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Localized epigenetic changes induced by DH recombination restricts recombinase to DJH junctions

Nature Immunology volume 13, pages 1205–1212 (2012)Cite this article

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Abstract

Genes encoding immunoglobulin heavy chains (Igh) are assembled by rearrangement of variable (VH), diversity (DH) and joining (JH) gene segments. Three critical constraints govern VH recombination. These include timing (VH recombination follows DH recombination), precision (VH gene segments recombine only to DJH junctions) and allele specificity (VH recombination is restricted to DJH-recombined alleles). Here we provide a model for these universal features of VH recombination. Analyses of DJH-recombined alleles showed that DJH junctions were selectively epigenetically marked, became nuclease sensitive and bound RAG recombinase proteins, which thereby permitted DH-associated recombination signal sequences to initiate the second step of Igh gene assembly. We propose that VH recombination is precise, because these changes did not extend to germline DH segments located 5′ of the DJH junction.

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Figure 1: Chromatin accessibility at a DSP2.2b-JH1–rearranged allele.
Figure 2: Histone modifications at unrearranged upstream DH gene segments in DJH-rearranged Igh alleles.
Figure 3: Histone modifications at Igh alleles with DFL16.1 and DQ52 rearrangements.
Figure 4: Chromatin accessibility at DSP2.9-JH2–rearranged alleles.
Figure 5: Chromatin accessibility at DJH junctions in primary pro-B cells.
Figure 6: Association of RAG-1 with DJH-rearranged Igh alleles.

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Acknowledgements

Supported by the Intramural Research Program of the National Institute on Aging (US National Institutes of Health; AI20047 to F.W.A., and AI32524 to D.G.S.) and the Howard Hughes Medical Institute (F.W.A. and D.G.S.).

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Author notes

  1. Tirtha Chakraborty & Yanhong Ji

    Present address: Present addresses: Department of Immunology & Microbiology, School of Medicine, Xian Jiaotong University, Xian Shaanxi, China (Y.J.), and ModeRNA Therapeutics, Cambridge, Massachusetts, USA (T.C.).,

Authors and Affiliations

  1. Laboratory of Molecular Biology and Immunology, National Institute on Aging, US National Institutes of Health, Baltimore, Maryland, USA

    Ramesh Subrahmanyam, Hansen Du, Irina Ivanova, Tirtha Chakraborty & Ranjan Sen

  2. Department of Immunobiology, Howard Hughes Medical Institute, Yale Medical School, New Haven, Connecticut, USA

    Yanhong Ji & David G Schatz

  3. Immune Disease Institute and Department of Genetics, Howard Hughes Medical Institute, The Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA

    Yu Zhang & Frederick W Alt

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Contributions

R. Subrahmanyam designed and did all the experiments; R. Subrahmanyam and R. Sen analyzed and interpreted the data; H.D. assisted with Southern blot analysis; I.I. did the ChIP analysis of H3K4me2; T.C. assisted in the initial characterization of DJH-rearranged cell lines; Y.J. and D.G.S. provided D345 cells and discussions of the ChIP analysis of RAG; Y.Z. and F.W.A. generated the Eμ-deficient cell lines; R. Subrahmanyam and R. Sen wrote the manuscript; and D.G.S. and F.W.A. read and critiqued the manuscript.

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Correspondence to Ranjan Sen.

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Subrahmanyam, R., Du, H., Ivanova, I. et al. Localized epigenetic changes induced by DH recombination restricts recombinase to DJH junctions. Nat Immunol 13, 1205–1212 (2012). https://doi.org/10.1038/ni.2447

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