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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #373386

Research Project: Improving Crop Efficiency Using Genomic Diversity and Computational Modeling

Location: Plant, Soil and Nutrition Research

Title: Widespread long-range cis-regulatory elements in the maize genome

item RICCI, WILLIAM - University Of Georgia
item LU, ZEFU - University Of Georgia
item JI, LEXIANG - University Of Georgia
item MARAND, ALEXANDRE - University Of Georgia
item ETHRIDGE, CHRISTINA - University Of Georgia
item MURPHY, NATHALIE - University Of Georgia
item NOSHAY, JACLYN - University Of Minnesota
item GALLI, MARY - Rutgers University
item MEJIA-GUERRA, MARIA - Cornell University
item COLOME-TATCHE, MARIA - Technical University Of Munich
item JOHANNES, FRANK - Technical University Of Munich
item ROWLEY, M. JORDAN - Emory University
item CORCES, VICTOR - Emory University
item ZHAI, JIXIAN - Southern University
item SCANLON, MICHAEL - Cornell University
item Buckler, Edward - Ed
item GALLAVOTTI, ANDREA - Rutgers University
item SPRINGER, NATHAN - University Of Minnesota
item SCHMITZ, ROBERT - University Of Georgia
item ZHANG, XIAOYU - University Of Georgia

Submitted to: Nature Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/9/2019
Publication Date: 11/18/2019
Citation: Ricci, W.A., Lu, Z., Ji, L., Marand, A.P., Ethridge, C.L., Murphy, N.G., Noshay, J.M., Galli, M., Mejia-Guerra, M.K., Colome-Tatche, M., Johannes, F., Rowley, M., Corces, V.G., Zhai, J., Scanlon, M.J., Buckler IV, E.S., Gallavotti, A., Springer, N.M., Schmitz, R.J., Zhang, X. 2019. Widespread long-range cis-regulatory elements in the maize genome. Nature Plants. 5:1237-1249.

Interpretive Summary: In maize, as in other crops, phenotypic variation of several agronomic traits is controlled by genes, together with the regions that regulate the turning on and off of the genes (i.e., cis-regulatory elements or CREs). However, different from genes that are easy to predict, identifying a CRE requires cumbersome experiments. Furthermore, even if the position of the CREs is known, assigning a CREs to the gene that it regulates is difficult in large genomes because CREs might be located far away from genes. Due to these challenges, the location and characteristics of CREs in crops remain poorly studied.

Technical Abstract: Genetic mapping studies on crops suggest that agronomic traits can be controlled by gene–distal intergenic loci. Despite the biological importance and the potential agronomic utility of these loci, they remain virtually uncharacterized in all crop species to date. Here, we provide genetic, epigenomic and functional molecular evidence to support the widespread existence of gene–distal (hereafter, distal) loci that act as long-range transcriptional cis-regulatory elements (CREs) in the maize genome. Such loci are enriched for euchromatic features that suggest their regulatory functions. Chromatin loops link together putative CREs with genes and recapitulate genetic interactions. Putative CREs also display elevated transcriptional enhancer activities, as measured by self-transcribing active regulatory region sequencing. These results provide functional support for the widespread existence of CREs that act over large genomic distances to control gene expression.