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transcription-coupled NER

Sunday 26 March 2006

Definition: Transcription-coupled repair (TCR) removes damage from actively transcribing genes while global genome repair (GGR) removes damage from the remainder of the genome.

Cells induce the expression of DNA-repair enzymes, activate cell-cycle checkpoints and, under some circumstances, undergo apoptosis in response to DNA-damaging agents.

The mechanisms by which these cellular responses are triggered are not well understood, but there is recent evidence that the transcription machinery might be used in DNA-damage surveillance and in triggering DNA-damage responses to suppress mutagenesis.

Transcription might also act as a DNA-damage dosimeter where the severity of blockage determines whether or not to induce cell death.

Transcription-coupled repair (TCR)

In global genome repair (GGR), damage such as ultraviolet induced cyclobutane pyrimidine dimers (CPD) or 6-4 photoproducts (6-4 PP) are recognized by proteins including the XPE (DDB2) and XPC gene products.

In TCR, the lesion appears to block the progress of RNA polymerase II in a process involving the CSA and CSB gene products.

Following initial damage recognition the pathways converge. The XPB (ERCC3) and XPD (ERCC2) helicases unwind the region surrounding the lesion along with the XPA and XPG (ERCC5) gene products, and replication protein A (RPA).

The XPF and XPG (ERCC5) endonucleases perform incisions to remove the lesion in a fragment of about 30 nucleotides. The resulting gap is filled in by de novo DNA synthesis.

This system is coordinated so that if one part of the pathway is mutated the entire pathway fails to function normally. Mutations in the genes in rectangles have been associated with clinical disease.

- The rate of NER in mammalian genes that are actively transcribed is faster than that in transcriptionally silent regions of the genome. Further studies showed that the increased kinetics of NER in transcriptionally active regions is accounted for by a faster rate of NER in the transcribed DNA strand compared with the non-transcribed strand.

- The mechanism of transcription-coupled NER (TCNER) has not been determined in the detail just described for NER in transcriptionally inactive regions.

- Significantly, humans and mice that are genetically defective in XPC retain the capacity for TCNER, leading to the conclusion that XPC is not required for this process.

- Damage recognition is subserved by the arrested RNA polymerase II transcription machinery. This arrested complex is thought to include additional proteins, which, although not necessarily components of the normal transcriptional machinery, are recruited to sites of arrested transcription.

- Among these are two proteins, CSA and CSB, that merit special attention because mutational inactivation of the genes encoding these proteins leads to a hereditary disease called Cockayne syndrome.

- The complex assembled at sites of arrested transcription is believed to include the NER components discussed above46, as well as other proteins. Hence, the ensuing biochemical events during TCNER are the same as those for global NER in transcriptionally silent DNA.

- The relationship between NER and RNA polymerase II transcription - reflected by the requirement for TFIIH in the DNA unwinding step during NER in both transcriptionally active and transcriptionally silent DNA - should not be confused with the relationship between NER and RNA polymerase II transcription that is reflected by the lesion-recognition step of TCNER.

Steps of TCNER

- 1. Many types of base damage arrest normal transcription by presenting a ’road block’ to the progress of the transcription machinery.

- 2. Arrested transcription by RNA polymerase II is believed to result in the recruitment of a large protein complex, the precise composition and function of which remains to be established. This complex includes one or more proteins involved in mismatch repair (represented generically as MSH), proteins called CSA and CSB, which, if inactivated, can result in a disease called Cockayne syndrome, the NER proteins XPB, XPD and XPG, proteins called BRCA1 and BRCA2, inactivation of which is associated with hereditary breast cancer, and a protein called XAB2 that binds to CSA (and to XPA involved in NER).

- 3. This putative TCNER complex is thought to dislocate the stalled transcription machinery from the site of base damage in the transcribed strand.

- 4. It provides access of this site to proteins required for the completion of NER or BER, depending on which of these two excision repair modes is appropriate for the base damage.

- 5. Following these processes, normal transcription can again occur.


- Bulky lesions such as UV-light-induced pyrimidine dimers and cisplatin adducts, which cause great distortion in the DNA helix, can act as both cytotoxic and mutagenic lesions depending on their localization in the genome. If they are located in the transcribed strand of active genes they are cytotoxic, as they can induce apoptosis by blocking transcription.

- The cytotoxicities of these lesions are suppressed by their removal through TCR, whereas similar lesions elsewhere in the genome are removed by another NER system, global genomic repair (GGR).

- TCR is a specialized repair pathway using RNA polymerase II stalled at DNA lesions for recruitment of DNA-repair enzymes, whereas GGR requires specialized proteins for the detection of DNA lesions and recruitment of DNA-repair factors.

- So, the function of TCR is primarily to counteract DNA-damage signalling and suppress apoptosis, whereas GGR removes pre-mutagenic lesions and thereby suppresses carcinogenesis. In fact, there is a strong correlation between the incident of lung and breast cancer and the capacity for NER of an individual.

Animal models

- In animals with defects in TCR, such as Csb-/- and Xpa-/- mice, the development of sunburn as a result of apoptosis occurs at much lower doses of UV light than in corresponding wild-type littermates.

- By contrast, Xpc-/- mice with proficient TCR but defective GGR show no hypersensitivity to UVB-light-induced sunburn.

- A similar hypersensitivity for UVB-light-induced induction of p53 has been shown in the skin of Xpa-/- and Csb-/- mice, but not in the skin of Xpc-/- mice.

- The hypersensitivity to UVB-light irradiation correlates closely with the reduced ability of these cells to recover RNA synthesis following irradiation.

- These results show that the triggering signal for p53 accumulation and the induction of apoptosis following exposure to agents inducing bulky adducts originates specifically from persistent lesions in the transcribed strand of active genes, indicating that blockage of transcription might be involved in p53 signalling and in the induction of apoptosis.

See also

- xeroderma pigmentosum
- DNA repair

  • nucleotide excision repair (NER)
  • base excision repair (BER)


- Laine JP, Egly JM. When transcription and repair meet: a complex system. Trends Genet. 2006 Aug;22(8):430-6. PMID: #16797777#

- Transcription — guarding the genome by sensing DNA damage. Mats Ljungman & David P. Lane. Nature Reviews Cancer 4, 727-737 (September 2004) | doi:10.1038/nrc1435


  • NER-associated transcription coupled repair