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

First author: William A. Ricci; Affiliations: University of Georgia (佐治亚大学): Athens, USA

Corresponding author: Xiaoyu Zhang

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.

作物的遗传图谱研究表明，农艺性状可以由基因-远端基因间位点控制。 尽管这些位点具有生物学上的重要性和潜在的农艺利用价值，但迄今为止，我们并不清楚它们在农作物中的具体作用。本文中，作者提供了遗传、表观和功能分子证据，显示在玉米基因组中作为长距离转录顺式调控元件（CRE）的基因-远端位点的广泛存在。 这些位点富集常染色体特征，说明其具有调控功能。 染色质环将假定的CRE与基因连接在一起，说明了他们之间会有遗传相互作用。通过自转录活性调控区测序，作者发现假定的CREs同时也显示出升高的转录增强子活性。 本文的研究结果为CRE的广泛存在提供了功能性证据，这些CRE会跨越较大的基因组距离来控制基因的表达。

通讯：Xiaoyu Zhang (https://research.franklin.uga.edu/xiaoyu/)

研究方向：植物表观遗传。

doi: https://doi.org/10.1038/s41477-019-0547-0

Journal: Nature Plants

Published date: November 18, 2019