Open AccessDirect DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution
Author(s) -
Qiancheng You,
Anthony Cheng,
Xi Gu,
Bryan T. Harada,
Miao Yu,
Tong Wu,
Bing Ren,
Zhengqing Ouyang,
Chuan He
Publication year - 2020
Publication title -
nature biotechnology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 15.358
H-Index - 445
eISSN - 1546-1696
pISSN - 1087-0156
DOI - 10.1038/s41587-020-0643-8
Subject(s) - chromatin , transcription (linguistics) , dna , chromosome conformation capture , biology , microbiology and biotechnology , biophysics , transcription factor , chemistry , genetics , gene , enhancer , linguistics , philosophy
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.