The histone methyltransferases Set5 and Set1 have overlapping functions in gene silencing and telomere maintenance

Abstract

Genes adjacent to telomeres are subject to transcriptional repression mediated by an integrated set of chromatin modifying and remodeling factors. The telomeres of Saccharomyces cerevisiae have served as a model for dissecting the function of diverse chromatin proteins in gene silencing, and their study has revealed overlapping roles for many chromatin proteins in either promoting or antagonizing gene repression. The H3K4 methyltransferase Set1, which is commonly linked to transcriptional activation, has been implicated in telomere silencing. Set5 is an H4 K5, K8, and K12 methyltransferase that functions with Set1 to promote repression at telomeres. Here, we analyzed the combined role for Set1 and Set5 in gene expression control at native yeast telomeres. Our data reveal that Set1 and Set5 promote a Sir proteinindependent mechanism of repression that may primarily rely on regulation of H4K5ac and H4K8ac at telomeric regions. Furthermore, cells lacking both Set1 and Set5 have highly correlated transcriptomes to mutants in telomere maintenance pathways and display defects in telomere stability, linking their roles in silencing to protection of telomeres. Our data therefore provide insight into and clarify potential mechanisms by which Set1 contributes to telomere silencing and shed light on the function of Set5 at telomeres.

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.…”

Chromosome Evolution in Connection with Repetitive Sequences and Epigenetics in Plants

“…Heterochromatin is essential for normal chromosome organization, centromere function, and telomere protection [ 109 , 110 , 111 ]. The epigenetic modification is frequently involved in the condensed heterochromatic regions [ 112 ].…”

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

“…Statistical analyses were performed using the R statistical computing environment. Datasets include previously published and analyzed RNA-sequencing experiments of set1 Δ cells ( Martín et al 2014 ; Jezek et al 2017 ; GEO accession number GSE52086) and publically available microarray datasets from Kemmeren et al 2014 (GEO accession number GSE42527, http://deleteome.holstegelab.nl/ ). Gene ontology (GO) analysis was performed using FunSpec ( Robinson et al 2002 ).…”

“…Chromatin immunoprecipitation (chIP) was performed as described ( Meluh and Broach 1999 ; Liu et al 2005 ; Jezek et al 2017 ). Briefly, 100 ml of mid-log phase yeast were fixed with 1% formaldehyde for 30 min.…”

“…In the case of subtelomeric genes, loss of silencing in set1 Δ cells has been proposed to be due to titration of the Sir protein complex, which deacetylates H4K16, away from subtelomeric chromatin ( Santos-Rosa et al 2004 ; Venkatasubrahmanyam et al 2007 ). However, data regarding other functional roles for Set1 , including its links to noncoding RNA production and genome stability pathways ( Corda et al 1999 ; Margaritis et al 2012 ; Jezek et al 2017 ), suggest alternate mechanisms for Set1 -mediated repression. Interestingly, Set1 -dependent repression in fission yeast appears to occur through both H3K4 methylation-dependent and independent mechanisms, and it works together with the histone deacetylase Clr3 to promote repression ( Lorenz et al 2014 ).…”