دورية أكاديمية
أعرض في EDS

TAD evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function.

التفاصيل البيبلوغرافية
العنوان: TAD evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function.
المؤلفون: Okhovat M; Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA. okhovat@ohsu.edu., VanCampen J; Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA., Nevonen KA; Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA., Harshman L; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.; Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA., Li W; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.; Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA., Layman CE; Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA., Ward S; Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA., Herrera J; Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA., Wells J; Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA., Sheng RR; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.; Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA., Mao Y; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China., Ndjamen B; Histology and Light Microscopy Core Facility, Gladstone Institutes, San Francisco, CA, USA., Lima AC; Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA., Vigh-Conrad KA; Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA., Stendahl AM; Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA., Yang R; Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA., Fedorov L; OHSU Transgenic Mouse Models Core Lab, Oregon Health and Science University, Portland, OR, USA., Matthews IR; Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, CA, USA., Easow SA; Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, CA, USA., Chan DK; Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, CA, USA., Jan TA; Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, USA., Eichler EE; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA., Rugonyi S; Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA., Conrad DF; Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA.; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA., Ahituv N; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA. nadav.ahituv@ucsf.edu.; Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA. nadav.ahituv@ucsf.edu., Carbone L; Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA. carbone@ohsu.edu.; Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA. carbone@ohsu.edu.; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA. carbone@ohsu.edu.; Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA. carbone@ohsu.edu.
المصدر: Nature communications [Nat Commun] 2023 Dec 07; Vol. 14 (1), pp. 8111. Date of Electronic Publication: 2023 Dec 07.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [London] : Nature Pub. Group
مواضيع طبية MeSH: Genomics* , Genome*, Animals ; Mice ; Humans ; Gene Expression Regulation ; Epigenomics ; Chromatin Immunoprecipitation Sequencing ; Chromatin ; Mammals/genetics
مستخلص: Topological associating domains (TADs) are self-interacting genomic units crucial for shaping gene regulation patterns. Despite their importance, the extent of their evolutionary conservation and its functional implications remain largely unknown. In this study, we generate Hi-C and ChIP-seq data and compare TAD organization across four primate and four rodent species and characterize the genetic and epigenetic properties of TAD boundaries in correspondence to their evolutionary conservation. We find 14% of all human TAD boundaries to be shared among all eight species (ultraconserved), while 15% are human-specific. Ultraconserved TAD boundaries have stronger insulation strength, CTCF binding, and enrichment of older retrotransposons compared to species-specific boundaries. CRISPR-Cas9 knockouts of an ultraconserved boundary in a mouse model lead to tissue-specific gene expression changes and morphological phenotypes. Deletion of a human-specific boundary near the autism-related AUTS2 gene results in the upregulation of this gene in neurons. Overall, our study provides pertinent TAD boundary evolutionary conservation annotations and showcases the functional importance of TAD evolution.
(© 2023. The Author(s).)
التعليقات: Update of: bioRxiv. 2023 Mar 07;:. (PMID: 36945527)
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معلومات مُعتمدة: P51 OD011092 United States OD NIH HHS; P51 OD011092 United States CD ODCDC CDC HHS; UM1 HG011966 United States HG NHGRI NIH HHS; R01 HG010333 United States HG NHGRI NIH HHS; S10 OD021717 United States OD NIH HHS; R01 HG002385 United States HG NHGRI NIH HHS
المشرفين على المادة: 0 (Chromatin)
تواريخ الأحداث: Date Created: 20231207 Date Completed: 20231216 Latest Revision: 20240329
رمز التحديث: 20240329
مُعرف محوري في PubMed: PMC10703881
DOI: 10.1038/s41467-023-43841-8
PMID: 38062027
قاعدة البيانات: MEDLINE
الوصف
تدمد:2041-1723
DOI:10.1038/s41467-023-43841-8