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AID stabilizes stem-cell phenotype by removing epigenetic memory of pluripotency genes

Abstract

The activation-induced cytidine deaminase (AID; also known as AICDA) enzyme is required for somatic hypermutation and class switch recombination at the immunoglobulin locus1. In germinal-centre B cells, AID is highly expressed, and has an inherent mutator activity that helps generate antibody diversity2. However, AID may also regulate gene expression epigenetically by directly deaminating 5-methylcytosine in concert with base-excision repair to exchange cytosine3. This pathway promotes gene demethylation, thereby removing epigenetic memory. For example, AID promotes active demethylation of the genome in primordial germ cells4. However, different studies have suggested either a requirement5 or a lack of function6 for AID in promoting pluripotency in somatic nuclei after fusion with embryonic stem cells. Here we tested directly whether AID regulates epigenetic memory by comparing the relative ability of cells lacking AID to reprogram from a differentiated murine cell type to an induced pluripotent stem cell. We show that Aid-null cells are transiently hyper-responsive to the reprogramming process. Although they initiate expression of pluripotency genes, they fail to stabilize in the pluripotent state. The genome of Aid-null cells remains hypermethylated in reprogramming cells, and hypermethylated genes associated with pluripotency fail to be stably upregulated, including many MYC target genes. Recent studies identified a late step of reprogramming associated with methylation status7, and implicated a secondary set of pluripotency network components8. AID regulates this late step, removing epigenetic memory to stabilize the pluripotent state.

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Figure 1: Cells lacking AID are initially hyper-responsive to transcription-factor-based reprogramming.
Figure 2: AID stabilizes pluripotency.
Figure 3: Cells lacking AID reprogram inefficiently, but those that do are pluripotent.
Figure 4: Cells lacking AID fail to activate expression of hypermethylated pluripotency genes.

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Gene Expression Omnibus

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All RNA-seq and RRBS data have been deposited in the Gene Expression Omnibus under accession GSE46700.

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Acknowledgements

We thank G. Mostoslavsky for the gift of reprogramming vectors. A. Melnick provided advice and consultation. We are grateful to T. Honjo for AID-knockout mice, and N. Papavasiliou for assistance in designing genotyping PCR primers. The Epigenomics Core Facility of Weill Cornell Medical College carried out the bisulphite sequencing and provided consultation. This study was supported by National Institutes of Health grant HL056182 (T.E.), AI072194 (J.C.) and National Science Foundation CAREER grant 1054964 (O.E.).

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R.K. conceived the study, carried out experiments, and wrote the manuscript. L.D., N.S., T.-C.L., P.F. and S.M.-D. carried out experiments. A.A.Z. and A.-K.H. provided essential reagents and expertise. J.C. conceived the study and wrote the manuscript. O.E. conceived the study, carried out computational and informatics analyses, and wrote the manuscript. T.E. conceived the study and wrote the manuscript.

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Correspondence to Todd Evans.

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The authors declare no competing financial interests.

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This file contains a list of abbreviations used in the text, Supplementary Figures 1-16 and Supplementary Tables 1-3. (PDF 6803 kb)

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Kumar, R., DiMenna, L., Schrode, N. et al. AID stabilizes stem-cell phenotype by removing epigenetic memory of pluripotency genes. Nature 500, 89–92 (2013). https://doi.org/10.1038/nature12299

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