The Cellular Response to Transcription-Blocking DNA Damage

Abstract

In response to transcription-blocking DNA lesions such as those generated by UV irradiation, cells activate a multipronged DNA damage response. This response encompasses repair of the lesions that stall RNA polymerase (RNAP) but also a poorly understood, genome-wide shutdown of transcription, even of genes that are not damaged. Over the past few years, a number of new results have shed light on this intriguing DNA damage response at the structural, biochemical, cell biological, and systems biology level. In this review we summarize the most important findings.

Keywords: Cockayne syndrome; DNA damage response; UV-sensitivity syndrome; nucleotide excision repair; transcription restart; transcription-coupled nucleotide excision repair.

Figure 1

Models for Transcription-Coupled Nucleotide Excision Repair (TC-NER). (1) After RNAPII stalls at a transcription-blocking lesion, CSB is recruited. CSB’s precise role is unclear, but it may remodel the stalled RNAPII complex, for example to dislodge elongation factors such as Spt4/Spt5 (also called DSIF in humans). (2) To make space for NER, RNAPII must be either completely removed from DNA or backtracked. Importantly, if backtracking occurs it is likely to be by as much as 30–40 nucleotides due to the space requirements of RNAPII, repair factors, and the gap-filling DNA polymerase (DNA Pol) on DNA. Such backtracking might require CSB dissociation and could conceivably be facilitated by TFIIH. Repair factors (and probably DNA Pol) are recruited. DNA incisions are made by ERCC1–XPF and XPG and removal of lesion-containing ssDNA oligonucleotides is performed by TFIIH. (3) DNA gap filling, dissociation of NER factors, and marking of chromatin with γH2AZ. (4) Transcript cleavage and forward translocation, probably stimulated by factors such as ELL. A number of unanswered issues about the molecular details of the process are listed on the right. Note that the DNA characteristics of RNAPII and NER (footprint, melted DNA, excised oligo, etc.) are drawn to scale where possible. However, nucleosomes, as well as the dramatic bending of DNA in the elongation complex, are omitted for simplicity.

Figure 2

Analogous Regulation of Transcription-Coupled Nucleotide Excision Repair (TC-NER) and General Genome Repair (GG-NER) by Ubiquitin. CSB and XPC are specific for TC-NER and GG-NER, respectively, yet analogous ubiquitin pathways regulate their function. The CRL4 ubiquitin ligase complex is required for their ubiquitylation but uses CSA and DDB2, respectively, as targeting subunits. Unsurprisingly, CSA and DDB2 are also known to be specifically required for TC-NER and GG-NER, respectively. Likewise, USP7 is required for deubiquitylation of both, which in the case of CSB is likely to occur through its interaction with a targeting subunit, UVSSA. Abbreviation: ub, ubiquitin. See text for details.

Figure 3

The Global Transcriptional Response to UV Irradiation. The different stages of transcriptional shutdown and restart in an average ‘long’ gene. Short genes (<20 kb) are often much less affected. See text for details.