Targeted DNase Hi-C.

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  • Author(s): Duan Z;Duan Z;Duan Z
  • Source:
    Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2021; Vol. 2157, pp. 65-83.
  • Publication Type:
    Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
  • Language:
    English
  • Additional Information
    • Source:
      Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029 (Electronic) Linking ISSN: 10643745 NLM ISO Abbreviation: Methods Mol Biol Subsets: MEDLINE
    • Publication Information:
      Publication: Totowa, NJ : Humana Press
      Original Publication: Clifton, N.J. : Humana Press,
    • Subject Terms:
      Deoxyribonucleases/*metabolism; Chromatin/metabolism ; Chromosomes/metabolism ; Deoxyribonucleases/genetics ; Genome/genetics ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae/metabolism
    • Abstract:
      Technology advance during the past decade has greatly expanded our understanding of the higher-order structure of the genome. The various chromosome conformation capture (3C)-based techniques such as Hi-C have provided the most widely used tools for interrogating three-dimensional (3D) genome organization. We recently developed a Hi-C variant, DNase Hi-C, for characterizing 3D genome organization. DNase Hi-C employs DNase I for chromatin fragmentation, aiming to overcome restriction enzyme digestion-related limitations associated with traditional Hi-C methods. By combining DNase Hi-C with DNA capture technology, we further implemented a high-throughput approach, called targeted DNase Hi-C, which enables to map fine-scale chromatin architecture at exceptionally high resolution and thereby is an ideal tool for mapping the physical landscapes of cis-regulatory networks and for characterizing phenotype-associated chromatin 3D signatures. Here, I describe a detailed protocol of targeted DNase Hi-C library preparation, which covers experimental steps starting from cell cross-linking to library amplification.
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    • Grant Information:
      U54 DK107979 United States DK NIDDK NIH HHS; UM1 HG011586 United States HG NHGRI NIH HHS
    • Contributed Indexing:
      Keywords: 3C; 3D genome; Chromatin; Chromosome; DNase Hi-C; Hi-C
    • Accession Number:
      0 (Chromatin)
      EC 3.1.- (Deoxyribonucleases)
    • Publication Date:
      Date Created: 20200822 Date Completed: 20210315 Latest Revision: 20220102
    • Publication Date:
      20231215
    • Accession Number:
      PMC8087163
    • Accession Number:
      10.1007/978-1-0716-0664-3_5
    • Accession Number:
      32820399