title: HiChIP: efficient and sensitive analysis of protein-directed genome architecture.
abstract: 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.
authors.affiliation: Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.|Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA.|Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Maxwell R
authors.initials: MR
authors.lastname: Mumbach
authors.affiliation: Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Adam J
authors.initials: AJ
authors.lastname: Rubin
authors.affiliation: Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.|Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Ryan A
authors.identifier: http://orcid.org/0000-0001-5013-0442
authors.initials: RA
authors.lastname: Flynn
authors.affiliation: Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.|Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Chao
authors.initials: C
authors.lastname: Dai
authors.affiliation: Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Paul A
authors.initials: PA
authors.lastname: Khavari
authors.affiliation: Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.|Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.|Department of Applied Physics, Stanford University, Stanford, California, USA.
authors.forename: William J
authors.initials: WJ
authors.lastname: Greenleaf
authors.affiliation: Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.|Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Howard Y
authors.initials: HY
authors.lastname: Chang
mesh_terms: D000818:Animals; D001402:B-Lymphocytes / Q000378:metabolism; D018797:Cell Cycle Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D002460:Cell Line; D002467:Cell Nucleus / Q000378:metabolism; D002843:Chromatin / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D002868:Chromosomal Proteins, Non-Histone / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D002874:Chromosome Mapping; D004247:DNA / Q000737:chemistry*; D053595:Embryonic Stem Cells / Q000378:metabolism; D023281:Genomics / Q000379:methods*; D006801:Humans; D051379:Mice; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D000097722:Cohesins
chemical_list: D018797:Cell Cycle Proteins; D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; D004247:DNA; D000097722:Cohesins