دورية أكاديمية
أعرض في EDS

The chromatin landscape of the euryarchaeon Haloferax volcanii.

التفاصيل البيبلوغرافية
العنوان: The chromatin landscape of the euryarchaeon Haloferax volcanii.
المؤلفون: Marinov GK; Department of Genetics, Stanford University, Stanford, CA, 94305, USA. GKM359@gmail.com., Bagdatli ST; Department of Genetics, Stanford University, Stanford, CA, 94305, USA., Wu T; Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA., He C; Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA.; Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA.; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA., Kundaje A; Department of Genetics, Stanford University, Stanford, CA, 94305, USA.; Department of Computer Science, Stanford University, Stanford, CA, 94305, USA., Greenleaf WJ; Department of Genetics, Stanford University, Stanford, CA, 94305, USA.; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA.; Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA.; Chan Zuckerberg Biohub, San Francisco, CA, USA.
المصدر: Genome biology [Genome Biol] 2023 Nov 06; Vol. 24 (1), pp. 253. Date of Electronic Publication: 2023 Nov 06.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't; Research Support, N.I.H., Extramural
اللغة: English
بيانات الدورية: Publisher: BioMed Central Ltd Country of Publication: England NLM ID: 100960660 Publication Model: Electronic Cited Medium: Internet ISSN: 1474-760X (Electronic) Linking ISSN: 14747596 NLM ISO Abbreviation: Genome Biol Subsets: MEDLINE
أسماء مطبوعة: Publication: London, UK : BioMed Central Ltd
Original Publication: London : Genome Biology Ltd., c2000-
مواضيع طبية MeSH: Haloferax volcanii*/genetics , Haloferax volcanii*/metabolism , Archaeal Proteins*/genetics, Chromatin ; Histones/genetics ; Nucleosomes ; Biological Evolution ; Eukaryota/genetics
مستخلص: Background: Archaea, together with Bacteria, represent the two main divisions of life on Earth, with many of the defining characteristics of the more complex eukaryotes tracing their origin to evolutionary innovations first made in their archaeal ancestors. One of the most notable such features is nucleosomal chromatin, although archaeal histones and chromatin differ significantly from those of eukaryotes, not all archaea possess histones and it is not clear if histones are a main packaging component for all that do. Despite increased interest in archaeal chromatin in recent years, its properties have been little studied using genomic tools.
Results: Here, we adapt the ATAC-seq assay to archaea and use it to map the accessible landscape of the genome of the euryarchaeote Haloferax volcanii. We integrate the resulting datasets with genome-wide maps of active transcription and single-stranded DNA (ssDNA) and find that while H. volcanii promoters exist in a preferentially accessible state, unlike most eukaryotes, modulation of transcriptional activity is not associated with changes in promoter accessibility. Applying orthogonal single-molecule footprinting methods, we quantify the absolute levels of physical protection of H. volcanii and find that Haloferax chromatin is similarly or only slightly more accessible, in aggregate, than that of eukaryotes. We also evaluate the degree of coordination of transcription within archaeal operons and make the unexpected observation that some CRISPR arrays are associated with highly prevalent ssDNA structures.
Conclusions: Our results provide the first comprehensive maps of chromatin accessibility and active transcription in Haloferax across conditions and thus a foundation for future functional studies of archaeal chromatin.
(© 2023. The Author(s).)
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معلومات مُعتمدة: U01 HG009431 United States HG NHGRI NIH HHS; R01 HG008140 United States HG NHGRI NIH HHS; U19AI057266 United States NH NIH HHS; U19 AI057266 United States AI NIAID NIH HHS; UM1 HG009436 United States HG NHGRI NIH HHS; UM1 HG009442 United States HG NHGRI NIH HHS; 1UM1HG009436 United States NH NIH HHS; RO1 HG008140 United States NH NIH HHS; 1DP2OD022870-01 United States NH NIH HHS; P50HG007735 United States NH NIH HHS; UM1HG009442 United States NH NIH HHS; P50 HG007735 United States HG NHGRI NIH HHS; 1U01HG009431 United States NH NIH HHS
المشرفين على المادة: 0 (Chromatin)
0 (Histones)
0 (Nucleosomes)
0 (Archaeal Proteins)
تواريخ الأحداث: Date Created: 20231107 Date Completed: 20231108 Latest Revision: 20240210
رمز التحديث: 20240210
مُعرف محوري في PubMed: PMC10626798
DOI: 10.1186/s13059-023-03095-5
PMID: 37932847
قاعدة البيانات: MEDLINE
الوصف
تدمد:1474-760X
DOI:10.1186/s13059-023-03095-5