Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution.

Document Type

Article

Publication Date

2-2021

Publication Title

Nature biotechnology

Keywords

JGM, Animals, CCCTC-Binding Factor, Chromatin, Cross-Linking Reagents, DNA, DNA (Cytosine-5-)-Methyltransferases, Enzyme Inhibitors, Genome, Mice, Mouse Embryonic Stem Cells, Nucleic Acid Conformation, Promoter Regions, Genetic, Transcription, Genetic

JAX Source

Nat Biotechnol 2021 Feb; 39(2):225-235

Volume

39

Issue

2

First Page

225

Last Page

235

ISSN

1546-1696

PMID

32839564

DOI

https://doi.org/10.1038/s41587-020-0643-8

Abstract

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.

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