HiChIP: efficient and sensitive analysis of protein-directed genome architecture

• Published in: Nature methods Vol. 13; no. 11; pp. 919 - 922
• Main Authors: Mumbach, Maxwell R, Rubin, Adam J, Flynn, Ryan A, Dai, Chao, Khavari, Paul A, Greenleaf, William J, Chang, Howard Y
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.11.2016; Nature Publishing Group
• Subjects: 631/1647/2210/2211; 631/208/177; 631/61/191; Animals; B-Lymphocytes - metabolism; Bioinformatics; Biological Microscopy; Biological Techniques; Biomedical Engineering/Biotechnology; brief-communication; Cell Cycle Proteins - chemistry; Cell Cycle Proteins - genetics; Cell Cycle Proteins - metabolism; Cell Line; Cell Nucleus - metabolism; Chromatin - chemistry; Chromatin - genetics; Chromatin - metabolism; Chromatin Immunoprecipitation - methods; Chromosomal Proteins, Non-Histone - chemistry; Chromosomal Proteins, Non-Histone - genetics; Chromosomal Proteins, Non-Histone - metabolism; Chromosome Mapping; Cohesins; DNA - chemistry; Embryonic Stem Cells - metabolism; Genes; Genomes; Genomics; Genomics - methods; Humans; Life Sciences; Mice; Proteins; Proteomics; Reproducibility of Results; Sensitivity analysis; Sensitivity and Specificity; United States
• ISSN: 1548-7091; 1548-7105
• DOI: 10.1038/nmeth.3999

HiChIP combines chromosome conformation capture with immunoprecipitation- and tagmentation-based library preparation to uncover the 3D chromatin architecture focused around a protein of interest. Genome conformation is central to gene control but challenging to interrogate. Here we present HiChIP, a protein-centric chromatin conformation method. HiChIP improves the yield of conformation-informative reads by over 10-fold and lowers the input requirement over 100-fold relative to that of ChIA-PET. HiChIP of cohesin reveals multiscale genome architecture with greater signal-to-background ratios than those of in situ Hi-C.