Evidence that Moderate Eviction of Spt5 and Promotion of Error-Free Transcriptional Bypass by Rad26 Facilitates Transcription Coupled Nucleotide Excision Repair

Selvam, Kathiresan; Ding, Baojin; Sharma, Rahul; Li, Shisheng

doi:10.1016/j.jmb.2019.02.010

Cited by 11 publications

(9 citation statements)

References 45 publications

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“…Previous studies have shown that the K328R mutation abolishes the DNA translocase activity of Rad26 in promoting Pol II transcription over DNA barriers (12). Additionally, mutations in the ATPase domain do not affect cellular Rad26 protein stability (26). Analysis of CPD-seq data revealed generally impaired TC-NER in the Rad26 ATPase-dead strain (Fig.…”

Section: Tc-ner Is Generally Impaired In Rad26-deficient Yeast Strainmentioning

confidence: 74%

Genome-wide role of Rad26 in promoting transcription-coupled nucleotide excision repair in yeast chromatin

Duan

Selvam

Wyrick

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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Transcription-coupled nucleotide excision repair (TC-NER) is an important DNA repair mechanism that removes RNA polymerase (RNAP)-stalling DNA damage from the transcribed strand (TS) of active genes. TC-NER deficiency in humans is associated with the severe neurological disorder Cockayne syndrome. Initiation of TC-NER is mediated by specific factors such as the human Cockayne syndrome group B (CSB) protein or its yeast homolog Rad26. However, the genome-wide role of CSB/Rad26 in TC-NER, particularly in the context of the chromatin organization, is unclear. Here, we used single-nucleotide resolution UV damage mapping data to show that Rad26 and its ATPase activity is critical for TC-NER downstream of the first (+1) nucleosome in gene coding regions. However, TC-NER on the transcription start site (TSS)-proximal half of the +1 nucleosome is largely independent of Rad26, likely due to high occupancy of the transcription initiation/repair factor TFIIH in this nucleosome. Downstream of the +1 nucleosome, the combination of low TFIIH occupancy and high occupancy of the transcription elongation factor Spt4/Spt5 suppresses TC-NER in Rad26-deficient cells. We show that deletion of SPT4 significantly restores TC-NER across the genome in a rad26∆ mutant, particularly in the downstream nucleosomes. These data demonstrate that the requirement for Rad26 in TC-NER is modulated by the distribution of TFIIH and Spt4/Spt5 in transcribed chromatin and Rad26 mainly functions downstream of the +1 nucleosome to remove TC-NER suppression by Spt4/Spt5.

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Section: Tc-ner Is Generally Impaired In Rad26-deficient Yeast Strainmentioning

confidence: 74%

Genome-wide role of Rad26 in promoting transcription-coupled nucleotide excision repair in yeast chromatin

Duan

Selvam

Wyrick

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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“…Accumulation of H3K36me behind a stalled Pol II may recruit Rad26 to initiate TC-NER. Moreover, Rad26 binds to the upstream (‘back’) side of Pol II to promote elongation past barriers and initiate TC-NER [ 62 , 63 ]. Accumulation of H3K36me upstream of Pol II during stalling may help properly orient Rad26 behind Pol II to perform these functions ( Fig 7 ).…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2022

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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., rad16Δ) 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.

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“…A previous genetic study in S. cerevisiae showed that Rpb4/7 promotes Rad26-dependent TC-NER while suppressing Rad26-independent TC-NER (27). On the other hand, Spt4/5, an elongation factor that binds both Rpb4/7 and the protrusion domain of Pol II (18, 19, 28), functions as an inhibitor of TC-NER (29). We propose that the steric exclusion of Spt4/5 by the lesion-induced strong interaction between Rad26 and Rpb4/7 is a major step in committing a lesion-stalled Pol II to TC-NER.…”

Section: Discussionmentioning

confidence: 99%

Elf1 promotes Rad26’s interaction with lesion-arrested Pol II for transcription-coupled repair

Sarsam,

Xu,

Lahiri

et al. 2023

Preprint

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Transcription-coupled nucleotide excision repair (TC-NER) is a highly conserved DNA repair pathway that removes bulky lesions in the transcribed genome. Cockayne syndrome B protein (CSB), or its yeast ortholog Rad26, has been known for decades to play important roles in the lesion-recognition steps of TC-NER. Another conserved protein ELOF1, or its yeast ortholog Elf1, was recently identified as a core transcription-coupled repair factor. How Rad26 distinguishes between RNA polymerase II (Pol II) stalled at a DNA lesion or other obstacles and what role Elf1 plays in this process remains unknown. Here, we present cryo-EM structures of Pol II-Rad26 complexes stalled at different obstacles that show that Rad26 uses a universal mechanism to recognize a stalled Pol II but interacts more strongly with a lesion-arrested Pol II. A cryo-EM structure of lesion-arrested Pol II-Rad26 bound to Elf1 revealed that Elf1 induces new interactions between Rad26 and Pol II when the complex is stalled at a lesion. Biochemical and genetic data support the importance of the interplay between Elf1 and Rad26 in TC-NER initiation.

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Evidence that Moderate Eviction of Spt5 and Promotion of Error-Free Transcriptional Bypass by Rad26 Facilitates Transcription Coupled Nucleotide Excision Repair

Cited by 11 publications

References 45 publications

Genome-wide role of Rad26 in promoting transcription-coupled nucleotide excision repair in yeast chromatin

Genome-wide role of Rad26 in promoting transcription-coupled nucleotide excision repair in yeast chromatin

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

Elf1 promotes Rad26’s interaction with lesion-arrested Pol II for transcription-coupled repair

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