H3 K36 Methylation Helps Determine the Timing of Cdc45 Association with Replication Origins

Abstract

BackgroundReplication origins fire at different times during S-phase. Such timing is determined by the chromosomal context, which includes the activity of nearby genes, telomeric position effects and chromatin structure, such as the acetylation state of the surrounding chromatin. Activation of replication origins involves the conversion of a pre-replicative complex to a replicative complex. A pivotal step during this conversion is the binding of the replication factor Cdc45, which associates with replication origins at approximately their time of activation in a manner partially controlled by histone acetylation.Methodology/Principal FindingsHere we identify histone H3 K36 methylation (H3 K36me) by Set2 as a novel regulator of the time of Cdc45 association with replication origins. Deletion of SET2 abolishes all forms of H3 K36 methylation. This causes a delay in Cdc45 binding to origins and renders the dynamics of this interaction insensitive to the state of histone acetylation of the surrounding chromosomal region. Furthermore, a decrease in H3 K36me3 and a concomitant increase in H3 K36me1 around the time of Cdc45 binding to replication origins suggests opposing functions for these two methylation states. Indeed, we find K36me3 depleted from early firing origins when compared to late origins genomewide, supporting a delaying effect of this histone modification for the association of replication factors with origins.Conclusions/SignificanceWe propose a model in which K36me1 together with histone acetylation advance, while K36me3 and histone deacetylation delay, the time of Cdc45 association with replication origins. The involvement of the transcriptionally induced H3 K36 methylation mark in regulating the timing of Cdc45 binding to replication origins provides a novel means of how gene expression may affect origin dynamics during S-phase.

A PWWP Domain-Containing Protein Targets the NuA3 Acetyltransferase Complex via Histone H3 Lysine 36 trimethylation to Coordinate Transcriptional Elongation at Coding Regions

“…In yeast, Set2 catalyzes all three forms of H3K36 methylation (33). To date, H3K36me1 is suggested to function in DNA replication (101), and although H3K36me2 and me3 are both linked to transcriptional elongation, H3K36me2 is essential for Rpd3S recruitment (18,(41)(42)(43)(44)(45)(46)(47), whereas H3K36me3 is implicated in nucleosomal positioning via Isw1b and repression of trans-histone exchange (50 -52). Interestingly, unlike H3K36me2, the establishment of H3K36me3 specifically requires Set2 association with the CTD of RNAPII, and H3K36me3 is positively correlated with the rate of transcription (13).…”

MYC and the Control of DNA Replication

“…As described above, chromatin remodeling enzymes, such as Rif1, regulate Cdc45 binding to chromatin, which is a rate-limiting step of origin activation (Pryde et al 2009;Wong et al 2011;Cornacchia et al 2012;Knott et al 2012;Yamazaki et al 2012). …”

Nucleosomes in the neighborhood

“…40 In support of this model, S phase to late-firing origins. 35 The abundance of H3K36me3 at origins also decreases throughout S phase at the same time that monomethylation of H3K36 (H3K36me1) increases. These observations correlate H3K36 methylation with early or late replication; do individual H3K36 methylation states directly affect replication?…”

“…39 Also, the recruitment of the origin initiation factor Cdc45 to yeast origins was correlated with high levels of H3K36me1 but low levels of H3K36me3. 35 Additional work shed light on how H3K36me3 may mediate an inhibitory effect. Eaf3 associates with both H3K36me3 and the Rpd3S deacetylase.…”

“…32,33 Unlike acetylation, which is typically associated with a general opening of chromatin and active genes, methylation has been shown to both activate and repress transcription and replication. 34,35 Additional complexity stems from the fact that the extent of methylation on a particular lysine can have opposite effects. 36,37 Thus, diverse histone methylation events may function along with acetylation to control the precise sequence of events that are required for efficient but regulated origin firing.…”