The prevalence, evolution and chromatin signatures of plant regulatory elements

First author: Zefu Lu; Affiliations: University of Georgia (佐治亚大学): Athens, USA

Corresponding author: Robert J. Schmitz

Chromatin accessibility and modification is a hallmark of regulatory DNA, the study of which led to the discovery of cis-regulatory elements (CREs). Here, we characterize chromatin accessibility, histone modifications and sequence conservation in 13 plant species. We identified thousands of putative CREs and revealed that distal CREs are prevalent in plants, especially in species with large and complex genomes. The majority of distal CREs have been moved away from their target genes by transposable-element (TE) proliferation, but a substantial number of distal CREs also seem to be created by TEs. Finally, plant distal CREs are associated with three major types of chromatin signatures that are distinct from metazoans. Taken together, these results suggest that CREs are prevalent in plants, highly dynamic during evolution and function through distinct chromatin pathways to regulate gene expression.

染色质可及性和修饰是调控DNA的一个标志，对于这方面的研究发现了顺式调控元件CRE。本文中，作者对13个植物物种进行了染色质可及性、组蛋白修饰以及序列保守性的分析。作者鉴定了数千个假定的CRE，并且揭示了远端CRE在植物中普遍存在，尤其是基因较大且复杂的植物。大多数远端CRE由于转座子的扩增从靶基因附近移除，但TE同时也创造了一定数量的新的远端CRE。最终，植物的远端CRE与三种主要的染色质特性相关，并且与后生动物完全不同。综上，本文的结果揭示了CRE在植物中普遍存在，在演化过程中高度动态波动，通过不同的染色质途径调控基因的表达。

通讯：Robert J. Schmitz (http://schmitzlab.genetics.uga.edu)

研究方向：植物表观遗传如何驱动表型变异。

doi: https://doi.org/10.1038/s41477-019-0548-z

Journal: Nature Plants

Published date: November 18, 2019