Transcription-targeted DNA deamination by the AID antibody diversification enzyme


Activation-induced cytidine deaminase (AID), which is specific to B lymphocytes, is required for class switch recombination (CSR)—a process mediating isotype switching of immunoglobulin—and somatic hypermutation—the introduction of many point mutations into the immunoglobulin variable region genes1,2. It has been suggested that AID may function as an RNA-editing enzyme3 or as a cytidine deaminase on DNA4,5. However, the precise enzymatic activity of AID has not been assessed in previous studies. Similarly, although transcription of the target immunoglobulin locus sequences is required for both CSR and somatic hypermutation, the precise role of transcription has remained speculative6,7,8,9. Here we use two different assays to demonstrate that AID can deaminate specifically cytidines on single-stranded (ss)DNA but not double-stranded (ds)DNA substrates in vitro. However, dsDNA can be deaminated by AID in vitro when the reaction is coupled to transcription. Moreover, a synthetic dsDNA sequence, which targets CSR in vivo in a manner dependent on transcriptional orientation10, was deaminated by AID in vitro with the same transcriptional-orientation-dependence as observed for endogenous CSR. We conclude that transcription targets the DNA deamination activity of AID to dsDNA by generating secondary structures that provide ssDNA substrates.

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Figure 1: DNA cytidine deaminase activity in AID-expressing cells.
Figure 2: ssDNA cytidine deaminase activity co-sediments with AID in glycerol gradients.
Figure 3: Immunoprecipitated AID contains ssDNA cytidine deaminase activity.
Figure 4: Transcription-coupled dsDNA deamination by AID.


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We thank T. Honjo for providing AID-deficient mice and B. Demple for helpful discussions. We also thank J. Manis, A. Zarrin, S. Ranganath and S. Saleque for suggestions and critical reading of the manuscript. This work was supported by a NIH grant (F.W.A.) and a NIH training grant (M.T.). K.C. is supported by a Pfizer Postdoctoral Fellowship in Rheumatology/Immunology and E.P. is supported by a Fondation pour la Recherche Medicale Postdoctoral Fellowship. F.W.A. is an Investigator and J.C. an Associate of the Howard Hughes Medical Institute.

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Correspondence to Frederick W. Alt.

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Chaudhuri, J., Tian, M., Khuong, C. et al. Transcription-targeted DNA deamination by the AID antibody diversification enzyme. Nature 422, 726–730 (2003).

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