MNase-chip of maize B73 immature ears, seedling shoots, and seedling roots

ABSTRACT: The eukaryotic nuclear genome is organized into the fundamental units of chromatin, nucleosomes. The positions and biochemical states of nucleosomes on DNA can regulate protein-DNA interactions, and in turn influence DNA-templated events. Despite the increasing number of genome-wide maps of nucleosome position, how global changes in nucleosome position relate to changes in gene expression is poorly understood. Using micrococcal nuclease (MNase) to map nucleosome positions, we show that in the maize genome, nucleosome occupancy signals are remarkably uniform between different tissues, whereas particular genomic regions are highly susceptible to variation. We demonstrate that much of this variation is associated with the degree to which chromatin is digested with MNase. Using high-density DNA microarrays, we exploited this digestion-linked variation to identify protein footprints in the maize genome that are hypersensitive to MNase digestion, a method we term Differential Nuclease-Sensitivity profiling (DNS-chip). Hypersensitive footprints were enriched at the 5’ and 3’ ends of genes, associated with gene-expression levels, and significantly overlapped with conserved noncoding sequences and the binding sites of the homeobox transcription-factor Knotted1, suggesting a functional role in genome regulation. We also found that the tissue-specific regulation of gene expression was linked to tissue-specific hypersensitive footprints in gene promoters. These results demonstrate the value of DNS-chip for revealing biochemical features of nucleosome organization that correlate with gene expression levels and colocalize with functional DNA elements. This approach to chromatin profiling should be broadly applicable to other species and should shed light on how chromatin organization might influence protein-DNA interactions and genome regulation.

ORGANISM(S): Zea mays

PROVIDER: GSE60089 | GEO | 2014/08/06

SECONDARY ACCESSION(S): PRJNA257467

REPOSITORIES: GEO