Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

A role for cohesin in T-cell-receptor rearrangement and thymocyte differentiation

Nature volume 476, pages 467–471 (2011)Cite this article

Subjects

Abstract

Cohesin enables post-replicative DNA repair and chromosome segregation by holding sister chromatids together from the time of DNA replication in S phase until mitosis1. There is growing evidence that cohesin also forms long-range chromosomal cis-interactions2,3,4 and may regulate gene expression2,3,4,5,6,7,8,9,10 in association with CTCF8,9, mediator4 or tissue-specific transcription factors10. Human cohesinopathies such as Cornelia de Lange syndrome are thought to result from impaired non-canonical cohesin functions7, but a clear distinction between the cell-division-related and cell-division-independent functions of cohesion—as exemplified in Drosophila11,12,13—has not been demonstrated in vertebrate systems. To address this, here we deleted the cohesin locus Rad21 in mouse thymocytes at a time in development when these cells stop cycling and rearrange their T-cell receptor (TCR) α locus (Tcra). Rad21-deficient thymocytes had a normal lifespan and retained the ability to differentiate, albeit with reduced efficiency. Loss of Rad21 led to defective chromatin architecture at the Tcra locus, where cohesion-binding sites flank the TEA promoter and the Eα enhancer, and demarcate Tcra from interspersed Tcrd elements and neighbouring housekeeping genes. Cohesin was required for long-range promoter–enhancer interactions, Tcra transcription, H3K4me3 histone modifications that recruit the recombination machinery14,15 and Tcra rearrangement. Provision of pre-rearranged TCR transgenes largely rescued thymocyte differentiation, demonstrating that among thousands of potential target genes across the genome4,8,9,10, defective Tcra rearrangement was limiting for the differentiation of cohesin-deficient thymocytes. These findings firmly establish a cell-division-independent role for cohesin in Tcra locus rearrangement and provide a comprehensive account of the mechanisms by which cohesin enables cellular differentiation in a well-characterized mammalian system.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Genetic cohesin depletion in non-dividing thymocytes.
Figure 2: Cohesin affects Tcra transcription and Rag recombinase recruitment.
Figure 3: Cohesin affects Tcra rearrangement.
Figure 4: Cohesin mediates long-range interactions between regulatory elements that control Tcra transcription.

Similar content being viewed by others

References

  1. Nasmyth, K. & Haering, C. H. Cohesin: its roles and mechanisms. Annu. Rev. Genet. 43, 525–558 (2009)

    Article  CAS  Google Scholar 

  2. Hadjur, S. et al. Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus. Nature 460, 410–413 (2009)

    Article  ADS  CAS  Google Scholar 

  3. Degner, S. C. et al. CCCTC-binding factor (CTCF) and cohesin influence the genomic architecture of the Igh locus and antisense transcription in pro-B cells. Proc. Natl Acad. Sci. USA 10.1073/pnas.1019391108 (23 May 2011)

  4. Kagey, M. H. et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 467, 430–435 (2010)

    Article  ADS  CAS  Google Scholar 

  5. Hagstrom, K. A. & Meyer, B. J. Condensin and cohesin: more than chromosome compactor and glue. Nature Rev. Genet. 4, 520–534 (2003)

    Article  CAS  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Strachan, T. Cornelia de Lange syndrome and the link between chromosomal function, DNA repair and developmental gene regulation. Curr. Opin. Genet. Dev. 15, 258–264 (2005)

    Article  CAS  Google Scholar 

  8. Parelho, V. et al. Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell 132, 422–433 (2008)

    Article  CAS  Google Scholar 

  9. Wendt, K. S. et al. Cohesin mediates transcriptional insulation by CCCTC-binding factor. Nature 451, 796–801 (2008)

    Article  ADS  CAS  Google Scholar 

  10. Schmidt, D. et al. A CTCF-independent role for cohesin in tissue-specific transcription. Genome Res. 20, 578–588 (2010)

    Article  CAS  Google Scholar 

  11. Schuldiner, O. et al. piggyBac-based mosaic screen identifies a postmitotic function for cohesin in regulating developmental axon pruning. Dev. Cell 14, 227–238 (2008)

    Article  CAS  Google Scholar 

  12. Pauli, A. et al. Cell-type-specific TEV protease cleavage reveals cohesin functions in Drosophila neurons. Dev. Cell 14, 239–251 (2008)

    Article  CAS  Google Scholar 

  13. Pauli, A. et al. A direct role for cohesin in gene regulation and ecdysone response in Drosophila salivary glands. Curr. Biol. 20, 1787–1798 (2010)

    Article  CAS  Google Scholar 

  14. Matthews, A. G. et al. RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination. Nature 450, 1106–1110 (2007)

    Article  ADS  CAS  Google Scholar 

  15. Liu, Y., Subrahmanyam, R., Chakraborty, T., Sen, R. & Desiderio, S. A plant homeodomain in Rag-2 that binds hypermethylated lysine 4 of histone H3 is necessary for efficient antigen-receptor-gene rearrangement. Immunity 27, 561–571 (2007)

    Article  CAS  Google Scholar 

  16. Kisielow, P. & von Boehmer, H. Development and selection of T cells: facts and puzzles. Adv. Immunol. 58, 87–209 (1995)

    Article  CAS  Google Scholar 

  17. Stanhope-Baker, P., Hudson, K. M., Shaffer, A. L., Constantinescu, A. & Schlissel, M. S. Cell type-specific chromatin structure determines the targeting of V(D)J recombinase activity in vitro . Cell 85, 887–897 (1996)

    Article  CAS  Google Scholar 

  18. Krangel, M. S. Mechanics of T cell receptor gene rearrangement. Curr. Opin. Immunol. 21, 133–139 (2009)

    Article  CAS  Google Scholar 

  19. Jhunjhunwala, S., van Zelm, M. C., Peak, M. M. & Murre, C. Chromatin architecture and the generation of antigen receptor diversity. Cell 138, 435–448 (2009)

    Article  CAS  Google Scholar 

  20. Desiderio, S., Lin, W. C. & Li, Z. The cell cycle and V(D)J recombination. Curr. Top. Microbiol. Immunol. 217, 45–59 (1996)

    CAS  PubMed  Google Scholar 

  21. Brekelmans, P. et al. Transferrin receptor expression as a marker of immature cycling thymocytes in the mouse. Cell. Immunol. 159, 331–339 (1994)

    Article  CAS  Google Scholar 

  22. Huesmann, M., Scott, B., Kisielow, P. & von Boehmer, H. Kinetics and efficacy of positive selection in the thymus of normal and T cell receptor transgenic mice. Cell 66, 533–540 (1991)

    Article  CAS  Google Scholar 

  23. Lee, P. P. et al. A critical role for Dnmt1 and DNA methylation in T cell development, function, and survival. Immunity 15, 763–774 (2001)

    Article  CAS  Google Scholar 

  24. Diaz, P., Cado, D. & Winoto, A. A locus control region in the T cell receptor α/δ locus. Immunity 1, 207–217 (1994)

    Article  CAS  Google Scholar 

  25. Magdinier, F., Yusufzai, T. M. & Felsenfeld, G. Both CTCF-dependent and -independent insulators are found between the mouse T cell receptor α and Dad1 genes. J. Biol. Chem. 279, 25381–25389 (2004)

    Article  CAS  Google Scholar 

  26. Zhong, X. P. & Krangel, M. S. Enhancer-blocking activity within the DNAse I hypersensitivity site 2 to 6 region between the T cell receptor α and Dad1 genes. J. Immunol. 163, 295–300 (1999)

    CAS  PubMed  Google Scholar 

  27. Abarrategui, I. & Krangel, M. S. Germline transcription: a key regulator of accessibility and recombination. Adv. Exp. Med. Biol. 650, 93–102 (2009)

    Article  CAS  Google Scholar 

  28. Ji, Y. et al. The in vivo pattern of binding of RAG1 and RAG2 to antigen receptor loci. Cell 141, 419–431 (2010)

    Article  CAS  Google Scholar 

  29. Guo, J. et al. Regulation of the TCRα repertoire by the survival window of CD4+CD8+ thymocytes. Nature Immunol. 3, 469–476 (2002)

    Article  Google Scholar 

  30. Dekker, J. The three ‘C’ s of chromosome conformation capture: controls, controls, controls. Nature Methods 3, 17–21 (2006)

    Article  CAS  Google Scholar 

  31. Spanopoulou, E. et al. Functional immunoglobulin transgenes guide ordered B-cell differentiation in Rag-1-deficient mice. Genes Dev. 8, 1030–1042 (1994)

    Article  CAS  Google Scholar 

  32. Hogquist, K. A. et al. T cell receptor antagonist peptides induce positive selection. Cell 76, 17–27 (1994)

    Article  CAS  Google Scholar 

  33. Kaye, J. et al. Selective development of CD4+ T cells in transgenic mice expressing a class II MHC-restricted antigen receptor. Nature 341, 746–749 (1989)

    Article  ADS  CAS  Google Scholar 

  34. Abarrategui, I. & Krangel, M. S. Regulation of T cell receptor-α gene recombination by transcription. Nature Immunol. 7, 1109–1115 (2006)

    Article  CAS  Google Scholar 

  35. Jackson, A., Kondilis, H. D., Khor, B., Sleckman, B. P. & Krangel, M. S. Regulation of T cell receptor β allelic exclusion at a level beyond accessibility. Nature Immunol. 6, 189–197 (2005)

    Article  CAS  Google Scholar 

  36. Toyoda, Y. & Yanagida, M. Coordinated requirements of human topo II and cohesin for metaphase centromere alignment under Mad2-dependent spindle checkpoint surveillance. Mol. Biol. Cell 17, 2287–2302 (2006)

    Article  CAS  Google Scholar 

  37. Kibbe, W. A. OligoCalc: an online oligonucleotide properties calculator. Nucleic Acids Res. 35, W43–W46 (2007)

    Article  Google Scholar 

  38. Fejes, A. P. et al. FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 24, 1729–1730 (2008)

    Article  CAS  Google Scholar 

  39. Lee, Y. N. et al. Differential utilization of T cell receptor TCRα/TCRδ locus variable region gene segments is mediated by accessibility. Proc. Natl Acad. Sci. USA 106, 17487–17492 (2009)

    Article  ADS  CAS  Google Scholar 

Download references

Acknowledgements

We thank S. Hadjur, D. Tough, L. Williams, Z. Webster, J. Godwin and H.-Y. Shih for help and advice, L. Game and M. Jones for high-throughput sequencing, A. Giess for sequence alignment, and J. Elliott and P. Hexley for cell sorting. Supported by the Medical Research Council, UK (V.S., T.L., H.M.-B., K.E.B., T.C., A.T., L.A., A.G.F., K.N., M.M.), the European Union FP6 integrated project HEROIC (H.M.), EU and the Marie Curie Research Training Network Chromatin Plasticity (H.M.-B.), the Boehringer Ingelheim Fonds (T.L.), the Wellcome Trust (D.J.A., K.N.) and the National Institutes of Health (B.H., M.S.K., G.T., D.G.S.). D.G.S. is an investigator of the Howard Hughes Medical Institute.

Author information

Author notes

  1. Vlad C. Seitan, Bingtao Hao and Kikuë Tachibana-Konwalski: These authors contributed equally to this work.

Authors and Affiliations

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

    Vlad C. Seitan, Thais Lavagnolli, Hegias Mira-Bontenbal, Karen E. Brown, Anna Terry, Amanda G. Fisher & Matthias Merkenschlager

  2. Cell Cycle Group, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK

    Vlad C. Seitan & Luis Aragon

  3. Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK

    Vlad C. Seitan, Thais Lavagnolli, Hegias Mira-Bontenbal, Karen E. Brown, Tom Carroll, Anna Terry, Luis Aragon, Amanda G. Fisher & Matthias Merkenschlager

  4. Department of Immunology, Duke University Medical Center, Durham, 27710, North Carolina, USA

    Bingtao Hao & Michael S. Krangel

  5. Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK

    Kikuë Tachibana-Konwalski & Kim Nasmyth

  6. Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, 06520-8011, Connecticut, USA

    Grace Teng & David G. Schatz

  7. Central Biological Services, Imperial College London, Du Cane Road, London W12 0NN, UK

    Katie Horan

  8. Department of Molecular Biology, Nijmegen Center for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, The Netherlands

    Hendrik Marks

  9. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK

    David J. Adams

  10. Howard Hughes Medical Institute, Yale University School of Medicine, 300 Cedar Street, New Haven, 06520-8011, Connecticut, USA

    David G. Schatz

Authors
  1. Vlad C. Seitan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Bingtao Hao
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kikuë Tachibana-Konwalski
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Thais Lavagnolli
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hegias Mira-Bontenbal
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Karen E. Brown
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Grace Teng
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Tom Carroll
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Anna Terry
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Katie Horan
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Hendrik Marks
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. David J. Adams
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. David G. Schatz
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Luis Aragon
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Amanda G. Fisher
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Michael S. Krangel
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Kim Nasmyth
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. Matthias Merkenschlager
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

V.S. and M.M. conceived the study with critical input from D.G.S., L.A., A.G.F., M.S.K. and K.N., V.S., B.H., K.T.-K., T.L., H.M.-B., K.E.B., G.T., K.H. and M.M. conducted experiments, K.T.-K., D.J.A., K.N., G.T. and D.G.S. designed and generated novel materials, T.C., A.T. and H.M. analysed data, V.S. and M.M. wrote the paper and all authors discussed the results and commented on the manuscript.

Corresponding authors

Correspondence to Michael S. Krangel, Kim Nasmyth or Matthias Merkenschlager.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-8 with legends and additional references. (PDF 5104 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature10312

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing