Set2 histone methyltransferase regulates transcription coupled-nucleotide excision repair in yeast

Helix-distorting DNA lesions, including ultraviolet (UV) light-induced damage, are repaired by the global genomic-nucleotide excision repair (GG-NER) and transcription coupled-nucleotide excision repair (TC-NER) pathways. Previous studies have shown that histone post-translational modifications (PTMs) such as histone acetylation and methylation can promote GG-NER in chromatin. Whether histone PTMs also regulate the repair of DNA lesions by the TC-NER pathway in transcribed DNA is unknown. Here, we report that histone H3 K36 methylation (H3K36me) by the Set2 histone methyltransferase in yeast regulates TC-NER. Mutations in Set2 or H3K36 result in UV sensitivity that is epistatic with Rad26, the primary TC-NER factor in yeast, and cause a defect in the repair of UV damage across the yeast genome. We further show that mutations in Set2 or H3K36 in a GG-NER deficient strain (i.e., rad16 Delta) partially rescue its UV sensitivity. Our data indicate that deletion of SET2 rescues UV sensitivity in a GG-NER deficient strain by activating cryptic antisense transcription, so that the non-transcribed strand (NTS) of yeast genes is repaired by TC-NER. These findings indicate that Set2 methylation of H3K36 establishes transcriptional asymmetry in repair by promoting canonical TC-NER of the transcribed strand (TS) and suppressing cryptic TC-NER of the NTS. Author summaryExposure to UV light causes damage to DNA, which must be efficiently repaired to avoid cell death or carcinogenesis. UV damage is repaired by the nucleotide excision repair pathway, which is triggered either by directly sensing UV damage (known as global genomic repair) or by sensing the stalling of an RNA polymerase enzyme at UV damage during transcription (known as transcription coupled repair). Repair of UV damage must take place in the context of DNA tightly packaged with histone proteins into chromatin. Previous studies have shown that global genomic repair can be facilitated by epigenetic modifications of histone proteins in chromatin. However, whether transcription coupled repair is also regulated by these or other histone modifications was previously unclear. Here, we show that a specific histone modification catalyzed by the Set2 protein in yeast promotes transcription coupled repair. Surprisingly, in the absence of Set2, a new form of transcription coupled repair is activated at sites of cryptic transcription, which can restore UV resistance to otherwise repair-deficient cells. Since Set2 homologs are frequently mutated in human cancers, these findings have potentially important implications for carcinogenesis and chemotherapeutic resistance.

Automated summary

This study reveals that the Set2 protein regulates transcription coupled-nucleotide excision repair (TC-NER) by catalyzing a specific histone modification. In the absence of Set2, a new form of TC-NER is activated at sites of cryptic transcription, which restores UV resistance to repair-deficient cells.