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The position and density of nucleosomes are controlled by a combination of chromatin
regulatory complexes and features intrinsic to DNA sequence. This organization results in
architectures that facilitate or impede DNA-binding interactions required for nuclear processes
such as transcription, replication, recombination, repair, and transposition. How epigenetic modifications affect the local chromatin
structure near specific genes is well documented, but how changes in nucleosome position might impact DNA-templated processes has not been clearly elucidated. This aspect of the project aims to characterize the distribution and dynamics of nucleosomes in the maize genome in the context of transcriptional regulation.Concept of nuclease sensitivity.
We utilize
custom-designed NimbleGen microarrays to characterize nucleosome distribution and dynamics. These microarrays are a cost-effective approach to
nucleosome distribution mapping, while providing a providing large amounts of information previously unattainable with conventional nucleosome mapping techniques. Each high-density nucleosome mapping microarray contains probes representing overlapping genomic sequences that allow the detection of nucleosomes at hundreds of genes simultaneously.
Using this approach, we have experimentally measured nucleosome distribution at 400 transcription start sites in different tissues, under different growing, and as a result of mutations in chromatin-associated genes. We are investigating the consequence of nucleosome position changes on transcriptional regulation and other nuclear processes. This data will also be used to train a support vector machine to predict the nucleosome occupancy likelihood of any given DNA sequence (Click here for more info). |