Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution
| Autor: | You, Qiancheng, Cheng, Anthony Youzhi, Gu, Xi, Harada, Bryan T, Yu, Miao, Wu, Tong, Ren, Bing, Ouyang, Zhengqing, He, Chuan |
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| Rok vydání: | 2021 |
| Předmět: |
CCCTC-Binding Factor
Genome 1.1 Normal biological development and functioning Mouse Embryonic Stem Cells Bioengineering DNA Stem Cell Research Chromatin Promoter Regions Mice Cross-Linking Reagents Genetic Underpinning research Genetics Animals Nucleic Acid Conformation DNA (Cytosine-5-)-Methyltransferases Generic health relevance Enzyme Inhibitors Transcription |
| Zdroj: | Nature biotechnology, vol 39, iss 2 |
| Popis: | Determining the spatial organization of chromatin in cells mainly relies on crosslinking-based chromosome conformation capture techniques, but resolution and signal-to-noise ratio of these approaches is limited by interference from DNA-bound proteins. Here we introduce chemical-crosslinking assisted proximity capture (CAP-C), a method that uses multifunctional chemical crosslinkers with defined sizes to capture chromatin contacts. CAP-C generates chromatin contact maps at subkilobase (sub-kb) resolution with low background noise. We applied CAP-C to formaldehyde prefixed mouse embryonic stem cells (mESCs) and investigated loop domains (median size of 200 kb) and nonloop domains (median size of 9 kb). Transcription inhibition caused a greater loss of contacts in nonloop domains than loop domains. We uncovered conserved, transcription-state-dependent chromatin compartmentalization at high resolution that is shared from Drosophila to human, and a transcription-initiation-dependent nuclear subcompartment that brings multiple nonloop domains in close proximity. We also showed that CAP-C could be used to detect native chromatin conformation without formaldehyde prefixing. |
| Databáze: | OpenAIRE |
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