Genome distribution of replication-independent histone H1 variants shows H1.0 associated with nucleolar domains and H1X associated with RNA polymerase II-enriched regions

J Biol Chem. 2015 Mar 20;290(12):7474-91. doi: 10.1074/jbc.M114.617324. Epub 2015 Feb 2.


Unlike core histones, the linker histone H1 family is more evolutionarily diverse, and many organisms have multiple H1 variants or subtypes. In mammals, the H1 family includes seven somatic H1 variants; H1.1 to H1.5 are expressed in a replication-dependent manner, whereas H1.0 and H1X are replication-independent. Using ChIP-sequencing data and cell fractionation, we have compared the genomic distribution of H1.0 and H1X in human breast cancer cells, in which we previously observed differential distribution of H1.2 compared with the other subtypes. We have found H1.0 to be enriched at nucleolus-associated DNA repeats and chromatin domains, whereas H1X is associated with coding regions, RNA polymerase II-enriched regions, and hypomethylated CpG islands. Further, H1X accumulates within constitutive or included exons and retained introns and toward the 3' end of expressed genes. Inducible H1X knockdown does not affect cell proliferation but dysregulates a subset of genes related to cell movement and transport. In H1X-depleted cells, the promoters of up-regulated genes are not occupied specifically by this variant, have a lower than average H1 content, and, unexpectedly, do not form an H1 valley upon induction. We conclude that H1 variants are not distributed evenly across the genome and may participate with some specificity in chromatin domain organization or gene regulation.

Keywords: Chromatin; Epigenetics; H1.0; H1X; Histone; Histone H1; Nucleolus; RNA Polymerase II; Variants.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Breast Neoplasms / genetics
  • Breast Neoplasms / pathology
  • Cell Line, Tumor
  • Cell Nucleolus / genetics*
  • Cell Proliferation
  • CpG Islands
  • DNA / genetics
  • DNA Primers
  • Exons
  • Genome, Human*
  • Histones / genetics*
  • Humans
  • Polymerase Chain Reaction
  • RNA Polymerase II / metabolism*
  • Repetitive Sequences, Nucleic Acid
  • Transcription, Genetic


  • DNA Primers
  • Histones
  • DNA
  • RNA Polymerase II

Associated data

  • GEO/GSE49345
  • GEO/GSE62766