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Yildirim O, Li R, Hung JH, Chen PB, Dong X, Ee LS et al. Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells. Cell 147: 1498-1510

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
Cell (Impact Factor: 32.24). 12/2011; 147(7):1498-510. DOI: 10.1016/j.cell.2011.11.054
Source: PubMed

ABSTRACT

Numerous chromatin regulators are required for embryonic stem (ES) cell self-renewal and pluripotency, but few have been studied in detail. Here, we examine the roles of several chromatin regulators whose loss affects the pluripotent state of ES cells. We find that Mbd3 and Brg1 antagonistically regulate a common set of genes by regulating promoter nucleosome occupancy. Furthermore, both Mbd3 and Brg1 play key roles in the biology of 5-hydroxymethylcytosine (5hmC): Mbd3 colocalizes with Tet1 and 5hmC in vivo, Mbd3 knockdown preferentially affects expression of 5hmC-marked genes, Mbd3 localization is Tet1-dependent, and Mbd3 preferentially binds to 5hmC relative to 5-methylcytosine in vitro. Finally, both Mbd3 and Brg1 are themselves required for normal levels of 5hmC in vivo. Together, our results identify an effector for 5hmC, and reveal that control of gene expression by antagonistic chromatin regulators is a surprisingly common regulatory strategy in ES cells.

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    • "Finally, as a negative control, we observed no changes in small reads over a random sampling of nucleosomes, demonstrating alterations in esBAF and Mbd3/NuRD are confined to specific regions of the genome. Smarca4 KD resulted in a substantial reduction in small read accumulation at several sites (Figure 1A; Data S1A), consistent with the function of esBAF to create open chromatin structure to facilitate binding of regulatory factors and the general transcription machinery (Ho et al., 2009a, 2009b, 2011; Novershtern and Hanna, 2011; Yildirim et al., 2011). Whereas KD of Mbd3 resulted in subtle changes in MNase footprinting at most sites relative to Smarca4 KD, we observed a strong increase in peaks of small reads at p300 binding sites in Mbd3 KD cells, consistent with the antagonistic roles of Mbd3/NuRD and p300 in enhancer function (Pasini et al., 2010; Reynolds et al., 2012). "
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    • "It has recently been shown that 5hmC acts not only as an intermediate of DNA demethylation but also as an epigenetic mark that recruits DNA-binding proteins. For example, it has been shown that the Mbd3/NURD complex regulates expression of 5hmC-marked genes in embryonic stem cells (ESCs) (Yildirim et al., 2011). It has also been reported that MeCP2 binds to 5hmC that is enriched within active genes as well as accessible chromatin in the nervous system (Mellé n et al., 2012). "
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    • "Recent research has begun to shed some light on the potential role of 5hmC. It has been found that 5mC and 5hmC, are diversely distributed in the genome where 5mC occurs preferentially in the promoter/enhancer regions, while 5hmC is increased in the intragenic gene body regions of genes undergoing active transcription in mouse embryonic stem (ES) cells (Stroud, Feng, Morey Kinney, Pradhan, & Jacobsen, 2011; Wu et al., 2011; Yildirim et al., 2011) and mouse cerebellum (J. U. Guo et al., 2011; Pastor et al., 2011; Wu et al., 2011). "
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