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Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution

Wenxiu Ma, Ferhat Ay, Choli Lee, Gunhan Gulsoy, Xinxian Deng, Savannah Cook, Jennifer Hesson, Christopher Cavanaugh, Carol B. Ware, Anton Krumm, Jay Shendure, C. Anthony Blau, Christine M. Disteche, William S. Noble, ZhiJun Duan
doi: https://doi.org/10.1101/184846
Wenxiu Ma
1Department of Genome Sciences, University of Washington, USA
8Present address: Department of Statistics, University of California, Riverside, USA
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Ferhat Ay
1Department of Genome Sciences, University of Washington, USA
9Present address: La Jolla Institute for Allergy and Immunology, USA
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Choli Lee
1Department of Genome Sciences, University of Washington, USA
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Gunhan Gulsoy
1Department of Genome Sciences, University of Washington, USA
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Xinxian Deng
2Department of Pathology, University of Washington, USA
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Savannah Cook
3Institute for Stem Cell and Regenerative Medicine, University of Washington, USA
4Department of Comparative Medicine, University of Washington, USA
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Jennifer Hesson
3Institute for Stem Cell and Regenerative Medicine, University of Washington, USA
4Department of Comparative Medicine, University of Washington, USA
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Christopher Cavanaugh
3Institute for Stem Cell and Regenerative Medicine, University of Washington, USA
4Department of Comparative Medicine, University of Washington, USA
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Carol B. Ware
3Institute for Stem Cell and Regenerative Medicine, University of Washington, USA
4Department of Comparative Medicine, University of Washington, USA
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Anton Krumm
5Department of Radiation Oncology, University of Washington, USA
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Jay Shendure
1Department of Genome Sciences, University of Washington, USA
7Howard Hughes Medical Institute Seattle, WA 98195-8056, USA
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C. Anthony Blau
3Institute for Stem Cell and Regenerative Medicine, University of Washington, USA
6Division of Hematology, Department of Medicine, University of Washington, USA
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Christine M. Disteche
2Department of Pathology, University of Washington, USA
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William S. Noble
1Department of Genome Sciences, University of Washington, USA
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  • For correspondence: william-noble@uw.edu zjduan@uw.edu
ZhiJun Duan
3Institute for Stem Cell and Regenerative Medicine, University of Washington, USA
6Division of Hematology, Department of Medicine, University of Washington, USA
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  • For correspondence: william-noble@uw.edu zjduan@uw.edu
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Abstract

The folding and three-dimensional (3D) organization of chromatin in the nucleus critically impacts genome function. The past decade has witnessed rapid advances in genomic tools for delineating 3D genome architecture. Among them, chromosome conformation capture (3C)-based methods such as Hi-C are the most widely used techniques for mapping chromatin interactions. However, traditional Hi-C protocols rely on restriction enzymes (REs) to fragment chromatin and are therefore limited in resolution. We recently developed DNase Hi-C for mapping 3D genome organization, which uses DNase I for chromatin fragmentation. DNase Hi-C overcomes RE-related limitations associated with traditional Hi-C methods, leading to improved methodological resolution. Furthermore, combining this method with DNA capture technology provides a high-throughput approach (targeted DNase Hi-C) that allows for mapping fine-scale chromatin architecture at exceptionally high resolution. Hence, targeted DNase Hi-C will be valuable for delineating the physical landscapes of cis-regulatory networks that control gene expression and for characterizing phenotype-associated chromatin 3D signatures. Here, we provide a detailed description of method design and step-by-step working protocols for these two methods.

Highlights

  • DNase Hi-C, a method for comprehensive mapping of chromatin contacts on a whole-genome scale, is based on random chromatin fragmentation by DNase I digestion instead of sequence-specific restriction enzyme (RE) digestion.

  • Targeted DNase Hi-C, which combines DNase Hi-C with DNA capture technology, is a high-throughput method for mapping fine-scale chromatin architecture of genomic loci of interest at a resolution comparable to that of genomic annotations of functional elements.

  • DNase Hi-C and targeted DNase Hi-C provide the first high-throughput way to overcome the RE-digestion-associated resolution limit of 3C-based methods.

  • Step-by-step whole-genome and targeted DNase Hi-C protocols for mapping global and local 3D genome architecture, respectively, are described.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted September 05, 2017.
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Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution
Wenxiu Ma, Ferhat Ay, Choli Lee, Gunhan Gulsoy, Xinxian Deng, Savannah Cook, Jennifer Hesson, Christopher Cavanaugh, Carol B. Ware, Anton Krumm, Jay Shendure, C. Anthony Blau, Christine M. Disteche, William S. Noble, ZhiJun Duan
bioRxiv 184846; doi: https://doi.org/10.1101/184846
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Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution
Wenxiu Ma, Ferhat Ay, Choli Lee, Gunhan Gulsoy, Xinxian Deng, Savannah Cook, Jennifer Hesson, Christopher Cavanaugh, Carol B. Ware, Anton Krumm, Jay Shendure, C. Anthony Blau, Christine M. Disteche, William S. Noble, ZhiJun Duan
bioRxiv 184846; doi: https://doi.org/10.1101/184846

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