دورية أكاديمية
Multi-contact 4C: long-molecule sequencing of complex proximity ligation products to uncover local cooperative and competitive chromatin topologies.
| العنوان: | Multi-contact 4C: long-molecule sequencing of complex proximity ligation products to uncover local cooperative and competitive chromatin topologies. |
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| المؤلفون: | Vermeulen C; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Allahyar A; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Bouwman BAM; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Krijger PHL; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Verstegen MJAM; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Geeven G; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Valdes-Quezada C; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Renkens I; Oncode Institute, Center for Molecular Medicine, University Medical Center, Utrecht University, Utrecht, the Netherlands., Straver R; Oncode Institute, Center for Molecular Medicine, University Medical Center, Utrecht University, Utrecht, the Netherlands., Kloosterman WP; Oncode Institute, Center for Molecular Medicine, University Medical Center, Utrecht University, Utrecht, the Netherlands., de Ridder J; Oncode Institute, Center for Molecular Medicine, University Medical Center, Utrecht University, Utrecht, the Netherlands. j.deridder-4@umcutrecht.nl., de Laat W; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands. w.delaat@hubrecht.eu. |
| المصدر: | Nature protocols [Nat Protoc] 2020 Feb; Vol. 15 (2), pp. 364-397. Date of Electronic Publication: 2020 Jan 13. |
| نوع المنشور: | Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't |
| اللغة: | English |
| بيانات الدورية: | Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101284307 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1750-2799 (Electronic) Linking ISSN: 17502799 NLM ISO Abbreviation: Nat Protoc Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: London, UK : Nature Pub. Group, 2006- |
| مواضيع طبية MeSH: | Chromatin/*chemistry , Chromatin/*genetics , Sequence Analysis, DNA/*methods, Humans ; K562 Cells ; Molecular Conformation |
| مستخلص: | We present the experimental protocol and data analysis toolbox for multi-contact 4C (MC-4C), a new proximity ligation method tailored to study the higher-order chromatin contact patterns of selected genomic sites. Conventional chromatin conformation capture (3C) methods fragment proximity ligation products for efficient analysis of pairwise DNA contacts. By contrast, MC-4C is designed to preserve and collect large concatemers of proximity ligated fragments for long-molecule sequencing on an Oxford Nanopore or Pacific Biosciences platform. Each concatemer of proximity ligation products represents a snapshot topology of a different individual allele, revealing its multi-way chromatin interactions. By inverse PCR with primers specific for a fragment of interest (the viewpoint) and DNA size selection, sequencing is selectively targeted to thousands of different complex interactions containing this viewpoint. A tailored statistical analysis toolbox is able to generate background models and three-way interaction profiles from the same dataset. These profiles can be used to distinguish whether contacts between more than two regulatory sequences are mutually exclusive or, conversely, simultaneously occurring at chromatin hubs. The entire procedure can be completed in 2 w, and requires standard molecular biology and data analysis skills and equipment, plus access to a third-generation sequencing platform. |
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| المشرفين على المادة: | 0 (Chromatin) |
| تواريخ الأحداث: | Date Created: 20200115 Date Completed: 20200420 Latest Revision: 20220420 |
| رمز التحديث: | 20231215 |
| DOI: | 10.1038/s41596-019-0242-7 |
| PMID: | 31932773 |
| قاعدة البيانات: | MEDLINE |
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Full Text Finder | تدمد: | 1750-2799 |
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| DOI: | 10.1038/s41596-019-0242-7 |