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Chromatin accessibility modulates access to DNA by diffusible factors and small molecules including transcription factors, replication and repair machinery, and small RNAs. The regulation of chromatin accessibility is increasingly becoming recognized as a critical feature regulating DNA-templated processes, yet remains poorly understood. This represents a significant gap in our knowledge. This aspect of the project aims to characterize the large-scale changes in chromatin accessibility in multiple contexts.
Nuclease sensitivity has long been used to characterize the accessibility
of chromatin at specific loci to soluble nuclear factors, and is associated
with transcriptional activation. Performing nuclease sensitivity assays
with microarray technology allows for a genome-wide analysis of
chromatin structure in maize. To understand the functional significance of
large-scale chromatin accessibility in the nucleus, we utilize NimbleGen microarrays to detect nuclease sensitivity genome-wide at a resolution of 14 kb. As proof of principle, we have detected genome-wide differences in chromatin structure across different growing conditions and tissue types. We are further utilizing this technology to investigate changes in chromatin structure as a result of development and other biological processes, with the goal of identifying relationships between changes in large-scale chromatin structure and
changes in local changes in nucleosome distribution, three-dimensional nuclear architecture, and gene expression. This work will characterize the functional significance of chromatin accessibility and will establish a new platform for the analysis of how the maize
genome regulates global chromatin structure under various
environmental conditions and developmental pathways. |