Article

Mbd3/NURD Complex Regulates Expression of 5-Hydroxymethylcytosine Marked Genes in Embryonic Stem Cells

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
Cell (Impact Factor: 33.12). 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.

Download full-text

Full-text

Available from: Thomas G Fazzio, Aug 31, 2015
0 Followers
 · 
456 Views
  • Source
    • "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). "
    [Show abstract] [Hide abstract]
    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.
    Cell Reports 10/2014; 9(1). DOI:10.1016/j.celrep.2014.08.071 · 8.36 Impact Factor
  • Source
    • "To investigate which pathway is responsible for the observed gene reactivation, we searched for potential TET interaction partners. So far, it has been shown that MBD3 colocalizes with TET1 regulating hmC-marked gene expression (53) and that TET1, TET2 and TET3 interact with OGT controlling protein stability, localization and histone modification (54–57). Also, several chromatin-binding factors, such as HDAC1, EZH2 and MeCP2, have been described to associate with TET1 (58). "
    [Show abstract] [Hide abstract]
    ABSTRACT: The discovery of hydroxymethyl-, formyl- and carboxylcytosine, generated through oxidation of methylcytosine by TET dioxygenases, raised the question how these modifications contribute to epigenetic regulation. As they are subjected to complex regulation in vivo, we dissected links to gene expression with in vitro modified reporter constructs. We used an Oct4 promoter-driven reporter gene and demonstrated that in vitro methylation causes gene silencing while subsequent oxidation with purified catalytic domain of TET1 leads to gene reactivation. To identify proteins involved in this pathway we screened for TET interacting factors and identified TDG, PARP1, XRCC1 and LIG3 that are involved in base-excision repair. Knockout and rescue experiments demonstrated that gene reactivation depended on the glycosylase TDG, but not MBD4, while NEIL1, 2 and 3 could partially rescue the loss of TDG. These results clearly show that oxidation of methylcytosine by TET dioxygenases and subsequent removal by TDG or NEIL glycosylases and the BER pathway results in reactivation of epigenetically silenced genes.
    Nucleic Acids Research 06/2014; 42(13). DOI:10.1093/nar/gku552 · 9.11 Impact Factor
  • Source
    • "Alternatively, BRG1 recruitment might be compromised by reduced NuRD recruitment to the b-globin locus in LDB1D4/5-expressing cells. Evidence has been presented for interaction between BRG1 and NuRD, and, furthermore, SWI/SNF and NuRD can each influence the occupancy of the other in different contexts (Datta et al. 2005; Ramirez-Carrozzi et al. 2006; Yildirim et al. 2011). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Many questions remain about how close association of genes and distant enhancers occurs and how this is linked to transcription activation. In erythroid cells, lim domain binding 1 (LDB1) protein is recruited to the β-globin locus via LMO2 and is required for looping of the β-globin locus control region (LCR) to the active β-globin promoter. We show that the LDB1 dimerization domain (DD) is necessary and, when fused to LMO2, sufficient to completely restore LCR–promoter looping and transcription in LDB1-depleted cells. The looping function of the DD is unique and irreplaceable by heterologous DDs. Dissection of the DD revealed distinct functional properties of conserved subdomains. Notably, a conserved helical region (DD4/5) is dispensable for LDB1 dimerization and chromatin looping but essential for transcriptional activation. DD4/5 is required for the recruitment of the coregulators FOG1 and the nucleosome remodeling and deacetylating (NuRD) complex. Lack of DD4/5 alters histone acetylation and RNA polymerase II recruitment and results in failure of the locus to migrate to the nuclear interior, as normally occurs during erythroid maturation. These results uncouple enhancer–promoter looping from nuclear migration and transcription activation and reveal new roles for LDB1 in these processes.
    Genes & development 06/2014; 28(12):1278-1290. DOI:10.1101/gad.239749.114 · 12.64 Impact Factor
Show more