Skip to main content
SpringerLink
Log in
Book cover

Cohesin and Condensin pp 197–216Cite as

Analysis of Cohesin Function in Gene Regulation and Chromatin Organization in Interphase

  • Protocol
  • First Online:

  • 1424 Accesses

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1515))

Abstract

Cohesin is essential for the maintenance of chromosomes through the cell cycle. In addition, cohesin contributes to the regulation of gene expression and the organization of chromatin in interphase cells. To study cohesin’s role in gene expression and chromatin organization, it is necessary to avoid secondary effects due to disruption of vital cohesin functions in the cell cycle. Here we describe experimental approaches to achieve this and the methods applied to define cohesin’s role in interphase.

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

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   139.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   109.99
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

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Aragon L, Martinez-Perez E, Merkenschlager M (2013) Condensin, cohesin and the control of chromatin states. Curr Opin Genet Dev 23:204–211. doi:10.1016/j.gde.2012.11.004

    Article  CAS  PubMed  Google Scholar 

  2. Nasmyth K, Haering CH (2005) The structure and function of SMC and kleisin complexes. Annu Rev Biochem 74:595–648. doi:10.1146/annurev.biochem.74.082803.133219

    Article  CAS  PubMed  Google Scholar 

  3. Losada A, Hirano M, Hirano T (1998) Identification of Xenopus SMC protein complexes required for sister chromatid cohesion. Genes Dev 12:1986–1997

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Sumara I, Vorlaufer E, Gieffers C et al (2000) Characterization of vertebrate cohesin complexes and their regulation in prophase. J Cell Biol 151:749–762. doi:10.1083/jcb.151.4.749

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Gerlich D, Koch B, Dupeux F et al (2006) Live-cell imaging reveals a stable cohesin-chromatin interaction after but not before DNA replication. Curr Biol 16:1571–1578. doi:10.1016/j.cub.2006.06.068

    Article  CAS  PubMed  Google Scholar 

  6. Wendt KS, Yoshida K, Itoh T et al (2008) Cohesin mediates transcriptional insulation by CCCTC-binding factor. Nature 451:796–801. doi:10.1038/nature06634

    Article  CAS  PubMed  Google Scholar 

  7. Merkenschlager M, Odom DT (2013) CTCF and cohesin: linking gene regulatory elements with their targets. Cell 152:1285–1297. doi:10.1016/j.cell.2013.02.029

    Article  CAS  PubMed  Google Scholar 

  8. Heidinger-Pauli JM, Mert O, Davenport C et al (2010) Systematic reduction of cohesin differentially affects chromosome segregation, condensation, and DNA repair. Curr Biol 20:957–963. doi:10.1016/j.cub.2010.04.018

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Schaaf C, Misulovin Z, Sahota G et al (2009) Regulation of the Drosophila enhancer of split and invected-engrailed gene complexes by sister chromatid cohesion proteins. PLoS One 4, e6202. doi:10.1371/journal.pone.0006202

    Article  PubMed  PubMed Central  Google Scholar 

  10. Deardorff M, Bando M, Nakato R et al (2012) HDAC8 mutations in Cornelia de Lange syndrome affect the cohesin acetylation cycle. Nature 489:313–317. doi:10.1038/nature11316

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Liu J, Krantz ID (2009) Cornelia de Lange syndrome, cohesin, and beyond. Clin Genet 76:303–314. doi:10.1111/j.1399-0004.2009.01271.x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Krantz ID, McCallum J, DeScipio C et al (2004) Cornelia de Lange syndrome is caused by mutations in NIPBL, the human homolog of Drosophila melanogaster Nipped-B. Nat Genet 36:631–635. doi:10.1038/ng1364

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Ball AR, Chen Y-Y, Yokomori K (2014) Mechanisms of cohesin-mediated gene regulation and lessons learned from cohesinopathies. Biochim Biophys Acta 1839:191–202. doi:10.1016/j.bbagrm.2013.11.002

    Article  CAS  PubMed  Google Scholar 

  14. Skibbens RV, Colquhoun JM, Green MJ et al (2013) Cohesinopathies of a feather flock together. PLoS Genet 9, e1004036. doi:10.1371/journal.pgen.1004036

    Article  PubMed  PubMed Central  Google Scholar 

  15. Liu J, Zhang Z, Bando M et al (2009) Transcriptional dysregulation in NIPBL and cohesin mutant human cells. PLoS Biol 7, e1000119. doi:10.1371/journal.pbio.1000119

    Article  PubMed  PubMed Central  Google Scholar 

  16. Kawauchi S, Calof AL, Santos R et al (2009) Multiple organ system defects and transcriptional dysregulation in the Nipbl(+/−) mouse, a model of Cornelia de Lange syndrome. PLoS Genet 5, e1000650. doi:10.1371/journal.pgen.1000650

    Article  PubMed  PubMed Central  Google Scholar 

  17. Seitan VC, Hao B, Tachibana-Konwalski K et al (2011) A role for cohesin in T-cell-receptor rearrangement and thymocyte differentiation. Nature 476:467–471. doi:10.1038/nature10312

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Parelho V, Hadjur S, Spivakov M et al (2008) Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell 132:422–433. doi:10.1016/j.cell.2008.01.011

    Article  CAS  PubMed  Google Scholar 

  19. Pauli A, van Bemmel JG, Oliveira RA et al (2010) A direct role for cohesin in gene regulation and ecdysone response in Drosophila salivary glands. Curr Biol 20:1787–1798. doi:10.1016/j.cub.2010.09.006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Rollins RA, Morcillo P, Dorsett D (1999) Nipped-B, a Drosophila homologue of chromosomal adherins, participates in activation by remote enhancers in the cut and Ultrabithorax genes. Genetics 152:577–593

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Kagey MH, Newman JJ, Bilodeau S et al (2010) Mediator and cohesin connect gene expression and chromatin architecture. Nature 467:430–435. doi:10.1038/nature09380

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Ding L, Paszkowski-Rogacz M, Nitzsche A et al (2009) A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity. Cell Stem Cell 4:403–415. doi:10.1016/j.stem.2009.03.009

    Article  CAS  PubMed  Google Scholar 

  23. Nitzsche A, Paszkowski-Rogacz M, Matarese F et al (2011) RAD21 cooperates with pluripotency transcription factors in the maintenance of embryonic stem cell identity. PLoS One 6, e19470. doi:10.1371/journal.pone.0019470

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Hu G, Kim J, Xu Q et al (2009) A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal. Genes Dev 23:837–848. doi:10.1101/gad.1769609.Freely

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Lavagnolli T, Gupta P, Hörmanseder E et al (2015) Initiation and maintenance of pluripotency gene expression in the absence of cohesin. Genes Dev 29:23–38. doi:10.1101/gad.251835.114

    Article  PubMed  PubMed Central  Google Scholar 

  26. Lin T, Chao C, Saito S et al (2005) p53 induces differentiation of mouse embryonic stem cells by suppressing Nanog expression. Nat Cell Biol 7:165–171. doi:10.1038/ncb1211

    Article  CAS  PubMed  Google Scholar 

  27. Maimets T, Neganova I, Armstrong L, Lako M (2008) Activation of p53 by nutlin leads to rapid differentiation of human embryonic stem cells. Oncogene 27:5277–5287. doi:10.1038/onc.2008.166

    Article  CAS  PubMed  Google Scholar 

  28. Li M, He Y, Dubois W et al (2012) Distinct regulatory mechanisms and functions for p53-activated and p53-repressed DNA damage response genes in embryonic stem cells. Mol Cell 46:30–42. doi:10.1016/j.molcel.2012.01.020

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Schuldiner O, Berdnik D, Levy JM et al (2008) piggyBac-based mosaic screen identifies a postmitotic function for cohesin in regulating developmental axon pruning. Dev Cell 14:227–238. doi:10.1016/j.devcel.2007.11.001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Sofueva S, Yaffe E, Chan W-C et al (2013) Cohesin-mediated interactions organize chromosomal domain architecture. EMBO J 32:1–11. doi:10.1038/emboj.2013.237

    Article  Google Scholar 

  31. Seitan VC, Faure AJ, Zhan Y et al (2013) Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments. Genome Res 23:2066–2077. doi:10.1101/gr.161620.113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Ing-simmons E, Seitan VC, Faure AJ et al (2015) Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin. Genome Res 25(4):504–513. doi:10.1101/gr.184986.114.8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Tedeschi A, Wutz G, Huet S et al (2013) Wapl is an essential regulator of chromatin structure and chromosome segregation. Nature 501:564–568. doi:10.1038/nature12471

    Article  CAS  PubMed  Google Scholar 

  34. Sengupta S, Harris CC (2005) p53: traffic cop at the crossroads of DNA repair and recombination. Nat Rev Mol Cell Biol 6:44–55. doi:10.1038/nrm1546

    Article  CAS  PubMed  Google Scholar 

  35. Dekker J, Marti-Renom M, Mirny L (2013) Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet 14:390–403. doi:10.1038/nrg3454

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Creyghton MP, Cheng AW, Welstead GG et al (2010) Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A 107:21931–21936. doi:10.1073/pnas.1016071107

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Rada-Iglesias A, Bajpai R, Swigut T et al (2011) A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470:279–283. doi:10.1038/nature09692

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgment

This work was supported by the Medical Reseach Council, UK, the Wellcome Trust, and a Commonwealth Scholarship.

Author information

Authors and Affiliations

  1. Lymphocyte Development Group, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK

    Preksha Gupta, Thais Lavagnolli, Hegias Mira-Bontenbal & Matthias Merkenschlager

  2. Department of Developmental Biology, Erasmus MC, University Medical Centre, 3015 CN, Rotterdam, The Netherlands

    Hegias Mira-Bontenbal

Authors
  1. Preksha Gupta
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Thais Lavagnolli
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hegias Mira-Bontenbal
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Matthias Merkenschlager
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Preksha Gupta .

Editor information

Editors and Affiliations

  1. Department of Biological Chemistry, School of Medicine University of California— Irvine, Irvine, California, USA

    Kyoko Yokomori

  2. Laboratory of Genome Structure and Function Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences The University of Tokyo, Tokyo, Japan

    Katsuhiko Shirahige

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media New York

About this protocol

Cite this protocol

Gupta, P., Lavagnolli, T., Mira-Bontenbal, H., Merkenschlager, M. (2017). Analysis of Cohesin Function in Gene Regulation and Chromatin Organization in Interphase. In: Yokomori, K., Shirahige, K. (eds) Cohesin and Condensin. Methods in Molecular Biology, vol 1515. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6545-8_12

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-6545-8_12

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6543-4

  • Online ISBN: 978-1-4939-6545-8

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation