Genomics

Dataset Information

92

Whole Genome Bisulfite Sequencing of HUES8 WT and HUES8 TET1/2/3 TKO hESCs


ABSTRACT: The TET enzymes oxidize 5-methylcytosine to 5-hydroxymethylcytosine, which can lead to DNA demethylation. However, direct connections between TET-mediated DNA demethylation and transcriptional output are difficult to establish due to challenges of distinguishing global versus locus-specific effects. Here we show that TET1/2/3 triple knockout (TKO) human embryonic stem cells (hESCs) exhibit preferential hypermethylation at bivalent promoters without corresponding gene expression changes in undifferentiated hESCs. In the absence of the TET proteins, abnormal accumulation of DNMT3B at bivalent promoters results in hypermethylation and impaired gene activation upon differentiation. Broadly, the competitive balance between the TET proteins and de novo methyltransferases at bivalent promoters could facilitate rapid changes of their methylation state to either activate or silence transcription in a cell-lineage and gene dependent manner. Overall design: For whole genome bisulfite sequencing genomic DNA was isolated from HUES8 WT and HUES8 TKO hESCs using the DNeasy Blood & Tissue Kit (Qiagen, 69504) following manufacturer’s guidelines. One replicate was done for each sample.

INSTRUMENT(S): Illumina HiSeq 2000 (Homo sapiens)

SUBMITTER: Nipun Verma  

PROVIDER: GSE89727 | GEO | 2017-12-01

SECONDARY ACCESSION(S): PRJNA353017

REPOSITORIES: GEO

Similar Datasets

| GSE89724 | GEO
| GSE89726 | GEO
| GSE90495 | GEO
| GSE99346 | GEO
| PRJNA352093 | ENA
| PRJNA352092 | ENA
| PRJNA388168 | ENA
2014-09-22 | E-GEOD-56986 | ArrayExpress
2014-04-14 | E-GEOD-55574 | ArrayExpress
2014-04-17 | E-GEOD-55049 | ArrayExpress