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Functional Maize Genome Resides in Open Chromatin, Researchers Find

NEW YORK (GenomeWeb) – Researchers from Cornell University and Florida State University have examined the portion of the maize genome that falls in open chromatin regions and found that it accounts for 40 percent of phenotypic variation.

The vast majority — 98 percent — of the maize genome is noncoding, but Cornell's Edward Buckler and his colleagues used differential MNase sensitivity and high-throughput sequencing (DNS-seq) to uncover open chromatin regions of the genome that might be functional.

They found that these regions are typically near active genes and appear to be recombination hotspots, as they reported in the Proceedings of the National Academy of Sciences this week. In addition, the researchers said that the genetic variation within these open chromatin regions accounts for some 40 percent of phenotypic variation in maize agronomic traits.

"In agriculture, epigenomic profiling with DNS-seq can strategically guide the predictive accuracy of genomic selection, narrow candidate regions for experimentation with reverse genetics, and define the functions of intergenic chromatin toward organismal fitness," Buckler and his colleagues wrote in their paper.

To identity the 1 percent or so of the maize genome that falls in open chromatin, the researchers performed DNS-seq mapping of DNA from roots and shoots obtained from maize seedlings. Micrococcal nuclease, or MNase, cleaves DNA between nucleosomes to reveal their occupancy, the researchers noted.

From this, they found 126,992 MNase hypersensitivity regions in roots and 89,455 in shoots.

Broadly, Buckler and his colleagues found that the density of MNase hotspots correlates with gene regions. While most of these regions aren't located within genes, they are enriched in regions flanking genes. After sorting nearly 36,500 maize genes based on their mRNA levels, the researchers used heat map analysis to study MNase hotspots at transcription start sites. Both gene expression levels and signal strength of MNase regions show a genome-wide positive correlation around TSSs, they noted.

This effect is so strong that the researchers speculated "one might be able to predict transcription rates directly from the DNS profiles without measuring transcript levels."

These hotspots are also associated with DNA hypomethylation, the researchers reported. CpG methylation outside of transposable elements in the maize genome falls from 70 percent some 2 kilobases away from an MNase hotspot to 5 percent within one, though the effect seems to be stronger downstream of the hotspot.

At the same time, the MNase hotspots appear to also be hotbeds for recombination, as Buckler and his colleagues uncovered significant and genomic context-specific MNase hotspot enrichment at recombination hotspots.

MNase hypersensitivity also marks known quantitative trait loci and the hotspots appear to explain them, the researchers said.

For instance, they noted that the QTL linked with increased tb1 gene expression — a domestication gene that's involved in the number of stalks present in the plant— maps to an upstream spot between two transposable elements where there's also an MNase hotspot.

To test whether there's a link between MNase hotspots and complex traits, Buckler and his colleagues examined whether these regions were enriched for genome-wide association study hits and found a two-fold enrichment of such hits in regions near MNase hotspots.

When they constructed a genetic relationship matrix of SNP sets in a controlled-cross maize population, the researchers found that while coding regions of the maize genome explain about 47.6 percent of heritable variance, MNase hotspots account for 39.3 percent of the variance.

"MNase [hotspot] regions are therefore on par with coding sequences as annotations that demarcate the functional parts of the maize genome," Buckler and his colleagues wrote. "These results imply that less than 3 percent of the maize genome (coding and MNase [hotspot] regions) may give rise to the overwhelming majority of phenotypic variation, greatly narrowing the scope of the functional genome."