RNF40 regulates gene expression in an epigenetic context-dependent manner

Abstract

BackgroundMonoubiquitination of H2B (H2Bub1) is a largely enigmatic histone modification that has been linked to transcriptional elongation. Because of this association, it has been commonly assumed that H2Bub1 is an exclusively positively acting histone modification and that increased H2Bub1 occupancy correlates with increased gene expression. In contrast, depletion of the H2B ubiquitin ligases RNF20 or RNF40 alters the expression of only a subset of genes.ResultsUsing conditional Rnf40 knockout mouse embryo fibroblasts, we show that genes occupied by low to moderate amounts of H2Bub1 are selectively regulated in response to Rnf40 deletion, whereas genes marked by high levels of H2Bub1 are mostly unaffected by Rnf40 loss. Furthermore, we find that decreased expression of RNF40-dependent genes is highly associated with widespread narrowing of H3K4me3 peaks. H2Bub1 promotes the broadening of H3K4me3 to increase transcriptional elongation, which together lead to increased tissue-specific gene transcription. Notably, genes upregulated following Rnf40 deletion, including Foxl2, are enriched for H3K27me3, which is decreased following Rnf40 deletion due to decreased expression of the Ezh2 gene. As a consequence, increased expression of some RNF40-“suppressed” genes is associated with enhancer activation via FOXL2.ConclusionTogether these findings reveal the complexity and context-dependency whereby one histone modification can have divergent effects on gene transcription. Furthermore, we show that these effects are dependent upon the activity of other epigenetic regulatory proteins and histone modifications.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-017-1159-5) contains supplementary material, which is available to authorized users.

H2B ubiquitination: Conserved molecular mechanism, diverse physiologic functions of the E3 ligase during meiosis

“…39 Whether these functions are used in meiosis or not still need further investigation. On the other hand, histone is not the only substrate of RNF20.…”

RNF40-dependent epigenetic regulation of actin cytoskeletal dynamics is required for HER2-driven mammary tumorigenesis

“…Past studies have reported an extension of H3K4me3 into the transcribed region of genes displaying a particularly high transcriptional elongation rate (31), as well as a close link between H2Bub1 and transcriptional elongation (23). Consistently, we recently demonstrated that loss of RNF40-mediated H2B monoubiquitination results in the narrowing of H3K4me3 domains near the transcriptional start site (TSS) of important cell fate-determining genes displaying high elongation rates (22).…”

“…We generated a tri-transgenic MMTV- Erbb2 ; MMTV-Cre; Rnf40 f lox mouse line with mammary tissue-specific co-expression of HER2 and Cre-recombinase, and a floxed Rnf40 allele. This approach enabled us to achieve a simultaneous HER2 overexpression and mammary epithelium-specific ablation of Rnf40 (18,22). Consistent with our findings in human HER2-positive BC lesions, MMTV- Erbb2; Rnf40 wt/wt tumors did not display a loss of either RNF40 or H2Bub1 (Fig.…”

“…Previous studies from other groups demonstrated a crosstalk between H2Bub1 and H3K4 tri-methylation (H3K4me3) both in yeast and human systems (26,29,30). Moreover, we recently demonstrated that RNF40-mediated H2B monoubiquitination specifically governs the transcriptional start site- (TSS-) proximal broadening of H3K4me3 into the transcribed region to facilitate transcriptional elongation of a number of moderately H2Bub1-marked genes in mouse embryo fibroblasts (MEFs) (22). To examine if RNF40 controls the expression of genes of the actin regulatory network by modulating H2Bub1 and H3K4me3 levels, we performed chromatin immunoprecipitation sequencing (ChIP-seq) analyses for H2Bub1 and H3K4me3 in HCC1954 cells (Fig.…”

“…At the molecular level, H2Bub1 is localized across the body of active genes (21) and is closely coupled to transcriptional elongation (22–25). Studies in both yeast and human cells have revealed a particular coupling of H2Bub1 and the trimethylation of lysines 4 and 79 of histone 3 (H3K4me3 and H3K79me3, respectively) near the transcriptional start site and transcribed regions, respectively, of active genes (22,26–30). Past studies have reported an extension of H3K4me3 into the transcribed region of genes displaying a particularly high transcriptional elongation rate (31), as well as a close link between H2Bub1 and transcriptional elongation (23).…”