Investigating Chromatin Structure at Multiple Scales in Maize

We have investigated genomic and epigenomic features of maize chromatin at several levels using computational, biochemical, and cytological approaches.  Recent findings from several studies will be presented.  These include [1] computational identification and characterization of motifs capable of forming non-duplex, G-Quadruplex (G4) DNA; [2] chromatin structure profiling using Differential Nuclease Sensitivity (DNS-seq) mapping; and [3] 3D molecular cytology of spatiotemporal patterns of DNA replication.  At the DNA level, maize chromosomes were shown to harbor thousands of G4 DNA motifs with hot-spots located on the template strands in the 5’ UTR and the beginning of the first intron.  Many of these genes function in metabolic signaling pathways responsive to low energy states such as hypoxia.  At the chromatin level, nuclease sensitivity profiles highlight functional genomic regions.  MNase hypersensitive (HS) sites at promoters predict transcriptional activity while intergenic MNase HS sites explain a large proportion of heritable phenotypic variation in structured populations.  DNS-seq maps biochemically defined epigenomic features associated with multiple types of open chromatin.  At the level of higher-order chromatin structure and nuclear architecture, we examined spatiotemporal patterns of DNA replication at early, middle, and late S-phase of EdU-pulse labeled nuclei from developing maize root tips.  Maize euchromatin was found to exist as an intermingled but distinct mixture of two components/compartments, distinguished by their condensation state and replication timing (early versus middle S) in mitotic and endocycling nuclei.  Together, these findings will help bridge the genotype-phenotype gap with integrative information and annotations that span multiple scales of epigenomic resolution.