Transcriptomics

Dataset Information

242

Tet1 and hydroxymethylcytosine in transcription and DNA methylation fidelity (Affymetrix gene expression data)


ABSTRACT: Enzymes catalyzing the methylation of the 5-position of cytosine (mC) have essential roles in regulating gene expression, genome stability, and maintaining cellular identity. Recently Tet1, which is highly expressed in embryonic stem (ES) cells, was found to oxidize the methyl group of mC converting it to 5-hydroxymethyl cytosine (hmC)3. Here, we present the genome-wide mapping of Tet1 and hmC in mouse ES cells. We show that Tet1 binds throughout the genome with the majority of binding sites located at transcription start sites (TSSs) and within genes. Similar to Tet1 and mC, also hmC is found throughout the genome and in particular in gene bodies. However, in contrast to mC, hmC is enriched at TSSs. Tet1 and hmC are associated with genes critical for the control of development and differentiation, which become methylated during differentiation. Surprisingly our results also suggest that Tet1 has a role in transcriptional repression. We show that Tet1 binds to a significant proportion of target genes that are positive for the Polycomb repressive histone mark H3K27me3, and that downregulation of Tet1 also leads to increased expression of a group of Tet1 target genes. In agreement with a potential repressive function, we show that Tet1 associates with the Sin3A co-repressor complex, which also co-localises with Tet1 throughout the genome. We propose that Tet1 fulfils dual functions in transcriptional regulation, where it fine-tunes DNA methylation and associates with the Sin3A co-repressor complex to prevent transcriptional activation. [GSM611209-GSM611217] Control (shScr) or two different Tet1 knockdown (shTet1#4 or shTet1#5) mouse ES cells were used. Each experiment was performed in triplicates. [GSM675884-GSM675889] Control (shScr) or Sin3A knockdown (shSin3A) mouse ES cells were used.Each experiment was performed in triplicates.

ORGANISM(S): Mus musculus  

SUBMITTER: Kristine Williams  

PROVIDER: E-GEOD-24842 | ArrayExpress | 2011-04-13

SECONDARY ACCESSION(S): GSE24842PRJNA133433

REPOSITORIES: GEO, ArrayExpress

altmetric image

Publications

TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity.

Williams Kristine K   Christensen Jesper J   Pedersen Marianne Terndrup MT   Johansen Jens V JV   Cloos Paul A C PA   Rappsilber Juri J   Helin Kristian K  

Nature 20110413 7347


Enzymes catalysing the methylation of the 5-position of cytosine (mC) have essential roles in regulating gene expression and maintaining cellular identity. Recently, TET1 was found to hydroxylate the methyl group of mC, converting it to 5-hydroxymethyl cytosine (hmC). Here we show that TET1 binds throughout the genome of embryonic stem cells, with the majority of binding sites located at transcription start sites (TSSs) of CpG-rich promoters and within genes. The hmC modification is found in gen  ...[more]

Similar Datasets

2011-04-13 | E-GEOD-24841 | ArrayExpress
2011-04-13 | GSE24841 | GEO
2011-04-13 | GSE24842 | GEO
2013-06-30 | E-GEOD-46402 | ArrayExpress
2013-06-30 | E-GEOD-46319 | ArrayExpress
2013-02-26 | PXD000143 | Pride
2011-06-24 | E-GEOD-30173 | ArrayExpress
| GSE40166 | GEO
2011-03-30 | E-GEOD-26830 | ArrayExpress
2013-07-30 | E-GEOD-42723 | ArrayExpress