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A comprehensive analysis of the effects of the deaminase AID on the transcriptome and methylome of activated B cells

Nature Immunology volume 14, pages 749–755 (2013)Cite this article

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Abstract

Beyond its well-characterized functions in antibody diversification, the cytidine deaminase AID can catalyze off-target DNA damage and has been hypothesized to edit RNA and mediate DNA demethylation. To comprehensively examine the effects of AID on the transcriptome and the pattern of DNA methylation ('methylome'), we analyzed AID-deficient (Aicda−/−), wild-type and AID-overexpressing activated B cells by high-throughput RNA sequencing (RNA-Seq) and reduced-representation bisulfite sequencing (RRBS). These analyses confirmed the known role of AID in immunoglobulin isotype switching and also demonstrated few other effects of AID on gene expression. Additionally, we detected no evidence of AID-dependent editing of mRNA or microRNA. Finally, the RRBS data did not support the proposed role for AID in regulating DNA methylation. Thus, despite evidence of its additional activities in other systems, antibody diversification seems to be the sole physiological function of AID in activated B cells.

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Figure 1: AID-dependent effects on the B cell transcriptome are limited to the Igh locus.
Figure 2: AID-dependent RNA-editing events are not detectable by comparative RNA-Seq.
Figure 3: AID overexpression affects neither the abundance nor the editing of small RNA.
Figure 4: AID overexpression does not affect global DNA methylation in switching B cells.
Figure 5: No AID-dependent DNA-methylation changes are detectable in activated B cells.

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Acknowledgements

We thank members of the F.N.P. laboratory for discussion; C. Hamilton and D. Schulz for comments on the manuscript; C. Mason (Weill Cornell Medical College) for ERCC spikes; G. Hovel-Miner for VSG constructs; K. Velinzon for cell sorting; S. Dewell for sequencing advice; and Y. Li for assistance with EpiTYPER assays. Supported by the National Cancer Institute (CA098495), the Starr Cancer Consortium (I4-A447), the Howard Hughes Medical Institute (T.T.) and the US National Institutes of Health (work in the T.T. laboratory).

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Authors and Affiliations

  1. Laboratory of Lymphocyte Biology, The Rockefeller University, New York, New York, USA

    Eric L Fritz, Brad R Rosenberg, Kenneth Lay & F Nina Papavasiliou

  2. The Rockefeller Graduate Program, The Rockefeller University, New York, New York, USA

    Eric L Fritz & Kenneth Lay

  3. John C. Whitehead Presidential Fellows Program, The Rockefeller University, New York, New York, USA

    Brad R Rosenberg

  4. Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA

    Aleksandra Mihailović & Thomas Tuschl

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Contributions

E.L.F., B.R.R. and F.N.P. designed experiments and analyses; E.L.F. and K.L. cultured cells; K.L. generated VSG spikes; A.M. prepared miRNA sequencing libraries with the supervision of T.T.; E.L.F. did all other experiments and analyzed the data; and E.L.F., B.R.R. and F.N.P. wrote the manuscript.

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Correspondence to Eric L Fritz or F Nina Papavasiliou.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–5 (PDF 1567 kb)

Supplementary Table 1

Genes with greater than 2-fold difference between conditions, and full gene expression tables (XLSX 6595 kb)

Supplementary Table 2

Annotation of I-C and JH-C transcripts for quantification by Cufflinks (TXT 38 kb)

Supplementary Table 3

VH segment usage by AID expression, as determined by RNA-Seq (XLSX 67 kb)

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Fritz, E., Rosenberg, B., Lay, K. et al. A comprehensive analysis of the effects of the deaminase AID on the transcriptome and methylome of activated B cells. Nat Immunol 14, 749–755 (2013). https://doi.org/10.1038/ni.2616

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