mc_hmC_development
Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation
Methylation at the 5Ã¢Â?Â? position of cytosine in DNA plays important roles in genome             function and is dynamically reprogrammed during early embryonic and germ cell             development1. The mammalian genome also contains 5-hydroxymethylcytosine             (5hmC), which appears to be generated by oxidation of 5-methylcytosine (5mC) by             the TET family of enzymes that are highly expressed in ES cells2-4. Here we use             antibodies against 5hmC and 5mC together with high throughput sequencing to             determine genome-wide patterns of methylation and hydroxymethylation in mouse             wildtype and mutant ES cells and differentiating embryoid bodies. We find that             5hmC is mostly associated with euchromatin and that while 5mC is underrepresented             at gene promoters and CpG islands, 5hmC is enriched and is associated             with increased transcriptional levels. Most, if not all, 5hmC in the genome depends             on pre-existing 5mC and the balance between these two modifications is different             between genomic regions. Knockdown of TET1 and 2 causes downregulation of a             group of genes that includes pluripotency-related genes (including Esrrb,             Stella/Dppa3, Klf2, Tcl1, Zfp42) and a concomitant increase in methylation of their             promoters, together with an increased propensity of ES cells for extraembryonic             lineage differentiation. Declining levels of TETs during differentiation are             associated with decreased hydroxymethylation levels at the promoters of ES cellspecific             genes together with increased methylation and gene silencing. We propose             that the balance between hydroxymethylation and methylation in the genome is             inextricably linked with the balance between pluripotency and lineage commitment.