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Series GSE69823 Query DataSets for GSE69823
Status Public on Jan 27, 2017
Title Gender Differences in Global but not Targeted Demethylation in iPSC Reprogramming
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary 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 AID-mediated downregulation of UHRF1 protein and abolishing demethylation leaves thousands of hypermethylated regions in the iPSCs 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.
 
Overall design mRNA-seq and BS-seq of different time-points during iPSC reprogramming
 
Contributor(s) Milagre I, Stubbs TM, King MR, Spindel J, Santos F, Krueger F, Bachman M, Segonds-Pichon A, Balasubramanian S, Andrews SR, Dean W, Reik W
Citation(s) 28147265
Submission date Jun 12, 2015
Last update date Feb 15, 2024
Contact name Felix Krueger
E-mail(s) fkrueger@altoslabs.com
Organization name Altos Labs
Department Bioinformatics
Street address Granta Park
City Cambridge
ZIP/Postal code CB21 6GP
Country United Kingdom
 
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (203)
GSM1709590 BS_seq_MEF_1
GSM1709591 BS_seq_MEF_2
GSM1709592 BS_seq_MEF_3
Relations
BioProject PRJNA286869
SRA SRP059433

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE69823_RAW.tar 7.8 Gb (http)(custom) TAR (of COV, TXT)
GSE69823_Reprogramming_iPSC_RNAseq_Wt.txt.gz 2.1 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record
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