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Biochemistry (Moscow)

, Volume 83, Issue 5, pp 586–594 | Cite as

An Inducible DamID System for Profiling Interactions of Nuclear Lamina Protein Component Lamin B1 with Chromosomes in Mouse Cells

  • E. N. KozhevnikovaEmail author
  • A. E. Leshchenko
  • A. V. Pindyurin
Article
  • 321 Downloads

Abstract

At the level of DNA organization into chromatin, there are mechanisms that define gene expression profiles in specialized cell types. Genes within chromatin regions that are located at the nuclear periphery are generally expressed at lower levels; however, the nature of this phenomenon remains unclear. These parts of chromatin interact with nuclear lamina proteins like Lamin B1 and, therefore, can be identified in a given cell type by chromatin profiling of these proteins. In this study, we created and tested a Dam Identification (DamID) system induced by Cre recombinase using Lamin B1 and mouse embryonic fibroblasts. This inducible system will help to generate genome-wide profiles of chromatin proteins in given cell types and tissues with no need to dissect tissues from organs or separate cells from tissues, which is achieved by using specific regulatory DNA elements and due to the high sensitivity of the method.

Keywords

inducible DamID system Lamin B1 CRISPR/Cas9 chromatin mouse embryonic fibroblasts 

Abbreviations

Amp[r]

ampicillin resistance gene

CMV

cytomegalovirus

Dam

DNA adenine methyltransferase

DamID

DNA adenine methyltransferase identification

gDNA

genomic DNA

mePCR

methyl PCR (amplification of Dam-methylated genome fragments)

ori

replication origin

RLA

Rosa Left Arm

RRA

Rosa Right Arm

STOP

transcription terminator

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References

  1. 1.
    Pickersgill, H., Kalverda, B., de Wit, E., Talhout, W., Fornerod, M., and van Steensel, B. (2006) Characterization of the Drosophila melanogaster genome at the nuclear lamina, Nat. Genet., 38, 1005–1014.CrossRefPubMedGoogle Scholar
  2. 2.
    Guelen, L., Pagie, L., Brasset, E., Meuleman, W., Faza, M. B., Talhout, W., Eussen, B. H., de Klein, A., Wessels, L., de Laat, W., and van Steensel, B. (2008) Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions, Nature, 453, 948–951.CrossRefPubMedGoogle Scholar
  3. 3.
    Peric-Hupkes, D., Meuleman, W., Pagie, L., Bruggeman, S. W., Solovei, I., Brugman, W., Gräf, S., Flicek, P., Kerkhoven, R. M., van Lohuizen, M., Reinders, M., Wessels, L., and van Steensel, B. (2010) Molecular maps of the reorganization of genome–nuclear lamina interactions during differentiation, Mol. Cell, 38, 603–613.CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Furey, T. S. (2012) ChIP-seq and beyond: new and improved methodologies to detect and characterize pro-tein–DNA interactions, Nat. Rev. Genet., 13, 840–852.CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Aughey, G. N., and Southall, T. D. (2016) Dam it’s good! DamID profiling of protein–DNA interactions, Wiley Interdiscip. Rev. Dev. Biol., 5, 25–37.CrossRefPubMedGoogle Scholar
  6. 6.
    Voong, L. N., Xi, L., Sebeson, A. C., Xiong, B., Wang, J. P., and Wang, X. (2016) Insights into nucleosome organization in mouse embryonic stem cells through chemical mapping, Cell, 167, 1555–1570.CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Mieczkowski, J., Cook, A., Bowman, S. K., Mueller, B., Alver, B. H., Kundu, S., Deaton, A. M., Urban, J. A., Larschan, E., Park, P. J., Kingston, R. E., and Tolstorukov, M. Y. (2016) MNase titration reveals differences between nucleosome occupancy and chromatin accessibility, Nat. Commun., 7, 11485.CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    van Steensel, B., and Henikoff, S. (2000) Identification of in vivo DNA targets of chromatin proteins using tethered Dam methyltransferase, Nat. Biotechnol., 18, 424–428.CrossRefPubMedGoogle Scholar
  9. 9.
    Greil, F., van der Kraan, I., Delrow, J., Smothers, J. F., de Wit, E., Bussemaker, H. J., van Driel, R., Henikoff, S., and van Steensel, B. (2003) Distinct HP1 and Su(var)3-9 com-plexes bind to sets of developmentally coexpressed genes depending on chromosomal location, Genes Dev., 17, 2825–2838.CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Greil, F., Moorman, C., and van Steensel, B. (2006) DamID: mapping of in vivo protein–genome interactions using tethered DNA adenine methyltransferase, Methods Enzymol., 410, 342–359.CrossRefPubMedGoogle Scholar
  11. 11.
    Wu, F., Olson, B. G., and Yao, J. (2016) DamID-seq: genome-wide mapping of protein–DNA interactions by high throughput sequencing of adenine-methylated DNA fragments, J. Vis. Exp., 107, e53620.Google Scholar
  12. 12.
    Germann, S., Juul-Jensen, T., Letarnec, B., and Gaudin, V. (2006) DamID, a new tool for studying plant chromatin profiling in vivo, and its use to identify putative LHP1 tar-get loci, Plant J., 48, 153–163.CrossRefPubMedGoogle Scholar
  13. 13.
    Venkatasubrahmanyam, S., Hwang, W. W., Meneghini, M. D., Tong, A. H., and Madhani, H. D. (2007) Genome-wide, as opposed to local, antisilencing is mediated redun-dantly by the euchromatic factors Set1 and H2A.Z, Proc. Natl. Acad. Sci. USA, 104, 16609–16614.CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Woolcock, K. J., Gaidatzis, D., Punga, T., and Bühler, M. (2011) Dicer associates with chromatin to repress genome activity in Schizosaccharomyces pombe, Nat. Struct. Mol. Biol., 18, 94–99.CrossRefPubMedGoogle Scholar
  15. 15.
    Towbin, B. D., Gonzalez-Aguilera, C., Sack, R., Gaidatzis, D., Kalck, V., Meister, P., Askjaer, P., and Gasser, S. M. (2012) Step-wise methylation of histone H3K9 positions heterochromatin at the nuclear periphery, Cell, 150, 934–947.CrossRefPubMedGoogle Scholar
  16. 16.
    Gonzalez-Aguilera, C., Ikegami, K., Ayuso, C., de Luis, A., Iniguez, M., Cabello, J., Lieb, J. D., and Askjaer, P. (2014) Genome-wide analysis links emerin to neuromuscu-lar junction activity in Caenorhabditis elegans, Genome Biol., 15, R21.Google Scholar
  17. 17.
    Schuster, E., McElwee, J. J., Tullet, J. M., Doonan, R., Matthijssens, F., Reece-Hoyes, J. S., Hope, I. A., Vanfleteren, J. R., Thornton, J. M., and Gems, D. (2010) DamID in C. elegans reveals longevity-associated targets of DAF-16/FoxO, Mol. Syst. Biol., 6, 399.CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Choksi, S. P., Southall, T. D., Bossing, T., Edoff, K., de Wit, E., Fischer, B. E., van Steensel, B., Micklem, G., and Brand, A. H. (2006) Prospero acts as a binary switch between self-renewal and differentiation in Drosophila neu-ral stem cells, Dev. Cell, 11, 775–789.CrossRefPubMedGoogle Scholar
  19. 19.
    Southall, T. D., Gold, K. S., Egger, B., Davidson, C. M., Caygill, E. E., Marshall, O. J., and Brand, A. H. (2013) Cell-type-specific profiling of gene expression and chro-matin binding without cell isolation: assaying RNA Pol II occupancy in neural stem cells, Dev. Cell, 26, 101–112.CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Pindyurin, A. V., Pagie, L., Kozhevnikova, E. N., van Arensbergen, J., and van Steensel, B. (2016) Inducible DamID systems for genomic mapping of chromatin pro-teins in Drosophila, Nucleic Acids Res., 44, 5646–5657.CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Luo, S. D., Shi, G. W., and Baker, B. S. (2011) Direct tar-gets of the D. melanogaster DSXF protein and the evolution of sexual development, Development, 138, 2761–2771.CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Laktionov, P. P., White-Cooper, H., Maksimov, D. A., and Beliakin, S. N. (2014) Transcription factor comr acts as a direct activator in the genetic program controlling sper-matogenesis in D. melanogaster, Mol. Biol. (Moscow), 48, 153–165.CrossRefGoogle Scholar
  23. 23.
    Ilyin, A. A., Ryazansky, S. S., Doronin, S. A., Olenkina, O. M., Mikhaleva, E. A., Yakushev, E. Y., Abramov, Y. A., Belyakin, S. N., Ivankin, A. V., Pindyurin, A. V., Gvozdev, V. A., Klenov, M. S., and Shevelyov, Y. Y. (2017) Piwi inter-acts with chromatin at nuclear pores and promiscuously binds nuclear transcripts in Drosophila ovarian somatic cells, Nucleic Acids Res., 45, 7666–7680.CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Pindyurin, A. V. (2017) Genome-wide cell type-specific mapping of in vivo chromatin protein binding using an FLP-inducible DamID system in Drosophila, Methods Mol. Biol., 1654, 99–124.CrossRefPubMedGoogle Scholar
  25. 25.
    Pindyurin, A. V. (2017) Genomic mapping of chromatin proteins by using Daminv modification of an FLP-depend-ent DamID approach, Dokl. Biochem. Biophys., 472, 15–18.CrossRefPubMedGoogle Scholar
  26. 26.
    Green, M. R., and Sambrook, J. (2012) Molecular Cloning: A Laboratory Manual, 4th Edn., Cold Spring Harbor Laboratory Press.Google Scholar
  27. 27.
    Gibson, D. G. (2011) Enzymatic assembly of overlapping DNA fragments, Methods Enzymol., 498, 349–361.CrossRefPubMedGoogle Scholar
  28. 28.
    Dekker, M., Brouwers, C., and te Riele, H. (2003) Targeted gene modification in mismatch-repair-deficient embryonic stem cells by single-stranded DNA oligonucleotides, Nucleic Acids res., 31, e27.CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Maddalo, D., Manchado, E., Concepcion, C. P., Bonetti, C., Vidigal, J. A., Han, Y. C., Ogrodowski, P., Crippa, A., Rekhtman, N., de Stanchina, E., Lowe, S. W., and Ventura, A. (2014) In vivo engineering of oncogenic chromosomal rearrangements with the CRISPR/Cas9 system, Nature, 516, 423–427.CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Xu, J. (2005) Preparation, culture, and immortalization of mouse embryonic fibroblasts, Curr. Protoc. Mol. Biol., 28, Unit 28.1.Google Scholar
  31. 31.
    van Steensel, B., Delrow, J., and Henikoff, S. (2001) Chromatin profiling using targeted DNA adenine methyl-transferase, Nat. Genet., 27, 304–308.CrossRefPubMedGoogle Scholar
  32. 32.
    van Steensel, B. (2005) Mapping of genetic and epigenetic regulatory networks using microarrays, Nat. Genet., 37, S18–S24.CrossRefPubMedGoogle Scholar
  33. 33.
    Chen, C. M., Krohn, J., Bhattacharya, S., and Davies, B. (2011) A comparison of exogenous promoter activity at the ROSA26 locus using a PhiC31 integrase mediated cassette exchange approach in mouse ES cells, PLoS One, 6, e23376.CrossRefPubMedPubMedCentralGoogle Scholar
  34. 34.
    Bouabe, H., and Okkenhaug, K. (2013) Gene targeting in mice: a review, Methods Mol. Biol., 1064, 315–336.CrossRefPubMedPubMedCentralGoogle Scholar
  35. 35.
    Tosti, L., Ashmore, J., Tan, B. S. N., Carbone, B., Mistri, T. K., Wilson, V., Tomlinson, S. R., and Kaji, K. (2018) Mapping transcription factor occupancy using minimal num-bers of cells in vitro and in vivo, Genome Res., 28, 592–605.CrossRefPubMedPubMedCentralGoogle Scholar
  36. 36.
    Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., and Zhang, F. (2013) Multiplex genome engineering using CRISPR/Cas systems, Science, 339, 819–823.CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    Hartman, S. C., and Mulligan, R. C. (1988) Two dominant-acting selectable markers for gene transfer studies in mam-malian cells, Proc. Natl. Acad. Sci. USA, 85, 8047–8051.CrossRefPubMedPubMedCentralGoogle Scholar
  38. 38.
    Amendola, M., and van Steensel, B. (2015) Nuclear lamins are not required for lamina-associated domain organization in mouse embryonic stem cells, EMBO Rep., 16, 610–617.CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
    Robson, M. I., and Schirmer, E. C. (2016) The application of DamID to identify peripheral gene sequences in differen-tiated and primary cells, Methods Mol. Biol., 1411, 359–386.CrossRefPubMedGoogle Scholar
  40. 40.
    Chu, V. T., Weber, T., Graf, R., Sommermann, T., Petsch, K., Sack, U., Volchkov, P., Rajewsky, K., and Kühn, R. (2016) Efficient generation of Rosa26 knock-in mice using CRISPR/Cas9 in C57BL/6 zygotes, BMC Biotechnol., 16, 4.CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2018

Authors and Affiliations

  • E. N. Kozhevnikova
    • 1
    • 2
    Email author
  • A. E. Leshchenko
    • 1
  • A. V. Pindyurin
    • 1
    • 2
  1. 1.Institute of Molecular and Cellular BiologySiberian Branch of the Russian Academy of SciencesNovosibirskRussia
  2. 2.Institute of Cytology and GeneticsSiberian Branch of the Russian Academy of SciencesNovosibirskRussia

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