The nucleosome map of the mammalian liver

Nat Struct Mol Biol. 2011 Jun;18(6):742-6. doi: 10.1038/nsmb.2060. Epub 2011 May 29.

Abstract

Binding to nucleosomal DNA is critical for 'pioneer' transcription factors such as the winged-helix transcription factors Foxa1 and Foxa2 to regulate chromatin structure and gene activation. Here we report the genome-wide map of nucleosome positions in the mouse liver, with emphasis on transcriptional start sites, CpG islands, Foxa2 binding sites and their correlation with gene expression. Despite the heterogeneity of liver tissue, we could clearly discern the nucleosome pattern of the predominant liver cell, the hepatocyte. By analyzing nucleosome occupancy and the distributions of heterochromatin protein 1 (Hp1), CBP (also known as Crebbp) and p300 (Ep300) in Foxa1- and Foxa2-deficient livers, we find that the maintenance of nucleosome position and chromatin structure surrounding Foxa2 binding sites is independent of Foxa1 and Foxa2.

Publication types

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

MeSH terms

  • Animals
  • Binding Sites
  • CREB-Binding Protein / analysis
  • Chromosomal Proteins, Non-Histone / analysis
  • DNA / chemistry*
  • DNA / genetics
  • DNA / metabolism*
  • E1A-Associated p300 Protein / analysis
  • Hepatocytes / chemistry*
  • Mice
  • Nucleosomes / chemistry*
  • Nucleosomes / metabolism*
  • Transcription Initiation Site

Substances

  • Chromosomal Proteins, Non-Histone
  • Nucleosomes
  • heterochromatin-specific nonhistone chromosomal protein HP-1
  • DNA
  • CREB-Binding Protein
  • Crebbp protein, mouse
  • E1A-Associated p300 Protein
  • Ep300 protein, mouse