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

SummaryNumerous 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.

Graphical AbstractFigure optionsDownload high-quality image (220 K)Download as PowerPoint slideHighlights
► Mbd3/NURD and esBAF oppositely regulate many common target genes in ES cells
► Mbd3 association with its in vivo targets requires 5-methylcytosine hydroxylase Tet1
► Mbd3 binds preferentially to hydroxymethylated DNA relative to methylated DNA
► Genomic 5-hydroxymethylcytosine levels are reduced in Mbd3 and Brg1 knockdown cells