ArticleGenome research2013
Mapping genomic hotspots of DNA damage by a single-strand-DNA-compatible and strand-specific ChIP-seq method.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 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.
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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
29 citing papers in PubMed, 44 citations in OpenAlex.
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- Cytoskeletal gene alterations linked to sorafenib resistance in hepatocellular carcinoma.World journal of surgical oncology · 2024Article
- Identification of an integrase-independent pathway of retrotransposition.Science advances · 2022Article
- KAS-seq: genome-wide sequencing of single-stranded DNA by NNature protocols · 2022Review
- Entailing the Next-Generation Sequencing and Metabolome for Sustainable Agriculture by Improving Plant Tolerance.International journal of molecular sciences · 2022Review
- Applications of nanodosimetry in particle therapy planning and beyond.Physics in medicine and biology · 2021Review
- Off-Target Analysis in Gene Editing and Applications for Clinical Translation of CRISPR/Cas9 in HIV-1 Therapy.Frontiers in genome editing · 2021Review
- Methodologies for detecting environmentally induced DNA damage and repair.Environmental and molecular mutagenesis · 2020Review
- Kethoxal-assisted single-stranded DNA sequencing captures global transcription dynamics and enhancer activity in situ.Nature methods · 2020Article
- Maf1-dependent transcriptional regulation of tRNAs prevents genomic instability and is associated with extended lifespan.Aging cell · 2020Article
- Terminal transfer amplification and sequencing for high-efficiency and low-bias copy number profiling of fragmented DNA samples.Protein & cell · 2019Article
- iGUIDE: an improved pipeline for analyzing CRISPR cleavage specificity.Genome biology · 2019Article
- Genome-wide Map of R-Loop-Induced Damage Reveals How a Subset of R-Loops Contributes to Genomic Instability.Molecular cell · 2018Article
- The organization of genome duplication is a critical determinant of the landscape of genome maintenance.Genome research · 2018Article
- Both DNA Polymerases δ and ε Contact Active and Stalled Replication Forks Differently.Molecular and cellular biology · 2017Article
- The functions of the multi-tasking Pfh1Current genetics · 2017Review
- Regulating retrotransposon activity through the use of alternative transcription start sites.EMBO reports · 2016Article
- Detecting DNA double-stranded breaks in mammalian genomes by linear amplification-mediated high-throughput genome-wide translocation sequencing.Nature protocols · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Spontaneous DNA damage may occur nonrandomly in the genome, especially when genome maintenance mechanisms are undermined. We developed single-strand DNA (ssDNA)-associated protein immunoprecipitation followed by sequencing (SPI-seq) to map genomic hotspots of DNA damage. We demonstrated this method with Rad52, a homologous recombination repair protein, which binds to ssDNA formed at DNA lesions. SPI-seq faithfully detected, in fission yeast, Rad52 enrichment at artificially induced double-strand breaks (DSBs) as well as endogenously programmed DSBs for mating-type switching. Applying Rad52 SPI-seq to fission yeast mutants defective in DNA helicase Pfh1 or histone H3K56 deacetylase Hst4, led to global views of DNA lesion hotspots emerging in these mutants. We also found serendipitously that histone dosage aberration can activate retrotransposon Tf2 and cause the accumulation of a Tf2 cDNA species bound by Rad52. SPI-seq should be widely applicable for mapping sites of DNA damage and uncovering the causes of genome instability.
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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.