Mammalian somatic cells can be directly reprogrammed into induced pluripotent stem cells (iPSCs) by introducing defined sets of transcription factors. Somatic cell reprogramming involves epigenomic reconfiguration, conferring iPSCs with characteristics similar to embryonic stem cells (ESCs). Human ESCs (hESCs) contain 5-hydroxymethylcytosine (5hmC), which is generated through the oxidation of 5-methylcytosine by the TET enzyme family. Here we show that 5hmC levels increase significantly during reprogramming to human iPSCs mainly owing to TET1 activation, and this hydroxymethylation change is critical for optimal epigenetic reprogramming, but does not compromise primed pluripotency. Compared with hESCs, we find that iPSCs tend to form large-scale (100 kb-1.3 Mb) aberrant reprogramming hotspots in subtelomeric regions, most of which exhibit incomplete hydroxymethylation on CG sites. Strikingly, these 5hmC aberrant hotspots largely coincide (∼ 80%) with aberrant iPSC-ESC non-CG methylation regions. Our results suggest that TET1-mediated 5hmC modification could contribute to the epigenetic variation of iPSCs and iPSC-hESC differences.
Bibliographical noteFunding Information:
We thank J. Suhl, M. Santoro, S. Bray and C. Strauss for critical reading of the manuscript. We thank X. Huang from the Viral Vector Core of the Emory Neuroscience NINDS Core Facilities for preparing the retrovirus/lentivirus used in this study. We are grateful to J. Mowrey, V. Patel, C. Street and S. Namburi for support on Illumina Hiseq2000/Miseq sequencing. This study was supported in part by the National Institutes of Health (NS079625 and HD073162 to P.J.; MH089606 and HD24064 to S.T.W.), the Emory Genetics Discovery Fund, and the Autism Speaks grant (#7660 to X.L.).
All Science Journal Classification (ASJC) codes
- Cell Biology