Open chromatin reveals the functional maize genome.

Area of Science:

• Plant genomics
• Epigenetics
• Molecular biology

Background:

• Nuclear DNA function is influenced by chromatin structure.
• Chromatin structural assays can identify regulatory elements and the functional noncoding genome.

Purpose of the Study:

• To identify open chromatin regions in the maize genome using a differential nuclease sensitivity assay.
• To investigate the relationship between these regions and gene activity, recombination, and phenotypic variation.

Main Methods:

• Utilized micrococcal nuclease (MNase) digestion to perform a differential nuclease sensitivity assay.
• Analyzed the localization of MNase-hypersensitive (MNase HS) regions in the maize genome.
• Correlated MNase HS regions with active genes, recombination hotspots, and heritable phenotypic variance.

Main Results:

• Discovered maize MNase HS regions are located near active genes and within recombination hotspots.
• Observed biased gene conversion focused at the flanks of MNase HS regions.
• Found that MNase HS regions, comprising <1% of the genome, explain ~40% of heritable phenotypic variance.

Conclusions:

• MNase HS regions are critical functional elements in the maize genome, comparable to coding sequences.
• A small fraction of the maize genome (<3%, including coding and MNase HS regions) may account for most phenotypic variation.
• This study significantly narrows the focus for identifying functional genomic regions in maize.