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

Nature Biotechnology volume 39, pages 225–235 (2021)Cite this article

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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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Fig. 1: CAP-C resolves high-resolution local chromatin structure.
Fig. 2: CAP-C identifies loop and nonloop domains as two distinct types of chromatin domains.
Fig. 3: Active promoters are involved in chromatin boundary formation.
Fig. 4: Induction of transcription on nonannotated TSS by DNMTi results in the formation of weak chromatin boundaries and compartment changes.
Fig. 5: CAP-C identifies conserved small-scale chromatin compartmentalization shared among species.
Fig. 6: TICs as a type of nuclear subcompartment.

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Data availability

CAP-C, in situ Hi-C, ChIP–seq and PLAC-seq raw sequencing data are available on Gene Expression Omnibus accession: GSE110061. ChIP–seq data can also be found in the following links on UCSD genome browser: CAP-C–mESC: https://genome.ucsc.edu/s/anton386/CAPC%2DmESC; CAP-C–CTCF-AID: https://genome.ucsc.edu/s/anton386/CAPC%2DCTCF%2DAID; CAP-C–induction: https://genome.ucsc.edu/s/anton386/CAPC%2DInduction. Source data are provided with this paper.

Code availability

Code for CAP-C and ChIP–seq analysis is available on GitHub: http://github.com/ouyang-lab/CAPC.

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Acknowledgements

We thank A. Andersen (Life Science Editors) for editing the manuscript, P.W. Faber for helping with high-throughput sequencing, and J. Fei and J. Zhang for helping with DNA–FISH experiments. This work was supported by grant nos. NIH F32CA221007 (B.T.H.), NIH RM1HG008935 (C.H.), NIH U54CA193419 (C.H.), the Ludwig Institute for Cancer Research (B.R. and C.H.) and NIH/NIGMS grant no. R35 GM124998 (Z.O.). C.H. is an investigator of the Howard Hughes Medical Institute.

Author information

Author notes

  1. These authors contributed equally: Qiancheng You, Anthony Youzhi Cheng, Xi Gu.

Authors and Affiliations

  1. Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA

    Qiancheng You, Xi Gu, Bryan T. Harada, Tong Wu & Chuan He

  2. Howard Hughes Medical Institute, Chicago, IL, USA

    Qiancheng You, Xi Gu, Bryan T. Harada, Tong Wu & Chuan He

  3. The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA

    Anthony Youzhi Cheng & Zhengqing Ouyang

  4. Department of Genetics and Genome Sciences and Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA

    Anthony Youzhi Cheng & Zhengqing Ouyang

  5. Ludwig Institute for Cancer Research, La Jolla, CA, USA

    Miao Yu & Bing Ren

  6. Center for Epigenomics, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, USA

    Bing Ren

  7. Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA, USA

    Zhengqing Ouyang

  8. Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA

    Chuan He

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Contributions

C.H. and Q.Y. conceived the original idea. Q.Y., A.Y.C., X.G., Z.O. and C.H. designed the experiments. Q.Y., X.G., T.W. and M.Y., performed the experiments, A.Y.C. and B.L. performed analysis of the sequencing data. B.T.H. aided in the analysis of the FISH data. A.Y.C., Q.Y., X.G., B.R., Z.O. and C.H. analyzed the data and interpreted the finding. Q.Y., X.G., B.T.H. and A.Y.C. wrote the manuscript with input from B.R., Z.O. and C.H.

Corresponding authors

Correspondence to Bing Ren, Zhengqing Ouyang or Chuan He.

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Competing interests

C.H. is a scientific founder and a member of the scientific advisory board of Accent Therapeutics, Inc. and a shareholder of Epican Genetech. B.R. is a co-founder and a member of the scienceitific advisory board of Arima Genomics Inc.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–30 and Notes 1–5.

Reporting Summary

Supplementary Table 1

DNA–FISH probes

Supplementary Table 2

The sequencing information of CAP-C and in situ Hi-C

Source data

Source Data Fig. 2

Statistical source data.

Source Data Fig. 3

Statistical source data.

Source Data Fig. 5

Statistical source data.

Source Data Fig. 6

Statistical source data.

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You, Q., Cheng, A.Y., Gu, X. et al. Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution. Nat Biotechnol 39, 225–235 (2021). https://doi.org/10.1038/s41587-020-0643-8

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