Gender Differences in Global but Not Targeted Demethylation in iPSC Reprogramming.
Global DNA demethylation is an integral part of reprogramming processes in vivo and in vitro, but whether it occurs in the derivation of induced pluripotent stem cells (iPSCs) is not known. Here, we show that iPSC reprogramming involves both global and targeted demethylation, which are separable mechanistically and by their biological outcomes. Cells at intermediate-late stages of reprogramming undergo transient genome-wide demethylation, which is more pronounced in female cells. Global demethylation requires activation-induced cytidine deaminase (AID)-mediated downregulation of UHRF1 protein, and abolishing demethylation leaves thousands of hypermethylated regions in the iPSC genome. Independently of AID and global demethylation, regulatory regions, particularly ESC enhancers and super-enhancers, are specifically targeted for hypomethylation in association with transcription of the pluripotency network. Our results show that global and targeted DNA demethylation are conserved and distinct reprogramming processes, presumably because of their respective roles in epigenetic memory erasure and in the establishment of cell identity.
Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK. Electronic address: ines.milagre@babraham.ac.uk.
Inês
I
Milagre
Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK.
Thomas M
TM
Stubbs
Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK.
Michelle R
MR
King
Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK.
Julia
J
Spindel
Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK.
Fátima
F
Santos
Bioinformatics Group, The Babraham Institute, Cambridge CB22 3AT, UK.
Felix
F
Krueger
Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK.
Martin
M
Bachman
Bioinformatics Group, The Babraham Institute, Cambridge CB22 3AT, UK.
Anne
A
Segonds-Pichon
Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK.
Shankar
S
Balasubramanian
Bioinformatics Group, The Babraham Institute, Cambridge CB22 3AT, UK.
Simon R
SR
Andrews
Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK.
Wendy
W
Dean
Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK. Electronic address: wolf.reik@babraham.ac.uk.
Wolf
W
Reik
D000818:Animals; D022762:CCAAT-Enhancer-Binding Proteins; D002478:Cells, Cultured; D065150:Cellular Reprogramming / Q000235:genetics* / Q000502:physiology; D003564:Cytidine Deaminase / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D053595:Embryonic Stem Cells / Q000502:physiology; D044127:Epigenesis, Genetic / Q000235:genetics; D057890:Epigenomics / Q000379:methods; D005260:Female; D005347:Fibroblasts; D005786:Gene Expression Regulation / Q000235:genetics; D016678:Genome / Q000235:genetics; D057026:Induced Pluripotent Stem Cells / Q000502:physiology*; D051379:Mice; D009687:Nuclear Proteins / Q000235:genetics; D012727:Sex Characteristics; D014158:Transcription, Genetic / Q000235:genetics; D044767:Ubiquitin-Protein Ligases
D022762:CCAAT-Enhancer-Binding Proteins; D009687:Nuclear Proteins; D044767:Ubiquitin-Protein Ligases; C117054:Uhrf1 protein, mouse; D003564:Cytidine Deaminase
AID; DNA methylation; UHRF1; gender differences; iPSCs; reprogramming