Repression of Middle Sporulation Genes in Saccharomyces cerevisiae by the Sum1-Rfm1-Hst1 Complex Is Maintained by Set1 and H3K4 Methylation

Abstract

The conserved yeast histone methyltransferase Set1 targets H3 lysine 4 (H3K4) for mono, di, and trimethylation and is linked to active transcription due to the euchromatic distribution of these methyl marks and the recruitment of Set1 during transcription. However, loss of Set1 results in increased expression of multiple classes of genes, including genes adjacent to telomeres and middle sporulation genes, which are repressed under normal growth conditions because they function in meiotic progression and spore formation. The mechanisms underlying Set1-mediated gene repression are varied, and still unclear in some cases, although repression has been linked to both direct and indirect action of Set1, associated with noncoding transcription, and is often dependent on the H3K4me2 mark. We show that Set1, and particularly the H3K4me2 mark, are implicated in repression of a subset of middle sporulation genes during vegetative growth. In the absence of Set1, there is loss of the DNA-binding transcriptional regulator Sum1 and the associated histone deacetylase Hst1 from chromatin in a locus-specific manner. This is linked to increased H4K5ac at these loci and aberrant middle gene expression. These data indicate that, in addition to DNA sequence, histone modification status also contributes to proper localization of Sum1. Our results also show that the role for Set1 in middle gene expression control diverges as cells receive signals to undergo meiosis. Overall, this work dissects an unexplored role for Set1 in gene-specific repression, and provides important insights into a new mechanism associated with the control of gene expression linked to meiotic differentiation.

Tri-methylation of histone H3 lysine 4 facilitates gene expression in ageing cells

“…H3K4 methylation has a remarkably complex effect on gene expression. Transcriptomic approaches have detected repressive functions ( Guillemette et al, 2011 ; Jaiswal et al, 2017 ; Lenstra et al, 2011 ; Margaritis et al, 2012 ; Venkatasubrahmanyam et al, 2007 ), although in most cases this can probably be attributed to H3K4me2 with the possible exception of ribosomal protein genes ( Weiner et al, 2012 ). Evidence that H3K4me3 can promote gene expression in yeast is rarer; this was reported in early studies but has not been effectively reproduced ( Miller et al, 2001 ; Santos-Rosa et al, 2002 ), see ( Margaritis et al, 2012 ) for a discussion of technical reasons for this.…”

Set4 is a chromatin-associated protein, promotes survival during oxidative stress, and regulates stress response genes in yeast

“…To test expression in WT (yEG001) and set4⌬ (yEG322), cultures were prepared as described for the H 2 O 2 survival assays, except that 0.4 mM H 2 O 2 treatment for 30 min was performed to provide acute stress but not dramatically decrease survival, as previously performed for measurement of gene expression changes following H 2 O 2 treatment in yeast (9,48,49). RNA isolation, removal of genomic DNA contamination, cDNA synthesis, and quantitative RT-PCR were performed as described previously (50,51). Gene-specific primers for the qPCR are listed in Table 3.…”

“…WT (yEG001) and SET4::FLAG-SET4 (yEG513) were grown as described for gene expression analysis, including treatment with 0.4 mM H 2 O 2 for 30 min in 100 ml of YPD. Cells were fixed with 1% formaldehyde for 45 min, and ChIP procedures were performed as described previously (51,52). Mouse anti-FLAG (Sigma; catalogue no.…”

“…F1804) was prebound to protein A/G magnetic beads (Pierce) and then incubated with ChIP lysates for 3 h at 4°C. qPCR was performed on eluted DNA, as described (51,52), with primers listed in Table 3. The percentage input was calculated relative to 10% input, and the signal for FLAG-Set4 was determined relative to WT (untagged) either with or without H 2 O 2 treatment.…”

Tri-methylation of Histone H3 Lysine 4 Facilitates Gene Expression in Ageing Cells

“…H3K4 methylation has a remarkably complex effect on gene expression. Transcriptomic approaches have detected repressive functions (Guillemette et al, 2011;Jaiswal et al, 2017;Lenstra et al, 2011;Margaritis et al, 2012;Venkatasubrahmanyam et al, 2007), although in most cases this can probably be attributed to H3K4me2, with the possible exception of ribosomal protein genes (Weiner et al, 2012). Evidence that H3K4me3 can promote gene expression in yeast is rarer; this was reported in early studies but has not been effectively reproduced (Miller et al, 2001;Santos-Rosa et al, 2002), see (Margaritis et al, 2012) for a discussion of technical reasons for this.…”