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E-GEOD-32362 - Hydroxylation of 5-methylcytosine by TET2 maintains the active state of the mammalian HOXA cluster (Infinium HumanMethylation450 Beadchip)

Status
Released on 2 May 2012, last updated on 25 June 2012
Organism
Homo sapiens
Samples (4)
Array (1)
Protocols (8)
Description
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. Genome wide DNA methylation profiling of uninduced and retinoic acid (RA) induced NTera2/D1 embryocarcinoma cells (NT2). Bisulphite converted DNA of uninduced, 7d RA and 14d RA treated NT2 cells were hybridised to the Illumina Infinium HumanMethylation450 Beadchip.
Experiment type
methylation profiling by array 
Contacts
michael thomas bocker <geo@ncbi.nlm.nih.gov>, Achim Breiling, Feng-Chun Yang, Francesca Tuorto, Frank Lyko, Günter Raddatz, Michael T Bocker, Mingjiang Xu, Tanja Musch
Citation
Hydroxylation of 5-methylcytosine by TET2 maintains the active state of the mammalian HOXA cluster. Bocker MT, Tuorto F, Raddatz G, Musch T, Yang FC, Xu M, Lyko F, Breiling A. , PMID:22569366
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-32362.idf.txt
Sample and data relationshipE-GEOD-32362.sdrf.txt
Processed data (1)E-GEOD-32362.processed.1.zip
Additional data (1)E-GEOD-32362.additional.1.zip
Array designA-GEOD-13534.adf.txt
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