The Rhox Homeobox Gene Cluster Is Imprinted and Selectively Targeted for Regulation by Histone H1 and DNA Methylation

Abstract

Histone H1 is an abundant and essential component of chromatin whose precise role in regulating gene expression is poorly understood. Here, we report that a major target of H1-mediated regulation in embryonic stem (ES) cells is the X-linked Rhox homeobox gene cluster. To address the underlying mechanism, we examined the founding member of the Rhox gene cluster-Rhox5-and found that its distal promoter (Pd) loses H1, undergoes demethylation, and is transcriptionally activated in response to loss of H1 genes in ES cells. Demethylation of the Pd is required for its transcriptional induction and we identified a single cytosine in the Pd that, when methylated, is sufficient to inhibit Pd transcription. Methylation of this single cytosine prevents the Pd from binding GA-binding protein (GABP), a transcription factor essential for Pd transcription. Thus, H1 silences Rhox5 transcription by promoting methylation of one of its promoters, a mechanism likely to extend to other H1-regulated Rhox genes, based on analysis of ES cells lacking DNA methyltransferases. The Rhox cluster genes targeted for H1-mediated transcriptional repression are also subject to another DNA methylation-regulated process: Xp imprinting. Remarkably, we found that only H1-regulated Rhox genes are imprinted, not those immune to H1-mediated repression. Together, our results indicate that the Rhox gene cluster is a major target of H1-mediated transcriptional repression in ES cells and that H1 is a candidate to have a role in Xp imprinting.

Zinc Finger Protein ZFP57 Requires Its Co-factor to Recruit DNA Methyltransferases and Maintains DNA Methylation Imprint in Embryonic Stem Cells via Its Transcriptional Repression Domain

“…ES cells have been increasingly employed as a model system for studying genomic imprinting (9,25,(42)(43)(44)(45)(46). Indeed, we found that ZFP57 maintains DNA methylation imprint at a large subset of imprinted regions in ES cells.…”

Failure of extra-embryonic progenitor maintenance in the absence of dosage compensation

“…Interestingly, genes known to escape XCI, such as Kdm5c, escaped XCI in X JF1 /X 129 Xist1Lox;GFP TS cells in a reciprocal pattern to that of X JF1 /X 129 Xist2Lox;GFP TS cells. Genes known to be imprinted in adult tissues, such as Rhox6 (Maclean et al, 2011), followed the patterns of genes subject to imprinted XCI. It should be noted that when Cre-expressing constructs were introduced into X JF1 /X 129 Xist2Lox;GFP TS cells, we were unable to recover X JF1 /X 129 Xist1Lox;GFP TS cells, whereas the same Cre constructs introduced into X/X Xist2Lox embryonic stem (ES) cells produced X/X Xist1Lox ES colonies.…”

The humanRHOXgene cluster: target genes and functional analysis of gene variants in infertile men

“…This is further supported by studies examining RHOX regulation. Both mouse and human RHOX family members have been demonstrated to be strongly regulated by DNA methylation (25)(26)(27) and there is an association between RHOX hypermethylation and abnormal sperm in idiopathic infertile patients (14).…”