Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast

Abstract

Histone methylation is now realized to be a pivotal regulator of gene transcription. Although recent studies have shed light on a trans-histone regulatory pathway that controls H3 Lys 4 and H3 Lys 79 methylation in Saccharomyces cerevisiae, the regulatory pathway that affects Set2-mediated H3 Lys 36 methylation is unknown. To determine the functions of Set2, and identify factors that regulate its site of methylation, we genomically tagged Set2 and identified its associated proteins. Here, we show that Set2 is associated with Rbp1 and Rbp2, the two largest subunits of RNA polymerase II (RNA pol II). Moreover, we find that this association is specific for the interaction of Set2 with the hyperphosphorylated form of RNA pol II. We further show that deletion of the RNA pol II C-terminal domain (CTD) kinase Ctk1, or partial deletion of the CTD, results in a selective abolishment of H3 Lys 36 methylation, implying a pathway of Set2 recruitment to chromatin and a role for H3 Lys 36 methylation in transcription elongation. In support, chromatin immunoprecipitation assays demonstrate the presence of Set2 methylation in the coding regions, as well as promoters, of genes regulated by Ctk1 or Set2. These data document a new link between histone methylation and the transcription apparatus and uncover a regulatory pathway that is selective for H3 Lys 36 methylation.

Expanding the Functional Repertoire of CTD Kinase I and RNA Polymerase II: Novel PhosphoCTD-Associating Proteins in the Yeast Proteome

“…Recent results lend credence to this hypothesis. For example, as mentioned earlier, deletion of either CTDK-I catalytic activity or the SRI region of Set2 leads to a specific loss of H3 K36 methylation, suggesting that binding of Set2 to the PCTD made by CTDK-I is central to its activity in vivo (37,38,65 (68), and splicing of newly synthesized transcripts can be assayed. In contrast to wild type, in which unspliced precursor is never observed (e.g., Figure 9B, lanes 2 and 3), ctk1Δ cells consistently contain significant amounts of the unspliced RPS17A transcript (lanes 5 and 6).…”

“…For example, CTD phosphorylation by CTDK-I also plays a role in recruiting the histone H3 Lys36 methyltransferase Set2, and ctk1Δ cells are defective for histone H3 Lys36 methylation (37,38). Moreover, five of eight mammalian phosphoCTD-associating proteins (PCAPs) recently identified play roles in DNA With a view to further elucidating the cellular role of CTDK-I, and believing that only a small subset of phosphoCTD-associating proteins had thus far been identified, we undertook a systematic search for yeast proteins that bound the hyperphosphorylated CTD made by CTDK-I.…”

Molecular implementation and physiological roles for histone H3 lysine 4 (H3K4) methylation

“…The biological ramifications of histone methylations in transcriptional regulation are quite diverse. Histone methylation could either be associated with actively transcribing RNA polymerase II (Pol II) or could be involved in setting the stage for transcriptional repression within heterochromatin, and sometimes could be both [6,9,[11][12][13]. For example, histone H3 lysine 9 methylation (H3K9), which is implemented by the SUV39 family of enzymes, is mostly associated with the silent regions within both euchromatin and heterochromatin [14][15][16][17][18].…”

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

“…These modifications affect chromatin structure by altering histone-DNA or histone-histone contacts (25), and/or by collectively establishing a code that is recognized by downstream effector proteins and complexes (24). The chromatin-modifying activities are recruited to certain loci by sequencespecific transcription factors (26,27), or by association with RNA polymerase II (27,28).…”