RNA Polymerase II Carboxyl-terminal Domain Phosphorylation Regulates Protein Stability of the Set2 Methyltransferase and Histone H3 Di- and Trimethylation at Lysine 36

Stephen M Fuchs,Kelby O Kizer,Hannes Braberg,Nevan J Krogan,Brian D Strahl

doi:10.1074/jbc.m111.273953

Stephen M Fuchs, Kelby O Kizer + Show 3 more

Open Access

https://doi.org/10.1074/jbc.m111.273953

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Abstract

Methylation of lysine 36 on histone H3 (H3K36) is catalyzed by the Set2 methyltransferase and is linked to transcriptional regulation. Previous studies have shown that trimethylation of H3K36 by Set2 is directed through its association with the phosphorylated repeats of the RNA polymerase C-terminal domain (RNAPII CTD). Here, we show that disruption of this interaction through the use of yeast mutants defective in CTD phosphorylation at serine 2 results in a destabilization of Set2 protein levels and H3K36 methylation. Consistent with this, we find that Set2 has a short half-life and is co-regulated, with RNAPII CTD phosphorylation levels, during logarithmic growth in yeast. To probe the functional consequence of uncoupling Set2-RNAPII regulation, we expressed a truncated and more stable form of Set2 that is capable of dimethylation but not trimethylation in vivo. Results of high throughput synthetic genetic analyses show that this Set2 variant has distinct genetics from either SET2 or set2Δ and is synthetically sick or lethal with a number of transcription elongation mutants. Collectively, these results provide molecular insight into the regulation of Set2 protein levels that influence H3K36 methylation states.

Highlights

Set2 catalyzes mono, di, and trimethylation of lysine 36 on histone H3 (H3K36)
Set2 and H3K36 Methylation Are Regulated Differentially during Cell Growth—It has been well established that methylation by Set2 is correlated with hyperphosphorylation of the C-terminal domain (CTD) of RNA polymerase II (RNAPII)
We found that Set2 protein levels changed under these same conditions and correlated strongly with the occurrence of RNAPII CTD phosphorylation (Fig. 1B)

Summary

Background

Results: Phosphorylation of the C-terminal domain of RNA polymerase II (RNAPII CTD) regulates Set protein levels and H3K36 methylation. The N-terminal tails of histones are richly decorated with post-translational modifications that regulate a variety of DNA-templated processes through the recruitment of additional factors to chromatin These factors interact with modifications such as acetylation, methylation, and phosphorylation through specific protein domains such as bromo-, chromo-,. H3K36me appears uniformly distributed across transcribed genes and is not correlated with transcription frequency, whereas H3K36me seems to be most prevalent at the 3Ј end of coding regions and is positively correlated with the rate of transcription These data suggest that the deposition of different levels of H3K36 methylation is controlled within the cell and that the different degrees of this modification likely direct distinct biological functions. Subsequent studies revealed that H3K36me is the preferred substrate for Rpd3(S) binding [12,13,14] and that a primary function for H3K36 methylation is to recruit the repressive activity of Rpd3(S) to genes to “reset” or reestablish

The abbreviations used are

EXPERIMENTAL PROCEDURES

RESULTS

DISCUSSION