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Dataset Information

40

Hydroxylation of 5-methylcytosine by TET2 maintains the active state of the mammalian HOXA cluster (MeDIP-Seq)


ABSTRACT: Differentiation is accompanied by extensive epigenomic reprogramming, leading to the repression of stemness factors and the transcriptional maintenance of activated lineage-specific genes. Here we used the mammalian Hoxa cluster of developmental genes as a model system to follow changes in DNA modification patterns during retinoic acid induced differentiation. We found the inactive cluster to be marked by defined patterns of 5-methylcytosine (5mC). Upon the induction of differentiation, the active anterior part of the cluster became increasingly enriched in 5-hydroxymethylcytosine (5hmC), following closely the colinear activation pattern of the gene array, which was paralleled by the reduction of 5mC. Depletion of the 5hmC generating dioxygenase Tet2 impaired the maintenance of Hoxa activity and partially restored 5mC levels. Our results indicate that gene specific 5mC-5hmC conversion by Tet2 is crucial for the maintenance of active chromatin states at lineage-specific loci. Overall design: Examination of 5-methylcytosine (MeDIP-seq) and 5-hydroxymethylcytosine (hMeDIP-seq) at the HOXA cluster in 2 different developmental stages of a pluripotent cancer cell line.

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

ORGANISM(S): Homo sapiens  

SUBMITTER: michael thomas bocker 

PROVIDER: GSE33129 | GEO |

SECONDARY ACCESSION(S): PRJNA156605

REPOSITORIES: GEO

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