Dynamics of gene expression regulatory proteins in the living cell nucleus

Abstract

The intricate physical interaction of transcription factors with specific target genes in the genome has long been regarded as a fundamental mechanism of cell-type specific gene expression. However, due to insufficient spatiotemporal resolution of microscopy techniques, direct visualization of protein dynamics within the nuclei of living cells had not been achieved for decades. Resolving existing limitations, recent advances in imaging techniques enabled the direct observation of protein dynamics, even at a single-molecule level. In addition, the new imaging techniques accomplished capturing higher-order chromatin structures that influence gene expression regulation along with transcription factor dynamics. This review discusses the recent applications of microscopy techniques to investigate the dynamics of nuclear proteins in living cells and their achievements.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2

References

  1. 1.

    M.E. Levine, J.A. Suarez, S. Brandhorst, P. Balasubramanian, C.-W. Cheng, F. Madia, L. Fontana, M.G. Mirisola, J. Guevara-Aguirre, J. Wan, Low protein intake is associated with a major reduction in IGF-1, cancer, and overall mortality in the 65 and younger but not older population. Cell. Metab. 19, 407 (2014)

    Article  Google Scholar 

  2. 2.

    S.T. Hess, T.P. Girirajan, M.D. Mason, Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys. J. 91, 4258 (2006)

    Article  ADS  Google Scholar 

  3. 3.

    M.J. Rust, M. Bates, X. Zhuang, Stochastic optical reconstruction microscopy (STORM) provides sub-diffraction-limit image resolution. Nat. Methods. 3, 793 (2006)

    Article  Google Scholar 

  4. 4.

    M.G. Gustafsson, Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J. Microsc. 198, 82 (2000)

    Article  Google Scholar 

  5. 5.

    S.W. Hell, J. Wichmann, Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy. Opt. Lett. 19, 780 (1994)

    Article  ADS  Google Scholar 

  6. 6.

    A.H. Voie, D. Burns, F. Spelman, Orthogonal-plane fluorescence optical sectioning: Three-dimensional imaging of macroscopic biological specimens. J. Microsc. 170, 229 (1993)

    Article  Google Scholar 

  7. 7.

    J. Dekker, K. Rippe, M. Dekker, N. Kleckner, Capturing chromosome conformation. Science 295, 1306 (2002)

    Article  ADS  Google Scholar 

  8. 8.

    M. Simonis, P. Klous, E. Splinter, Y. Moshkin, R. Willemsen, E. De Wit, B. Van Steensel, W. De Laat, Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C). Nat. Genet. 38, 1348 (2006)

    Article  Google Scholar 

  9. 9.

    J.D. Lieb, X. Liu, D. Botstein, P.O. Brown, Promoter-specific binding of Rap1 revealed by genome-wide maps of protein–DNA association. Nat. Genet. 28, 327 (2001)

    Article  Google Scholar 

  10. 10.

    J. Kazakevych, S. Sayols, B. Messner, C. Krienke, N. Soshnikova, Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells. Nucleic Acids Res. 45, 5770 (2017)

    Article  Google Scholar 

  11. 11.

    M. Lisby, U.H. Mortensen, R. Rothstein, Colocalization of multiple DNA double-strand breaks at a single Rad52 repair centre. Nat. Cell Biol. 5, 572 (2003)

    Article  Google Scholar 

  12. 12.

    B. Huang, M. Bates, X. Zhuang, Super-resolution fluorescence microscopy. Annu. Rev. Biochem. 78, 993 (2009)

    Article  Google Scholar 

  13. 13.

    D.M. Shcherbakova, A.A. Shemetov, A.A. Kaberniuk, V.V. Verkhusha, Natural photoreceptors as a source of fluorescent proteins, biosensors, and optogenetic tools. Annu. Rev. Biochem. 84, 519 (2015)

    Article  Google Scholar 

  14. 14.

    I.I. Cisse, I. Izeddin, S.Z. Causse, L. Boudarene, A. Senecal, L. Muresan, C. Dugast-Darzacq, B. Hajj, M. Dahan, X. Darzacq, Real-time dynamics of RNA polymerase II clustering in live human cells. Science 341, 664 (2013)

    Article  ADS  Google Scholar 

  15. 15.

    W.-K. Cho, J.-H. Spille, M. Hecht, C. Lee, C. Li, V. Grube, I.I. Cisse, Mediator and RNA polymerase II clusters associate in transcription-dependent condensates. Science 361, 412 (2018)

    Article  ADS  Google Scholar 

  16. 16.

    J. Xu, H. Ma, J. Jin, S. Uttam, R. Fu, Y. Huang, Y. Liu, Super-resolution imaging of higher-order chromatin structures at different epigenomic states in single mammalian cells. Cell Rep. 24, 873 (2018)

    Article  Google Scholar 

  17. 17.

    C. Xia, H.P. Babcock, J.R. Moffitt, X. Zhuang, Multiplexed detection of RNA using MERFISH and branched DNA amplification. Sci. Rep. 9, 1 (2019)

    Article  Google Scholar 

  18. 18.

    M.G. Gustafsson, L. Shao, P.M. Carlton, C.R. Wang, I.N. Golubovskaya, W.Z. Cande, D.A. Agard, J.W. Sedat, Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination. Biophys. J. 94, 4957 (2008)

    Article  Google Scholar 

  19. 19.

    J. Chojnacki, C. Eggeling, Super-resolution fluorescence microscopy studies of human immunodeficiency virus. Retrovirology 15, 41 (2018)

    Article  Google Scholar 

  20. 20.

    B.-C. Chen, W.R. Legant, K. Wang, L. Shao, D.E. Milkie, M.W. Davidson, C. Janetopoulos, X.S. Wu, J.A. Hammer, Z. Liu, Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution. Science 346, 1257998 (2014)

    Article  Google Scholar 

  21. 21.

    W.-K. Cho, N. Jayanth, B.P. English, T. Inoue, J.O. Andrews, W. Conway, J.B. Grimm, J.-H. Spille, L.D. Lavis, T. Lionnet, RNA Polymerase II cluster dynamics predict mRNA output in living cells. Elife 5, e13617 (2016)

    Article  Google Scholar 

  22. 22.

    B.R. Sabari, A. Dall’Agnese, A. Boija, I.A. Klein, E.L. Coffey, K. Shrinivas, B.J. Abraham, N.M. Hannett, A.V. Zamudio, J.C. Manteiga, Coactivator condensation at super-enhancers links phase separation and gene control. Science 361, eaar3958 (2018)

    Article  Google Scholar 

  23. 23.

    Z. Liu, W.R. Legant, B.-C. Chen, L. Li, J.B. Grimm, L.D. Lavis, E. Betzig, R. Tjian, 3D imaging of Sox2 enhancer clusters in embryonic stem cells. Elife 3, e04236 (2014)

    Article  Google Scholar 

  24. 24.

    P. Filippakopoulos, J. Qi, S. Picaud, Y. Shen, W.B. Smith, O. Fedorov, E.M. Morse, T. Keates, T.T. Hickman, I. Felletar, Selective inhibition of BET bromodomains. Nature 468, 1067 (2010)

    Article  ADS  Google Scholar 

  25. 25.

    J. Lovén, H.A. Hoke, C.Y. Lin, A. Lau, D.A. Orlando, C.R. Vakoc, J.E. Bradner, T.I. Lee, R.A. Young, Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell 153, 320 (2013)

    Article  Google Scholar 

  26. 26.

    E. Gomes, J. Shorter, The molecular language of membraneless organelles. J. Biol. Chem. 294, 7115 (2019)

    Article  Google Scholar 

  27. 27.

    A.A. Hyman, C.A. Weber, F. Jülicher, Liquid-liquid phase separation in biology. Annu. Rev. Cell Dev. Biol. 30, 39 (2014)

    Article  Google Scholar 

  28. 28.

    T.K. Meyvis, S.C. De Smedt, P. Van Oostveldt, J. Demeester, Fluorescence recovery after photobleaching: a versatile tool for mobility and interaction measurements in pharmaceutical research. Pharm. Res. 16, 1153 (1999)

    Article  Google Scholar 

  29. 29.

    J. Dekker, L. Mirny, The 3D genome as moderator of chromosomal communication. Cell 164, 1110 (2016)

    Article  Google Scholar 

  30. 30.

    J.R. Dixon, S. Selvaraj, F. Yue, A. Kim, Y. Li, Y. Shen, M. Hu, J.S. Liu, B. Ren, Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376 (2012)

    Article  ADS  Google Scholar 

  31. 31.

    A.S. Hansen, I. Pustova, C. Cattoglio, R. Tjian, X. Darzacq, CTCF and cohesin regulate chromatin loop stability with distinct dynamics. Elife 6, e25776 (2017)

    Article  Google Scholar 

  32. 32.

    S.S. Rao, M.H. Huntley, N.C. Durand, E.K. Stamenova, I.D. Bochkov, J.T. Robinson, A.L. Sanborn, I. Machol, A.D. Omer, E.S. Lander, A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665 (2014)

    Article  Google Scholar 

  33. 33.

    A.D. Schmitt, M. Hu, I. Jung, Z. Xu, Y. Qiu, C.L. Tan, Y. Li, S. Lin, Y. Lin, C.L. Barr, A compendium of chromatin contact maps reveals spatially active regions in the human genome. Cell Rep 17, 2042 (2016)

    Article  Google Scholar 

Download references

Acknowledgements

This article is written by researchers supported by Basic Science Research Programs through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2019R1A6A1A10073887) and the Ministry of Science and ICT (2020R1C1C1014599; 2019M3A9H1103711).

Author information

Affiliations

Authors

Corresponding author

Correspondence to Won-Ki Cho.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Shim, H., Park, T.L. & Cho, WK. Dynamics of gene expression regulatory proteins in the living cell nucleus. J. Korean Phys. Soc. 78, 379–385 (2021). https://doi.org/10.1007/s40042-020-00043-5

Download citation

Keywords

  • Fluorescence microscopy
  • Super-resolution
  • Gene expression regulation
  • Protein dynamics