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

William A. Ricci, Zefu Lu, Lexiang Ji, Alexandre P. Marand, Christina L. Ethridge, Nathalie G. Murphy, Jaclyn M. Noshay, Mary Galli, María Katherine Mejía-Guerra, Maria Colomé-Tatché, Frank Johannes, M. Jordan Rowley, Victor G. Corces, Jixian Zhai, Michael J. Scanlon, Edward S. Buckler, Andrea Gallavotti, Nathan M. Springer, Robert J. Schmitz, Xiaoyu Zhang

Research output: Contribution to journalArticlepeer-review

201 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)1237-1249
Number of pages13
JournalNature Plants
Issue number12
StatePublished - Dec 1 2019
Externally publishedYes

ASJC Scopus subject areas

  • Plant Science


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