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

Nat Methods. 2016 Nov;13(11):919-922. doi: 10.1038/nmeth.3999. Epub 2016 Sep 19.

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.

MeSH terms

  • Animals
  • B-Lymphocytes / metabolism
  • 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
  • DNA / chemistry*
  • Embryonic Stem Cells / metabolism
  • Genomics / methods*
  • Humans
  • Mice
  • Reproducibility of Results
  • Sensitivity and Specificity

Substances

  • Cell Cycle Proteins
  • Chromatin
  • Chromosomal Proteins, Non-Histone
  • cohesins
  • DNA