DNA slip-outs cause RNA polymerase II arrest in vitro: potential implications for genetic instability

• Published in: Nucleic acids research Vol. 39; no. 17; pp. 7444 - 7454
• Main Authors: Salinas-Rios, Viviana, Belotserkovskii, Boris P., Hanawalt, Philip C.
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.09.2011
• Subjects: copy number; DNA; DNA - chemistry; DNA-directed RNA polymerase; DNA-Directed RNA Polymerases - antagonists & inhibitors; Genome Integrity, Repair and; HeLa Cells; Humans; Mammalian cells; Neurodegenerative diseases; Nucleic Acid Conformation; Polyglutamine; Repeated DNA sequences; RNA Polymerase II - antagonists & inhibitors; Transcription; Transcription, Genetic; transcription-coupled repair; Trinucleotide Repeat Expansion; Trinucleotide Repeats; Viral Proteins - antagonists & inhibitors
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkr429

The abnormal number of repeats found in triplet repeat diseases arises from 'repeat instability', in which the repetitive section of DNA is subject to a change in copy number. Recent studies implicate transcription in a mechanism for repeat instability proposed to involve RNA polymerase II (RNAPII) arrest caused by a CTG slip-out, triggering transcription-coupled repair (TCR), futile cycles of which may lead to repeat expansion or contraction. In the present study, we use defined DNA constructs to directly test whether the structures formed by CAG and CTG repeat slip-outs can cause transcription arrest in vitro. We found that a slip-out of (CAG)20 or (CTG)20 repeats on either strand causes RNAPII arrest in HeLa cell nuclear extracts. Perfect hairpins and loops on either strand also cause RNAPII arrest. These findings are consistent with a transcription-induced repeat instability model in which transcription arrest in mammalian cells may initiate a 'gratuitous' TCR event leading to a change in repeat copy number. An understanding of the underlying mechanism of repeat instability could lead to intervention to slow down expansion and delay the onset of many neurodegenerative diseases in which triplet repeat expansion is implicated.