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August 13, 2021
from Kathleen Haughney, Florida State University
Gaining a full understanding of how genes are regulated is an important goal of scientists around the world. Now a professor at Florida State University and his research partners have developed a technique that can map almost all likely regulatory switches in a genome.
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This knowledge could prove to be crucial for agriculture, where scientists are constantly trying to improve crop yields by making various crops such as maize or wheat more resistant to external influences such as drought, floods or plant viruses.
» Knowing the landscape of the genome structure should help focus genome editing and accelerate larger applied research efforts such as those leading precision agriculture and medicine, « said Hank Bass, professor of biological sciences.
Regulatory switches that controlled by transcription factors are almost like light switches for genes. All genes have specific functions, but some are only briefly active at various stages of development. If this process goes wrong, it could affect a plant’s ability to develop properly or fight off disease.
« By creating a robust, accurate map of regulatory sites and transcription factors in corn, gene expression can be targeted by targeting them Places to be optimized, « said Savannah Savadel, the article’s first author and an FSU alumna who is now at Baylor Medical School. studies university of medicine. « This could mean healthier plants, higher nutrient levels, better growth or drought resistance, which is especially important in areas where farming is difficult. »
Knowing where a transcription factor binds to the gene enables allows researchers to understand the biochemistry of gene regulation in both normal and pathological contexts.
Corn is a complicated plant that has been studied by hundreds of researchers as it is a good genetic model species that can also contribute to shed light on the genetics of other plants. The maize genome has about two billion base pairs – units of double-stranded nucleic acids that are the building blocks of DNA. For comparison: humans have around 2.9 billion base pairs.
Bass and his colleagues used their technique called MOA-seq to map DNA sequences in small chunks of around 30 base pairs. The procedure extracts cell nuclei and applies an enzyme that acts as a probe. It diffuses into the nucleus and identifies areas of DNA that can be modified by binding transcription factors.
Narrowing the DNA map to smaller footprints of 30 base pairs would allow researchers to use gene editing tools like CRISPR to modify certain areas of the gene.
« We found the light switches with high precision in a proof-of-concept test fabric, the developing ear of a corn plant, » said Bass. « The ability to get to this level of sequence means that one can look for genetic variations within the binding sites for these switches. This enables precision farming. »
Bass has been using the chromatin sensitivity profiling technique for the past decade refined. He worked on this paper with Thomas Hartwig, a researcher from the Max Planck Institute in Germany, who proposed a collaboration after attending a workshop that taught researchers how to use the method. Savadel conducted many of the experiments as part of her Honors in the Major Thesis at Florida State.
Jonathan Dennis, Associate Professor of Biology at FSU, and Jinfeng Zhang, Associate Professor of Statistics, along with graduate students Zachary Turpin, Pei -Yau Lung and Xin Sui and former FSU PhD student Daniel Vera contributed to this research. Wolf Frommer and Max Blank from the Max Planck Institute also contributed to this study.
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