Integrative analysis of haplotype-resolved epigenomes across human tissues

Nature. 2015 Feb 19;518(7539):350-354. doi: 10.1038/nature14217.


Allelic differences between the two homologous chromosomes can affect the propensity of inheritance in humans; however, the extent of such differences in the human genome has yet to be fully explored. Here we delineate allelic chromatin modifications and transcriptomes among a broad set of human tissues, enabled by a chromosome-spanning haplotype reconstruction strategy. The resulting large collection of haplotype-resolved epigenomic maps reveals extensive allelic biases in both chromatin state and transcription, which show considerable variation across tissues and between individuals, and allow us to investigate cis-regulatory relationships between genes and their control sequences. Analyses of histone modification maps also uncover intriguing characteristics of cis-regulatory elements and tissue-restricted activities of repetitive elements. The rich data sets described here will enhance our understanding of the mechanisms by which cis-regulatory elements control gene expression programs.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetylation
  • Alleles*
  • Chromatin / genetics
  • Chromatin / metabolism
  • Chromosomes, Human / genetics
  • Datasets as Topic
  • Enhancer Elements, Genetic / genetics
  • Epigenesis, Genetic / genetics*
  • Epigenomics*
  • Genetic Variation / genetics
  • Haplotypes / genetics*
  • Histones / metabolism
  • Humans
  • Nucleotide Motifs
  • Organ Specificity / genetics
  • Transcription, Genetic / genetics


  • Chromatin
  • Histones

Associated data

  • GEO/GSE16256
  • GEO/GSE58752