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Deep-sequencing identification of the genomic targets of the cytidine deaminase AID and its cofactor RPA in B lymphocytes

Nature Immunology volume 12, pages 62–69 (2011)Cite this article

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Abstract

The cytidine deaminase AID hypermutates immunoglobulin genes but can also target oncogenes, leading to tumorigenesis. The extent of AID's promiscuity and its predilection for immunoglobulin genes are unknown. We report here that AID interacted broadly with promoter-proximal sequences associated with stalled polymerases and chromatin-activating marks. In contrast, genomic occupancy of replication protein A (RPA), an AID cofactor, was restricted to immunoglobulin genes. The recruitment of RPA to the immunoglobulin loci was facilitated by phosphorylation of AID at Ser38 and Thr140. We propose that stalled polymerases recruit AID, thereby resulting in low frequencies of hypermutation across the B cell genome. Efficient hypermutation and switch recombination required AID phosphorylation and correlated with recruitment of RPA. Our findings provide a rationale for the oncogenic role of AID in B cell malignancy.

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Figure 1: Extent of AID recruitment in activated B cells.
Figure 2: AID targets are somatically hypermutated.
Figure 3: AID recruitment is biased toward actively transcribed genes associated with an open chromatin configuration.
Figure 4: Epigenetic signature of AID recruitment.
Figure 5: Genome-wide correlation between AID and PolII occupancy.
Figure 6: AID hypermutates basal promoters.
Figure 7: Recruitment of RPA to on-target sites of AID.

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Acknowledgements

We thank D. Schatz for comments on the manuscript; J. Chaudhuri (Memorial Sloan-Kettering Cancer Center) and F. Alt (Harvard University) for antibodies to AID; J. Simone for cell sorting; G. Gutierrez for technical assistance with the genome analyzer; and C. Ansarah-Sobrinho and S. Nelson for help with sequencing. Supported by the National Institutes of Health (Intramural Research Program of the National Institute of Arthritis and Musculoskeletal and Skin Diseases; and AI037526 to M.C.N.) and the Howard Hughes Medical Institute (M.C.N.).

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Author notes

  1. Arito Yamane and Wolfgang Resch: These authors contributed equally to this work.

Authors and Affiliations

  1. Genomics & Immunity, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA

    Arito Yamane, Wolfgang Resch, Nan Kuo, Stefan Kuchen, Zhiyu Li & Rafael Casellas

  2. Biodata Mining and Discovery, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA

    Hong-wei Sun

  3. Laboratory of Molecular Immunology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA

    Davide F Robbiani, Kevin McBride & Michel C Nussenzweig

  4. Center of Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA

    Rafael Casellas

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Contributions

A.Y. did deep sequencing, cloning and conventional sequencing experiments; W.R. and H.-w.S. analyzed data; N.K. contributed data; Z.L. maintained the mouse colonies and cultured cells; D.F.R. contributed the Igk-AID mice; M.C.N. made suggestions for experiments and reviewed and wrote sections of the manuscript; R.C. designed the experiments and wrote the manuscript.

Corresponding authors

Correspondence to Michel C Nussenzweig or Rafael Casellas.

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The authors declare no competing financial interests.

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Yamane, A., Resch, W., Kuo, N. et al. Deep-sequencing identification of the genomic targets of the cytidine deaminase AID and its cofactor RPA in B lymphocytes. Nat Immunol 12, 62–69 (2011). https://doi.org/10.1038/ni.1964

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