ArticleScientific reports2019
Highly interacting regions of the human genome are enriched with enhancers and bound by DNA repair proteins.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 18 citations in OpenAlex.
- Conserved 3D genome reorganization during DNA repair.Life science alliance · 2026Review
- Transcription-coupled repair: tangled up in convoluted repair.The FEBS journal · 2025Review
- C-terminal determinants for RNA binding motif 7 protein stability and RNA recognition.Biophysical chemistry · 2023Article
- Role of the redox state of the Pirin-bound cofactor on interaction with the master regulators of inflammation and other pathways.PloS one · 2023Article
- Long-distance association of topological boundaries through nuclear condensates.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Integrating Long-Range Regulatory Interactions to Predict Gene Expression Using Graph Convolutional Networks.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- Disparities in COVID-19 severities and casualties across ethnic groups around the globe and patterns of ACE2 and PIR variants.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2021Article
- Article
- Assessing stationary distributions derived from chromatin contact maps.BMC bioinformatics · 2020Article
- The Cajal Body Protein WRAP53β Prepares the Scene for Repair of DNA Double-Strand Breaks by Regulating Local Ubiquitination.Frontiers in molecular biosciences · 2019Review
- Super hotspots and super coldspots in the repair of UV-induced DNA damage in the human genome.The Journal of biological chemistryArticle
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In specific cases, chromatin clearly forms long-range loops that place distant regulatory elements in close proximity to transcription start sites, but we have limited understanding of many loops identified by Chromosome Conformation Capture (such as Hi-C) analyses. In efforts to elucidate their characteristics and functions, we have identified highly interacting regions (HIRs) using intra-chromosomal Hi-C datasets with a new computational method based on looking at the eigenvector that corresponds to the smallest eigenvalue (here unity). Analysis of these regions using ENCODE data shows that they are in general enriched in bound factors involved in DNA damage repair and have actively transcribed genes. However, both highly transcribed regions as well as transcriptionally inactive regions can form HIRs. The results also indicate that enhancers and super-enhancers in particular form long-range interactions within the same chromosome. The accumulation of DNA repair factors in most identified HIRs suggests that protection from DNA damage in these regions is essential for avoidance of detrimental rearrangements.
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