Skip to main content

The Cell Nucleus and Its Compartments

  • Chapter
  • First Online:
Cellular Mechanics and Biophysics

Part of the book series: Biological and Medical Physics, Biomedical Engineering ((BIOMEDICAL))

  • 1061 Accesses

Abstract

This chapter presents the basic knowledge about the function of cell division and the cell cycle process. In fine detail, the architecture and function of the largest compartment of the eukaryotic cell, the nucleus and its components, such as the nuclear envelope, nuclear pore complex, chromosomes and nucleoskeleton, are emphasized. Centrioles play an important role in cell division and are being discussed, including their replication. It is discussed how forces are transmitted from the cellular microenvironment, which are sensed by cell–matrix adhesion receptors, coupled via focal adhesion proteins to the cell’s cytoskeletal network, and subsequently they have an impact on the mechanical phenotype of the innermost organelle of the cell, the cell nucleus. The biophysical aspects of these main functions of cells under normal physiological conditions and under pathological conditions such as cancer and acute or chronic inflammation are at the center of attention. Finally, the effect of mechanical force on gene expression is addressed, how the cells deal with it.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 189.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 249.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • J.R. Abney, B. Cutler, M.L. Fillbach, D. Axelrod, B.A. Scalettar, Chromatin dynamics in interphase nuclei and its implications for nuclear structure. J. Cell Biol. 137, 1459–1468 (1997)

    Google Scholar 

  • S.A. Adam, R. Sterne-Marr, L. Gerace, In vitro nuclear protein import using permeabilized mammalian cells. Methods Cell Biol. 35, 469–482 (1991)

    Google Scholar 

  • R.L. Adams, S.R. Wente, Uncovering nuclear pore complexity with innovation. Cell 152, 1218–1221 (2013)

    Google Scholar 

  • C. Ader, S. Frey, W. Maas, H.B. Schmidt, D. Görlich, M. Baldus, Amyloid-like interactions within nucleoporin FG hydrogels. Proc. Natl. Acad. Sci. U. S. A. 107, 6281–6285 (2010)

    ADS  Google Scholar 

  • J.D. Aitchison, M.P. Rout, The road to ribosomes. Filling potholes in the export pathway. J. Cell Biol. 151, F23–F26 (2000)

    Google Scholar 

  • A. Akhtar, S.M. Gasser, The nuclear envelope and transcriptional control. Nat. Rev. Genet. 8, 507–517 (2007)

    Google Scholar 

  • F. Alber, S. Dokudovskaya, L.M. Veenhoff et al., The molecular architecture of the nuclear pore complex. Nature 450, 695–701 (2007)

    ADS  Google Scholar 

  • A.R. Alcazar-Roman, E.J. Tran, S. Guo, S.R. Wente, Inositol hexakisphosphate and Gle1 activate the DEAD-box protein Dbp5 for nuclear mRNA export. Nat. Cell Biol. 8, 711–716 (2006)

    Google Scholar 

  • N.P. Allen, L. Huang, A. Burlingame, M. Rexach, Proteomic analysis of nucleoporin interacting proteins. J. Biol. Chem. 276, 29268–29274 (2001)

    Article  Google Scholar 

  • T.D. Allen, J.M. Cronshaw, S. Bagley, E. Kiseleva, M.W. Goldberg, The nuclear pore complex: mediator of translocation between nucleus and cytoplasm. J. Cell Sci. 113(Pt 10), 1651–1659 (2000)

    Google Scholar 

  • S. Amlacher, P. Sarges, D. Flemming, V. van Noort, R. Kunze, D.P. Devos, M. Arumugam, P. Bork, E. Hurt, Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile. Cell 146, 277–289 (2011)

    Article  Google Scholar 

  • K.R. Andersen, E. Onischenko, J.H. Tang, P. Kumar, J.Z. Chen, A. Ulrich, J.T. Liphardt, K. Weis, T.U. Schwartz, Scaffold nucleoporins Nup188 and Nup192 share structural and functional properties with nuclear transport receptors. eLife 2, e00745 (2013)

    Google Scholar 

  • D.J. Anderson, M.W. Hetzer, Nuclear envelope formation by chromatin-mediated reorganization of the endoplasmic reticulum. Nat. Cell Biol. 9, 1160–1166 (2007)

    Article  Google Scholar 

  • D.J. Anderson, M.W. Hetzer, Reshaping of the endoplasmic reticulum limits the rate for nuclear envelope formation. J. Cell Biol. 182, 911–924 (2008)

    Article  Google Scholar 

  • D.J. Anderson, J.D. Vargas, J.P. Hsiao, M.W. Hetzer, Recruitment of functionally distinct membrane proteins to chromatin mediates nuclear envelope formation in vivo. J. Cell Biol. 186, 183–191 (2009)

    Article  Google Scholar 

  • J.T. Anderson, S.M. Wilson, K.V. Datar, M.S. Swanson, NAB2: a yeast nuclear polyadenylated RNA-binding protein essential for cell viability. Mol. Cell. Biol. 13, 2730–2741 (1993)

    Article  Google Scholar 

  • E.D. Andrulis, A.M. Neiman, D.C. Zappulla, R. Sternglanz, Perinuclear localization of chromatin facilitates transcriptional silencing. Nature 394, 592–595 (1998)

    Article  Google Scholar 

  • W. Antonin, C. Franz, U. Haselmann, C. Antony, I.W. Mattaj, The integral membrane nucleoporin pom121 functionally links nuclear pore complex assembly and nuclear envelope formation. Mol. Cell 17, 83–92 (2005)

    Article  Google Scholar 

  • W. Antonin, R. Ungricht, U. Kutay, Traversing the NPC along the pore membrane: targeting of membrane proteins to the INM. Nucleus 2, 87–91 (2011)

    Article  Google Scholar 

  • A. Arjomand, M.A. Baker, C. Li, A.M. Buckle, D.A. Jans, K.L. Loveland, Y. Miyamoto, The alpha-importome of mammalian germ cell maturation provides novel insights for importin biology. FASEB J. 28(8), 3480–3493 (2014)

    Article  Google Scholar 

  • H. Asakawa, H.J. Yang, T.G. Yamamoto, C. Ohtsuki, Y. Chikashige, K. Sakata-Sogawa, M. Tokunaga, M. Iwamoto, Y. Hiraoka, T. Haraguchi, Characterization of nuclear pore complex components in fission yeast Schizosaccharomyces pombe. Nucleus 5, 149–162 (2014)

    Article  Google Scholar 

  • A.G. Balakin, L. Smith, M.J. Fournier, The RNA world of the nucleolus: two major families of small RNAs defined by different box elements with related functions. Cell 86, 823–834 (1996)

    Article  Google Scholar 

  • A. Banerjee, L.H. Apponi, G.K. Pavlath, A.H. Corbett, PABPN1: molecular function and muscle disease. FEBS J. 280, 4230–4250 (2013)

    Article  Google Scholar 

  • D.W. Bauer, J.G. Gall, Coiled bodies without coilin. Mol. Biol. Cell 8, 73–82 (1997)

    Article  Google Scholar 

  • G. Bauren, L. Wieslander, Splicing of Balbiani ring 1 gene pre-mRNA occurs simultaneously with transcription. Cell 76, 183–192 (1994)

    Article  Google Scholar 

  • M. Beck, J.S. Glavy, Toward understanding the structure of the vertebrate nuclear pore complex. Nucleus 5, 119–123 (2014)

    Article  Google Scholar 

  • M. Beck, F. Forster, M. Ecke, J.M. Plitzko, F. Melchior, G. Gerisch, W. Baumeister, O. Medalia, Nuclear pore complex structure and dynamics revealed by cryoelectron tomogaphy. Science 306, 1387–1390 (2004)

    Article  Google Scholar 

  • M. Beck, V. Lucic, F. Forster, W. Baumeister, O. Medalia, Snapshots of nuclear pore complexes in action captured by cryo-electron tomography. Nature 449, 611–615 (2007)

    Article  Google Scholar 

  • N. Belaadi, J. Aureille, C. Guilluy, Under pressure: mechanical stress management in the nucleus. Cells 5(2), 27 (2016)

    Article  Google Scholar 

  • N. Belgareh, G. Rabut, S.W. Baï et al., An evolutionarily conserved NPC subcomplex, which redistributes in part to kinetochores in mammalian cells. J. Cell Biol. 154, 1147–1160 (2001)

    Article  Google Scholar 

  • A.S. Belmont, S. Dietzel, A.C. Nye, Y.G. Strukov, T. Tumbar, Large-scale chromatin structure and function. Curr. Opin. Cell Biol. 11, 307–311 (1999)

    Article  Google Scholar 

  • D. Bentley, Coupling RNA polymerase II transcription with pre-mRNA processing. Curr. Opin. Cell Biol. 11(347–351), 1–5 (1999)

    Google Scholar 

  • R. Berezney, D.S. Coffey, Identification of a nuclear protein matrix. Biochem. Biophys. Res. Commun. 60, 1410–1417 (1974)

    Article  Google Scholar 

  • I.C. Berke, T. Boehmer, G. Blobel, T.U. Schwartz, Structural and functional analysis of Nup133 domains reveals modular building blocks of the nuclear pore complex. J. Cell Biol. 167, 591–597 (2004)

    Article  Google Scholar 

  • A. Bestembayeva, Nanoscale stiffness topography reveals structure and mechanics of the transport barrier in intact nuclear pore complexes. Nat Nanotechnol. 10, 60–64 (2014)

    Article  Google Scholar 

  • A.L. Beyer, Y.N. Osheim, Splice site selection, rate of splicing, and alternative splicing on nascent transcripts. Genes Dev. 2, 754–765 (1988)

    Article  Google Scholar 

  • S. Bilokapic, T.U. Schwartz, 3D ultrastructure of the nuclear pore complex. Curr. Opin. Cell Biol. 24, 86–91 (2012a)

    Article  Google Scholar 

  • S. Bilokapic, T.U. Schwartz, Molecular basis for Nup37 and ELY5/ELYS recruitment to the nuclear pore complex. Proc. Natl. Acad. Sci. U. S. A. 109, 15241–15246 (2012b)

    Article  Google Scholar 

  • G. Blobel, Gene gating: a hypothesis. Proc. Natl. Acad. Sci. U. S. A. 82(24), 8527–8529 (1985)

    Article  Google Scholar 

  • T. Boehmer, S. Jeudy, I.C. Berke, T.U. Schwartz, Structural and functional studies of Nup107/Nup133 interaction and its implications for the architecture of the nuclear pore complex. Mol. Cell 30, 721–731 (2008)

    Article  Google Scholar 

  • K. Bohmann, J.A. Ferreira, A.I. Lamond, Mutational analysis of p80 coilin indicates a functional interaction between coiled bodies and the nucleolus. J. Cell Biol. 131, 817–831 (1995)

    Article  Google Scholar 

  • A. Boni, A.Z. Politi, P. Strnad, W. Xiang, M.J. Hossain, J. Ellenberg, Live imaging and modeling of inner nuclear membrane targeting reveals its molecular requirements in mammalian cells. J. Cell Biol. 209, 705–720 (2015)

    Article  Google Scholar 

  • E.A. Booth-Gauthier, T.A. Alcoser, G. Yang, K.N. Dahl, Force-induced changes in subnuclear movement and rheology. Biophys. J. 103, 2423–2431 (2012)

    Google Scholar 

  • J. Borden, L. Manuelidis, Movement of the X chromosome in epilepsy. Science 242, 1687–1691 (1988)

    Article  Google Scholar 

  • D.C. Bouck, K. Bloom, Pericentric chromatin is an elastic component of the mitotic spindle. Curr. Biol. 17, 741–748 (2007)

    Article  Google Scholar 

  • K. Boudonck, L. Dolan, P.J. Shaw, The movement of coiled bodies visualized in living plant cells by the green fluorescent protein. Mol. Biol. Cell 10, 2297–2307 (1999)

    Article  Google Scholar 

  • H. Bretes, J.O. Rouviere, T. Leger, M. Oeffinger, F. Devaux, V. Doye, B. Palancade, Sumoylation of the THO complex regulates the biogenesis of a subset of mRNPs. Nucleic Acids Res. 42(8), 5043–5058 (2014)

    Article  Google Scholar 

  • J.F. Briand, F. Navarro, O. Gadal, P. Thuriaux, Cross talk between tRNA and rRNA synthesis in Saccharomyces cerevisiae. Mol. Cell. Biol. 21, 189–195 (2001)

    Article  Google Scholar 

  • D.G. Brickner, Ahmed, S.L. Meldi, A. Thompson, W. Light, M. Young, T.L. Hickman, F. Chu, E. Fabre, J.H. Brickner, Transcription factor binding to a DNA zip code controls interchromosomal clustering at the nuclear periphery. Dev. Cell 22, 1234–1246 (2012)

    Article  Google Scholar 

  • Brickner J H and Walter P 2004 Gene recruitment of the activated INO1 locus to the nuclear membrane PLoS Biol. 2 e342

    Google Scholar 

  • J.M. Bridger, H. Herrmann, C. Munkel, P. Lichter, Identification of an interchromosomal compartment by polymerization of nuclear-targeted vimentin. J. Cell Sci. 111, 1241–1253 (1998)

    Google Scholar 

  • S.G. Brohawn, N.C. Leksa, E.D. Spear, K.R. Rajashankar, T.U. Schwartz, Structural evidence for common ancestry of the nuclear pore complex and vesicle coats. Science 322, 1369–1373 (2008)

    Article  Google Scholar 

  • S.G. Brohawn, J.R. Partridge, J.R. Whittle, T.U. Schwartz, The nuclear pore complex has entered the atomic age. Structure 17, 1156–1168 (2009)

    Article  Google Scholar 

  • K.E. Brown, J. Baxter, D. Graf, M. Merkenschlager, A.G. Fisher, Dynamic repositioning of genes in the nucleus of lymphocytes preparing for cell division. Mol. Cell 3, 207–217 (1999)

    Article  Google Scholar 

  • K.E. Brown, S.S. Guest, S.T. Smale, K. Hahm, M. Merkenschlager, A.G. Fisher, Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin. Cell 91, 845–854 (1997)

    Article  Google Scholar 

  • K.H. Bui, A. von Appen, A.L. DiGuilio et al., Integrated structural analysis of the human nuclear pore complex scaffold. Cell 155, 1233–1243 (2013)

    Article  Google Scholar 

  • B. Burke, C.L. Stewart, The nuclear lamins: flexibility in function. Nat. Rev. Mol. Cell Biol. 14, 13–24 (2013)

    Article  Google Scholar 

  • R.A. Burrell, N. McGranahan, J. Bartek, C. Swanton, The causes and consequences of genetic heterogeneity in cancer evolution. Nature 501, 338–345 (2013)

    Article  Google Scholar 

  • H. Busch, K.S. Narayan, J. Hamilton, Isolation of nucleoli in a medium containing spermine and magnesium acetate. Exp. Cell Res. 47, 329–336 (1967)

    Article  Google Scholar 

  • V. Butin-Israeli, S.A. Adam, A.E. Goldman, R.D. Goldman, Nuclear lamin functions and disease. Trends Genet. 28, 464–471 (2012)

    Article  Google Scholar 

  • H.G. Callan, J.G. Gall, Association of RNA with the B and C snurposomes of Xenopus oocyte nuclei. Chromosoma 101, 69–82 (1991)

    Article  Google Scholar 

  • X. Cao, E. Moeendarbary, P. Isermann, P.M. Davidson, X. Wang, M.B. Chen, A.K. Burkart, J. Lammerding, R.D. Kamm, V.B. Shenoy, A chemomechanical model for nuclear morphology and stresses during cell transendothelial migration. Biophys. J. 111, 1541–1552 (2016)

    Google Scholar 

  • M. Carmo-Fonseca, L. Mendes-Soares, I. Campos, To be or not to be in the nucleolus. Nat. Cell Biol. 2, E107–E112 (2000)

    Article  Google Scholar 

  • M. Carroll, K.L. Borden, The oncogene eIF4E: using biochemical insights to target cancer. J. Interferon Cytokine Res. 33, 227–238 (2013)

    Article  Google Scholar 

  • K.C. Carter, D. Bowman, W. Carrington, K. Fogarty, J.A. McNeil, F.S. Fay, J.B. Lawrence, A three-dimensional view of precursor messenger RNA metabolism within the mammalian nucleus. Science 259, 1330–1335 (1993)

    Article  Google Scholar 

  • K.C. Carter, K.L. Taneja, J.B. Lawrence, Discrete nuclear domains of poly(A) RNA and their relationship to the functional organization of the nucleus. J. Cell Biol. 115, 1191–1202 (1991)

    Article  Google Scholar 

  • T. Carvalho, F. Almeida, A. Calapez, M. Lafarga, M.T. Berciano, M. Carmo-Fonseca, The spinal muscular atrophy disease gene product, SMN: a link between snRNP biogenesis and the Cajal (coiled) body. J. Cell Biol. 147, 715–728 (1999)

    Article  Google Scholar 

  • A. Castello, B. Fischer, M.W. Hentze, T. Preiss, RNA-binding proteins in Mendelian disease. Trends Genet. 29, 318–327 (2013)

    Article  Google Scholar 

  • K.J. Chalut, M. Hopfler, F. Lautenschlager, L. Boyde, C.J. Chan, A. Ekpenyong, A. Martinez-Arias, J. Guck, Chromatin decondensation and nuclear softening accompany Nanog downregulation in embryonic. Stem. Cells Biophys. J. 103, 2060–2070 (2012)

    Google Scholar 

  • H. Cheng, K. Dufu, C.S. Lee, J.L. Hsu, A. A. Dias A and Reed R 2006 Human mRNA export machinery recruited to the 5′ end of mRNA. Cell 127, 1389–1400 (2006)

    Google Scholar 

  • M. Chiquet, L. Gelman, R. Lutz, S. Maier, From mechanotransduction to extracellular matrix gene expression in fibroblasts. Biochim. Biophys. Acta (BBA)-Mol. Cell Res. 1793(5), 911–920

    Google Scholar 

  • S. Cho, J. Irianto, D.E. Discher, Mechanosensing by the nucleus: from pathways to scaling relationships. J. Cell Biol. 216, 1–11 (2017)

    Article  Google Scholar 

  • H. Chug, S. Trakhanov, B.B. Hülsmann, T. Pleiner, D. Görlich, Crystal structure of the metazoan Nup62•Nup58•Nup54 nucleoporin complex. Science 350, 106–110 (2015)

    Google Scholar 

  • G. Cingolani, C. Petosa, K. Weis, C.W. Muller, Structure of importin-beta bound to the IBB domain of importin-alpha. Nature 399, 221–229 (1999)

    Article  Google Scholar 

  • S.C. Cloutier, W.K. Ma, L.T. Nguyen, E.J. Tran, The DEAD-box RNA helicase Dbp2 connects RNA quality control with repression of aberrant transcription. J. Biol. Chem. 287, 26155–26166 (2012)

    Article  Google Scholar 

  • D. Cmarko, P.J. Verschure, T.E. Martin, M.E. Dahmus, S. Krause, X.D. Fu, R. van Driel, S. Fakan, Ultrastructural analysis of transcription and splicing in the cell nucleus after bromo-UTP microinjectio. Mol. Biol. Cell 10, 211–223 (1999)

    Article  Google Scholar 

  • T.H. Coady, C.L. Lorson, SMN in spinal muscular atrophy and snRNP biogenesis Wiley Interdiscip. Rev. RNA 2, 546–564 (2011)

    Google Scholar 

  • M. Cockell, S.M. Gasser, Nuclear compartments and gene regulation. Curr. Opin. Genet. Dev. 9, 199–205 (1999)

    Article  Google Scholar 

  • T.V. Cohen, L. Hernandez, C.L. Stewart, Functions of the nuclear envelope and lamina in development and disease. Biochem. Soc. Trans. 36, 1329–1334 (2008)

    Article  Google Scholar 

  • E. Conti, C.W. Muller, M. Stewart, Karyopherin flexibility in nucleocytoplasmic transport. Curr. Opin. Struct. Biol. 16, 237–244 (2006)

    Article  Google Scholar 

  • E. Conti, M. Uy, L. Leighton, G. Blobel, J. Kuriyan, Crystallographic analysis of the recognition of a nuclear localization signal by the nuclear import factor karyopherin alpha. Cell 94, 193–204 (1998)

    Article  Google Scholar 

  • A.G. Cook, E. Conti, Nuclear export complexes in the frame. Curr. Opin. Struct. Biol. 20(2), 247–252 (2010)

    Article  Google Scholar 

  • P.R. Cook, The organization of replication and transcription Science 284, 1790–1795 (1999)

    Google Scholar 

  • T.A. Cooper, L. Wan, G. Dreyfuss, RNA and disease Cell 136, 777–793 (2009)

    Google Scholar 

  • E.A. Corbin, O.O. Adeniba, R.H. Ewoldt, R. Bashir, Dynamic mechanical measurement of the viscoelasticity of single adherent cells. Appl. Phys. Lett. 108(9), 093701 (2016)

    Article  Google Scholar 

  • T. Cremer, C. Cremer, T. Schneider, H. Baumann, E.K. Luedtke, K. Sperling, V. Teuber, C. Zorn, Rabl’s model of the interphase chromosome arrangement tested in Chinese hamster cells by premature chromosome condensation and laser UV-microbeam experiments. Hum. Genet. 60, 46–56 (1982)

    Article  Google Scholar 

  • T. Cremer, G. Kreth, H. Koester, R.H.A. Fink, R. Heintzmann, M. Cremer, I. Solovei, D. Zink, C. Cremer, Chromosome territories, interchromatin domain compartment and nuclear matrix: an integrated view of the functional nuclaer architecture. Crit. Rev. Gene Expr. 12, 179–212 (2000)

    Google Scholar 

  • T. Cremer, P. Lichter, J. Borden, D.C. Ward, L. Manuelidis, Detection of chromosome aberrations in metaphase and interphase tumor cells by in-situ hybridization using chromosome specific library probes. Hum. Genet. 80, 235–246 (1988)

    Article  Google Scholar 

  • M. Crisp, Q. Liu, K. Roux, J. Rattner, C. Shanahan, B. Burke, P.D. Stahl, D. Hodzic, Coupling of the nucleus and cytoplasm: role of the LINC complex. J. Cell Biol. 172, 41–53 (2006)

    Article  Google Scholar 

  • J.M. Cronshaw, A.N. Krutchinsky, W. Zhang, B.T. Chait, M.J. Matunis, Proteomic analysis of the mammalian nuclear pore complex. J. Cell Biol. 158, 915–927 (2002)

    Article  Google Scholar 

  • M.A. D’Angelo, J.S. Gomez-Cavazos, A. Mei, D.H. Lackner, M.W. Hetzer, A change in nuclear pore complex composition regulates cell differentiation. Dev. Cell 22, 446–458 (2012)

    Article  Google Scholar 

  • M.A. D’Angelo, M. Raices, S.H. Panowski, M.W. Hetzer, Age-dependent deterioration of nuclear pore complexes causes a loss of nuclear integrity in postmitotic cells. Cell 136, 284–295 (2009)

    Article  Google Scholar 

  • A. D’Urso, J.H. Brickner, Mechanisms of epigenetic memory. Trends Genet. 30(6), 230–236 (2014)

    Article  Google Scholar 

  • M.A. D’Angelo, M.W. Hetzer, The role of the nuclear envelope in cellular organization. Cell. Mol. Life Sci. 63, 316–332 (2006)

    Article  Google Scholar 

  • M.A. D’Angelo, M.W. Hetzer, Structure, dynamics and function of nuclear pore complexes. Trends Cell Biol. 18, 456–466 (2008)

    Google Scholar 

  • K.N. Dahl, A. Kalinowski, Nucleoskeleton mechanics at a glance. J. Cell Sci. 124, 675–678 (2011)

    Article  Google Scholar 

  • K.N. Dahl, A.J. Engler, J.D. Pajerowski, D.E. Discher, Power-law rheology of isolated nuclei with deformation mapping of nuclear substructures. Biophys. J. 89(4), 2855–2864 (2005)

    Article  Google Scholar 

  • K.N. Dahl, S.M. Kahn, K.L. Wilson, D.E. Discher, The nuclear envelope lamina network has elasticity and a compressibility limit suggestive of a molecular shock absorber. J. Cell Sci. 117, 4779–4786 (2004)

    Google Scholar 

  • B. Daneholt, Transcription in polytene chromosomes. Cell 4, 1–9 (1975)

    Google Scholar 

  • I. Davis, D. Ish-Horowicz, Apical localization of pair-rule transcripts requires 3 h sequences and limits protein diffusion in the Drosophila blastoderm embryo. Cell 67, 927–940 (1991)

    Google Scholar 

  • R. de Leeuw, Y. Gruenbaum, O. Medalia, Nuclear lamins: thin filaments with major functions. Trends Cell Biol. 28(1), 34–45 (2018)

    Google Scholar 

  • E.W. Debler, Y. Ma, H.S. Seo, K.C. Hsia, T.R. Noriega, G. Blobel, A. Hoelz, A fence-like coat for the nuclear pore membrane. Mol. Cell 32, 815–826 (2008)

    Google Scholar 

  • T. Dechat, K. Gesson, R. Foisner, Lamina-independent lamins in the nuclear interior serve important functions. Cold. Spring. Harb. Symp. Quant. Biol. 75, 533–543 (2010)

    Google Scholar 

  • T. Dechat, K. Pfleghaar, K. Sengupta, T. Shimi, D.K. Shumaker, L. Solimando, R.D. Goldman, Nuclear lamins: major factors in the structural organization and function of the nucleus and chromatin. Genes Dev. 22, 832–853 (2008)

    Google Scholar 

  • J.A. Degrasse, D. Devos, A functional proteomic study of the Trypanosoma brucei nuclear pore complex: an informatic strategy. Methods Mol. Biol. 673, 231–238 (2010)

    Google Scholar 

  • J.A. Degrasse, K.N. DuBois, D. Devos, T.N. Siegel, A. Sali, M.C. Field, M.P. Rout, B.T. Chait, Evidence for a shared nuclear pore complex architecture that is conserved from the last common eukaryotic ancestor. Mol. Cell. Proteomics 8, 2119–2130 (2009)

    Google Scholar 

  • C.M. Denais, R.M. Gilbert, P. Isermann, A.L. McGregor, M. te Lindert, B. Weigelin, P.M. Davidson, P. Friedl, K. Wolf, J. Lammerding, Nuclear envelope rupture and repair during cancer cell migration. Science 352, 353–358 (2016)

    ADS  Google Scholar 

  • D.P. Denning, S.S. Patel, V. Uversky, A.L. Fink, M. Rexach, Disorder in the nuclear pore complex: the FG repeat regions of nucleoporins are natively unfolded. Proc. Natl. Acad. Sci. U. S. A. 100, 2450–2455 (2003)

    ADS  Google Scholar 

  • A.F. Dernburg, K.W. Broman, J.C. Fung, W.F. Marshall, J. Philips, D.A. Agard, J.W. Sedat, Perturbation of nuclear architecture by long-distance chromosome interactions. Cell 85, 745–759 (1996)

    Google Scholar 

  • H. de Thé, C. Chomienne, M. Lanotte, L. Degas, A. Dejan, The t(15;17) translocation of acute promyelocytic leukemia fuses the retinoic acid receptor alpha gene to a novel transcribed locus. Nature 367, 558–561 (1990)

    Google Scholar 

  • D.P. Devos, R. Gräf, M.C. Field, Evolution of the nucleus. Curr. Opin. Cell Biol. 28C, 8–15 (2014)

    Google Scholar 

  • D. Devos, S. Dokudovskaya, F. Alber, R. Williams, B.T. Chait, A. Sali, M.P. Rout, Components of coated vesicles and nuclear pore complexes share a common molecular architecture. PLoS Biol. 2, e380 (2004)

    Google Scholar 

  • D. Devos, S. Dokudovskaya, R. Williams, F. Alber, N. Eswar, B.T. Chait, M.P. Rout, A. Sali, Simple fold composition and modular architecture of the nuclear pore complex. Proc. Natl. Acad. Sci. U. S. A. 103, 2172–2177 (2006)

    ADS  Google Scholar 

  • R.W. Dirks, K.C. Daniel, A.K. Raap, RNAs radiate from gene to cytoplasm as revealed by fluorescence in situ hybridization. J. Cell Sci. 108, 2565–2572 (1995)

    Google Scholar 

  • M.T. Doolin, T.S. Ornstein, K.M. Stroka, nuclear deformation in response to mechanical confinement is cell type dependent. Cells 8(5), 427 (2019)

    Google Scholar 

  • D. Dorner, J. Gotzmann, R. Foisner, Nucleoplasmic lamins and their interaction partners, LAP2a, Rb, and BAF, in transcriptional regulation. FEBS J. 274, 1362–1373 (2007)

    Google Scholar 

  • C.M. Doucet, M.W. Hetzer, Nuclear pore biogenesis into an intact nuclear envelope. Chromosoma 119, 469–477 (2010)

    Google Scholar 

  • T. Dousset, C. Wang, C. Verheggen, D. Chen, D. Hernandez-Verdun, S. Huang, Initiation of nucleolar assembly is independent of RNA polymerase I transcription. Mol. Biol. Cell 11, 2705–2717 (2000)

    Google Scholar 

  • T.P. Driscoll, B.D. Cosgrove, S.-J. Heo, Z.E. Shurden, R.L. Mauck, Cytoskeletal to nuclear strain transfer regulates YAP signaling in mesenchymal stem cells. Biophys. J. 108, 2783–2793 (2015)

    Google Scholar 

  • L. Du, S.L. Warren, A functional interaction between the carboxy-terminal domain of RNA polymerase II and pre-mRNA splicing. J. Cell Biol. 136, 5–18 (1997)

    Google Scholar 

  • E. Dultz, J. Ellenberg, Live imaging of single nuclear pores reveals unique assembly kinetics and mechanism in interphase. J. Cell Biol. 191, 15–22 (2010)

    Google Scholar 

  • E. Dultz, E. Zanin, C. Wurzenberger, M. Braun, G. Rabut, L. Sironi, J. Ellenberg, Systematic kinetic analysis of mitotic dis- and reassembly of the nuclear pore in living cells. J. Cell Biol. 180, 857–865 (2008)

    Google Scholar 

  • M. Dundr, T. Misteli, Functional architecture in the cell nucleus. Biochem. J. 356, 297–310 (2001)

    Google Scholar 

  • M. Dundr, I. Raska, Nonisotopic ultrastructural mapping of transcription sites within the nucleolus. Exp. Cell Res. 208, 275–281 (1993)

    Google Scholar 

  • M. Dundr, T. Misteli, M.O.J. Olson, The dynamics of postmitotic reassembly of the nucleolus. J. Cell Biol. 150, 433–446 (2000)

    Google Scholar 

  • J.A. Dyck, G.G. Maul, W.H. Miller, J.D. Chen, A. Kakizuka, R.M. Evans, A novel macromolecular structure is a target of the promyelocyte-retinoic acid receptor oncoprotein. Cell 76, 333–343 (1994)

    Google Scholar 

  • B.A. Edgar, M.P. White, G. Schubiger, T. Kornberg, Repression and turnover pattern of fusi tarazu RNA in the early Drosophila embryo. Cell 47, 747–754 (1986)

    Google Scholar 

  • D. Egecioglu, J.H. Brickner, Gene positioning and expression. Curr. Opin. Cell Biol. 23, 338–345 (2011)

    Google Scholar 

  • M. Eibauer, M. Pellanda, Y. Turgay, A. Dubrovsky, A. Wild, O. Medalia, Structure and gating of the nuclear pore complex. Nat. Commun. 6, 7532 (2015)

    ADS  Google Scholar 

  • N. Eisenhardt, J. Redolfi, W. Antonin, Interaction of Nup53 with Ndc1 and Nup155 is required for nuclear pore complex assembly. J. Cell Sci. 127, 908–921 (2014)

    Google Scholar 

  • C. Eriksson, C. Rustum, E. Hallberg, Dynamic properties of nuclear pore complex proteins in gp210 deficient cells. FEBS Lett. 572, 261–265 (2004)

    Google Scholar 

  • F. Esra Demircioglu, V.E. Cruz, T.U. Schwartz, Purification and structural analysis of SUN and KASH domain proteins. Methods Enzymol. 569, 63–78 (2016)

    Google Scholar 

  • S. Fakan, Perichromatin fibrils are in situ forms of nascent transcripts. Trends Cell Biol. 4, 86–90 (1994)

    Article  Google Scholar 

  • M.B. Fasken, A.H. Corbett, Process or perish: quality control in mRNA biogenesis. Nat. Struct. Mol. Biol. 12, 482–488 (2005)

    Article  Google Scholar 

  • D.W. Fawcett, On the occurrence of a fibrous lamina on the inner aspect of the nuclear envelope in certain cells of vertebrates. Am. J. Anat. 119, 129–145 (1996)

    Article  Google Scholar 

  • N. Fay, N. Pante, Nuclear entry of DNA viruses. Front. Microbiol. 6, 467 (2015)

    Article  Google Scholar 

  • C.M. Feldherr, D. Akin, The location of the transport gate in the nuclear pore complex. J. Cell Sci. 110(Pt 24), 3065–3070 (1997)

    Google Scholar 

  • J. Fernandez-Martinez, M.P. Rout, A jumbo problem: mapping the structure and functions of the nuclear pore complex. Curr. Opin. Cell Biol. 24, 92–99 (2012)

    Article  Google Scholar 

  • J. Fernandez-Martinez, J. Phillips, M.D. Sekedat et al., Structure–function mapping of a heptameric module in the nuclear pore complex. J. Cell Biol. 196, 419–434 (2012)

    Article  Google Scholar 

  • D. Ferrera, C. Canale, R. Marotta, N. Mazzaro, M. Gritti, M. Mazzanti, S. Capellari, P. Cortelli, L. Gasparini, Lamin B1 overexpression increases nuclear rigidity in autosomal dominant leukodystrophy fibroblasts. FASEB J. 28(9), 3906–3918 (2014)

    Google Scholar 

  • R. Festenstein, D. Kioussis, Locus control regions and epigenetic chromatin modifiers. Curr. Opin. Genet. Dev. 10, 199–203 (2000)

    Google Scholar 

  • M.C. Field, L. Koreny, M.P. Rout, Enriching the pore: splendid complexity from humble origins. Traffic 15, 141–156 (2014)

    Google Scholar 

  • J. Fischer, R. Teimer, S. Amlacher, R. Kunze, E. Hurt, Linker Nups connect the nuclear pore complex inner ring with the outer ring and transport channel. Nat. Struct. Mol. Biol. 22, 774–781 (2015)

    Google Scholar 

  • J. Fiserova, M.W. Goldberg, Relationships at the nuclear envelope: lamins and nuclear pore complexes in animals and plants. Biochem. Soc. Trans. 38, 829–831 (2010)

    Google Scholar 

  • J. Fiserova, E. Kiseleva, M.W. Goldberg, Nuclear envelope and nuclear pore complex structure and organization in tobacco BY-2 cells. Plant J. 59, 243–255 (2009)

    Google Scholar 

  • D. Flemming, D.P. Devos, J. Schwarz, S. Amlacher, M. Lutzmann, E. Hurt, Analysis of the yeast nucleoporin Nup188 reveals a conserved S-like structure with similarity to karyopherins. J Struct Biol. 177, 99–105 (2012)

    Google Scholar 

  • A.W. Folkmann, S.E. Collier, X. Zhan, P. Aditi, M.D. Ohi, S.R. Wente, Gle1 functions during mRNA export in an oligomeric complex that is altered in human disease. Cell 155, 582–593 (2013)

    Google Scholar 

  • A.W. Folkmann, T.R. Dawson, S.R. Wente, Insights into mRNA export-linked molecular mechanisms of human disease through a Gle1 structure–function analysis. Adv. Biol. Regul. 54, 74–91 (2014)

    Google Scholar 

  • M. Fornerod, M. Ohno, M. Yoshida, I.W. Mattaj, CRM1 is an export receptor for leucine-rich nuclear export signals. Cell 90, 1051–1060 (1997)

    Google Scholar 

  • C. Francastel, D. Schuebler, D.I.K. Martin, M. Groudine, Nuclear compartmentalization and gene activity. Nat. Rev. Mol. Cell Biol. 1, 137–143 (2000)

    Google Scholar 

  • C. Franz, P. Askjaer, W. Antonin, C.L. Iglesias, U. Haselmann, M. Schelder, A. de Marco, M. Wilm, C. Antony, I.W. Mattaj, Nup155 regulates nuclear envelope and nuclear pore complex formation in nematodes and vertebrates. EMBO J 24, 3519–3531 (2005)

    Google Scholar 

  • C. Franz, R. Walczak, S. Yavuz, R. Santarella, M. Gentzel, P. Askjaer, V. Galy, M. Hetzer, I.W. Mattaj, W. Antonin, MEL-28/ELYS is required for the recruitment of nucleoporins to chromatin and postmitotic nuclear pore complex assembly. EMBO Rep. 8, 165–172 (2007)

    Google Scholar 

  • M.R. Frey, A.G. Matera, Coiled bodies contain U7 small nuclear RNA and associate with specific DNA sequence in interphase human cells. Proc. Natl. Acad. Sci. U. S. A. 92, 5915–5919 (1995)

    Article  Google Scholar 

  • M.R. Frey, A.D. Bailey, A.M. Weiner, A.G. Matera, Association of snRNA genes with coiled bodies is mediated by nascent snRNA transcripts. Curr. Biol. 9, 126–135 (1999)

    Article  Google Scholar 

  • S. Frey, R.P. Richter, D. Gorlich, FG-rich repeats of nuclear pore proteins form a three-dimensional meshwork with hydrogel-like properties. Science 314, 815–817 (2006)

    Article  Google Scholar 

  • A. Fridkin, A. Penkner, V. Jantsch, Y. Gruenbaum, SUN-domain and KASH-domain proteins during development, meiosis and disease. Cell Mol. Life Sci. 66, 1518–1533 (2009)

    Google Scholar 

  • J.G. Gall, Cajal Bodies: the first 100 years. Annu. Rev. Cell. Dev. Biol. 16, 273–300 (2000)

    Article  Google Scholar 

  • J.G. Gall, H.G. Callan, H3-uridine incorporation in lampbrush chromosomes. Proc. Natl. Acad. Sci. U. S. A. 48, 562–570 (1962)

    Article  Google Scholar 

  • V. Galy, I.W. Mattaj, P. Askjaer, Caenorhabditis elegans nucleoporins Nup93 and Nup205 determine the limit of nuclear pore complex size exclusion in vivo. Mol. Biol. Cell 14, 5104–5115 (2003)

    Google Scholar 

  • P. Ganot, B.E. Jady, M.L. Bortolin, X. Darzacq, T. Kiss, Nucleolar factors direct the 2 h-O-ribose methylation and pseudouridylation of U6 spliceosomal RNA. Mol. Cell. Biol. 19, 6906–6917 (1999)

    Article  Google Scholar 

  • L. Gao, M.R. Frey, A.G. Matera, Human genes encoding U3 snRNA associate with coiled bodies in interphase cells and are clustered on chromosome 17p11.2 in a complex inverted repeat structure. Nucleic Acids Res. 25, 4740–4747 (1997)

    Google Scholar 

  • J.S. Gomez-Cavazos, M.W. Hetzer, The nucleoporin gp210/Nup210 controls muscle differentiation by regulating nuclear envelope/ER homeostasis. J. Cell Biol. 208, 671–681 (2015)

    Google Scholar 

  • D.E. Gottschling, O.M. Aparicio, B.L. Billington, V.A. Zakian, Position effect at S. cerevisiae telomeres: reversible repression of pol II transcription. Cell (Cambridge, Mass.) 63, 751–762 (1990)

    Google Scholar 

  • M.A. Grande, I. van der Kraan, L. de Jong, R. van Driel, Nuclear distribution of transcription factors in relation to sites of transcription and RNA polymerase II. J. Cell Sci. 110, 1781–1791 (1997)

    Google Scholar 

  • P. Grandi, V. Doye, E.C. Hurt, Purification of NSP1 reveals complex formation with “GLFG” nucleoporins and a novel nuclear pore protein NIC96. Embo J. 12, 3061–3071 (1993)

    Google Scholar 

  • E. Grossman, O. Medalia, M. Zwerger, Functional architecture of the nuclear pore complex. Annu. Rev. Biophys. 41, 557–584 (2012)

    Article  Google Scholar 

  • Y. Gruenbaum, U. Aebi, Intermediate filaments: a dynamic network that controls cell mechanics. F1000Prime Rep. 6, 54 (2014)

    Google Scholar 

  • Y. Gruenbaum, O. Medalia, Lamins: the structure and protein complexes. Curr. Opin. Cell Biol. 32, 7–12 (2015)

    Google Scholar 

  • Y. Gruenbaum, A. Margalit, R.D. Goldman, D.K. Shumaker, K.L. Wilson, The nuclear lamina comes of age. Nat. Rev. Mol. Cell Biol. 6(1), 21–31 (2005)

    Article  Google Scholar 

  • Y. Gruenbaum, K.L. Wilson, A. Harel, M. Goldberg, M. Cohen, Review: nuclear lamins–structural proteins with fundamental functions. J. Struct. Biol. 129, 313–323 (2000)

    Google Scholar 

  • D. Grunwald, R.H. Singer, M. Rout, Nuclear export dynamics of RNA–protein complexes. Nature 475, 333–341 (2000)

    Google Scholar 

  • F. Guilak, J.R. Tedrow, R. Burgkart, Viscoelastic properties of the cell nucleus. Biochem. Biophys. Res. Commun. 269(3), 781–786 (2000)

    Article  Google Scholar 

  • C. Guilluy, L.D. Osborne, L. Van Landeghem, L. Sharek, R. Superfine, R. Garcia-Mata, K. Burridge, Isolated nuclei adapt to force and reveal a mechanotransduction pathway in the nucleus. Nat. Cell Biol. 16(4), 376–381 (2014)

    Article  Google Scholar 

  • T. Guttler, D. Gorlich, Ran-dependent nuclear export mediators: a structural perspective EMBO J. 30, 3457–3474 (2011)

    Google Scholar 

  • C. Gwizdek, N. Iglesias, M.S. Rodriguez, B. Ossareh-Nazari, M. Hobeika, G. Divita, F. Stutz, C. Dargemont, Ubiquitin-associated domain of Mex67 synchronizes recruitment of the mRNA export machinery with transcription. Proc. Natl. Acad. Sci. U. S. A. 103, 16376–16381 (2006)

    Article  Google Scholar 

  • K. Haase, J.K.L. Macadangdang, C.H. Edrington, C.M. Cuerrier, S. Hadjiantoniou, J.L. Harden, I.S. Skerjanc, A.E. Pelling, Extracellular forces cause the nucleus to deform in a highly controlled anisotropic manner. Sci. Rep. 6, 21300 (2016)

    Article  Google Scholar 

  • W.J. Hadden, J.L. Young, A.W. Holle, M.L. McFetridge, D.Y. Kim, P. Wijesinghe, H. Taylor-Weiner, J.H. Wen, A.R. Lee, K. Bieback, B.N. Vo, D.D. Sampson, B.F. Kennedy, J.P. Spatz, A.J. Engler, Y.S. Choi, Stem cell migration and mechanotransduction on linear stiffness gradient hydrogels. Proc. Natl. Acad. Sci. U. S. A. 114(22), 5647–5652 (2017)

    Article  Google Scholar 

  • N. Handa, M. Kukimoto-Niino, R. Akasaka, et al., The crystal structure of mouse Nup35 reveals atypical RNP motifs and novel homodimerization of the RRM domain. J Mol Biol. 363, 114–124 (2006)

    Google Scholar 

  • L. Hanson, W. Zhao, H.Y. Lou, Z.C. Lin, S.W. Lee, P. Chowdary, Y. Cui, B. Cui, Vertical nanopillars for in situ probing of nuclear mechanics in adherent cells. Nat. Nanotechnol. 10(6), 554–562 (2015)

    Article  Google Scholar 

  • T. Harada, J. Swift, J. Irianto, J.-W. Shin, K.R. Spinler, A. Athirasala, R. Diegmiller, P.C.D.P. Dingal, I.L. Ivanovska, D.E. Discher, Nuclear lamin stiffness is a barrier to 3D migration, but softness can limit survival. J. Cell Biol. 204, 669–682 (2014)

    Article  Google Scholar 

  • A. Harel, A.V. Orjalo, T. Vincent, A. Lachish-Zalait, S. Vasu, S. Shah, E. Zimmerman, M. Elbaum, D.J. Forbes, Removal of a single pore subcomplex results in vertebrate nuclei devoid of nuclear pores. Mol. Cell 11, 853–864 (2003)

    Article  Google Scholar 

  • K. Harris, The Birth of the Cell (Yale University Press, New Haven, 1999)

    Google Scholar 

  • Hawryluk-Gara LA, Platani M, Santarella R, Wozniak R W and Mattaj I W 2008 Nup53 is required for nuclear envelope and nuclear pore complex assembly Mol Biol Cell 9(4) 1753–62

    Google Scholar 

  • A. Hayakawa, A. Babour, L. Sengmanivong, C. Dargemont, Ubiquitylation of the nuclear pore complex controls nuclear migration during mitosis in S. cerevisiae. J. Cell Biol. 196, 19–27 (2012)

    Article  Google Scholar 

  • M.D. Hebert, A.G. Matera, Self-association of p80 coilin reveals a common theme in nuclear body formation. Mol. Biol. Cell 11, 4159–4171 (2000)

    Article  Google Scholar 

  • S. Heessen, M. Fornerod, The inner nuclear envelope as a transcription factor resting place. EMBO Rep. 8, 914–919 (2007)

    Article  Google Scholar 

  • S.-J. Heo, T.P. Driscoll, S.D. Thorpe, et al., Differentiation alters stem cell nuclear architecture, mechanics, and mechano-sensitivity. Elife 5, 283–293 (2016a)

    Google Scholar 

  • S.-J. Heo, W.M. Han, S.E. Szczesny, B.D. Cosgrove, D.M. Elliott, D.A. Lee, R.L. Duncan, R.L. Mauck, Mechanically induced chromatin condensation requires cellular contractility in Mesenchymal stem cells. Biophys. J. 111, 864–874 (2016b)

    Google Scholar 

  • H. Herrmann, U. Aebi, Intermediate filaments: structure and assembly. Cold. Spring. Harb. Perspect. Biol. 8, a018242 (2016)

    Article  Google Scholar 

  • H.M. Herz, A. Garruss, A. Shilatifard, SET for life: biochemical activities and biological functions of SET domain-containing proteins. Trends Biochem. Sci. 38, 621–639 (2013)

    Article  Google Scholar 

  • M.W. Hetzer, The nuclear envelope. Cold. Spring. Harb. Perspect. Biol. 2, a000539 (2010)

    Article  Google Scholar 

  • M.W. Hetzer, S.R. Wente, Border control at the nucleus: biogenesis and organization of the nuclear membrane and pore complexes. Dev. Cell. 17, 606–616 (2009)

    Article  Google Scholar 

  • M. Hetzer, T.C. Walther, I.W. Mattaj, Pushing the envelope: structure, function, and dynamics of the nuclear periphery. Annu. Rev. Cell. Dev. Biol. 21, 367–380 (2005)

    Google Scholar 

  • D.A. Hill, A.N. Imbalzano, Human SWI/SNF nucleosome remodeling activity is partially inhibited by linker histone H1. Biochemistry 39, 11649–11656 (2000)

    Google Scholar 

  • Y. Hirose, J.L. Manley, RNA polymerase II and the integration of nuclear events. Genes Dev. 14, 1415–1429 (2000)

    Google Scholar 

  • J.H. Ho, G. Kallstrom, A.W. Johnson, Nmd3p is a Crm1p-dependent adapter protein for nuclear export of the large ribosomal subunit. J. Cell Biol. 151, 1057–1066 (2000)

    Article  Google Scholar 

  • L.E. Hough, K. Dutta, S. Sparks, D.B. Temel, A. Kamal, J. Tetenbaum-Novatt, M.P. Rout, D. Cowburn, The molecular mechanism of nuclear transport revealed by atomic-scale measurements. Elife 4, 635 (2015)

    Article  Google Scholar 

  • A.B. Houtsmuller, S. Rademakers, A.L. Nigg, D. Hoogstraten, J.H. Hoeijmakers, W. Vermeulen, Action of DNA repair endonuclease ERCC1/XPF in living cells. Science 284, 958–961 (1999)

    ADS  Google Scholar 

  • P. Hozak, P.R. Cook, C. Schofer, W. Mosgoller, F. Wachtler, Site of transcription of ribosomal RNA and intranucleolar structure in HeLa cells. J. Cell Sci. 107, 639–648 (1994)

    Google Scholar 

  • S. Huang, D.E. Ingber, Cell tension, matrix mechanics, and cancer development. Cancer Cell 8, 175–176 (2005)

    Google Scholar 

  • S. Huang, D.L. Spector, Intron-dependent recruitment of pre-mRNA splicing factors to sites of transcription. J. Cell Biol. 131, 719–732 (1996)

    Google Scholar 

  • S. Huang, T.J. Deerinck, M.H. Ellisman, D.L. Spector, The dynamic organization of the perinucleolar compartment in the cell nucleus. J. Cell Biol. 137, 965–974 (1997)

    Google Scholar 

  • M.D. Huber, T. Guan, L. Gerace, Overlapping functions of nuclear envelope proteins NET25 (Lem2) and emerin in regulation of extracellular signal-regulated kinase signaling in myoblast differentiation. Mol. Cell. Biol. 29, 5718–5728 (2009)

    Google Scholar 

  • B.B. Hülsmann, A.A. Labokha, D. Görlich, The permeability of reconstituted nuclear pores provides direct evidence for the selective phase model. Cell 150, 738–751 (2012)

    Google Scholar 

  • E. Hurt, M. Beck, Towards understanding nuclear pore complex architecture and dynamics in the age of integrative structural analysis. Curr. Opin. Cell Biol. 34, 31–38 (2015)

    Google Scholar 

  • N. Iglesias, E. Tutucci, C. Gwizdek, P. Vinciguerra, E. Von Dach, A.H. Corbett, C. Dargemont, F. Stutz, Ubiquitin-mediated mRNP dynamics and surveillance prior to budding yeast mRNA export. Genes Dev. 24, 1927–1938 (2010)

    Google Scholar 

  • D.E. Ingber, Mechanical control of tissue morphogenesis during embryological development. Int. J. Dev. Biol. 50, 255–266 (2006)

    Google Scholar 

  • R.V. Intine, A.L. Sakulich, S.B. Koduru, Y. Huang, E. Pierstorff, J.L. Goodier, L. Phan, R.J. Maraia, Control of transfer RNA maturation by phosphorylation of the human La antigen on serine 366. Mol. Cell 6, 339–348 (2000)

    Google Scholar 

  • J. Irianto, C.R. Pfeifer, R.R. Bennett, Y. Xia, I.L. Ivanovska, A.J. Liu, R.A. Greenberg, D.E. Discher, Nuclear constriction segregates mobile nuclear proteins away from chromatin. Mol. Biol. Cell 27, 4011–4020 (2016)

    Google Scholar 

  • J. Irianto, Y. Xia, C.R. Pfeifer et al., DNA damage follows repair factor depletion and portends genome variation in cancer cells after pore migration. Curr. Biol. 27(2), 210–223 (2017)

    Google Scholar 

  • J. Irianto, Y. Xia, C.R. Pfeifer, R.A. Greenberg, D.E. Discher, As a nucleus enters a small pore, chromatin stretches and maintains integrity, even with DNA breaks. Biophys. J. 112, 446–449 (2017b)

    Google Scholar 

  • C. Isaac, Y. Yang, U.T. Meier, Nopp140 functions as a molecular link between the nucleolus and the coiled bodies. J. Cell Biol. 142(2), 319–329 (1998)

    Google Scholar 

  • A.M. Ishov, A.G. Sotnikov, D. Negorev, O.V. Vladimirova, N. Neff, T. Kamitani, E.T. Yeh, J.F. Strauss, G.G. Maul, PML is critical for ND10 formation and recruits the PML-interacting protein Daxx to this nuclear structure when modified by SUMO-1. J. Cell Biol. 147, 221–234 (1999)

    Google Scholar 

  • I.L. Ivanovska, J. Swift, K. Spinler, D. Dingal, S. Cho, D.E. Discher, Cross-linked matrix rigidity and soluble retinoids synergize in nuclear lamina regulation of stem cell differentiation. Mol. Biol. Cell. 28(14), 2010–2022 (2017)

    Google Scholar 

  • M. Iwamoto, H. Asakawa, Y. Hiraoka, T. Haraguchi, Nucleoporin Nup98: a gate-keeper in the eukaryotic kingdoms. Genes Cells 15, 661–669 (2015)

    Google Scholar 

  • M. Iwamoto, C. Mori, T. Kojidani, F. Bunai, T. Hori, T. Fukagawa, Y. Hiraoka, T. Haraguchi, Two distinct repeat sequences of Nup98 nucleoporins characterize dual nuclei in the binucleated ciliate Tetrahymena. Curr. Biol. 19, 843–847 (2009)

    Google Scholar 

  • D.A. Jackson, A.B. Hassan, R.J. Errington, P.R. Cook, Visualization of focal sites of transcription within human nuclei. EMBO J. 12, 1059–1065 (1993)

    Google Scholar 

  • D.A. Jackson, F.J. Iborra, E.M. Manders, P.R. Cook, Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei. Mol. Biol. Cell 9, 1523–1536 (1998)

    Google Scholar 

  • D.A. Jackson, A. Pombo, F. Iborra, The balance sheet for transcription: an analysis of nuclear RNA metabolism in mammalian cells. FASEB J. 14, 242–254 (2000)

    Google Scholar 

  • E.Y. Jacobs, M.R. Frey, W. Wu, T.C. Ingledue, T.C. Gebuhr, L. Gao, W.F. Marzluff, A.G. Matera, Coiled bodies preferentially associate with U4, U11, and U12 small nuclear RNA genes in interphase HeLa cells but not with U6 and U7 genes. Mol. Biol. Cell 10, 1653–1663 (1999)

    Google Scholar 

  • B.E. Jady, T. Kiss, A small nucleolar guide RNA functions both in 2 h-O-ribose methylation and pseudouridylation of the U5 spliceosomal RNA. EMBO J. 20, 541–551 (2001)

    Google Scholar 

  • J. Janevski, P.C. Park, U. De Boni, Changes in morphology and spatial position of coiled bodies during NGF-induced neuronal differentiation of PC12 cells. J. Histochem. Cytochem. 45, 1523–1531 (1997)

    Google Scholar 

  • N. Jarrous, J.S. Wolenski, D. Wesolowski, C. Lee, S. Altman, Localization in the nucleolus and coiled bodies of protein subunits of the ribonucleoprotein ribonuclease P. J. Cell Biol. 146, 559–572 (1999)

    Google Scholar 

  • S. Jeudy, T. Schwartz, Crystal structure of nucleoporin Nic96 reveals a novel, intricate helical domain architecture. J Biol Chem. 282, 34904–34912 (2007)

    Google Scholar 

  • Y. Jia, V. Polunovsky, P.B. Bitterman, C.R. Wagner, Cap-dependent translation initiation factor eIF4E: an emerging anticancer drug target. Med. Res. Rev. 32, 786–814 (2012)

    Google Scholar 

  • L.F. Jimenez-Garcia, D.L. Spector, vivo evidence that transcription and splicing are coordinated by a recruiting mechanism. Cell 73, 47–59 (1993)

    Google Scholar 

  • C. Jolly, Y. Usson, R.I. Morimoto, Rapid and reversible relocalization of heat shock factor 1 within seconds to nuclear stress granules. Proc. Natl. Acad. Sci. U. S. A. 96, 6769–6774 (1999)

    ADS  Google Scholar 

  • M. Kampmann, G. Blobel, Three-dimensional structure and flexibility of a membrane-coating module of the nuclear pore complex. Nat. Struct. Mol. Biol. 16, 782–788 (2009)

    Google Scholar 

  • T. Kanda, K.F. Sullivan, G.M. Wahl, Histone-GFP fusion protein enables sensitive analysis of chromosome dynamics in living mammalian cells. Curr. Biol. 26, 377–385 (1998)

    Google Scholar 

  • L.E. Kapinos, R.L. Schoch, R.S. Wagner, K.D. Schleicher, R.Y. Lim, Karyopherin-centric control of nuclear pores based on molecular occupancy and kinetic analysis of multivalent binding with FG nucleoporins. Biophys. J. 106, 1751–1762 (2014)

    Google Scholar 

  • H. Karcher, J. Lammerding, H. Huang, R.T. Lee, R.D. Kamm, M.R. Kaazempur-Mofrad, A three-dimensional viscoelastic model for cell deformation with experimental verification. Biophys. J. 85(5), 3336–3349 (2003)

    ADS  Google Scholar 

  • G.H. Karpen, J.E. Schaefer, C.D. Laird, A Drosophila rRNA gene located in euchromatin is active in transcription and nucleolus formation. Genes Dev. 2, 1745–1763 (1988)

    Google Scholar 

  • S.S. Katta, C.J. Smoyer, S.L. Jaspersen, Destination: inner nuclear membrane. Trends Cell Biol. 24, 221–229 (2014)

    Google Scholar 

  • K. Kelley, K.E. Knockenhauer, G. Kabachinski, T.U. Schwartz, Atomic structure of the Y complex of the nuclear pore. Nat. Struct. Mol. Biol. 22, 425–431 (2015)

    Google Scholar 

  • S.M. Kelly, S.W. Leung, C. Pak, A. Banerjee, K.H. Moberg, A.H. Corbett, A conserved role for the zinc finger polyadenosine RNA binding protein, ZC3H14, in control of poly(a) tail length. RNA 20(5), 681–688 (2014)

    Google Scholar 

  • S. Kelly, C. Pak, M. Garshasbi, A. Kuss, A.H. Corbett, K. Moberg, New kid on the ID block: neural functions of the Nab2/ZC3H14 class of Cys(3)His tandem zinc-finger polyadenosine RNA binding proteins. RNA Biol. 9, 555–562 (2012)

    Google Scholar 

  • S.B. Khatau, R.J. Bloom, S. Bajpai et al., The distinct roles of the nucleus and nucleus-cytoskeleton connections in three-dimensional cell migration. Sci. Rep. 2, 488 (2012)

    Google Scholar 

  • T.R. Kiehl, A. Nechiporuk, K.P. Figueroa, M.T. Keating, D.P. Huynh, S.M. Pulst, Generation and characterization of Sca2 (ataxin-2) knockout mice. Biochem. Biophys. Res. Commun. 33, 917–924 (2006)

    Google Scholar 

  • D.I. Kim, B. Kc, W. Zhu, K. Motamedchaboki, V. Doye, K.J. Roux, Probing nuclear pore complex architecture with proximity-dependent biotinylation. Proc. Natl. Acad. Sci. U. S. A., 201406459 (2014a)

    Google Scholar 

  • E. Kim, L. Du, D.B. Bregman, S.L. Warren, Splicing factors associate with hyperphosphorylated RNA polymerase II in the absence of pre-mRNA. J. Cell Biol. 136, 19–28 (1997)

    Google Scholar 

  • J.-K. Kim, A. Louhghalam, G. Lee, B.W. Schafer, D. Wirtz, D.-H. Kim, Nuclear lamin A/C harnesses the perinuclear apical actin cables to protect nuclear morphology. Nat. Commun. 8(1), 2123 (2017)

    ADS  Google Scholar 

  • S.J. Kim, J. Fernandez-Martinez, P. Sampathkumar, et al., Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex. Mol. Cell Proteomics 13, 2911–2926 (2014b)

    Google Scholar 

  • T. Kim, M.L. Gardel, E. Munro, Determinants of fluidlike behavior and effective viscosity in cross-linked actin networks. Biophys. J. 106(3), 526–534 (2014)

    ADS  Google Scholar 

  • N. Kimura, M. Takizawa, K. Okita, O. Natori, K. Igarashi, M. Ueno, K. Nakashima, I. Nobuhisa, T. Taga, Identification of a novel transcription factor, ELYS, expressed predominantly in mouse foetal haematopoietic tissues. Genes Cells 7, 435–446 (2002)

    Google Scholar 

  • M.C. King, C.P. Lusk, G. Blobel, Karyopherin-mediated import of integral inner nuclear membrane proteins. Nature 442, 1003–1007 (2006)

    ADS  Google Scholar 

  • T.J. Kirby, J. Lammerding, Emerging views of the nucleus as a cellular mechanosensor. Nat. Cell Biol. 20(4), 373–381 (2018)

    Google Scholar 

  • T. Kirchhausen, D. Owen, S.C. Harrison, Molecular structure, function, and dynamics of clathrin-mediated membrane traffic. Cold Spring Harb. Perspect. Biol. 6, a016725 (2014)

    Google Scholar 

  • G.L. Kite, The relative permeability of the surface and interior portions of the cytoplasm of animal and plant cells. Biol. Bull. 25, 1–7 (1913)

    Google Scholar 

  • K.E. Knockenhauer, T.U. Schwartz, The nuclear pore complex as a flexible and dynamic gate. Cell 164(6), 1162–1171 (2016)

    Google Scholar 

  • B. Kobe, A.V. Kajava, When protein folding is simplified to protein coiling: the continuum of solenoid protein structures. Trends Biochem. Sci. 25, 509–515 (2000)

    Google Scholar 

  • A.J. Koch, J.M. Holaska, Emerin in health and disease. Semin. Cell Dev. Biol. 29, 95–106 (2014)

    Google Scholar 

  • J. Koh, G. Blobel, Allosteric regulation in gating the central channel of the nuclear pore complex. Cell 161, 1361–1373 (2015)

    Google Scholar 

  • M.H. Koken, G. Linares-Cruz, F. Quignon, A. Viron, K. Chelbi-Alix, J. Sobczak-Thepot, L. Juhlin, L. Degos, F. Calvo, H. de The, The PML growth-suppressor has an altered expression in human oncogenesis. Oncogene 10, 1315–1324 (1995)

    Google Scholar 

  • M.H. Koken, F. Puvion-Dutilleul, M.C. Guillemin, et al., The t(15;17) translocation alters a nuclear body in a retinoic acid-reversible fashion. EMBO J. 13, 1073–1083 (1994)

    Google Scholar 

  • H. Kondo, C. Rabouille, R. Newman, T.P. Levine, D. Pappin, P. Freemont, G. Warren, p47 is a cofactor for p97-mediated membrane fusion. Nature 388, 75–78 (1997)

    Google Scholar 

  • B.E. Koop, J.L. Lewis, A model of fracture testing of soft viscoelastic tissues. J. Biomech. 36(4), 605–608 (2003)

    Article  Google Scholar 

  • V.L. Koumandou, B. Wickstead, M.L. Ginger, M. van der Giezen, J.B. Dacks, M.C. Field, Molecular paleontology and complexity in the last eukaryotic common ancestor. Crit. Rev. Biochem. Mol. Biol. 48, 373–396 (2013)

    Article  Google Scholar 

  • D.M. Kraemer, C. Strambio-de-Castillia, G. Blobel, M.P. Rout, The essential yeast nucleoporin NUP159 is located on the cytoplasmic side of the nuclear pore complex and serves in karyopherin-mediated binding of transport substrate. J. Biol. Chem. 270, 19017–19021 (1995)

    Article  Google Scholar 

  • A. Kralt, J.B. Jagalur, V. van den Boom, R.K. Lokareddy, A. Steen, G. Cingolani, M. Fornerod, L.M. Veenhoff, Conservation of inner nuclear membrane targeting sequences in mammalian Pom121 and yeast Heh2 membrane proteins. Mol. Biol. Cell 26, 3301–3312 (2015)

    Google Scholar 

  • D. Kressler, P. Linder, J. de La Cruz, Protein trans-acting factors involved in ribosome biogenesis in Saccharomyces cerevisiae. Mol. Cell. Biol. 19, 7897–7912 (1999)

    Article  Google Scholar 

  • M.J. Kruhlak, M.A. Lever, W. Fischle, E. Verdin, D.P. Bazett-Jones, M.J. Hendzel, Reduced mobility of the alternate splicing factor (ASF) through the nucleoplasm and steady state speckle compartments. J. Cell Biol. 150, 41–51 (2000)

    Google Scholar 

  • H.H. Ku, Notes on the use of propagation of error formulas. J. Res. Natl. Bur. Stand. 79, 75–79 (1966)

    Google Scholar 

  • U. Kubitscheck, P. Wedekind, O. Zeidler, M. Grote, R. Peters, Single nuclear pores visualized by confocal microscopy and image processing. Biophys. J. 70, 2067–2077 (1996)

    ADS  Google Scholar 

  • A. Kumar, M. Mazzanti, M. Mistrik et al., ATR mediates a checkpoint at the nuclear envelope in response to mechanical stress. Cell 158, 633–646 (2014)

    Google Scholar 

  • A. Kurz, S. Lampel, J.E. Nickolenko, J. Bradl, A. Benner, R.M. Zirbel, T. Cremer, P. Lichter, Active and inactive genes localize preferentially in the periphery of chromosome territories. J. Cell Biol. 135, 1195–1205 (1996)

    Google Scholar 

  • U. Kutay, S. Guttinger, Leucine-rich nuclear-export signals: born to be weak. Trends Cell Biol. 15, 121–124 (2005)

    Google Scholar 

  • A.A. Labokha, S. Gradmann, S. Frey, B.B. Hülsmann, H. Urlaub, M. Baldus, D. Görlich, Systematic analysis of barrier-forming FG hydrogels from Xenopus nuclear pore complexes Embo J. 32, 204–218 (2013)

    Google Scholar 

  • H. Laklai, Y.A. Miroshnikova, M.W. Pickup et al., Genotype tunes pancreatic ductal adenocarcinoma tissue tension to induce matricellular fibrosis and tumor progression. Nat. Med. 22, 497–505 (2016)

    Google Scholar 

  • S. Lall, H. Francis-Lang, A. Flament, A. Norvell, T. Schupbach, D. Ish-Horowicz, Squid hnRNP proteins promotes apical cytoplasmic transport and localization of Drosophila pair-rule transcripts. Cell 98, 171–180 (1999)

    Google Scholar 

  • J. Lammerding, Mechanics of the nucleus. Compr. Physiol. 1(2), 783–807 (2011)

    Google Scholar 

  • A. Lange, R.E. Mills, C.J. Lange, M. Stewart, S.E. Devine, A.H. Corbett, Classical nuclear localization signals: definition, function, and interaction with importin alpha. J. Biol. Chem. 282, 5101–5105 (2007)

    Google Scholar 

  • T.S. Lange, S.A. Gerbi, Transient nucleolar localization of U6 small nuclear RNA in Xenopus laevis oocytes. Mol. Biol. Cell 11, 2419–2448 (2000)

    Article  Google Scholar 

  • K. Lau, H. Tao, H. Liu et al., Anisotropic stress orients remodelling of mammalian limb bud ectoderm. Nat. Cell Biol. 17(5), 569–579 (2015)

    Article  Google Scholar 

  • A. Laugesen, K. Helin, Chromatin repressive complexes in stem cells, development, and cancer. Cell Stem Cell 14, 735–751 (2014)

    Google Scholar 

  • H.Q. Le, S. Ghatak, C.-Y.C. Yeung et al., Mechanical regulation of transcription controls Polycomb-mediated gene silencing during lineage commitment. Nat. Cell Biol. 18, 864–875 (2016)

    Google Scholar 

  • B.J. Lee, A.E. Cansizoglu, S.E. Suel, T.H. Louis, Z. Zhang, Y.M. Chook, Rules for nuclear localization sequence recognition by karyopherin beta 2. Cell 126, 543–558 (2006)

    Google Scholar 

  • M.S. Lee, M. Henry, P.A. Silver, A protein that shuttles between the nucleus and the cytoplasm is an important mediator of RNA export. Genes Dev. 10, 1233–1246 (1996)

    Article  Google Scholar 

  • S.J. Lee, Y. Matsuura, S.M. Liu, M. Stewart, Structural basis for nuclear import complex dissociation by RanGTP. Nature 435, 693–696 (2005)

    Article  Google Scholar 

  • H. Lei, B. Zhai, S. Yin, S. Gygi, R. Reed, Evidence that a consensus element found in naturally intronless mRNAs promotes mRNA export. Nucleic Acids Res. 41, 2517–2525 (2013)

    Article  Google Scholar 

  • C. Lemaître, W.A. Bickmore, Chromatin at the nuclear periphery and the regulation of genome functions. Histochem. Cell Biol. 144, 111–122 (2015)

    Article  Google Scholar 

  • H. Leonhardt, H.-P. Rahn, P. Weinzierl, A. Sporbert, T. Cremer, D. Zink, M.C. Cardoso, Dynamics of DNA replication factories in living cells. J. Cell Biol. 149, 271–279 (2000)

    Article  Google Scholar 

  • K.R. Levental, H. Yu, L. Kass et al., Matrix crosslinking forces tumor progression by enhancing integrin signaling. Cell 139, 891–906 (2009)

    Article  Google Scholar 

  • M.A. Lever, J.P. Thng, X. Sun, M.J. Hendzel, Rapid exchange of histone H1.1 on chromatin in living cells. Nature 408, 873–876 (2000)

    Google Scholar 

  • S.J. Li, M. Hochstrasser, A new protease required for cell-cycle progression in yeast. Nature 398, 246–251 (1999)

    Article  Google Scholar 

  • W.H. Light, J.H. Brickner, Nuclear pore proteins regulate chromatin structure and transcriptional memory by a conserved mechanism. Nucleus 4, 357–360 (2013)

    Article  Google Scholar 

  • W.H. Light, D.G. Brickner, V.R. Brand, J.H. Brickner, Interaction of a DNA zip code with the nuclear pore complex promotes H2A.Z incorporation and INO1 transcriptional memory. Mol. Cell 40, 112–125 (2010)

    Article  Google Scholar 

  • W.H. Light, J. Freaney, V. Sood, A. Thompson, A. D’Urso, C.M. Horvath, J.H. Brickner, A conserved role for human Nup98 in altering chromatin structure and promoting epigenetic transcriptional memory. PLoS Biol. 11, e1001524 (2013)

    Google Scholar 

  • R.Y.H. Lim, B. Fahrenkrog, J. Köser, K. Schwarz-Herion, J. Deng, U. Aebi, Nanomechanical basis of selective gating by the nuclear pore complex. Science 318, 640–643 (2007)

    Article  Google Scholar 

  • H. Liu, J. Wen, Y. Xiao, J. Liu, S. Hopyan, M. Radisic, C.A. Simmons, Y. Sun, In situ mechanical characterization of the cell nucleus by atomic force microscopy. ACS Nano 8(4), 3821–3828 (2014)

    Article  Google Scholar 

  • J. Liu, M.D. Hebert, Y. Ye, D.J. Templeton, H. Kung, A.G. Matera, Cell cycle-dependent localization of the CDK2-cyclin E complex in Cajal (coiled) bodies. J. Cell Sci. 113, 1543–1552 (2000)

    Google Scholar 

  • L. Liu, Q. Luo, J. Sun, S. Guanbin, Nucleus and nucleus-cytoskeleton connections in 3D cell migration. Experimental Cell Res. 348, 56–65 (2016)

    Google Scholar 

  • X. Liu, X. Liu, J.M. Mitchell, R.W. Wozniak, G. Blobel, J. Fan, J. Fan, Structural evolution of the membrane-coating module of the nuclear pore complex. Proc. Natl. Acad. Sci. U. S. A. 109, 16498–16503 (2012)

    Article  Google Scholar 

  • I. Loïodice, A. Alves, G. Rabut, M. Van Overbeek, J. Ellenberg, J.B.Sibarita, V. Doye, The entire Nup107–160 complex, including three new members, is targeted as one entity to kinetochores in mitosis. Mol. Biol. Cell 15, 3333–3344 (2004)

    Google Scholar 

  • R.K. Lokareddy, R.A. Hapsari, M. van Rheenen, R.A. Pumroy, A. Bhardwaj, A. Steen, L. M. Veenhoff, G. Cingolani, Distinctive properties of the nuclear localization signals of inner nuclear membrane proteins Heh1 and Heh2. Structure 23, 1305–1316 (2015)

    Google Scholar 

  • M.L. Lombardi, M. Zwerger, J. Lammerding, Biophysical assays to probe the mechanical properties of the interphase cell nucleus: substrate strain application and microneedle manipulation. J. Vis. Experim. JoVE 55

    Google Scholar 

  • E.A. López-Guerra, S.D. Solares, Modeling viscoelasticity through spring–dashpot models in intermittent-contact atomic force microscopy. Beilstein. J. Nanotechnol. 5, 2149 (2014)

    Article  Google Scholar 

  • C.L. Lorson, J. Strasswimmer, J.D. Yao, J.D. Baleja, E. Hahnen, T. Wirth, T. Le, A.H. Burghes, E.J. Androphy, SMN oligomerization defect correlates with spinal muscular atrophy severity. Nat. Genet. 19, 63–66 (1998)

    Article  Google Scholar 

  • A.R. Lowe, J.H. Tang, J. Yassif, M. Graf, W.Y.C. Huang, J. Groves, K. Weis, J.T. Liphardt, Importin-β modulates the permeability of the nuclear pore complex in a Ran-dependent manner. eLife 4, e04052 (2015)

    Google Scholar 

  • L. Lu, M.S. Ladinsky, T. Kirchhausen, Cisternal organization of the endoplasmic reticulum during mitosis. Mol. Biol. Cell 15, 3471–3480 (2009)

    Google Scholar 

  • M.K. Lund, C. Guthrie, The DEAD-box protein Dbp5p is required to dissociate Mex67p from exported mRNPs at the nuclear rim. Mol. Cell 20, 645–651 (2005)

    Google Scholar 

  • F. Lupu, A. Alves, K. Anderson, V. Doye, E. Lacy, Nuclear pore composition regulates neural stem/progenitor cell differentiation in the mouse embryo. Dev. Cell 14, 831–842 (2008)

    Google Scholar 

  • G.W. Luxton, E.R. Gomes, E.S. Folker, H.J. Worman, G.G. Gundersen, TAN lines: a novel nuclear envelope structure involved in nuclear positioning. Nucleus 2, 173–181 (2011)

    Google Scholar 

  • C.E. Lyon, K. Bohmann, J. Sleeman, A.I. Lamond, Inhibition of protein dephosphorylation results in the accumulation of splicing snRNPs and coiled bodies within the nucleolus. Exp. Cell Res. 230, 84–93 (1997)

    Google Scholar 

  • M.F. Lyon, Gene action in the X chromosome of the mouse. Nature 190, 372–373 (1961)

    ADS  Google Scholar 

  • H. Ma, J. Samarabandu, R.S. Devdhar, R. Acharya, P.C. Cheng, C. Meng, R. Berezney, Spatial and temporal dynamics of DNA replication sites in mammalian cells. J. Cell Biol. 143, 1415–1425 (1998)

    Google Scholar 

  • W.K. Ma, S.C. Cloutier, E.J. Tran, The DEAD-box protein Dbp2 functions with the RNA-binding protein Yra1 to promote mRNP assembly. J. Mol. Biol. 425, 3824–3838 (2013)

    Google Scholar 

  • X.M. Ma, J. Blenis, Molecular mechanisms of mTOR-mediated translational control. Nat. Rev. Mol. Cell Biol. 10, 307–318 (2009)

    Google Scholar 

  • M. Machowska, K. Piekarowicz, R. Rzepecki, Regulation of lamin properties and functions: does phosphorylation do it all? Open Biol. 5, 150094 (2015)

    Google Scholar 

  • B.E. Maden, J.M. Hughes, Eukaryotic ribosomal RNA: the recent excitement in the nucleotide modification problem. Chromosoma 105, 391–400 (1997)

    Google Scholar 

  • T. Maimon, N. Elad, I. Dahan, O. Medalia, The human nuclear pore complex as revealed by cryo-electron tomography. Structure 20, 998–1006 (2012)

    Google Scholar 

  • M. Malatesta, C. Zancanaro, T.E. Martin, E.K. Chan, F. Amalric, R. Luhrmann, P. Vogel, S. Fakan, Cytochemical and immunocytochemical characterization of nuclear bodies during hibernation. Eur. J. Cell Biol. 65, 82–93 (1994)

    Google Scholar 

  • B.J. Mans, V. Anantharaman, L. Aravind, E.V. Koonin, Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex. Cell Cycle 3, 1612–1637 (2004)

    Google Scholar 

  • J. Mansfeld, S. Guttinger, L.A. Hawryluk-Gara, et al., The conserved transmembrane nucleoporin NDC1 is required for nuclear pore complex assembly in vertebrate cells. Mol Cell, 22, 93–103 (2006)

    Google Scholar 

  • L. Manuelidis, Different central nervous system cell types display distinct and nonrandom arrangements of satellite DNA sequences. Proc. Natl. Acad. Sci. U. S. A. 81, 3123–3127 (1984)

    ADS  Google Scholar 

  • L. Manuelidis, A view of interphase chromosomes. Science 250, 1533–1540 (1990)

    ADS  Google Scholar 

  • M. Marelli, D.J. Dilworth, R.W. Wozniak, J.D. Aitchison, The dynamics of karyopherin-mediated nuclear transport. Biochem. Cell Biol. 79, 603–612 (2001)

    Google Scholar 

  • W.F. Marshall, A. Straight, J.F. Marko, J. Swedlow, A. Dernburg, A. Belmont, A.W. Murray, D.A. Agard, J.W. Sedat, Interphase chromosomes undergo constrained diffusional motion in living cells. Curr. Biol. 7, 930–939 (1997)

    Google Scholar 

  • R.P. Martins, J.D. Finan, F. Guilak, D.A. Lee, Mechanical regulation of nuclear structure and function. Annu. Rev. Biomed. Eng. 14, 431–455 (2012)

    Google Scholar 

  • M. Masaeli, D. Gupta, S. O’Byrne et al., Multiparameter mechanical and morphometric screening of cells. Sci. Rep. 6, 37863 (2016)

    ADS  Google Scholar 

  • A.G. Matera, Nuclear bodies: multifaceted subdomains of the interchromatin space. Trends Cell Biol. 9, 302–309 (1999)

    Google Scholar 

  • K.A. Matreyek, A. Engelman, Viral and cellular requirements for the nuclear entry of retroviral preintegration nucleoprotein complexes. Viruses 5, 2483–2511 (2013)

    Google Scholar 

  • A. Mattout, D.S. Cabianca, S.M. Gasser, Chromatin states and nuclear organization in development—a view from the nuclear lamina. Genome Biol. 16, 174 (2015)

    Google Scholar 

  • A. Mattout, T. Dechat, S.A. Adam, R.D. Goldman, Y. Gruenbaum, Nuclear lamins, diseases and aging. Curr. Opin. Cell Biol. 18, 335–341 (2006)

    Google Scholar 

  • G.G. Maul, Nuclear domain 10, the site of DNA virus transcription and replication. Bioessays 20, 660–667 (1998)

    Google Scholar 

  • G.G. Maul, D. Negorev, P. Bell, A.M. Ishov, Review: properties and assembly mechanisms of ND10, PML bodies, or PODs. J. Struct. Biol. 129, 278–287 (2000)

    Google Scholar 

  • J.G. McNally, W.G. Muller, D. Walker, R. Wolford, G.L. Hager, The glucocorticoid receptor: rapid exchange with regulatory sites in living cells. Science 287, 1262–1265 (2000)

    ADS  Google Scholar 

  • A.C. Meinema, J.K. Laba, R.A. Hapsari, R. Otten, F.A.A. Mulder, A. Kralt, G. van den Bogaart, C.P. Lusk, B. Poolman, L.M. Veenhoff, Long unfolded linkers facilitate membrane protein import through the nuclear pore complex. Science 333, 90–93 (2011)

    ADS  Google Scholar 

  • I. Melcak, S. Cermanova, K. Jirsova, K. Koberna, J. Malinsky, I. Raska, Nuclear pre-mRNA compartmentalization: trafficking of released transcripts to splicing factor reservoirs. Mol. Biol. Cell 11, 497–510 (2000)

    Google Scholar 

  • I. Melcák, A. Hoelz, G. Blobel, Structure of Nup58/45 suggests flexible nuclear pore diameter by intermolecular sliding. Science 315, 1729–1732 (2007)

    Google Scholar 

  • T. Melese, Z. Xue, The nucleolus: an organelle formed by the act of building a ribosome. Curr. Opin. Cell Biol. 7, 319–324 (1995)

    Google Scholar 

  • C.T. Mierke, Physical role of nuclear and cytoskeletal confinements in cell migration mode selection and switching. AIMS Biophys. 4(4), 615–658 (2017)

    Google Scholar 

  • E.A. Miller, R. Schekman, COPII - a flexible vesicle formation system. Curr. Opin. Cell Biol. 25, 420–427 (2013)

    Google Scholar 

  • S. Milles, D. Mercadante, I.V. Aramburu et al., Plasticity of an ultrafast interaction between nucleoporins and nuclear transport receptors. Cell 163, 734–745 (2015)

    Google Scholar 

  • P.J. Mintz, S.D. Patterson, A.F. Neuwal, C.S. Spahr, D.L. Spector, Purification and biochemical characterization of interchromatin granule clusters. EMBO J. 18, 4308–4320 (1999)

    Google Scholar 

  • Y.A. Miroshnikova, M.M. Nava, S.A. Wickström, Emerging roles of mechanical forces in chromatin regulation. J. Cell Sci. 130(14), 2243–2250 (2017)

    Google Scholar 

  • Y.A. Miroshnikova, I. Cohen, E. Ezhkova, S.A. Wickström, Epigenetic gene regulation, chromatin structure, and force-induced chromatin remodelling in epidermal development and homeostasis. Curr. Opin. Genet. Dev. 55, 46–51 (2019)

    Google Scholar 

  • T. Misteli, Cell biology of transcription and pre-mRNA splicing: nuclear architecture meets nuclear function. J. Cell Sci. 113, 1841–1849 (2000)

    Google Scholar 

  • T. Misteli, Protein dynamics: implications for nuclear architecture and gene expression. Science 291, 843–847 (2001)

    ADS  Google Scholar 

  • T. Misteli, D.L. Spector, RNA polymerase II targets pre-mRNA splicing factors to transcription sites in vivo. Mol. Cell 3, 697–705 (1999)

    Google Scholar 

  • T. Misteli, A. Agresti, P. Scaffidi et al., Beyond the sequence: cellular organization of genome function. Cell 128, 787–800 (2007)

    Google Scholar 

  • T. Misteli, J.F. Caceres, D.L. Spector, The dynamics of a pre-mRNA splicing factor in living cells. Nature (London) 387, 523–527 (1997)

    ADS  Google Scholar 

  • T. Misteli, A. Gunjan, R. Hock, M. Bustin, D.T. Brown, Dynamic binding of histone H1 to chromatin in living cells. Nature 408, 877–881 (2000)

    Google Scholar 

  • Y. Miyamoto, M.A. Baker, P.A. Whiley, A. Arjomand, J. Ludeman, C. Wong, D.A. Jans, K.L. Loveland, Towards delineation of a developmental alpha-importome in the mammalian male germline. Biochim. Biophys. Acta 1833, 731–742 (2013)

    Google Scholar 

  • D. Mohr, S. Frey, T. Fischer, T. Güttler, D. Görlich, Characterisation of the passive permeability barrier of nuclear pore complexes Embo J. 28, 2541–2553 (2009)

    Google Scholar 

  • A. Monneron, W. Bernhard, Fine structural organization of the interphase nucleus in some mammalian cells. J. Ultrastruct. Res. 27, 266–288 (1969)

    Google Scholar 

  • M.J. Moore, N.J. Proudfoot, Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 136, 688–700 (2009)

    Google Scholar 

  • A. Mor, S. Suliman, R. Ben-Yishay, S. Yunger, Y. Brody, Y. Shav-Tal, Dynamics of single mRNP nucleocytoplasmic transport and export through the nuclear pore in living cells. Nat. Cell Biol. 12, 543–552 (2010)

    Google Scholar 

  • A. Mor, M.A. White, B.M. Fontoura, Nuclear trafficking in health and disease. Curr. Opin. Cell Biol. 28C, 28–35 (2014)

    Google Scholar 

  • F. Mora-Bermudez, D. Gerlich, J. Ellenberg, Maximal chromosome compaction occurs by axial shortening in anaphase and depends on Aurora kinase. Nat. Cell Biol. 9, 822–831 (2007)

    Google Scholar 

  • S. Morchoisne-Bolhy, M.C. Geoffroy, I.B. Bouhlel, A. Alves, N. Audugé, X. Baudin, K. Van Bortle, M.A. Powers, V. Doye, Intranuclear dynamics of the Nup107–160 complex. Mol. Biol. Cell 26, 2343–2356 (2015)

    Google Scholar 

  • G.T. Morgan, O. Doyle, C. Murphy, J.G. Gall, RNA polymerase II in Cajal bodies of amphibian oocytes. J. Struct. Biol. 129, 258–268 (2000)

    Google Scholar 

  • T. Moriuchi, M. Kuroda, F. Kusumoto, T. Osumi, F. Hirose, Lamin A reassembly at the end of mitosis is regulated by its SUMO-interacting motif. Exp. Cell Res. 342, 83–94 (2016)

    Google Scholar 

  • L. Mounkes, S. Kozlov, B. Burke, C.L. Stewart, The laminopathies: nuclear structure meets disease. Curr. Opin. Genet. Dev. 13, 223–230 (2003)

    Google Scholar 

  • R. Moussavi-Baygi, Y. Jamali, R. Karimi, M.R. Mofrad, Brownian dynamics simulation of nucleocytoplasmic transport: a coarse-grained model for the functional state of the nuclear pore complex. PLoS Comput. Biol. 7, e1002049 (2011)

    MathSciNet  ADS  Google Scholar 

  • A. Muchir, H.J. Worman, The nuclear envelope and human disease. Physiology 19, 309–314 (2004)

    Google Scholar 

  • M. Muratani, D. Gerlich, S.M. Janicki, M. Gebhard, R. Eils, D.L. Spector, Metabolic-energy-dependent movement of PML bodies within the mammalian cell nucleus. Nat. Cell Biol. 4, 106–111 (2002)

    Google Scholar 

  • S. Nakielny, U. Fischer, W.M. Michael, G. Dreyfuss, RNA transport. Annu. Rev. Neurosci. 20, 269–301 (1997)

    Google Scholar 

  • A. Narayanan, W. Speckmann, R. Terns, M.P. Terns, Role of the box C/D motif in localization of small nucleolar RNAs to coiled bodies and nucleoli. Mol. Biol. Cell 10, 2131–2147 (1999)

    Google Scholar 

  • E.G. Neilan, Laminopathies, other progeroid disorders, and aging: Common pathogenic themes and possible treatments. Am. J. Med. Genet. A 149A, 563–566 (2009)

    Google Scholar 

  • N. Neumann, D. Lundin, A.M. Poole, Comparative genomic evidence for a complete nuclear pore complex in the last eukaryotic common ancestor. PLoS ONE 5, e13241 (2010)

    ADS  Google Scholar 

  • J. Nickerson, Experimental observations of a nuclear matrix. J. Cell Sci. 114, 463–474 (2001)

    Google Scholar 

  • C.A. Nino, A. Hayakawa, C. Dargemont, A. Babour, Mapping ubiquitin modifications reveals new functions for the yeast nuclear pore complex. Cell Logist. 2, 43–45 (2012)

    Google Scholar 

  • C.A. Nino, L. Herissant, A. Babour, C. Dargemont, mRNA nuclear export in yeast. Chem. Rev. 113, 8523–8545 (2013)

    Google Scholar 

  • L. Niu, T. Ma, F. Yang et al., Atlastin-mediated membrane tethering is critical for cargo mobility and exit from the endoplasmic reticulum. Proc. Natl. Acad. Sci. U. S. A. 116(28), 14029–14038 (2019)

    Google Scholar 

  • H.O. Nousiainen, M. Kestila, N. Pakkasjarvi, H. Honkala, S. Kuure, J. Tallila, K. Vuopala, J. Ignatius, R. Herva, L. Peltonen, Mutations in mRNA export mediator GLE1 result in a fetal motoneuron disease. Chem. Genet. 40, 155–157 (2008)

    Google Scholar 

  • R.T. O’Keefe, S.C. Henderson, D.L. Spector, Dynamic organization of DNA replication in mammalian cell nuclei: spatially and temporally defined replication of chromosome-specific alpha-satellite DNA sequences. J. Cell Biol. 116, 1095–1110 (1992)

    Google Scholar 

  • M. Oakes, J.P. Aris, J.S. Brockenbrough, H. Wai, L. Vu, M. Nomura, Mutational analysis of the structure and localization of the nucleolus in the yeast Saccharomyces cerevisiae. J. Cell Biol. 143, 23–34 (1998)

    Google Scholar 

  • M. Oakes, Y. Nogi, M.W. Clark, M. Nomura, Structural alterations of the nucleolus in mutants of Saccharomyces cerevisiae defective in RNA polymerase I. Mol. Cell. Biol. 13, 2441–2555 (1993)

    Google Scholar 

  • R.L. Ochs, T.W. Stein, E.M. Tan, Coiled bodies in the nucleolus of breast cancer cells. J. Cell Sci. 107, 385–399 (1994)

    Google Scholar 

  • M. Ohsugi, K. Adachi, R. Horai, S. Kakuta, K. Sudo, H. Kotaki, N. Tokai-Nishizumi, H. Sagara, Y. Iwakura, T. Yamamoto, Kid-mediated chromosome compaction ensures proper nuclear envelope formation. Cell 132, 771–782 (2008)

    Google Scholar 

  • A.L. Ollins, G. Rhodes, D.B. Welch, M. Zwerger, D.E. Ollins, Lamin B receptor: multitasking at the nuclear envelope. Nucleus 1, 53–70 (2010)

    Google Scholar 

  • M.O.J. Olson, M. Dundr, A. Szebeni, The nucleolus: An old factory with unexpected capabilities Trends Cell Biol. 10, 189–196 (2000)

    Google Scholar 

  • E. Onischenko, L.H. Stanton, A.S. Madrid, T. Kieselbach, K. Weis, Role of the Ndc1 interaction network in yeast nuclear pore complex assembly and maintenance. J. Cell Biol., 185, 475–491 (2009)

    Google Scholar 

  • A. Ori, N. Banterle, M. Iskar et al., Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines. Mol. Syst. Biol. 9, 648 (2013)

    Google Scholar 

  • E. Orias, M.D. Cervantes, E.P. Hamilton, Tetrahymena thermophila, a unicellular eukaryote with separate germline and somatic genomes. Res. Microbiol. 162, 578–586 (2011)

    Article  Google Scholar 

  • B. Ossareh-Nazari, F. Bachelerie, C. Dargemont, Evidence for a role of CRM1 in signal-mediated nuclear protein export. Science 278, 141–144 (1997)

    Google Scholar 

  • S. Pagliara, K. Franze, C.R. McClain, G.W. Wylde, C.L. Fisher, R.J.M. Franklin, A.J. Kabla, U.F. Keyser, K.J. Chalut, Auxetic nuclei in embryonic stem cells exiting pluripotency. Nat. Mater. 13, 638–644 (2014)

    Article  Google Scholar 

  • J.S. Paige, K.Y. Wu, S.R. Jaffrey, RNA mimics of green fluorescent protein. Science 333, 642–646 (2011)

    Article  Google Scholar 

  • J.D. Pajerowski, K.N. Dahl, F.L. Zhong, P.J. Sammak, D.E. Discher, Physical plasticity of the nucleus in stem cell differentiation. Proc. Natl. Acad. Sci. U. S. A. 104, 15619–15624 (2007)

    Article  Google Scholar 

  • C. Pak, M. Garshasbi, K. Kahrizi et al., Mutation of the conserved polyadenosine RNA binding protein, ZC3H14/dNab2, impairs neural function in Drosophila and humans. Proc. Natl. Acad. Sci. U. S. A. 108, 12390–12395 (2011)

    Article  Google Scholar 

  • N. Pante, M. Kann, Nuclear pore complex is able to transport macromolecules with diameters of about 39 nm. Mol. Biol. Cell 13, 425–434 (2002)

    Google Scholar 

  • P.C. Park, U. De Boni, Transposition of DNase hypersensitive chromatin to the nuclear periphery coincides temporally with nerve growth factor-induced up-regulation of gene expression in PC12 cells. Proc. Natl. Acad. Sci. U. S. A. 93, 11646–11651 (1996)

    ADS  Google Scholar 

  • G. Parry, Assessing the function of the plant nuclear pore complex and the search for specificity. J. Exp. Bot. 64, 833–845 (2013)

    Google Scholar 

  • S.S. Patel, B.J. Belmont, J.M. Sante, M.F. Rexach, Natively unfolded nucleoporins gate protein diffusion across the nuclear pore complex. Cell 129, 83–96 (2007)

    Google Scholar 

  • S. Pawar, R. Ungricht, P. Tiefenboeck, J.C. Leroux, U. Kutay, Efficient protein targeting to the inner nuclear membrane requires Atlastin-dependent maintenance of ER topology. eLife 6, e28202 (2017)

    Google Scholar 

  • T. Pederson, Half a century of ‘‘the nuclear matrix’’. Mol. Biol. Cell 11, 799–805 (2000)

    Google Scholar 

  • T. Pederson, J.C. Politz, The nucleolus and the four ribonucleoproteins of translation. J. Cell Biol. 148, 1091–1095 (2000)

    Google Scholar 

  • O. Peleg, R.Y.H. Lim, Converging on the function of intrinsically disordered nucleoporins in the nuclear pore complex. Biol Chem. 391, 719–730 (2010)

    Google Scholar 

  • L. Pellizzoni, B. Charroux, J. Rappsilber, M. Mann, G. Dreyfuss, A functional interaction between the survival motor neuron complex and RNA polymerase II. J. Cell Biol. 152, 75–86 (2001)

    Google Scholar 

  • P.Y. Perche, C. Vourch, L. Konecny, C. Souchier, M. Robert-Nicoud, S. Dimitrov, S. Khochbin, Higher concentration of histone macro-H2A in the Barr body are correlated with higher nucleosome density. Curr. Biol. 10, 1531–1534 (2000)

    Google Scholar 

  • D. Pérez-Calixto, G. Genaro Vázquez-Victorio, M. Hautefeuille, A viscoelastic nuclear model predicting mechanical memory and convergence rate of nuclear spreading as a function of stiffness bioRxiv (preprint first posted online Feb. 6, 2019). http://dx.doi.org/10.1101/542274)

  • R. Peters, Translocation through the nuclear pore: Kaps pave the way. BioEssays 31, 466–477 (2009)

    Google Scholar 

  • R.D. Phair, T. Misteli, High mobility of proteins in the mammalian cell nucleus. Nature 404, 604–609 (2000)

    Article  Google Scholar 

  • M. Platani, I. Goldberg, J.R. Swedlow, A.I. Lamond, In vivo analysis of Cajal body movement, separation, and joining in live human cells. J. Cell Biol. 151, 1561–1574 (2000)

    Article  Google Scholar 

  • Y.-C. Poh, S.P. Shevtsov, F. Chowdhury, D.C. Wu, S. Na, M. Dundr, N. Wang, Dynamic force-induced direct dissociation of protein complexes in a nuclear body in living cells. Nat. Commun. 3(1), 1038 (2012)

    Article  Google Scholar 

  • J.C. Politz, T. Pederson, Movement of mRNA from transcription site to nuclear pores. J. Struct. Biol. 129, 252–257 (2000)

    Article  Google Scholar 

  • J.C. Politz, E.S. Browne, D.E. Wolf, T. Pederson, Intranuclear diffusion and hybridization state of oligonucleotides measured by fluorescence correlation spectroscopy in living cells. Proc. Natl. Acad. Sci. U. S. A. 95, 6043–6048 (1998)

    ADS  Google Scholar 

  • J.C. Politz, R.A. Tuft, T. Pederson, R.H. Singer, Movement of nuclear poly(A) RNA throughout the interchromatin space in living cells. Curr. Biol. 9, 285–291 (1999)

    Google Scholar 

  • J.C. Politz, S. Yarovoi, S.M. Kilroy, K. Gowda, C. Zwieb, T. Pederson, Signal recognition particle components in the nucleolus. Proc. Natl. Acad. Sci. U. S. A. 97, 55–60 (2000)

    ADS  Google Scholar 

  • B.D. Price, A.D. D’Andrea, Chromatin remodeling at DNA double-strand breaks. Cell 152, 1344–1354 (2013)

    Google Scholar 

  • C. Prives, P.A. Hall, The p53 pathway. J. Pathol. 187, 112–126 (1999)

    Article  Google Scholar 

  • F. Puvion-Dutilleul, S. Mazan, M. Nicoloso, E. Pichard, P. Bachellerie, E. Puvion, Alterations of nucleolar ultrastructure and ribosome biogenesis by actinomycin D. Implications for U3 snRNP function. Eur. J. Cell Biol. 58, 149–162 (1992)

    Google Scholar 

  • F. Puvion-Dutilleul, E. Puvion, J.P. Bachellerie, Early stages of pre-rRNA formation within the nucleolar ultrastructure of mouse cells studied by in situ hybridization with a 5hETS leader probe. Chromosoma 105, 496–505 (1997)

    Google Scholar 

  • X. Qu, S. Lykke-Andersen, T. Nasser, C. Saguez, E. Bertrand, T.H. Jensen, C. Moore, Assembly of an export-competent mRNP is needed for efficient release of the 3′-end processing complex after polyadenylation. Mol. Cell. Biol. 29, 5327–5338 (2009)

    Google Scholar 

  • F. Quignon, F. De Bels, M. Koken, J. Feunteun, J.C. Ameisen, H. de Th, PML induces a novel caspase-independent death process. Nat. Genet. 20, 259–265 (1998)

    Google Scholar 

  • B.B. Quimby, M. Dasso, The small GTPase Ran: interpreting the signs. Curr. Opin. Cell Biol. 15, 338–344 (2003)

    Google Scholar 

  • M. Raab, M. Gentili, H. de Belly et al., ESCRT III repairs nuclear envelope ruptures during cell migration to limit DNA damage and cell death Science 352, 359–362 (2016)

    Google Scholar 

  • M. Rabineau, F. Flick, C. Ehlinger et al., Chromatin de-condensation by switching substrate elasticity. Sci. Rep. 8, 12655 (2018)

    ADS  Google Scholar 

  • G. Rabut, V. Doye, J. Ellenberg, Mapping the dynamic organization of the nuclear pore complex inside single living cells. Nat. Cell Biol. 6, 1114–1121 (2004)

    Google Scholar 

  • M. Raices, M.A. D’Angelo, Nuclear pore complex composition: a new regulator of tissue-specific and developmental functions. Nat. Rev. Mol. Cell Biol. 13, 687–699 (2012)

    Google Scholar 

  • D. Rajgor, J.A. Mellad, F. Autore, Q. Zhang, C.M. Shanahan, Multiple novel nesprin-1 and nesprin-2 variants act as versatile tissue-specific intracellular scaffolds. PLoS ONE 7, e40098

    Google Scholar 

  • K. Ramadan, R. Bruderer, F.M. Spiga, O. Popp, T. Baur, M. Gotta, H.H. Meyer, Cdc48/p 97 promotes reformation of the nucleus by extracting the kinase Aurora B from chromatin. Nature 450, 1258–1262 (2007)

    Google Scholar 

  • B.A. Rasala, A.V. Orjalo, Z. Shen, S. Briggs, D.J. Forbes, ELYS is a dual nucleoporin/kinetochore protein required for nuclear pore assembly and proper cell division. Proc. Natl. Acad. Sci. 103, 17801–17806 (2006)

    ADS  Google Scholar 

  • I. Raska, L.E. Andrade, R.L. Ochs, E.K. Chan, C.M. Chang, G. Roos, E.M. Tan, Immunological and ultrastructural studies of the nuclear coiled body with autoimmune antibodies. Exp. Cell Res. 195, 27–37 (1991)

    Google Scholar 

  • K.L. Reddy, J.M. Zullo, E. Bertolino, H. Singh, Transcriptional repression mediated by repositioning of genes to the nuclear lamina. Nature 452, 243–247 (2008)

    ADS  Google Scholar 

  • R. Reichelt, A. Holzenburg, E.L. Buhle, M. Jarnik, A. Engel, U. Aebi, Correlation between structure and mass distribution of the nuclear pore complex and of distinct pore complex components. J Cell Biol. 110, 883–894 (1990)

    Google Scholar 

  • K. Ribbeck, D. Görlich, Kinetic analysis of translocation through nuclear pore complexes. EMBO J. 20, 1320–1330 (2001)

    Google Scholar 

  • K. Ribbeck, D. Gorlich, The permeability barrier of nuclear pore complexes appears to operate via hydrophobic exclusion. EMBO J. 21, 2664–2671 (2002)

    Google Scholar 

  • G. Rigaud, J. Roux, R. Pictet, T. Grange, vivo footprinting of rat TAT gene: dynamic interplay between the glucocorticoid receptor and a liver-specific factor. Cell 67, 977–986 (1991)

    Google Scholar 

  • C. Robinett, A. Straight, G. Li, C. Willhelm, G. Sudlow, A. Murray, A. Belmont, In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition. J. Cell Biol. 135, 1685–1700 (1996)

    Google Scholar 

  • A. Rothballer, U. Kutay, Poring over pores: nuclear pore complex insertion into the nuclear envelope. Trends Biochem. Sci. 38, 292–301 (2013a)

    Google Scholar 

  • A. Rothballer, U. Kutay, The diverse functional LINCs of the nuclear envelope to the cytoskeleton and chromatin. Chromosoma 122, 415–429 (2013b)

    Google Scholar 

  • A. Rothballer, T.U. Schwartz, U. Kutay, LINCing complex functions at the nuclear envelope: what the molecular architecture of the LINC complex can reveal about its function. Nucleus 4, 29–36 (2013)

    Google Scholar 

  • M.P. Rout, J.D. Aitchison, A. Suprapto, K. Hjertaas, Y. Zhao, B.T. Chait, The yeast nuclear pore complex: composition, architecture, and transport mechanism. J. Cell Biol. 148(4), 635–651 (2000)

    Google Scholar 

  • J.O. Rouviere, M.C. Geoffroy, B. Palancade, Multiple crosstalks between mRNA biogenesis and SUMO. Chromosoma 122, 387–399 (2013)

    Google Scholar 

  • K.J. Roux, M.L. Crisp, Q. Liu, D. Kim, S. Kozlov, C.L. Stewart, B. Burke, Nesprin 4 is an outer nuclear membrane protein that can induce kinesin-mediated cell polarization. Proc. Natl. Acad. Sci. U. S. A. 106, 2194–2199 (2009)

    Google Scholar 

  • A.C. Rowat, J. Lammerding, J.H. Ipsen, Mechanical properties of the cell nucleus and the effect of emerin deficiency. Biophys. J. 91, 4649–4664 (2006)

    Google Scholar 

  • A.C. Rowat, D.E. Jaalouk, M. Zwerger, W.L. Ung, I.A. Eydelnant, D.E. Olins, A.L. Olins, H. Herrmann, D.A. Weitz, J. Lammerding, Nuclear envelope composition determines the ability of neutrophil-type cells to passage through micron-scale constrictions. J. Biol. Chem. 288(12), 8610–8618 (2013).

    Google Scholar 

  • D. Ruggero, Z.G. Wang, P.P. Pandolfi, The puzzling multiple lives of PML and its role in the genesis of cancer. BioEssays 22, 827–835 (2000)

    Google Scholar 

  • K.M. Sakthivel, P. Sehgal, A novel role of lamins from genetic disease to cancer biomarkers. Oncol. Rev. 10, 309 (2016)

    Google Scholar 

  • P. Sampathkumar, S.J. Kim, P. Upla, et al., Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex. Structure 21, 560–571 (2013)

    Google Scholar 

  • J. Sapudom, S. Rubner, S. Martin, T. Kurth, S. Riedel, C.T. Mierke, T. Pompe, The phenotype of cancer cell invasion controlled by fibril diameter and pore size of 3D collagen networks. Biomaterials 52, 367–375 (2015)

    Google Scholar 

  • J.N. Savas, B.H. Toyama, T. Xu, J.R. Yates, M.W. Hetzer, Extremely long-lived nuclear pore proteins in the rat brain. Science 335, 942 (2012)

    ADS  Google Scholar 

  • P. Scaffidi, T. Misteli, Lamin A-dependent nuclear defects in human aging. Science 312, 1059–1063 (2006)

    ADS  Google Scholar 

  • U. Scheer, R. Hock, Structure and function of the nucleolus. Curr. Opin. Cell Biol. 11, 385–390 (1999)

    Google Scholar 

  • E.C. Schirmer, R. Foisner, Proteins that associate with lamins: many faces, many functions. Exp. Cell Res. 313, 2167–2179 (2007)

    Google Scholar 

  • E.C. Schirmer, L. Gerace, The nuclear membrane proteome: extending the envelope. Trends Biochem. Sci. 30, 551–558 (2005)

    Google Scholar 

  • E.C. Schirmer, L. Florens, T. Guan, J.R. Yates, L. Gerace, Nuclear membrane proteins with potential disease links found by subtractive proteomics. Science 301, 1380–1382 (2003)

    Google Scholar 

  • K.D. Schleicher, S.L. Dettmer, L.E. Kapinos, S. Pagliara, U.F. Keyser, S. Jeney, R.Y.H. Lim, Selective transport control on molecular velcro made from intrinsically disordered proteins. Nat. Nanotechnol. 9, 525–530 (2014)

    ADS  Google Scholar 

  • M. Schmid, T.H. Jensen, Nuclear quality control of RNA polymerase II transcripts. Wiley Interdiscip. Rev. RNA 1, 474–485 (2010)

    Google Scholar 

  • H.B. Schmidt, D. Görlich, Nup98 FG domains from diverse species spontaneously phase-separate into particles with nuclear pore-like permselectivity. eLife 4, e04251 (2015)

    Google Scholar 

  • C. Schmitt, C. von Kobbe, A. Bachi, et al., 1999 Dbp5, a DEAD-box protein required for mRNA export, is recruited to the cytoplasmic fibrils of nuclear pore complex via a conserved interaction with CAN/Nup159p. EMBO J. 18, 4332–4347 (2105)

    Google Scholar 

  • R.L. Schoch, L.E. Kapinos, R.Y. Lim, Nuclear transport receptor binding avidity triggers a self-healing collapse transition in FG-nucleoporin molecular brushes. Proc. Natl. Acad. Sci. U. S. A. 109, 16911–16916 (2012)

    ADS  Google Scholar 

  • A. Schooley, B. Vollmer, W. Antonin, Building a nuclear envelope at the end of mitosis: coordinating membrane reorganization, nuclear pore complex assembly, and chromatin de-condensation. Chromosoma 121, 539–554 (2012)

    Google Scholar 

  • N. Schrader, P. Stelter, D. Flemming, R. Kunze, E. Hurt, I.R. Vetter, Structural basis of the nic96 subcomplex organization in the nuclear pore channel. Mol. Cell 29, 46–55 (2008)

    Google Scholar 

  • K.H. Schreiber, B.K. Kennedy, When lamins go bad: nuclear structure and disease. Cell 152, 1365–1375 (2013)

    Google Scholar 

  • S.M. Schreiner, P.K. Koo, Y. Zhao, S.G. Mochrie, M.C. King, The tethering of chromatin to the nuclear envelope supports nuclear mechanics Nature communications 6, 7159 (2015)

    Google Scholar 

  • W. Schul, I. van Der Kraan, A.G. Matera, R. van Driel, L. de Jong, Nuclear domains enriched in RNA 3 h-processing factors associate with coiled bodies and histone genes in a cell cycle-dependent manner. Mol. Biol. Cell 10, 3815–3824 (1999)

    Google Scholar 

  • W. Schul, R. van Driel, L. de Jong, Coiled bodies and U2 snRNA genes adjacent to coiled bodies are enriched in factors required for snRNA transcription. Mol. Biol. Cell 9, 1025–1036 (1998)

    Google Scholar 

  • W. Schul. B. Groenhout, K. Koberna, Y. Takagaki, A. Jenny, E.M. Manders, I. Raska, R. van Driel, L. de Jong, The RNA 3 h cleavage factors CstF 64 kDa and CPSF 100 kDa are concentrated in nuclear domains closely associated with coiled bodies and newly synthesized RNA. EMBO J. 15, 2883–2892 (1996)

    Google Scholar 

  • T.U. Schwartz, Modularity within the architecture of the nuclear pore complex. Curr. Opin. Struct. Biol. 15, 221–226 (2005)

    Google Scholar 

  • A. Segref, K. Sharma, V. Doye, A. Hellwig, J. Huber, R. Luhrmann, E. Hurt, Mex67p, a novel factor for nuclear mRNA export, binds to both poly(A) + RNA and nuclear pores. EMBO J. 16, 3256–3271 (1997)

    Google Scholar 

  • O. Seksek, J. Biwersi, A.S. Verkman, Translational diffusion of macromolecule-sized solutes in cytoplasm and nucleus. J. Cell Biol. 138, 131–142 (1997)

    Google Scholar 

  • W.T. Senapedis, E. Baloglu, Y. Landesman, Clinical translation of nuclear export inhibitors in cancer. Semin. Cancer Biol. 27C, 74–86 (2014)

    Google Scholar 

  • H.S. Seo, B.J. Blus, N.Z. Jankovic, G. Blobel, Structure and nucleic acid binding activity of the nucleoporin Nup157. Proc. Natl. Acad. Sci. U. S. A. 110, 16450–16455 (2013)

    Google Scholar 

  • J. Seong, A. Tajik, J. Sun, J.-L. Guan, M.J. Humphries, S.E. Craig, A. Shekaran, Distinct biophysical mechanisms of focal adhesion kinase mechanoactivation by different extracellular matrix proteins. Proc. Natl. Acad. Sci. U. S. A. 110, 19372–19377 (2013)

    ADS  Google Scholar 

  • C. Shiels, S.A. Islam, R. Vatcheva, P. Sasieni, M.J. Sternberg, P.S. Freemont, D. Sheer, PML bodies associate specifically with the MHC gene cluster in interphase nuclei. J. Cell Sci. 114, 3705–3716 (2001)

    Google Scholar 

  • J.-W. Shin, K.R. Spinler, J. Swift, J.A. Chasis, N. Mohandas, D.E. Discher, Lamins regulate cell trafficking and lineage maturation of adult human hematopoietic cells. Proc. Natl. Acad. Sci. USA 110, 18892–18897 (2013)

    ADS  Google Scholar 

  • L.S. Shopland, M. Byron, J.L. Stein, J.B. Lian, G.S. Stein, J.B. Lawrence, Replication-dependent histone gene expression is related to Cajal body (cb) association but does not require sustained cb contact. Mol. Biol. Cell 12, 565–576 (2001)

    Google Scholar 

  • A.K. Simi, A.S. Piotrowski, C.M. Nelson, Mechanotransduction, metastasis and genomic instability, in Genomic Instability and Cancer Metastasis (Springer International Publishing), pp. 139–158

    Google Scholar 

  • G.D. Sinclair, K. Brasch, The reversible action of a-amanitin on nuclear structure and molecular composition. Exp. Cell Res. 111, 1–14 (1978)

    Google Scholar 

  • O.P. Singh, B. Bjorkroth, S. Masich, L. Wieslander, B. Daneholt, The intranuclear movement of Balbiani ring premessenger ribonucleoprotein particles. Exp. Cell Res. 251, 135–146 (1999)

    Google Scholar 

  • S. Siniossoglou, M. Lutzmann, H. Santos-Rosa, K. Leonard, S. Mueller, U. Aebi, E. Hurt, Structure and assembly of the Nup84p complex. J. Cell Biol. 149, 41–54 (2000)

    Google Scholar 

  • S. Siniossoglou, C. Wimmer, M. Rieger, V. Doye, H. Tekotte, C. Weise, S. Emig, A. Segref, E.C. Hurt, A novel complex of nucleoporins, which includes Sec13p and a Sec13p homolog, is essential for normal nuclear pores. Cell 84, 265–275 (1996)

    Google Scholar 

  • J.E. Sleeman, A.I. Lamond, Newly assembled snRNPs associate with coiled bodies before speckles, suggesting a nuclear snRNP maturation pathway. Curr. Biol. 9, 1065–1074 (1999)

    Google Scholar 

  • C.J. Smoyer, S.L. Jaspersen, Breaking down the wall: the nuclear envelope during mitosis. Curr. Opin. Cell Biol. 26, 1–9 (2014)

    Google Scholar 

  • S. Snaar, K. Wiesmeijer, A.G. Jochemsen, H.J. Tanke, R.W. Dirks, Mutational analysis of fibrillarin and its mobility in living human cells. J. Cell Biol. 151, 653–662 (2000)

    Google Scholar 

  • C.A. Snay-Hodge, H.V. Colot, A.L. Goldstein, C.N. Cole, Dbp5p/Rat8p is a yeast nuclear pore-associated DEAD-box protein essential for RNA export. EMBO J. 17, 2663–2676 (1998)

    Google Scholar 

  • N.T. Snider, M.B. Omary, Post-translational modifications of intermediate filament proteins: mechanisms and functions. Nat. Rev. Mol. Cell Biol. 15, 163–177 (2014)

    Google Scholar 

  • B. Sollner-Webb, K. Tyc, J.A. Steitz, Ribosomal RNA processing in eukaryotes, in Ribosomal RNA: Structure, Evolution, Processing and Function in Protein Synthesis, ed. by R. Zimmerman, A. Dahlberg (CRC Press, Boca Raton, FL, 1996), pp. 469–490

    Google Scholar 

  • S.R. Solmaz, G. Blobel, I. Melcák, Ring cycle for dilating and constricting the nuclear pore. Proc. Natl. Acad. Sci. U. S. A. 110, 5858–5863 (2013)

    ADS  Google Scholar 

  • I. Solovei, A.S. Wang, K. Thanisch, C.S. Schmidt, S. Krebs, M. Zwerger, T.V. Cohen, D. Devys, R. Foisner, L. Peichl, H. Herrmann, H. Blum, D. Engelkamp, C.L. Stewart, H. Leonhardt, B. Joffe, LBR and lamin A/C sequentially tether peripheral heterochromatin and inversely regulate differentiation. Cell 152(3), 584–598 (2013)

    Google Scholar 

  • B.A. Sosa, U. Kutay, T.U. Schwartz, Structural insights into LINC complexes. Curr. Opin. Struct. Biol. 23, 285–291 (2013)

    Google Scholar 

  • B.A. Sosa, A. Rothballer, U. Kutay, T.U. Schwartz, LINC complexes form by binding of three KASH peptides to domain interfaces of trimeric SUN proteins. Cell 149, 1035–1047 (2012)

    Google Scholar 

  • S. Soucek, A.H. Corbett, M.B. Fasken, The long and the short of it: the role of the zinc finger polyadenosine RNA binding protein, Nab2, in control of poly(A) tail length. Biochim. Biophys. Acta 1819, 546–554 (2012)

    Google Scholar 

  • B. Soullam, H.J. Worman, Signals and structural features involved in integral membrane protein targeting to the inner nuclear membrane. J Cell Biol. 130, 15–27 (1995)

    Google Scholar 

  • S.T. Spagnol, K.N. Dahl, Spatially resolved quantification of chromatin condensation through differential local rheology in cell nuclei fluorescence lifetime imaging. PLoS ONE 11(1), e0146244 (2016)

    Google Scholar 

  • D.L. Spector, G. Lark, S. Huang, Differences in snRNP localization between transformed and nontransformed cells. Mol. Biol. Cell 3, 555–569 (1992)

    Google Scholar 

  • K. Stade, C.S. Ford, C. Guthrie, K. Weis, Exportin 1 (Crm1p) is an essential nuclear export factor. Cell 90, 1041–1050 (1997)

    Google Scholar 

  • D.A. Starr, M. Han, ANChors away: an actin based mechanism of nuclear positioning. J. Cell Sci. 116, 211–216 (2003)

    Google Scholar 

  • F. Stavru, B.B. Hülsmann, A. Spang, E. Hartmann, V.C. Cordes, D. Görlich, NDC1: a crucial membrane-integral nucleoporin of metazoan nuclear pore complexes. J Cell Biol. 173, 509–519 (2006)

    Google Scholar 

  • D.L. Stenoien, K. Patel, M.G. Mancini, M. Dutertre, C.L. Smith, B.W. O’Malley, M.A. Mancini, FRAP reveals that mobility of oestrogen receptor-α is ligand and proteasome-dependent. Nat. Cell Biol. 3, 15–23 (2001)

    Google Scholar 

  • A.D. Stephens, E.J. Banigan, S.A. Adam, R.D. Goldman, J.F. Marko, Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus. Mol. Biol. Cell 28(14), 1984–1996 (2017)

    Google Scholar 

  • T. Sternsdorf, T. Grotzinger, K. Jensen, H. Will, Nuclear dots: actors on many stages. Immunobiology 198, 307–331 (1997)

    Google Scholar 

  • C.L. Stewart, B. Burke, The missing LINC: a mammalian KASH-domain protein coupling meiotic chromosomes to the cytoskeleton. Nucleus 5, 3–10 (2014)

    Google Scholar 

  • C.L. Stewart, K.J. Roux, B. Burke, Blurring the boundary: the nuclear envelope extends its reach. Science 318, 1408–1412 (2007)

    ADS  Google Scholar 

  • M. Stewart, Nuclear export of mRNA. Trends Biochem. Sci. 35, 609–617 (2010)

    Google Scholar 

  • Y. Strahm, B. Fahrenkrog, D. Zenklusen, E. Rychner, J. Kantor, M. Rosbach, F. Stutz, The RNA export factor Gle1p is located on the cytoplasmic fibrils of the NPC and physically interacts with the FG-nucleoporin Rip1p, the DEAD-box protein Rat8p/ Dbp5p and a new protein Ymr 255p. EMBO J. 18, 5761–5777 (1999)

    Google Scholar 

  • K. Strasser, E. Hurt, Yra1p, a conserved nuclear RNA-binding protein, interacts directly with Mex67p and is required for mRNA export. EMBO J. 19, 410–420 (2000)

    Google Scholar 

  • K. Strasser, J. Bassler, E. Hurt, Binding of the Mex67p/Mtr2p heterodimer to FXFG, GLFG, and FG repeat nucleoporins is essential for nuclear mRNA export. J. Cell Biol. 150, 695–706 (2000)

    Google Scholar 

  • L.A. Strawn, T. Shen, N. Shulga, D.S. Goldfarb, S.R. Wente, Minimal nuclear pore complexes define FG repeat domains essential for transport. Nat Cell Biol. 6, 197–206 (2004)

    Google Scholar 

  • S. Strudwick, K.L. Borden, Finding a role for PML in APL pathogenesis: a critical assessment of potential PML activities. Leukemia 16, 1906–1917 (2002)

    Google Scholar 

  • T. Stuwe, C.J. Bley, K. Thierbach et al., Architecture of the fungal nuclear pore inner ring complex. Science 350, 56–64 (2015a)

    ADS  Google Scholar 

  • T. Stuwe, A.R. Correia, D.H. Lin, M. Paduch, V.T. Lu, A.A. Kossiakoff, A. Hoelz, Nuclear pores. Architecture of the nuclear pore complex coat. Science 347, 1148–1152 (2015b)

    ADS  Google Scholar 

  • T. Stuwe, D.H. Lin, L.N. Collins, E. Hurt, A. Hoelz, Evidence for an evolutionary relationship between the large adaptor nucleoporin Nup192 and karyopherins. Proc. Natl. Acad. Sci. U. S. A. 111, 2530–2535 (2014)

    Google Scholar 

  • K.E. Suel, H. Gu, Y.M. Chook, Modular organization and combinatorial energetics of proline-tyrosine nuclear localization signals. PLoS Biol. 6, e137 (2008)

    Article  Google Scholar 

  • B.O. Sun, Y. Fang, Z. Li, Z. Chen, J. Xiang, Role of cellular cytoskeleton in epithelial-mesenchymal transition process during cancer progression Biomed. Rep. 3, 603–610 (2015)

    Google Scholar 

  • H. Sun, N. Hattori, W. Chien et al., KPT-330 has antitumour activity against non-small cell lung cancer. Br. J. Cancer 111, 281–291 (2014)

    Article  Google Scholar 

  • J. Swift, D.E. Discher, The nuclear lamina is mechano-responsive to ECM elasticity in mature tissue. J. Cell Sci. 127, 3005–3015 (2014)

    Article  Google Scholar 

  • J. Swift, I.L. Ivanovska, A. Buxboim et al., Nuclear Lamin-A scales with tissue stiffness and enhances matrix-directed differentiation. Science 341, 1240104 (2013)

    Article  Google Scholar 

  • K. Tahara, M. Takagi, M. Ohsugi et al., Importin-b and the small guanosine triphosphatase Ran mediate chromosome loading of the human chromokinesin Kid. J. Cell Biol. 180, 493–506 (2008)

    Article  Google Scholar 

  • A. Tajik, Y. Zhang, F. Wei, J. Sun, Q. Jia, W. Zhou, R. Singh, N. Khanna, A.S. Belmont, N. Wang, Transcription upregulation via force-induced direct stretching of chromatin. Nat. Mater. 15(12), 1287–1296 (2016)

    Google Scholar 

  • K. Tamura, Y. Fukao, M. Iwamoto, T. Haraguchi, I. Hara-Nishimura, Identification and characterization of nuclear pore complex components in Arabidopsis thaliana. Plant Cell 22, 4084–4097 (2010)

    Article  Google Scholar 

  • W. Tao, A.J. Levine, P19(ARF) stabilizes p53 by blocking nucleocytoplasmic shuttling of Mdm2. Proc. Natl. Acad. Sci. U. S. A. 96, 6937–6941 (1999)

    Article  Google Scholar 

  • S. Taranum, I. Sur, R. Muller, W. Lu, R.N. Rashmi, M. Munck, S. Neumann, I. Karakesisoglou, A.A. Noegel, Cytoskeletal interactions at the nuclear envelope mediated by nesprins. Int. J. Cell Biol. 2012, 736524 (2012)

    Article  Google Scholar 

  • Z. Tariq, H. Zhang, A. Chia-Liu, Y. Shen, Y. Gete, Z.-M. Xiong, C. Tocheny, L. Campanello, D. Wu, W. Losert, Lamin A and microtubules collaborate to maintain nuclear morphology. Nucleus 8, 433–446 (2017)

    Article  Google Scholar 

  • B. Terris, V. Baldin, S. Dubois, C. Degott, J.F. Flejou, D. Henin, A. Dejean, PML nuclear bodies are general targets for inflammation and cell proliferation. Cancer Res. 55, 1590–1597 (1995)

    Google Scholar 

  • L.J. Terry, S.R. Wente, Flexible gates: dynamic topologies and functions for FG nucleoporins in nucleocytoplasmic transport. Eukaryot. Cell 8, 1814–1827 (2009)

    Article  Google Scholar 

  • L.J. Terry, E.B. Shows, S.R. Wente, Crossing the nuclear envelope: Hierarchical regulation of nucleocytoplasmic transport. Science 318, 1412–1416 (2007)

    ADS  Google Scholar 

  • P. Tessarz, T. Kouzarides, Histone core modifications regulating nucleosome structure and dynamics. Nat. Rev. Mol. Cell Biol. 15, 703–708 (2014)

    Google Scholar 

  • J. Tetenbaum-Novatt, L.E. Hough, R. Mironska, A.S. McKenney, M.P. Rout, Nucleocytoplasmic transport: a role for nonspecific competition in karyopherin–nucleoporin interactions. Mol. Cell. Proteomics 11, 31–46 (2012)

    Google Scholar 

  • L. Texari, G. Dieppois, P. Vinciguerra, M.P. Contreras, A. Groner, A. Letourneau, F. Stutz, The nuclear pore regulates GAL1 gene transcription by controlling the localization of the SUMO protease Ulp1. Mol. Cell 51, 807–818 (2013)

    Google Scholar 

  • G. Theerthagiri, N. Eisenhardt, W. Schwarz Hand Antonin, The nucleoporin Nup188 controls passage of membrane proteins across the nuclear pore complex. J. Cell Biol. 189, 1129–1142 (2010)

    Google Scholar 

  • H.-R. Thiam, P. Vargas, N. Carpi et al., Perinuclear Arp2/3- driven actin polymerization enables nuclear deformation to facilitate cell migration through complex environments. Nat. Commun. 7, 10997 (2016)

    ADS  Google Scholar 

  • M. Thiry, T. Cheutin, M.F. O’Donohue, H. Kaplan, D. Ploton, Dynamics and three-dimensional localization of ribosomal RNA within the nucleolus. RNA 6, 1750–1761 (2000)

    Google Scholar 

  • V.J. Tocco, Y. Li, K.G. Christopher, J.H. Matthews, V. Aggarwal, L. Paschall, H. Luesch, J.D. Licht, R.B. Dickinson, T.P. Lele, The nucleus is irreversibly shaped by motion of cell boundaries in cancer and non-cancer cells. J. Cell. Physiol. 233(2), 1446–1454 (2018)

    Google Scholar 

  • D. Tollervey, T. Kiss, Function and synthesis of small nucleolar RNAs. Curr. Opin. Cell Biol. 9, 337–342 (1997)

    Google Scholar 

  • M. Torbati, T.P. Lele, A. Agrawal, An unresolved LINC in the nuclear envelope. Cell. Mol. Bioeng. 9, 252–257 (2016)

    Google Scholar 

  • B.H. Toyama, J.N. Savas, S.K. Park, M.S. Harris, N.T. Ingolia, J.R. Yates, M.W. Hetzer, Identification of long-lived proteins reveals exceptional stability of essential cellular structures. Cell 154, 971–982 (2013)

    Google Scholar 

  • E.J. Tran, S.R. Wente, Dynamic nuclear pore complexes: life on the edge. Cell 125, 1041–1053 (2006)

    Google Scholar 

  • E.J. Tran, M.C. King, A.H. Corbett, Macromolecular transport between the nucleus and the cytoplasm: advances in mechanism and emerging links to disease. Biochim. Biophys. Acta 1843(11), 2784–2795 (2014)

    Google Scholar 

  • R.J. Tran, Y. Zhou, A.H. Corbett, S.R. Wente, The DEAD-box protein Dbp5 controls mRNA export by triggering specific RNA: protein remodeling events. Mol. Cell 28, 850–859 (2007)

    Google Scholar 

  • T. Tsukamoto, N. Hashiguchi, S.M. Janicki, T. Tumbar, A.S. Belmont, D.L. Spector, Visualization of gene activity in living cells. Nat. Cell Biol. 2, 871–878 (2000)

    Google Scholar 

  • L.C. Tu, G. Fu, A. Zilman, S.M. Musser, Large cargo transport by nuclear pores: implications for the spatial organization of FG-nucleoporins EMBO J. 32, 3220–3230 (2013)

    Google Scholar 

  • T. Tumbar, A.S. Belmont, Interphase movements of a DNA chromosome region modulated by VP16 transcriptional activator. Nat. Cell Biol. 3, 134–139 (2001)

    Google Scholar 

  • T. Tumbar, G. Sudlow, A.S. Belmont, Large-scale chromatin unfolding and remodeling induced by VP16 acidic activation domain. J. Cell Biol. 145, 1341–1353 (1999)

    Google Scholar 

  • S. Tyagi, V. Vandelinder, N. Banterle, G. Fuertes, S. Milles, M. Agez, E.A. Lemke, Continuous throughput and long-term observation of single-molecule FRET without immobilization. Nat. Methods 11, 297–300 (2014)

    Google Scholar 

  • Y.B. Tzur, K.L. Wilson, Y. Gruenbaum, SUN-domain proteins: ‘Velcro’ that links the nucleoskeleton to the cytoskeleton. Nat. Rev. Mol. Cell Biol. 7, 782–788 (2006)

    Google Scholar 

  • C. Uhler, G.V. Shivashankar, Nuclear mechanopathology and cancer diagnosis. Trends in Cancer 4, 320–331 (2019)

    Google Scholar 

  • S. Ulbert, M. Platani, S. Boue, I.W. Mattaj, Direct membrane protein-DNA interactions required early in nuclear envelope assembly. J. Cell Biol. 173, 469–476 (2006)

    Google Scholar 

  • A. Ulrich, J.R. Partridge, T.U. Schwartz, The stoichiometry of the nucleoporin 62 subcomplex of the nuclear pore in solution. Mol. Biol. Cell 25, 1484–1492 (2014)

    Google Scholar 

  • R. Ungricht, U. Kutay, Establishment of NE asymmetry—targeting of membrane proteins to the inner nuclear membrane. Curr. Opin Cell Biol. 34, 135–141 (2015)

    Google Scholar 

  • R. Ungricht, U. Kutay, Mechanisms and functions of nuclear envelope remodelling. Nat. Rev. Mol. Cell Biol. 18, 229–245 (2017)

    Google Scholar 

  • R. Ungricht, M. Klann, P. Horvath, U. Kutay, Diffusion and retention are major determinants of protein targeting to the inner nuclear membrane. J. Cell Biol. 209, 687–703 (2015)

    Google Scholar 

  • R. Ungricht, S. Pawar, U. Kutay, An in vitro assay to study targeting of membrane proteins to the inner nuclear membrane. Methods Mol. Biol. 1411, 461–477 (2016)

    Google Scholar 

  • P. Valencia, A.P. Dias, R. Reed, Splicing promotes rapid and efficient mRNA export in mammalian cells. Proc. Natl. Acad. Sci. U. S. A. 105, 3386–3391 (2008)

    ADS  Google Scholar 

  • C. Verheggen, G. Almouzni, D. Hernandez-Verdun, The ribosomal RNA processing machinery is recruited to the nucleolar domain before RNA polymerase I during Xenopus laevis development. J. Cell Biol. 149, 293–306 (2000)

    Google Scholar 

  • P.J. Verschure, I. van der Kraan, E.M.M. Manders, R. van Driel, Spatial relationship between transcription sites and chromosome territories. J. Cell Biol. 147, 13–24 (1999)

    Google Scholar 

  • I.R. Vetter, A. Arndt, U. Kutay, D. Gorlich, A. Wittinghofer, Structural view of the Ran–Importin beta interaction at 2.3 A resolution. Cell 97, 635–646 (1999)

    Google Scholar 

  • J.F. Vincent, Structural Biomaterials (Princeton University Press, 2012)

    Google Scholar 

  • A. Vitaliano-Prunier, A. Babour, L. Herissant, L. Apponi, T. Margaritis, F.C. Holstege, A.H. Corbett, C. Gwizdek, C. Dargemont, H2B ubiquitylation controls the formation of export-competent mRNP. Mol. Cell 45, 132–139 (2012)

    Google Scholar 

  • S. Vlcek, R. Foisner, Lamins and lamin-associated proteins in aging and disease. Curr. Opin. Cell Biol. 19, 298–304 (2007)

    Google Scholar 

  • G.K. Voeltz, W.A. Prinz, Sheets, ribbons and tubules-how organelles get their shape. Nat. Rev. Mol. Cell Biol. 8, 258–264 (2007)

    Google Scholar 

  • B. Vollmer, W. Antonin, The diverse roles of the Nup93/Nic96 complex proteins—structural scaffolds of the nuclear pore complex with additional cellular functions. Biol. Chem. 395, 515–528 (2014)

    Google Scholar 

  • L. Volpon, M.J. Osborne, H. Zahreddine, A.A. Romeo, K.L. Borden, Conformational changes induced in the eukaryotic translation initiation factor eIF4E by a clinically relevant inhibitor, ribavirin triphosphate. Biochem. Biophys. Res. Commun. 434, 614–619 (2013)

    Google Scholar 

  • A. von Appen, J. Kosinski, L. Sparks et al., In situ structural analysis of the human nuclear pore complex. Nature 526, 140–143 (2015)

    Article  Google Scholar 

  • J.M. Wallace, Applications of atomic force microscopy for the assessment of nanoscale morphological and mechanical properties of bone. Bone 50, 420–427 (2012)

    Google Scholar 

  • T.C. Walther, A. Alves, H. Pickersgill, et al., The conserved Nup107-160 complex is critical for nuclear pore complex assembly. Cell 113, 195–206 (2003)

    Google Scholar 

  • J. Wang, C. Shiels, P. Sasieni, P.J. Wu, S.A. Islam, P.S. Freemont, D. Sheer, Promyelocytic leukemia nuclear bodies associate with transcriptionally active genomic regions. J. Cell Biol. 164, 515–526 (2004)

    Google Scholar 

  • N. Wang, J.D. Tytell, D.E. Ingber, Mechanotransduction at a distance: mechanically coupling the extracellular matrix with the nucleus. Nat. Rev. Mol. Cell Biol. 10(1), 75–82 (2009)

    Google Scholar 

  • X. Wang, H. Liu, M. Zhu, et al., Mechanical stability of the cell nucleus—roles played by the cytoskeleton in nuclear deformation and strain recovery. J. Cell Sci. 131, jcs209627 (2018)

    Google Scholar 

  • D.G. Wansink, W. Schul, I. van der Kraan, B. van Steensel, R. van Driel, L. de Jong, Fluorescent labeling of nascent RNA reveals transcription by RNA polymerase II in domains scattered throughout the nucleus. J. Cell Biol. 122, 283–293 (1993)

    Google Scholar 

  • M. Wasser, W. Chia, The EAST protein of Drosophila controls an expandable nuclear endoskeleton. Nat. Cell Biol. 2, 268–275 (2000)

    Google Scholar 

  • M.L. Watson, The nuclear envelope; its structure and relation to cytoplasmic membranes. J. Biophys. Biochem. Cytol. 1, 257–270 (1955)

    Google Scholar 

  • J.D. Weber, L.J. Taylor, M.F. Roussel, C.J. Sherr, D. Bar-Sagi, Nucleolar Arf sequesters Mdm2 and activates p53. Nat. Cell Biol. 1, 20–27 (1999)

    Google Scholar 

  • C.S. Weirich, J.P. Erzberger, J.S. Flick, J.M. Berger, J. Thorner, K. Weis, Activation of the DExD/H-box protein Dbp5 by the nuclear-pore protein Gle1 and its coactivator InsP6 is required for mRNA export. Nat. Cell Biol. 8, 668–676 (2006)

    Google Scholar 

  • K. Weis, The nuclear pore complex: oily spaghetti or gummy bear? Cell 130, 405–407 (2007)

    Google Scholar 

  • S.R. Wente, L. Burns, From hypothesis to mechanism: uncovering nuclear pore complex links to gene expression. Mol. Biol. Cell 34(12), 2114–2120 (2014)

    Google Scholar 

  • S.R. Wente, M.P. Rout, The nuclear pore complex and nuclear transport. Cold Spring Harb. Perspect. Biol. 2, a000562 (2010)

    Google Scholar 

  • J.R.R. Whittle, T.U. Schwartz, Architectural nucleoporins Nup157/170 and Nup133 are structurally related and descend from a second ancestral element. J Biol Chem. 284, 28442–28452 (2009)

    Google Scholar 

  • K. Wiesmeijer, C. Molenaar, I.M. Bekeer, H.J. Tanke, R.W. Dirks, Mobile foci of Sp100 do not contain PML: PML bodies are immobile but PML and Sp100 proteins are not. J. Struct. Biol. 140, 180–188 (2002)

    Google Scholar 

  • P. Wild, C. Senn, C.L. Manera, E. Sutter, E.M. Schraner, K. Tobler, M. Ackermann, U. Ziegler, M.S. Lucas, A. Kaech, Exploring the nuclear envelope of herpes simplex virus 1-infected cells by high-resolution microscopy. J. Virol. 83, 408–419 (2009)

    Google Scholar 

  • K. Wilhelmsen, M. Ketema, H. Truong, A. Sonnenberg, KASH-domain proteins in nuclear migration, anchorage and other processes. J. Cell Sci. 119, 5021–5029 (2006)

    Google Scholar 

  • K. Wilhelmsen, S.H. Litjens, I. Kuikman, N. Tshimbalanga, H. Janssen, I. van den Bout, K. Raymond, A. Sonnenberg, Nesprin-3, a novel outer nuclear membrane protein, associates with the cytoskeletal linker protein plectin. J. Cell Biol. 171, 799–810 (2005)

    Google Scholar 

  • S.L. Wolin, A.G. Matera, The trials and travels of tRNA. Genes Dev. 13, 1–10 (1999)

    Google Scholar 

  • J.L. Workman, R.E. Kingston, Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu. Rev. Biochem. 67, 545–579 (1998)

    Google Scholar 

  • H.J. Worman, G. Bonne, “Laminopathies”: awide spectrum of human diseases. Exp. Cell Res. 313, 2121–2133 (2007)

    Google Scholar 

  • H.J. Worman, J.C. Courvalin, The inner nuclear membrane. J. Membr. Biol. 177, 1–11 (2000)

    Google Scholar 

  • Y. Xing, J.B. Lawrence, Nuclear RNA tracks: structural basis for transcription and splicing? Trends Cell Biol. 3, 346–353 (1993)

    Google Scholar 

  • Y. Xing, C.V. Johnson, P.R. Dobner, J.B. Lawrence, Higher level organization of individual gene transcription and RNA splicing. Science 259, 1326–1330 (1993)

    ADS  Google Scholar 

  • Y. Xing, C.V. Johnson, P.T. Moen, J.A. McNeil, J.B. Lawrence, Nonrandom gene organization: Structural arrangements of specific pre-mRNA transcription and splicing with SC-35 domains. J. Cell Biol. 131, 1635–1647 (1995)

    Google Scholar 

  • C. Xu, Z. Li, H. He, A. Wernimont, Y. Li, P. Loppnau, J. Min, Crystal structure of human nuclear pore complex component NUP43. FEBS Lett. 589, 3247–3253 (2015)

    Google Scholar 

  • D. Xu, A. Farmer, Y.M. Chook, Recognition of nuclear targeting signals by Karyopherin-beta proteins. Curr. Opin. Struct. Biol. 20, 782–790 (2010)

    Google Scholar 

  • Q. Yang, M.P. Rout, C.W. Akey, Three-dimensional architecture of the isolated yeast nuclear pore complex: functional and evolutionary implications. Mol. Cell 1, 223–234 (1998)

    Google Scholar 

  • Y. Yang, C. Isaac, C. Wang, F. Dragon, V. Pogacic, U.T. Meier, Conserved composition of mammalian box H/ACA and box C/D small nucleolar ribonucleoprotein particles and their interaction with the common factor Nopp140. Mol. Biol. Cell 11, 567–577 (2000)

    Google Scholar 

  • Y. Ye, H.H. Meyer, T.A. Rapoport, Function of the p 97- Ufd1-Npl4 complex in retrotranslocation from the ER to the cytosol: Dual recognition of nonubiquitinated polypeptide segments and polyubiquitin chains. J. Cell Biol. 162, 71–84 (2003)

    Google Scholar 

  • Z. Zachar, J. Kramer, P.M. Bingham, Evidence for channeled diffusion of pre-mRNAs during nuclear RNA transport in metazoans. J. Cell Biol. 121, 729–742 (1993)

    Google Scholar 

  • M.H. Zaman, L.M. Trapani, A.L. Sieminski, D. Mackellar, H. Gong, R.D. Kamm, A. Wells, D.A. Lauffenburger, P. Matsudaira, Migration of tumor cells in 3D matrices is governed by matrix stiffness along with cell-matrix adhesion and proteolysis. Proc. Natl. Acad. Sci. U. S. A. 103, 10889–10894 (2006)

    ADS  Google Scholar 

  • G. Zanetti, K.B. Pahuja, S. Studer, S. Shim, R. Schekman, COPII and the regulation of protein sorting in mammals Nat Cell Biol. 14, 20–28 (2012)

    Google Scholar 

  • Q. Zhang, C. Ragnauth, M.J. Greener, C.M. Shanahan, R.G. Roberts, The nesprins are giant actin-binding proteins, orthologous to Drosophila melanogaster muscle protein MSP-300. Genomics 80, 473–481 (2002)

    Google Scholar 

  • Q. Zhang, J.N. Skepper, F. Yang, J.D. Davies, L. Hegyi, R.G. Roberts, P.L. Weissberg, J.A. Ellis, C.M. Shanahan, Nesprins: a novel family of spectrin-repeat-containing proteins that localize to the nuclear membrane in multiple tissues. J. Cell Sci. 114(Pt 24), 4485–4498

    Google Scholar 

  • Y. Zhang, Y. Xiong, Mutations in human ARF exon 2 disrupt its nucleolar localization and impair its ability to block nuclear export of MDM2 and p53. Mol. Cell 3, 579–591 (1999)

    Google Scholar 

  • Y. Zhao, I. Meier, Efficient plant male fertility depends on vegetative nuclear movement mediated by two families of plant outer nuclear membrane proteins. Proc. Natl. Acad. Sci. U. S. A 111(32), 11900–11905 (2014)

    ADS  Google Scholar 

  • Y. Zheng, S. Gery, H. Sun, S. Shacham, M. Kauffman, H.P. Koeffler, KPT-330 inhibitor of XPO1-mediated nuclear export has anti-proliferative activity in hepatocellular carcinoma. Cancer Chemother. Pharmacol. 74(3), 487–495 (2014)

    Google Scholar 

  • X. Zhou, I. Meier, How plants LINC the SUN to KASH. Nucleus 4, 206–215 (2013)

    Google Scholar 

  • X. Zhou, K. Graumann, D.E. Evans, I. Meier, Novel plant SUN-KASH bridges are involved in RanGAP anchoring and nuclear shape determination. J. Cell Biol. 196, 203–211 (2012)

    Google Scholar 

  • Z. Zhou, M.J. Luo, K. Straesser, J. Katahira, E. Hurt, R. Reed, The protein Aly links pre-messenger-RNA splicing to nuclear export in metazoans. Nature 407, 401–405 (2000)

    ADS  Google Scholar 

  • M. Zwerger, C.Y. Ho, J. Lammerding, Nuclear mechanics in disease. Annu. Rev. Biomed. Eng. 13, 397–428 (2011)

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Claudia Tanja Mierke .

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Mierke, C.T. (2020). The Cell Nucleus and Its Compartments. In: Cellular Mechanics and Biophysics. Biological and Medical Physics, Biomedical Engineering. Springer, Cham. https://doi.org/10.1007/978-3-030-58532-7_10

Download citation

Publish with us

Policies and ethics