Cockayne syndrome B protein is implicated in transcription and associated chromatin dynamics in homeostatic and genotoxic conditions

TL;DR

This study shows how the Cockayne syndrome B protein (CSB) affects transcription and chromatin structure in normal and stressed cells, revealing new roles beyond DNA repair.

Contribution

The study reveals novel roles of CSB in transcription and chromatin dynamics, independent of its known DNA repair function.

Findings

CSB absence causes delayed transcription progression and more compact chromatin structure.

CSB-deficient cells show increased retention of RNA transcripts and elongating RNA polymerase II after UV exposure.

Transcription initiation remains active in CSB-deficient cells despite chromatin changes.

Abstract

The integrity of the actively transcribed genome against helix‐distorting DNA lesions relies on a multilayered cellular response that enhances Transcription‐Coupled Nucleotide Excision Repair (TC‐NER). When defective, TC‐NER is causatively associated with Cockayne‐Syndrome (CS), a rare severe human progeroid disorder. Although the presence of unresolved transcription‐blocking lesions is considered a driver of the aging process, the molecular features of the transcription‐driven response to genotoxic stress in CS‐B cells remain largely unknown. Here, an in‐depth view of the transcriptional and associated chromatin dynamics that occur in CS‐B cells illuminates the role of CSB therein. By employing high‐throughput genome‐wide approaches, we observed that absence of a functional CSB protein results in a delay in transcription progression, more positioned +1 nucleosomes, and less dynamic chromatin structure, compared to normal cells. We found that early after exposure to UV, CS‐B cells released RNA polymerase II (RNAPII) from promoter‐proximal pause sites into elongation. However, the magnitude of this response and the progression of RNAPII were reduced compared to normal counterparts. Notably, we detected increased post‐UV retainment of unprocessed nascent RNA transcripts and chromatin‐associated elongating RNAPII molecules. Contrary to the prevailing models, we found that transcription initiation is operational in CS‐B fibroblasts early after UV and that chromatin accessibility showed a marginal increase. Our study provides robust evidence for the role of CSB in shaping the transcription and chromatin landscape both in homeostasis and in response to genotoxic insults, which is independent of its known role in TC‐NER, and which may underlie major aspects of the CS phenotype.

Early after exposure to UV, RNAPII is released from promoter‐proximal pause sites to elongation in both normal and CS‐B fibroblasts. However, RNAPII progression speed is slower in CS‐B compared to normal fibroblasts. Additionally, UV‐exposed CS‐B cells are characterized by increased retention of nascent RNA transcripts and elongating RNAPII molecules in gene bodies, minimal changes in chromatin accessibility and, more compact chromatin structure, compared to irradiated normal cells.

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