1
|
Ma W, Ay F, Lee C, Gulsoy G, Deng X, Cook S, Hesson J, Cavanaugh C, Ware CB, Krumm A, Shendure J, Blau CA, Disteche CM, Noble WS, Duan Z. Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution. Methods 2018; 142:59-73. [PMID: 29382556 PMCID: PMC5993575 DOI: 10.1016/j.ymeth.2018.01.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 12/14/2017] [Accepted: 01/25/2018] [Indexed: 01/09/2023] Open
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.
Collapse
Affiliation(s)
- Wenxiu Ma
- Department of Genome Sciences, University of Washington, USA
| | - Ferhat Ay
- Department of Genome Sciences, University of Washington, USA
| | - Choli Lee
- Department of Genome Sciences, University of Washington, USA
| | - Gunhan Gulsoy
- Department of Genome Sciences, University of Washington, USA
| | - Xinxian Deng
- Department of Pathology, University of Washington, USA
| | - Savannah Cook
- Institute for Stem Cell and Regenerative Medicine, University of Washington, USA; Department of Comparative Medicine, University of Washington, USA
| | - Jennifer Hesson
- Institute for Stem Cell and Regenerative Medicine, University of Washington, USA; Department of Comparative Medicine, University of Washington, USA
| | - Christopher Cavanaugh
- Institute for Stem Cell and Regenerative Medicine, University of Washington, USA; Department of Comparative Medicine, University of Washington, USA
| | - Carol B Ware
- Institute for Stem Cell and Regenerative Medicine, University of Washington, USA; Department of Comparative Medicine, University of Washington, USA
| | - Anton Krumm
- Department of Radiation Oncology, University of Washington, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, USA; Howard Hughes Medical Institute, Seattle, WA 98195-8056, USA
| | - C Anthony Blau
- Institute for Stem Cell and Regenerative Medicine, University of Washington, USA; Division of Hematology, Department of Medicine, University of Washington, USA
| | | | - William S Noble
- Department of Genome Sciences, University of Washington, USA.
| | - ZhiJun Duan
- Institute for Stem Cell and Regenerative Medicine, University of Washington, USA; Division of Hematology, Department of Medicine, University of Washington, USA.
| |
Collapse
|
2
|
Ma W, Ay F, Lee C, Gulsoy G, Deng X, Cook S, Hesson J, Cavanaugh C, Ware CB, Krumm A, Shendure J, Blau CA, Disteche CM, Noble WS, Duan Z. Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes. Nat Methods 2014; 12:71-8. [PMID: 25437436 PMCID: PMC4281301 DOI: 10.1038/nmeth.3205] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 10/17/2014] [Indexed: 12/18/2022]
Abstract
High-throughput methods based on chromosome conformation capture have greatly advanced our understanding of the three-dimensional (3D) organization of genomes but are limited in resolution by their reliance on restriction enzymes. Here we describe a method called DNase Hi-C for comprehensively mapping global chromatin contacts. DNase Hi-C uses DNase I for chromatin fragmentation, leading to greatly improved efficiency and resolution over that of Hi-C. Coupling this method with DNA-capture technology provides a high-throughput approach for targeted mapping of fine-scale chromatin architecture. We applied targeted DNase Hi-C to characterize the 3D organization of 998 large intergenic noncoding RNA (lincRNA) promoters in two human cell lines. Our results revealed that expression of lincRNAs is tightly controlled by complex mechanisms involving both super-enhancers and the Polycomb repressive complex. Our results provide the first glimpse of the cell type-specific 3D organization of lincRNA genes.
Collapse
Affiliation(s)
- Wenxiu Ma
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Ferhat Ay
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Choli Lee
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Gunhan Gulsoy
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Xinxian Deng
- Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Savannah Cook
- 1] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA. [2] Department of Comparative Medicine, University of Washington, Seattle, Washington, USA
| | - Jennifer Hesson
- 1] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA. [2] Department of Comparative Medicine, University of Washington, Seattle, Washington, USA
| | - Christopher Cavanaugh
- 1] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA. [2] Department of Comparative Medicine, University of Washington, Seattle, Washington, USA
| | - Carol B Ware
- 1] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA. [2] Department of Comparative Medicine, University of Washington, Seattle, Washington, USA
| | - Anton Krumm
- Department of Radiation Oncology, University of Washington, Seattle, Washington, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Carl Anthony Blau
- 1] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA. [2] Division of Hematology, University of Washington, Seattle, Washington, USA
| | | | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Zhijun Duan
- 1] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA. [2] Division of Hematology, University of Washington, Seattle, Washington, USA
| |
Collapse
|