Transcription-coupled repair: an update

Abstract

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Nucleotide excision repair (NER) is a versatile pathway that removes helix-distorting DNA lesions from the genomes of organisms across the evolutionary scale, from bacteria to humans. NER involves recognition of lesions, adducts or structures that disrupt the DNA double helix, removal of a short oligonucleotide containing the offending lesion, synthesis of a repair patch copying the opposite undamaged strand, and ligation, to restore the DNA to its original form. Transcription-coupled repair (TCR) is a subpathway of NER dedicated to the repair of lesions that, by virtue of their location on the transcribed strands of active genes, encumber elongation by RNA polymerases. Mutations that result in null or reduced functionality of NER proteins cause mild to extreme photosensitivity in humans. Of particular interest are Cockayne and UV-sensitive syndromes: individuals with these diseases are proficient in NER but lack TCR of lesions that significantly distort the DNA double helix. Smaller lesions, such as those caused by oxidation, are repaired by the base excision repair (BER) pathway. To elucidate whether a lesion resulting from oxidation of DNA, 8-oxo-Guanine, is subject to TCR, we developed an ultrasensitive approach combining single-cell electrophoresis (the comet assay) with fluorescent in situ hybridization (FISH) using strand-specific probes. The method allowed the quantification of low, physiologically relevant levels of specific DNA lesions in each strand of defined DNA sequences. We determined that 8-oxo-Guanine is preferentially repaired on the transcribed strand of the ATM gene in human cells, and this requires actively transcribing RNA polymerase II, CSB, UVSSA, hOGG1 and XPA, suggesting the participation of both BER and NER in this process [4]. I will review the biochemical pathways for TCR in the bacterium Escherichia coli, the yeast Saccharomyces cerevisiae, and human cells, and discuss how and when cells might choose to utilize TCR for repair and for restoration of transcription [1-5].