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

Authors: RICCI, WILLIAM - University Of Georgia; LU, ZEFU - University Of Georgia; JI, LEXIANG - University Of Georgia; MARAND, ALEXANDRE - University Of Georgia; ETHRIDGE, CHRISTINA - University Of Georgia; MURPHY, NATHALIE - University Of Georgia; NOSHAY, JACLYN - University Of Minnesota; GALLI, MARY - Rutgers University; MEJIA-GUERRA, MARIA - Cornell University; COLOME-TATCHE, MARIA - Technical University Of Munich; JOHANNES, FRANK - Technical University Of Munich; ROWLEY, M. JORDAN - Emory University; CORCES, VICTOR - Emory University; ZHAI, JIXIAN - Southern University; SCANLON, MICHAEL - Cornell University; Buckler, Edward - Ed; GALLAVOTTI, ANDREA - Rutgers University; SPRINGER, NATHAN - University Of Minnesota; SCHMITZ, ROBERT - University Of Georgia; 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. https://doi.org/10.1038/s41477-019-0547-0.
DOI: https://doi.org/10.1038/s41477-019-0547-0

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.