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Highly interacting regions of the human genome are enriched with enhancers and bound by DNA repair proteins
Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).ORCID iD: 0000-0002-8186-1085
Umeå University, Faculty of Science and Technology, Department of Physics. (Integrated Science Lab (Icelab))ORCID iD: 0000-0002-7268-9519
Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
Umeå University, Faculty of Science and Technology, Department of Physics. (Integrated Science Lab (Icelab))
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2019 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 4577Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Nature Publishing Group, 2019. Vol. 9, article id 4577
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Biochemistry and Molecular Biology
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URN: urn:nbn:se:umu:diva-157750DOI: 10.1038/s41598-019-40770-9ISI: 000461159600054PubMedID: 30872630Scopus ID: 2-s2.0-85063013118OAI: oai:DiVA.org:umu-157750DiVA, id: diva2:1303275
Available from: 2019-04-09 Created: 2019-04-09 Last updated: 2019-04-09Bibliographically approved

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Sobhy, HaithamKumar, RajendraLewerentz, JacobLizana, LudvigStenberg, Per

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