دورية أكاديمية
أعرض في EDS

Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions.

التفاصيل البيبلوغرافية
العنوان: Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions.
المؤلفون: Miller HE; Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX, USA.; Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX, USA.; Bioinformatics Research Network, Atlanta, GA, USA., Montemayor D; Department of Medicine, UT Health San Antonio, San Antonio, TX, USA.; Center for Precision Medicine, UT Health San Antonio, San Antonio, TX, USA., Abdul J; Bioinformatics Research Network, Atlanta, GA, USA.; Department of Biology, University of Ottawa, Ottawa, Canada., Vines A; Bioinformatics Research Network, Atlanta, GA, USA.; Faculty of Arts, University of Bristol, Bristol, U.K., Levy SA; Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX, USA.; Bioinformatics Research Network, Atlanta, GA, USA.; Sam & Ann Barshop Institute for Longevity & Aging Studies, UT Health San Antonio, San Antonio, TX, USA.; Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA., Hartono SR; Department of Molecular and Cellular Biology, UC Davis, Davis, CA, USA., Sharma K; Department of Medicine, UT Health San Antonio, San Antonio, TX, USA.; Center for Precision Medicine, UT Health San Antonio, San Antonio, TX, USA., Frost B; Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX, USA.; Sam & Ann Barshop Institute for Longevity & Aging Studies, UT Health San Antonio, San Antonio, TX, USA.; Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA., Chédin F; Department of Molecular and Cellular Biology, UC Davis, Davis, CA, USA., Bishop AJR; Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX, USA.; Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX, USA.; May's Cancer Center, UT Health San Antonio, San Antonio, TX, USA.
المصدر: Nucleic acids research [Nucleic Acids Res] 2022 Jul 22; Vol. 50 (13), pp. 7260-7286.
نوع المنشور: Journal Article; Meta-Analysis; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
اللغة: English
بيانات الدورية: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE
أسماء مطبوعة: Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.
مواضيع طبية MeSH: R-Loop Structures* , RNA*/chemistry , RNA*/genetics, Consensus ; DNA/chemistry ; Nucleic Acid Hybridization
مستخلص: R-loops are three-stranded nucleic acid structures formed from the hybridization of RNA and DNA. While the pathological consequences of R-loops have been well-studied to date, the locations, classes, and dynamics of physiological R-loops remain poorly understood. R-loop mapping studies provide insight into R-loop dynamics, but their findings are challenging to generalize. This is due to the narrow biological scope of individual studies, the limitations of each mapping modality, and, in some cases, poor data quality. In this study, we reprocessed 810 R-loop mapping datasets from a wide array of biological conditions and mapping modalities. From this data resource, we developed an accurate R-loop data quality control method, and we reveal the extent of poor-quality data within previously published studies. We then identified a set of high-confidence R-loop mapping samples and used them to define consensus R-loop sites called 'R-loop regions' (RL regions). In the process, we identified a stark divergence between RL regions detected by S9.6 and dRNH-based mapping methods, particularly with respect to R-loop size, location, and colocalization with RNA binding factors. Taken together, this work provides a much-needed method to assess R-loop data quality and offers novel context regarding the differences between dRNH- and S9.6-based R-loop mapping approaches.
(© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)
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معلومات مُعتمدة: R01 CA241554 United States CA NCI NIH HHS; R35 GM139549 United States GM NIGMS NIH HHS; F31 AG072902 United States AG NIA NIH HHS; P30 CA054174 United States CA NCI NIH HHS; R01 CA152063 United States CA NCI NIH HHS; RT6187 United Kingdom CRUK_ Cancer Research UK
المشرفين على المادة: 63231-63-0 (RNA)
9007-49-2 (DNA)
تواريخ الأحداث: Date Created: 20220627 Date Completed: 20220725 Latest Revision: 20230311
رمز التحديث: 20240628
مُعرف محوري في PubMed: PMC9303298
DOI: 10.1093/nar/gkac537
PMID: 35758606
قاعدة البيانات: MEDLINE
الوصف
تدمد:1362-4962
DOI:10.1093/nar/gkac537