Jump to main content
Jump to site search

Issue 12, 2009
Previous Article Next Article

Genome-wide analysis predicts DNA structural motifs as nucleosome exclusion signals

Author affiliations

Abstract

Several factors are known to determine chromatin organization. However, the role of non-canonical DNA structure has not been studied in this context. Our recent observations indicated a widespread role of a particular non-canonical DNA structure, the G-quadruplex, or G4 motifs, in gene regulation. Herein, we first analyzed potential G4 (PG4) motif occurrence vis-à-visnucleosome occupancy signals. Genome-wide analysis using reported nucleosome positions in Saccharomyces cerevisiae and human (ENCODE regions and 3239 promoters) showed exclusion of nucleosomes by regions that have a relatively high density of PG4 motifs (P < 0.0001). This was supported by the enrichment of PG4 motifs within DNase I hypersensitive sites, which generally exclude nucleosomes. Based on these, we asked whether PG4 motifs had any distinct regulatory function. Two non-overlapping gene-sets in humans were tested—with PG4-enriched (Set I) or nucleosome-enriched (Set II) promoters. Gene-sets I and II were enriched in distinct functions: apoptosis and cellular signaling vs. development and immunity-related, respectively (P < 0.01). Sets I and II also showed different tissue-specific expression in 35 normal human tissues. In S. cerevisiae, we noted significant enrichment of PG4 motif regulated genes in cellular response to heat-shock, while genes with nucleosome-enriched promoters were not significantly represented. Our results show a structural motif as a possible nucleosome exclusion signal for the first time, and predict an alternate/additional regulatory role of G4 motifs, which could be distinct from gene regulation by remodeling of nucleosomes.

Graphical abstract: Genome-wide analysis predicts DNA structural motifs as nucleosome exclusion signals

Back to tab navigation
Please wait while Download options loads

Supplementary files

Publication details

The article was received on 20 Mar 2009, accepted on 15 Apr 2009 and first published on 29 May 2009


Article type: Paper
DOI: 10.1039/B905132E
Citation: Mol. BioSyst., 2009,5, 1703-1712
  •   Request permissions

    Genome-wide analysis predicts DNA structural motifs as nucleosome exclusion signals

    K. Halder, R. Halder and S. Chowdhury, Mol. BioSyst., 2009, 5, 1703
    DOI: 10.1039/B905132E

Search articles by author