MNase Profiling of the Chromatin Landscapes in the Maize Genome

Nucleosomes are the fundamental units of chromatin structure with important roles in genome function and regulation.  In order to investigate the chromatin landscape in a complex eukaryotic genome, we developed new microarray-based chromatin mapping assays for the plant genetic model system maize (Zea  mays).  We  found that nucleosome occupancy signals were consistent regardless of the source tissue or the nuclei isolation buffer used.  In contrast to these global observations, we noticed persistent variation across multiple experiments at many small genomic regions within and between genes.  We could show that these hypervariable regions were caused by technical differences in nuclease digestion conditions.  We exploited this property to further identify biochemically defined hypersensitive and hyper-resistant regions throughout the maize genome.  MNase hypersensitive regions were enriched just upstream of many genes, in 3’ UTRs of most intron-containing genes, and just downstream of most genes.  In addition, we found the strength of the TSS-associated hypersensitivity was correlated with gene expression levels.  Hyper-resistant regions tended to be enriched in protein-coding exonic regions, as well as numerous intergenic regions.  We found that MNase hypersensitive regions co-localized with recently published datasets of conserved noncoding sequences (CNS) and the transcription factor binding sites for the homeobox protein Knotted1.  The ability to measure nucleosome occupancy and to map functionally relevant nuclease hypersensitivity regions provides valuable new information for comparative and functional plant genomics.

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