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

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

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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.

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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.

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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.

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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

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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.

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The authors declare no competing financial interests.

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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

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