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


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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    ABSTRACT: Functional interactions between gene regulatory factors and chromatin architecture have been difficult to directly assess. Here, we use micrococcal nuclease (MNase) footprinting to probe the functions of two chromatin-remodeling complexes. By simultaneously quantifying alterations in small MNase footprints over the binding sites of 30 regulatory factors in mouse embryonic stem cells (ESCs), we provide evidence that esBAF and Mbd3/NuRD modulate the binding of several regulatory proteins. In addition, we find that nucleosome occupancy is reduced at specific loci in favor of subnucleosomes upon depletion of esBAF, including sites of histone H2A.Z localization. Consistent with these data, we demonstrate that esBAF is required for normal H2A.Z localization in ESCs, suggesting esBAF either stabilizes H2A.Z-containing nucleosomes or promotes subnucleosome to nucleosome conversion by facilitating H2A.Z deposition. Therefore, integrative examination of MNase footprints reveals insights into nucleosome dynamics and functional interactions between chromatin structure and key gene-regulatory factors.
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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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    ABSTRACT: The development of cancer is driven not only by genetic mutations but also by epigenetic alterations. Here, we show that TET1-mediated production of 5-hydroxymethylcytosine (5hmC) is required for the tumorigenicity of glioblastoma cells. Furthermore, we demonstrate that chromatin target of PRMT1 (CHTOP) binds to 5hmC. We found that CHTOP is associated with an arginine methyltransferase complex, termed the methylosome, and that this promotes the PRMT1-mediated methylation of arginine 3 of histone H4 (H4R3) in genes involved in glioblastomagenesis, including EGFR, AKT3, CDK6, CCND2, and BRAF. Moreover, we found that CHTOP and PRMT1 are essential for the expression of these genes and that CHTOP is required for the tumorigenicity of glioblastoma cells. These results suggest that 5hmC plays a critical role in glioblastomagenesis by recruiting the CHTOP-methylosome complex to selective sites on the chromosome, where it methylates H4R3 and activates the transcription of cancer-related genes.
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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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    ABSTRACT: The etiology of many brain diseases remains allusive to date after intensive investigation of genomic background and symptomatology from the day of birth. Emerging evidences indicate that a third factor, epigenetics prior to the birth, can exert profound influence on the development and functioning of the brain and over many neurodevelopmental syndromes. This chapter reviews how aversive environmental exposure to parents might predispose or increase vulnerability of offspring to neurodevelopmental deficit through alteration of epigenetics. These epigenetic altering environmental factors will be discussed in the category of addictive agents, nutrition or diet, prescriptive medicine, environmental pollutant, and stress. Epigenetic alterations induced by these aversive environmental factors cover all aspects of epigenetics including DNA methylation, histone modification, noncoding RNA, and chromatin modification. Next, the mechanisms how these environmental inputs influence epigenetics will be discussed. Finally, how environmentally altered epigenetic marks affect neurodevelopment is exemplified by the alcohol-induced fetal alcohol syndrome. It is hoped that a thorough understanding of the nature of prenatal epigenetic inputs will enable researchers with a clear vision to better unravel neurodevelopmental deficit, late-onset neuropsychiatric diseases, or idiosyncratic mental disorders.
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