ArticleBiochemistry2012
Transcription blockage by bulky end termini at single-strand breaks in the DNA template: differential effects of 5' and 3' adducts.
Article in Biochemistry, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
21 citing papers in PubMed, 34 citations in OpenAlex.
- Oxidative stress triggers RNAPII arrest through PARylation and DNA damage.Nature communications · 2026Article
- F2,6BP restores mitochondrial genome integrity in Huntington's disease.The Journal of biological chemistry · 2026Article
- Fructose-2,6-bisphosphate restores DNA repair activity of PNKP and ameliorates neurodegenerative symptoms in Huntington's disease.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Fructose-2,6-bisphosphate restores DNA repair activity of PNKP and ameliorates neurodegenerative symptoms in Huntington's disease.bioRxiv : the preprint server for biology · 2024Article
- Supercoiled DNA percentage: A key in-process control of linear DNA template for mRNA drug substance manufacturing.Molecular therapy. Nucleic acids · 2024Article
- Site-specific acetylation of polynucleotide kinase 3'-phosphatase regulates its distinct role in DNA repair pathways.Nucleic acids research · 2024Article
- RNAPII response to transcription-blocking DNA lesions in mammalian cells.The FEBS journal · 2023Review
- Role of Histone Tails and Single Strand DNA Breaks in Nucleosomal Arrest of RNA Polymerase.International journal of molecular sciences · 2023Article
- Highly Sensitive Radioactivity-Based DNA 3'-Phosphatase Activity Assay for Polynucleotide Kinase 3'-Phosphatase.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Topologically switchable and gated transcription machinery.Chemical science · 2022Article
- Article
- RNA polymerase pausing, stalling and bypass during transcription of damaged DNA: from molecular basis to functional consequences.Nucleic acids research · 2022Review
- XRCC1 protects transcription from toxic PARP1 activity during DNA base excision repair.Nature cell biology · 2021Article
- Parp1 hyperactivity couples DNA breaks to aberrant neuronal calcium signalling and lethal seizures.EMBO reports · 2021Article
- When transcription goes on Holliday: Double Holliday junctions block RNA polymerase II transcription in vitro.Biochimica et biophysica acta. Gene regulatory mechanisms · 2017Article
- Classical non-homologous end-joining pathway utilizes nascent RNA for error-free double-strand break repair of transcribed genes.Nature communications · 2016Article
- Transcription blockage by stable H-DNA analogs in vitro.Nucleic acids research · 2015Article
- RNA polymerase II transcriptional fidelity control and its functional interplay with DNA modifications.Critical reviews in biochemistry and molecular biology · 2015Review
- Review
- Molecular basis of transcriptional fidelity and DNA lesion-induced transcriptional mutagenesis.DNA repair · 2014Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
RNA polymerases from phage-infected bacteria and mammalian cells have been shown to bypass single-strand breaks (SSBs) with a single-nucleotide gap in the template DNA strand during transcription elongation; however, the SSB bypass efficiency varies significantly depending upon the backbone end chemistries at the break. Using a reconstituted T7 phage transcription system (T7 RNAP) and RNA polymerase II (RNAPII) in HeLa cell nuclear extracts, we observe a slight reduction in the level of transcription arrest at SSBs with no gap as compared to those with a single-nucleotide gap. We have shown that biotin and carbon-chain moieties linked to the 3' side, and in select cases the 5' side, of an SSB in the template strand strongly increase the level of transcription arrest when compared to unmodified SSBs. We also find that a small carbon-chain moiety linked to the upstream side of an SSB aids transcriptional bypass of SSBs for both T7 RNAP and RNAP II. Analysis of transcription across SSBs flanked by bulky 3' adducts reveals the ability of 3' end chemistries to arrest T7 RNAP in a size-dependent manner. T7 RNAP is also completely arrested when 3' adducts or 3'-phosphate groups are placed opposite 5'-phosphate groups at an SSB. We have also observed that a biotinylated thymine in the template strand (without a break) does not pose a strong block to transcription. Taken together, these results emphasize the importance of the size of 3', but usually not 5', end chemistries in arresting transcription at SSBs, substantiating the notion that bulky 3' lesions (e.g., topoisomerase cleavable complexes, 3'-phosphoglycolates, and 3'-unsaturated aldehydes) pose very strong blocks to transcribing RNA polymerases. These findings have implications for the processing of DNA damage through SSB intermediates and the mechanism of SSB bypass by T7 RNAP and mammalian RNAPII.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.