Effectors of Lysine 4 Methylation of Histone H3 in Saccharomyces cerevisiae Are Negative Regulators of PHO5 and GAL1-10

Abstract

Post-translational modifications of histone amino-terminal tails are a key determinant in gene expression. Histone methylation plays a dual role in gene regulation. Methylation of lysine 9 of histone H3 in higher eukaryotes is associated with transcriptionally inactive heterochromatin, whereas H3 lysine 4 methylation correlates with active chromatin. Methylation of lysine 4 of H3 via Set1, a component of the Saccharomyces cerevisiae COMPASS complex, is regulated by the transcriptional elongation Paf1-Rtf1 and histone ubiquitination Rad6-Bre1 complexes, which are required for the expression of a subset of genes. This suggests that lysine 4 methylation of histone H3 may play an activating role in transcription; however, the mechanism of Set1 function remains unclear. We show here that H3 lysine 4 methylation also negatively regulated gene expression, as strains without Set1 showed enhanced expression of PHO5, wherein chromatin structure plays an important transcriptional regulatory role. Di-and trimethylation of H3 lysine 4 was detected at the PHO5 promoter, and a strain expressing a mutant version of histone H3 with lysine 4 changed to arginine, (which cannot be methylated) exhibited PHO5 derepression. Moreover, PHO5 was derepressed in strains that lacked components of either the Paf1-Rtf1 elongation or Rad6-Bre1 histone ubiquitination complexes. Lastly, PHO84 and GAL1-10 transcription was also increased in set1⌬ cells. These results suggest that H3 methylation at lysine 4, in conjunction with transcriptional elongation, may function in a negative feedback pathway for basal transcription of some genes, although being a positive effector at others.In eukaryotes, DNA is packaged with histone proteins to form nucleosomes that are further condensed into higher order chromatin structures. Generally, this compaction serves as a barrier for the binding of factors that elicit important cellular processes such as transcription and DNA replication. Thus, genes found in heavily condensed regions, such as heterochromatin, are transcriptionally silent. Expression of genes located in euchromatic regions, which are typically less compacted, is also regulated by chromatin structure.Post-translational modifications of the amino-terminal tails of histone proteins are a key determinant in defining active and repressed chromatin. These modifications may alter chromatin structure directly by affecting histone-DNA and histone-histone interactions (1). They also allow for the recruitment of transcriptional activators or repressors. Acetylation of histone H3 at lysines 9 and 14 is strongly correlated with transcriptionally active and accessible chromatin. Histone methylation is associated with both active and repressed chromatin states. In eukaryotes other than budding yeast, heterochromatic silencing is marked by methylation of histone H3 at lysine 9. Conversely, euchromatic regions are associated with histone methylation of histone H3 at lysine 4 (H3 Lys-4) (2). Set1 is the catalytic subunit of a large complex named COMPASS (3), which...

Functional Analysis of H2B-Lys-123 Ubiquitination in Regulation of H3-Lys-4 Methylation and Recruitment of RNA Polymerase II at the Coding Sequences of Several Active Genes in Vivo

“…Thus, H3-Lys-4 methylation does not seem to play an active role in the regulation of transcriptional elongation of these genes. However, several studies (8,16,60,62) have demonstrated the role of Set1p or H3-Lys-4 methylation in transcription of a subset of genes, consistent with the fact that H3-Lys-4 methylation is associated with active chromatin in a wide range of eukaryotic organisms (8, 45, 49 -53) and is correlated with transcription (43, 54 -56). Currently, it is not known how H3-Lys-4 methylation can be involved in different transcriptional states.…”

Chromatin and Transcription in Yeast

“…Indeed, while H3K4 methylation is associated with actively transcribed genes, in some cases it can be repressive (Carvin and Kladde 2004). A hint regarding the biological role for H3K4 methylation in transcriptional control comes from the above-noted role for another 59-directed mark, H2A.Z, in control of antisense transcription (Zofall et al 2009).…”

Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae

“…Since H3K4 trimethylation correlates with active chromatin states (Noma and Grewal 2002), the silencing defects observed in the absence of Set1 could reflect its role in facilitating the production of noncoding RNAs, which in turn may target silencing factors to corresponding DNA regions. An earlier study showed that PHO84 and GAL1-10, two genes that were shown recently to produce and to be regulated negatively by antisense transcripts (Camblong et al 2007;Houseley et al 2008;Xu et al 2009), become derepressed in the absence of Set1 (Carvin and Kladde 2004). Notably, a recent genome wide study showed that in S. cerevisiae, H3K4 methylation is not only promoter-associated but also present within ORFs and at the 39 end of a number of genes (Kirmizis et al 2007).…”