In order to understand genetic regulation more completely, a team of researchers has developed a technique that can map out nearly all of the likely regulatory switches across a genome. In their proof-of-concept study using developing maize ears, they showed that their assay, which uses micrococcal nuclease (MNase) as a structural probe, detects known transcription factor (TF)-binding sites. Expanding the knowledge regarding genetic regulation in maize, and other plants, could prove critical for the agriculture field where scientists are constantly trying to improve crop yield by making different plants more resistant to external forces like drought, flooding, or plant viruses.

This research is published in PLOS Genetics in the paper, “The native cistrome and sequence motif families of the maize ear.

An ear of maize (Zea mays) from the FSU study.
[Jonathan Doster]

Corn is a useful model species, in part because of its complexity, that can help shed light on the genetics of other plants. The corn genome has about two billion base pairs; humans have about 2.9 billion base pairs.

Regulatory switches are controlled by transcription factors. These switches control gene expression, particularly during different stages of development. When the process goes awry, it could disrupt a plant’s ability to develop correctly or fight off disease.

A team led by Hank Bass, PhD, professor of biological science at Florida State University (FSU), developed a technique known as MNase-defined cistrome-Occupancy Analysis (MOA-seq) to map DNA sequences in small chunks of about 30 base pairs. The method extracts cell nuclei and applies MNase as a structural probe to simultaneously reveal regions of accessible chromatin in addition to high-resolution footprints with signatures of TF-occupied cis-elements. It diffuses into the nucleus and identifies areas of the DNA that are open to modification by transcription factor binding.

“By creating a robust, precise map of regulatory sites and transcription factors in maize, gene expression can be optimized by targeting these sites,” said Savannah Savadel, first author on the paper and an FSU alumna who is now in medical school at Baylor College of Medicine. “This could mean healthier plants, higher nutrient content, better growth, or drought resistance, which is an especially important concern in areas where farming is difficult.”

The authors wrote that they used MOA-seq on developing maize ears as a proof of concept, able to define a cistrome of 145,000 MOA footprints (MFs). While a substantial majority (76%), “of the known ATAC-seq ACRs intersected with the MFs, only a minority of MFs overlapped with the ATAC peaks, indicating that the majority of MFs were novel and not detected by ATAC-seq,” the authors wrote.

“We found the light switches with high precision in a proof-of-concept test tissue, the developing ear of a maize plant,” Bass said. “The ability to get down to this sequence level means you can look for genetic variation within the binding sites for these switches. This enables precision agriculture.” Narrowing the DNA map to smaller footprints of 30 base pairs would allow researchers to use gene editing tools such as CRISPR to modify specific areas of the gene.

This genome-wide assay, the authors wrote, “not only defines chromatin landscapes, but crucially enables global discovery and mapping of sequence motifs underlying small footprints of ~30 bp to produce an atlas of candidate TF occupancy.”

“Knowledge of the landscape of the genome structure should help focus genome editing and accelerate larger applied research efforts such as those guiding precision agriculture and medicine,” said Bass.

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