Functional Genomics in Maize using Differential Nuclease Sensitivity (DNS­-seq) Chromatin Profiling

Nucleosomes are the fundamental units of chromatin structure with important but poorly characterized roles in genome function and regulation.  Maize (Zea mays) chromatin structural dynamics was measured at the nucleosomal level using a genome-wide chromatin profiling assay based on differential nuclease sensitivity, DNS (Vera, et al., 2014; Plant Cell 26:3883).  Chromatin structure was probed in fixed and isolated nuclei with different concentrations of nuclease, and fragment protection assay plots for light versus heavy digests uncovered specific regions of divergence, classified as MNase sensitive or resistant. Analysis of these DNS hot spots confirmed that they map to functionally important genomic loci.  In particular, the MNase hypersensitive sites (aka MSF or MNase HS) included specialized or so-called fragile nucleosomes and also non-nucleosomal structures including transcription factor binding sites and conserved noncoding sequence motifs.  At genes, the promoter-associated MNase HS signals co-varied with transcript abundance, suggesting that DNS profiling may accurately report transcription rate information genome-wide.  In addition to promoters, MSFs are enriched at the 3’ ends of genes, and in between genes, where GWAS approaches show that MNase HS sites explain a remarkable amount of heritable phenotypic variation.  Overall, DNS-chip or DNS-seq can be used to discover biochemically defined epigenomic features associated with open chromatin of nearly all types.  The ability to reduce the vast genomic landscape to dramatically smaller functional regions solves a major challenge in plant genome research while bridging the genotype-phenotype gap.