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Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome

Nature Methods volume 13, pages 1009–1011 (2016)Cite this article

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Abstract

We present Micro-C XL, an improved method for analysis of chromosome folding at mononucleosome resolution. Using long crosslinkers and isolation of insoluble chromatin, Micro-C XL increases signal-to-noise ratio. Micro-C XL maps of budding and fission yeast genomes capture both short-range chromosome fiber features such as chromosomally interacting domains and higher order features such as centromere clustering. Micro-C XL provides a single assay to interrogate chromosome folding at length scales from the nucleosome to the full genome.

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Figure 1: Overview of Micro-C XL.
Figure 2: Analysis of chromosome folding in S. pombe.
Figure 3: Comparison of chromosome folding between S. cerevisiae and S. pombe.

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Acknowledgements

We thank L. Mirny and members of the Rando lab for insightful discussions. Work was supported in part by NIH grant GM079205 to O.J.R. G.F. and A.G. were supported by 4D Nucleome Program grants R01 GM114190 and U54 DK107980. T.-H.S.H. is an HHMI international student research fellow.

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA

    Tsung-Han S Hsieh & Oliver J Rando

  2. Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Geoffrey Fudenberg & Anton Goloborodko

  3. Center for 3D Structure and Physics of the Genome, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Geoffrey Fudenberg & Anton Goloborodko

Authors
  1. Tsung-Han S Hsieh
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  2. Geoffrey Fudenberg
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  3. Anton Goloborodko
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  4. Oliver J Rando
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Contributions

T.-H.S.H. and O.J.R. conceived the study. T.-H.S.H. performed all experiments. G.F. and T.-H.S.H. analyzed data. T.-H.S.H., G.F., A.G., and O.J.R. wrote the manuscript.

Corresponding author

Correspondence to Oliver J Rando.

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The authors declare no competing financial interests.

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Supplementary Figures 1–18 and Supplementary Protocol (PDF 10017 kb)

Supplementary Data

Read numbers and interactions vs. distance for all datasets. (XLSX 813 kb)

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Hsieh, TH., Fudenberg, G., Goloborodko, A. et al. Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome. Nat Methods 13, 1009–1011 (2016). https://doi.org/10.1038/nmeth.4025

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