The histone methylase Set2p and the histone deacetylase Rpd3p repress meiotic recombination at the HIS4 meiotic recombination hotspot in Saccharomyces cerevisiae

Abstract

The rate of meiotic recombination in the yeast Saccharomyces cerevisiae varies widely in different regions of the genome with some genes having very high levels of recombination (hotspots). A variety of experiments done in yeast suggest that hotspots are a feature of chromatin structure rather than a feature of primary DNA sequence. We examined the effects of mutating a variety of enzymes that affect chromatin structure on the recombination activity of the well-characterized HIS4 hotspot including the Set2p and Dot1p histone methylases, the Hda1p and Rpd3p histone deacetylases, the Sin4p global transcription regulator, and a deletion of one of the two copies of the genes encoding histone H3-H4. Loss of Set2p or Rpd3p substantially elevated HIS4 hotspot activity, and loss of Hda1p had a smaller stimulatory effect; none of the other alterations had a significant effect. The increase of HIS4 hotspot activity in set2 and rpd3 strains is likely to be related to the recent finding that histone H3 methylation by Set2p directs deacetylation of histones by Rpd3p. IntroductionThe rate of meiotic recombination varies considerably at different positions in the yeast genome (1,2). This variation reflects differences in the frequency of local meiosis-specific doublestrand DNA breaks (DSBs), the recombination-initiating lesion (3,4) catalyzed by Spo11p and associated proteins (5). There are several lines of evidence that the frequency of DSBs is regulated by elements of chromatin structure rather than primary DNA sequence (2). First, recombination hotspots exhibit hypersensitivity to nucleases (6-10). Some loci (8,9) undergo meiosis-specific alterations in nuclease sensitivity prior to DSB formation, although no such changes are observed at other loci (6). Since all nuclease-hypersensitive regions are not meiotic Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.Conflicts of interest None. NIH Public AccessAuthor Manuscript DNA Repair (Amst) (6,10), "open" chromatin appears necessary, but not sufficient, for meiotic recombination hotspot activity. Second, insertion of a nucleosome-excluding sequence into the yeast genome creates a recombination hotspot (11). Third, the activity of some hotspots requires the binding of transcription factors, but not high levels of transcription (2). This result has been interpreted as indicating that chromatin modifications associated with transcription factor binding stimulate both transcription and recombination. Finally, some mutants that affect chromatin modifications reduce the frequency of meiosis-specific DSBs. In the yeast S. pombe, mutatio...

Functional Roles of Acetylated Histone Marks at Mouse Meiotic Recombination Hot Spots

“…7D; Table S4). Our findings strongly support the notion that histone acetylation is necessary for meiotic recombination, and they are consistent with analyses of hot spot activity in epigenetic mutant strains of yeasts and plants (21,(85)(86)(87). For example, deletion of the S. pombe HAT gene Gcn5, which directs hyperacetylation of the ade6-M26 hot spot, leads to reductions in DSBs and CO rates at this hot spot (21).…”

“…For example, deletion of the S. pombe HAT gene Gcn5, which directs hyperacetylation of the ade6-M26 hot spot, leads to reductions in DSBs and CO rates at this hot spot (21). Conversely, deletion of the S. cerevisiae HDAC gene Rpd3 augments HIS4 hot spot activity (86). However, our HDAC inhibitor studies with the CAST/DBA mouse strain, in which the HS22 hot spot is inactive, have also shown that augmenting histone acetylation (Fig.…”

Homodimeric PHD Domain-containing Rco1 Subunit Constitutes a Critical Interaction Hub within the Rpd3S Histone Deacetylase Complex

“…The histone methyltransferase Set2 directly binds to elongating polymerase II (23)(24)(25)(26)(27) and co-transcriptionally methylates histone H3K36. H3K36me in turn recruits and activates the Rpd3S histone deacetylases and the Isw1a chromatin remodeler to maintain hypoacetylated coding regions (22,28), which suppress cryptic transcription initiation (29 -31) and recombination (32). H3K36me is also responsible for directing the histone acetyltransferases NuA4 and NuA3b to coding regions to facilitate transcription elongation (33)(34)(35).…”

Bypassing the Requirement for an Essential MYST Acetyltransferase

“…It is important to note that sir2Δ strains have similar high rDNA recombination levels (Gottlieb and Esposito 1989;Clarke et al 2006); however, the high recombination rate is restricted to specific genomic areas (Su et al 2000;Mieczkowski et al 2007). In the esa1Δ sds3Δ sir2Δ strain, the genomic areas susceptible to recombination may be more dispersed than in sir2Δ cells as Rpd3 has a role in repressing mitotic recombination (Dora et al 1999;Merker et al 2008).Finally, to test if the DNA damage resistance of the esa1Δ sds3Δ sir2Δ strain was due to a pseudodiploid state, we transformed a MATa esa1Δ sds3Δ strain with a plasmidborne MATa locus. Enhanced suppression of the DNAdamage-sensitive phenotype was not observed ( Figure 5D).…”