Genome-Wide Chromatin Remodeling Identified at GC-Rich Long Nucleosome-Free Regions

Karin Schwarzbauer, Ulrich Bodenhofer, Sepp Hochreiter

Research output: Contribution to journalArticlepeer-review

10 Citations (Scopus)

Abstract

To gain deeper insights into principles of cell biology, it is essential to understand how cells reorganize their genomes by chromatin remodeling. We analyzed chromatin remodeling on next generation sequencing data from resting and activated T cells to determine a whole-genome chromatin remodeling landscape. We consider chromatin remodeling in terms of nucleosome repositioning which can be observed most robustly in long nucleosome-free regions (LNFRs) that are occupied by nucleosomes in another cell state. We found that LNFR sequences are either AT-rich or GC-rich, where nucleosome repositioning was observed much more prominently in GC-rich LNFRs - a considerable proportion of them outside promoter regions. Using support vector machines with string kernels, we identified a GC-rich DNA sequence pattern indicating loci of nucleosome repositioning in resting T cells. This pattern appears to be also typical for CpG islands. We found out that nucleosome repositioning in GC-rich LNFRs is indeed associated with CpG islands and with binding sites of the CpG-island-binding ZF-CXXC proteins KDM2A and CFP1. That this association occurs prominently inside and also prominently outside of promoter regions hints at a mechanism governing nucleosome repositioning that acts on a whole-genome scale.

Original languageEnglish
Article numbere47924
JournalPLoS ONE
Volume7
Issue number11
DOIs
Publication statusPublished - 5 Nov 2012

Keywords

  • Animals
  • Base Composition
  • Base Sequence
  • CD4-Positive T-Lymphocytes/metabolism
  • Chromatin/metabolism
  • Chromatin Assembly and Disassembly/genetics
  • Chromosome Mapping
  • Consensus Sequence
  • CpG Islands
  • GC Rich Sequence
  • Genome, Human
  • Humans
  • Mice
  • Models, Genetic
  • Molecular Sequence Annotation
  • Nucleosomes/genetics
  • Sequence Analysis, DNA

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