High-density nucleosome occupancy map of human chromosome 9p21-22 reveals chromatin organization of the type I interferon gene cluster

Jonathan E. Freaney, Quanwei Zhang, Erbay Yigit, Rebecca Kim, Jonathan Widom, Ji Ping Wang, Curt M. Horvath

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Genome-wide investigations have dramatically increased our understanding of nucleosome positioning and the role of chromatin in gene regulation, yet some genomic regions have been poorly represented in human nucleosome maps. One such region is represented by human chromosome 9p21-22, which contains the type I interferon gene cluster that includes 16 interferon alpha genes and the single interferon beta, interferon epsilon, and interferon omega genes. A high-density nucleosome mapping strategy was used to generate locus-wide maps of the nucleosome organization of this biomedically important locus at a steady state and during a time course of infection with Sendai virus, an inducer of interferon gene expression. Detailed statistical and computational analysis illustrates that nucleosomes in this locus exhibit preferences for particular dinucleotide and oligomer DNA sequence motifs in vivo, which are similar to those reported for lower eukaryotic nucleosome-DNA interactions. These data were used to visualize the region's chromatin architecture and reveal features that are common to the organization of all the type I interferon genes, indicating a common nucleosome-mediated gene regulatory paradigm. Additionally, this study clarifies aspects of the dynamic changes that occur with the nucleosome occupying the transcriptional start site of the interferon beta gene after virus infection.

Original languageEnglish (US)
Pages (from-to)676-685
Number of pages10
JournalJournal of Interferon and Cytokine Research
Volume34
Issue number9
DOIs
StatePublished - Sep 1 2014
Externally publishedYes

Fingerprint

Chromosomes, Human, Pair 22
Interferon Type I
Nucleosomes
Human Chromosomes
Multigene Family
Chromatin
Interferon-beta
Genes
Interferon Inducers
Sendai virus
Nucleotide Motifs
Virus Diseases
Regulator Genes
Interferon-alpha
Genome
Gene Expression
DNA

ASJC Scopus subject areas

  • Immunology
  • Cell Biology
  • Virology

Cite this

High-density nucleosome occupancy map of human chromosome 9p21-22 reveals chromatin organization of the type I interferon gene cluster. / Freaney, Jonathan E.; Zhang, Quanwei; Yigit, Erbay; Kim, Rebecca; Widom, Jonathan; Wang, Ji Ping; Horvath, Curt M.

In: Journal of Interferon and Cytokine Research, Vol. 34, No. 9, 01.09.2014, p. 676-685.

Research output: Contribution to journalArticle

Freaney, Jonathan E. ; Zhang, Quanwei ; Yigit, Erbay ; Kim, Rebecca ; Widom, Jonathan ; Wang, Ji Ping ; Horvath, Curt M. / High-density nucleosome occupancy map of human chromosome 9p21-22 reveals chromatin organization of the type I interferon gene cluster. In: Journal of Interferon and Cytokine Research. 2014 ; Vol. 34, No. 9. pp. 676-685.
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