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RAG-1 and ATM coordinate monoallelic recombination and nuclear positioning of immunoglobulin loci

Nature Immunology volume 10, pages 655–664 (2009)Cite this article

A Corrigendum to this article was published on 01 April 2010

An Addendum to this article was published on 01 April 2010

A Corrigendum to this article was published on 01 September 2009

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Abstract

Coordinated recombination of homologous antigen receptor loci is thought to be important for allelic exclusion. Here we show that homologous immunoglobulin alleles pair in a stage-specific way that mirrors the recombination patterns of these loci. The frequency of homologous immunoglobulin pairing was much lower in the absence of the RAG-1–RAG-2 recombinase and was restored in Rag1−/− developing B cells with a transgene expressing a RAG-1 active-site mutant that supported DNA binding but not cleavage. The introduction of DNA breaks on one immunoglobulin allele induced ATM-dependent repositioning of the other allele to pericentromeric heterochromatin. ATM activated by the cleaved allele acts in trans on the uncleaved allele to prevent biallelic recombination and chromosome breaks or translocations.

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Figure 1: Homologous pairing of Igh and Igk alleles occurs during recombination.
Figure 2: RAG-1 contributes to homologous pairing of Igh and Igk alleles.
Figure 3: RAG-1 cleavage marks paired immunoglobulin alleles differently so that one allele is in euchromatic and the other is in heterochromatic regions of the nucleus.
Figure 4: RAG-1 binding, not cleavage, also directs repositioning of Igk alleles.
Figure 5: ATM directs the repositioning of one immunoglobulin allele to pericentromeric heterochromatin.
Figure 6: ATM prevents biallelic RAG-mediated cleavage during immunoglobulin V(D)J rearrangement.
Figure 7: ATM prevents biallelic Igk chromosome breaks and translocations.
Figure 8: Igh pairing can occur beyond the pro–B cell stage if locus accessibility is maintained.

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  • 18 May 2009

    NOTE: In the version of this article initially published, some of the funding was stated incorrectly or missing; the Competing Financial Interests section was missing; and the citation to reference 15 was missing. The correct funding statement should be as follows: Supported by the Wellcome Trust (085096 to J.A.S.), the New York University School of Medicine (J.A.S.), the US National Institutes of Health (R37 AI32524 to D.G.S.; R01 GM086852A to J.A.S.; R01 CA125195 to C.H.B.; and RO1 AI050737 to M.A.F.), the Pew Scholars Program (C.H.B. and M.A.F.), the Cancer Research Institute (M.A.F.), the Cancer Research Institute Predoctoral Emphasis Pathway in Tumor Immunology (B.Y.), Boehringer Ingelheim (M.B.), Genome Research in Austria (M.B.) and the Howard Hughes Medical Institute (D.G.S.). The correct Competing Financial Interests statement should be ?The authors declare competing financial interests?; in the PDF, the statement also includes “details accompany the full-text HTML version of the paper at http://www.nature.com/natureimmunology/.” The citation for reference 15 should be on the first page as follows: “Studies of the rearrangement status of Igh alleles in mature B cell hybridomas and in developing B cells that have been transformed by Abelson murine leukemia virus15 have suggested?.” The errors have been corrected in the HTML and PDF versions of the article.

  • 19 August 2009

    NOTE: In the version of this article initially published, the values for scoring coincident loci are incorrect on page 660 and in the legend for Figure 7b. The correct value should be 1.0 μm. The error has been corrected in the HTML and PDF versions of the article.

  • 12 March 2010

    In the version of this article initially published, two values on page 657, the title to Figure 3 and several Supplementary Table citations are incorrect. Sentence 2 of paragraph 2 on page 657, column 2, should end “than those in similar wild-type populations (55% and 61%, respectively).” The title for Figure 3 should begin “RAG-1 cleavage marks paired immunoglobulin alleles differently....” The Supplementary Table citations should be as follows: Figure 3 legend, “(complete statistical results, Supplementary Tables 4–6)”; Figure 5 legend, “(complete statistical results, Supplementary Tables 1, 2, 4, 5, 7 and 8)”; Figure 8 legend, “(complete statistical results, Supplementary Tables 1, 5 and 12)”; and page 662, column 2, sentence 2 “Supplementary Tables 1 and 4.” The errors have been corrected in the HTML and PDF versions of the article.

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Acknowledgements

We thank M. Nussenzweig (Rockefeller University) for BAC HG and members of the Skok lab for critical reading of this manuscript. Supported by the Wellcome Trust (085096 to J.A.S.), the New York University School of Medicine (J.A.S.), the US National Institutes of Health (R37 AI32524 to D.G.S.; R01 GM086852A to J.A.S.; R01 CA125195 to C.H.B.; and RO1 AI050737 to M.A.F.), the Pew Scholars Program (C.H.B. and M.A.F.), the Cancer Research Institute (M.A.F.), the Cancer Research Institute Predoctoral Emphasis Pathway in Tumor Immunology (B.Y.), Boehringer Ingelheim (M.B.), Genome Research in Austria (M.B.) and the Howard Hughes Medical Institute (D.G.S.).

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Author notes

  1. Craig H Bassing and Jane A Skok: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Pathology, New York University School of Medicine, New York, New York, USA

    Susannah L Hewitt, Julie Chaumeil, Katarzyna Marszalek, Jeannette Tenthorey & Jane A Skok

  2. Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Abramson Family Cancer Research Institute, Philadelphia, Pennsylvania, USA

    Bu Yin, Natalie Steinel & Craig H Bassing

  3. Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA

    Yanhong Ji & David G Schatz

  4. Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria

    Giorgia Salvagiotto & Meinrad Busslinger

  5. Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA

    Laura B Ramsey & Michael A Farrar

  6. Institut Curie, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 146, Centre Universitaire, Orsay, France

    Jacques Ghysdael

  7. Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA

    Barry P Sleckman

  8. Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, USA

    David G Schatz

  9. Department of Immunology and Molecular Pathology, Division of Infection and Immunity, University College London, London, UK

    Jane A Skok

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Contributions

S.L.H. and B.Y. contributed equally to this work. S.L.H. sorted cells (Supplementary Figs. 1 and 2), did the three-dimensional DNA FISH (Figs. 1,2,3,4,5 and Supplementary Figs. 3 and 4) and did the confocal analysis of γ-H2AX association on immunoglobulin alleles (Fig. 5 and Supplementary Figs. 3 and 4); B.Y. contributed data for Figure 6 and Supplementary Figure 5; Y.J. and D.G.S. provided bones from Rag1−/−, Rag1−/−Rag1D708A, B1.8, Rag1−/−B1.8 and Rag1−/−Rag1D708A B1.8 mice; J.C. improved the immuno-FISH protocol used in Figure 5; K.M. grew and labeled BAC probes and helped with sorting; J.T. set up the initial immuno-FISH experiments used for analysis of γ-H2AX association on immunoglobulin alleles; G.S. sorted cells from caStat5a mice, did the ligation-mediated PCR experiments (Supplementary Fig. 7) and flow cytometry analysis (Supplementary Fig. 8); N.S. did flow cytometry analysis (Fig. 7 and Supplementary Fig. 6); L.B.R. provided bones from caStat5b mice; J.G. and M.A.F. provided caStat5a mice; D.G.S. and M.A.F. provided critical comments on the manuscript; B.P.S. made the Abelson-transformed cells used in Figure 6 and Supplementary Figure 5 and provided critical comments on the manuscript; M.B. provided the Pax5−/− pro–B cells and caStat5a mice and collaborated on the manuscript; C.H.B. provided Atm−/− mice and data in Figure 6 and Supplementary Figures 5 and 6 and collaborated on the manuscript; and J.A.S. did confocal analysis of experiments in Figures 1,2,3,4 and 7, did three-dimensional DNA FISH (Figs. 1 and 7 and Supplementary Fig. 7) and wrote the manuscript.

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Correspondence to Jane A Skok.

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M.B. received support from Boehringer Ingelheim.

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Hewitt, S., Yin, B., Ji, Y. et al. RAG-1 and ATM coordinate monoallelic recombination and nuclear positioning of immunoglobulin loci. Nat Immunol 10, 655–664 (2009). https://doi.org/10.1038/ni.1735

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