Two Distinct Repressive Mechanisms for Histone 3 Lysine 4 Methylation through Promoting 3′-End Antisense Transcription

Abstract

Histone H3 di- and trimethylation on lysine 4 are major chromatin marks that correlate with active transcription. The influence of these modifications on transcription itself is, however, poorly understood. We have investigated the roles of H3K4 methylation in Saccharomyces cerevisiae by determining genome-wide expression-profiles of mutants in the Set1 complex, COMPASS, that lays down these marks. Loss of H3K4 trimethylation has virtually no effect on steady-state or dynamically-changing mRNA levels. Combined loss of H3K4 tri- and dimethylation results in steady-state mRNA upregulation and delays in the repression kinetics of specific groups of genes. COMPASS-repressed genes have distinct H3K4 methylation patterns, with enrichment of H3K4me3 at the 3′-end, indicating that repression is coupled to 3′-end antisense transcription. Further analyses reveal that repression is mediated by H3K4me3-dependent 3′-end antisense transcription in two ways. For a small group of genes including PHO84, repression is mediated by a previously reported trans-effect that requires the antisense transcript itself. For the majority of COMPASS-repressed genes, however, it is the process of 3′-end antisense transcription itself that is the important factor for repression. Strand-specific qPCR analyses of various mutants indicate that this more prevalent mechanism of COMPASS-mediated repression requires H3K4me3-dependent 3′-end antisense transcription to lay down H3K4me2, which seems to serve as the actual repressive mark. Removal of the 3′-end antisense promoter also results in derepression of sense transcription and renders sense transcription insensitive to the additional loss of SET1. The derepression observed in COMPASS mutants is mimicked by reduction of global histone H3 and H4 levels, suggesting that the H3K4me2 repressive effect is linked to establishment of a repressive chromatin structure. These results indicate that in S. cerevisiae, the non-redundant role of H3K4 methylation by Set1 is repression, achieved through promotion of 3′-end antisense transcription to achieve specific rather than global effects through two distinct mechanisms.

Coordination of Cell Cycle Progression and Mitotic Spindle Assembly Involves Histone H3 Lysine 4 Methylation by Set1/COMPASS

“…We asked whether the benomyl phenotype correlated with defects in H3K4 methylation status that we previously associated with Set1C mutants (Schneider et al 2005;Dehe and Geli 2006;Margaritis et al 2012). Dset1, Dswd1, and Dswd3 strains are deficient in formation of H3K4 me1, me2, and me3 and Dsdc1 and Dbre2 mutants are deficient in formation of me2 and me3, with less impact on me1; Dspp1 is mainly deficient in me3 but maintains robust levels of me1 and me2; Dshg1 is dispensable for methylation activity and even results in higher level of me2 and me3 (Dehe and Geli 2006;Margaritis et al 2012).…”

“…Dset1, Dswd1, and Dswd3 strains are deficient in formation of H3K4 me1, me2, and me3 and Dsdc1 and Dbre2 mutants are deficient in formation of me2 and me3, with less impact on me1; Dspp1 is mainly deficient in me3 but maintains robust levels of me1 and me2; Dshg1 is dispensable for methylation activity and even results in higher level of me2 and me3 (Dehe and Geli 2006;Margaritis et al 2012). Figure 1C shows analyses of mutants derived from BY4741 background strains.…”

“…H3K4 dimethylation recruits deacetylase complexes to antagonize nucleosome acetylation and remodelling downstream of promoters (Kim and Buratowski 2009;Pinskaya et al 2009). Repressive function frequently involves regulation of antisense transcription (Margaritis et al 2012;Castelnuovo et al 2014).…”

“…Possibly, this is due to the more frequent analyses of steady-state conditions, for which H3K4 methylation appears to have a rather limited impact on mRNA levels, compared to dynamic gene expression processes, which appear to be impacted more strongly (Margaritis et al 2012;Weiner et al 2012). A notable exception is the Set1-dependent expression of genes required for ergosterol synthesis, which provides cells with resistance to the antifungal compound Brefeldin A (South et al 2013).…”

Interaction of the Jhd2 Histone H3 Lys-4 Demethylase with Chromatin Is Controlled by Histone H2A Surfaces and Restricted by H2B Ubiquitination

“…Although the role for H3K4me1 in Saccharomyces cerevisiae or the budding yeast is not yet known, it is present at "poised" developmental enhancers in embryonic stem cells (13) and implicated in gene repression in mammals (14). H3K4me2 and H3K4me3 are found predominantly at transcriptionally active loci (15)(16)(17), but recent studies in budding yeast have also linked these marks to transcriptional repression (9,18,19). H3K4 methylation is a dynamic modification.…”