Regulation of histone modifications and cryptic transcription by the Bur1 kinase

Abstract

RNA polymerase II-directed transcription is a complex process, which occurs in the context of chromatin. To understand how transcription elongation factors are involved in transcription regulation in the context of chromatin, we started from a genetic screen and forward biochemical analysis focusing on the functions of the Bur1-Bur2 kinase. BUR1 encodes a cyclin-dependent protein kinase in yeast that has an important role in transcription and is essential for normal growth. BUR2 encodes a cyclin that is required for Burl kinase activity. To obtain deeper insight into Bur1-Bur2's function, we took a genetic approach, looking for mutations that could suppress the growth defect of a bur1Delta strain. Two suppressors with mutations in SET2 were obtained. SET2 encodes a methyltransferase that targets histone H3K36. Our genetic data further demonstrate that the methyltransferase activity of Set2 and histone H3K36 methylation are required to inhibit the growth of bur1Delta cells.;To explore the exact biochemical relationship between Bur1 and H3K36 methylation, we examined the K36 methylation level in several elongation factors mutant strains. We found that K36 tri-methylation was reduced in bur1, bur2 and paf1 mutant strains. To examine whether the reduced tri-methylation was correlated with a change in histone acetylation, we did ChIP assays to measure histone H3 and H4 acetylation in paf1Delta and bur2Delta strains. Surprisingly, our results led us to identify new functions of the Bur1-Bur2 and Paf1 complexes in histone acetylation. Firstly, acetylation is increased at the 5' end of open reading frames in paf1A and bur2A strains, indicating Bur2 and Paf1 have roles in controlling histone acetylation. Secondly, acetylation is increased at the 3' end in paf1Delta set2Delta and bur2Delta set2Delta strains, indicating the (Bur1-Bur2)-Paf1 pathway has a redundant role with Set2 in controlling histone acetylation at the 3' end of some genes. Thirdly, internal cryptic transcription is enhanced in pafDelta set2Delta and bur2A set2A strains, indicating the (Bur1-Bur2)-Paf1 pathway has a redundant role with Set2 in repressing spurious transcription.;In conclusion, our studies establish strong connections between the Bur1-Bur2 kinase and H3K36 methylation and reveal new roles of the Bur1-Bur2 kinase and the Paf1 complex in controlling histone modifications and repressing internal cryptic transcription.