Letter | Published:

Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping

Nature volume 541, pages 237241 (12 January 2017) | Download Citation

Abstract

Chromatin structure at the length scale encompassing local nucleosome–nucleosome interactions is thought to play a crucial role in regulating transcription and access to DNA1,2,3. However, this secondary structure of chromatin remains poorly understood compared with the primary structure of single nucleosomes or the tertiary structure of long-range looping interactions4. Here we report the first genome-wide map of chromatin conformation in human cells at the 1–3 nucleosome (50–500 bp) scale, obtained using ionizing radiation-induced spatially correlated cleavage of DNA with sequencing (RICC-seq) to identify DNA–DNA contacts that are spatially proximal. Unbiased analysis of RICC-seq signal reveals regional enrichment of DNA fragments characteristic of alternating rather than adjacent nucleosome interactions in tri-nucleosome units, particularly in H3K9me3-marked heterochromatin. We infer differences in the likelihood of nucleosome–nucleosome contacts among open chromatin, H3K27me3-marked, and H3K9me3-marked repressed chromatin regions. After calibrating RICC-seq signal to three-dimensional distances, we show that compact two-start helical fibre structures with stacked alternating nucleosomes are consistent with RICC-seq fragmentation patterns from H3K9me3-marked chromatin, while non-compact structures and solenoid structures are consistent with open chromatin. Our data support a model of chromatin architecture in intact interphase nuclei consistent with variable longitudinal compaction of two-start helical fibres.

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Acknowledgements

We acknowledge R. Das for conversations and help with capillary sequencing, E. Koslover, A. Spakowitz, and A. Schep for sharing code and sample data, discussions, and reading the manuscript, A. Kathiria for technical assistance, J. Buenrostro and C. Araya for advice and sharing code, I. Whitehouse for sharing a protocol, C. Fuller for nucleosome reconstitution help, P. Zhu and G. Li for sharing their chromatin fibre model, T. Phillips, G. J. Gu, O. Rando and W. Johnson for discussions, and G. Wang for BJ cells. BJ-5ta cells were a gift from J. Cochran. V.I.R. acknowledges the support of the Walter V. and Idun Berry Postdoctoral Fellowship. S.K.D. acknowledges support from a National Institutes of Health (NIH) Predoctoral Molecular Biophysics Training Program grant to Stanford University and from a National Science Foundation Graduate Fellowship. A.F.S. acknowledges support from National Institutes of Health (NIH) grant R01GM106005. W.J.G. acknowledges NIH grants R21HG007726, and P50HG00773501. This work was supported by the Rita Allen Foundation, the Baxter Foundation, and the Human Frontier Science Program.

Author information

Affiliations

  1. Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA

    • Viviana I. Risca
    •  & William J. Greenleaf
  2. Biophysics Program, Stanford University, Stanford, California 94305, USA

    • Sarah K. Denny
    •  & William J. Greenleaf
  3. Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA

    • Aaron F. Straight
  4. Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA

    • Aaron F. Straight
  5. Department of Applied Physics, Stanford University School of Medicine, Stanford, California 94305, USA

    • William J. Greenleaf

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Contributions

V.I.R., S.K.D., A.F.S., and W.J.G. designed experiments. V.I.R. and S.K.D. performed experiments. V.I.R. and S.K.D. analysed data. V.I.R., A.F.S., and W.J.G. interpreted the results and wrote the paper.

Competing interests

Stanford University has filed a patent application on these results with V.I.R., S.J.K.D., and W.J.G. named as co-inventors.

Corresponding author

Correspondence to William J. Greenleaf.

Reviewer Information

Nature thanks S. Grigoryev and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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https://doi.org/10.1038/nature20781

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