DamC reveals principles of chromatin folding in vivo without crosslinking and ligation
Autor: | Eskeatnaf Mulugeta, Wouter de Laat, Jop Kind, Mariya Kryzhanovska, Luca Giorgetti, Isabel Guerreiro, Christian Valdes-Quezada, Guido Tiana, Vytautas Iesmantavicius, Josef Redolfi, Sébastien A. Smallwood, Tim Pollex, Ralph S. Grand, Yinxiu Zhan |
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Přispěvatelé: | Cell biology, Hubrecht Institute for Developmental Biology and Stem Cell Research |
Rok vydání: | 2019 |
Předmět: |
CCCTC-Binding Factor
Site-Specific DNA-Methyltransferase (Adenine-Specific) Recombinant Fusion Proteins Chromosomes Article Cell Line Chromosome conformation capture 03 medical and health sciences chemistry.chemical_compound Mice 0302 clinical medicine Bacterial Proteins Structural Biology Animals Molecular Biology 030304 developmental biology 0303 health sciences Chromosome Mouse Embryonic Stem Cells Methylation DNA Methylation Chromatin Cell biology Folding (chemistry) chemistry CTCF DNA methylation Nucleic Acid Conformation 030217 neurology & neurosurgery DNA |
Zdroj: | Nature Structural & Molecular Biology Nature Structural & Molecular Biology, 26(6), 471-+. Nature Publishing Group Nature structural & molecular biology Nature Structural & Molecular Biology, 26(6), 471-480. Nature Publishing Group |
ISSN: | 1545-9985 1545-9993 |
Popis: | Current understanding of chromosome folding is largely reliant on chromosome conformation capture (3C)-based experiments, where chromosomal interactions are detected as ligation products after chromatin crosslinking. To measure chromosome structure in vivo, quantitatively and without crosslinking and ligation, we implemented a modified version of DNA adenine methyltransferase identification (DamID) named DamC, which combines DNA methylation-based detection of chromosomal interactions with next-generation sequencing and biophysical modeling of methylation kinetics. DamC performed in mouse embryonic stem cells provides the first in vivo validation of the existence of topologically associating domains (TADs), CTCF loops and confirms 3C-based measurements of the scaling of contact probabilities. Combining DamC with transposon-mediated genomic engineering shows that new loops can be formed between ectopic and endogenous CTCF sites, which redistributes physical interactions within TADs. DamC provides the first crosslinking- and ligation-free demonstration of the existence of key structural features of chromosomes and provides novel insights into how chromosome structure within TADs can be manipulated. |
Databáze: | OpenAIRE |
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