The bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elements

First author: Zijuan Li; Affiliations: Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (中国科学院上海植物生理生态学研究所): Shanghai, China

Corresponding author: Yijing Zhang

Bread wheat is an allohexaploid species with a 16-Gb genome that has large intergenic regions, which presents a big challenge for pinpointing regulatory elements and further revealing the transcriptional regulatory mechanisms. Chromatin profiling to characterize the combinatorial patterns of chromatin signatures is a powerful means to detect functional elements and clarify regulatory activities in human studies. In the present study, through comprehensive analyses of the open chromatin, DNA methylome, seven major chromatin marks, and transcriptomic data generated for seedlings of allohexaploid wheat, we detected distinct chromatin architectural features surrounding various functional elements, including genes, promoters, enhancer-like elements, and transposons. Thousands of new genic regions and cis-regulatory elements are identified based on the combinatorial pattern of chromatin features. Roughly 1.5% of the genome encodes a subset of active regulatory elements, including promoters and enhancer-like elements, which are characterized by a high degree of chromatin openness and histone acetylation, an abundance of CpG islands, and low DNA methylation levels. A comparison across sub-genomes reveals that evolutionary selection on gene regulation is targeted at the sequence and chromatin feature levels. The divergent enrichment of cis-elements between enhancer-like sequences and promoters implies these functional elements are targeted by different transcription factors. We herein present a systematic epigenomic map for the annotation of cis-regulatory elements in the bread wheat genome, which provides new insights into the connections between chromatin modifications and cis-regulatory activities in allohexaploid wheat.

育种小麦是异源六倍体物种，基因组大小约为16Gb，基因组上间隔区很大，所以精确定位调控元件及转录调控机制的研究十分困难。在人类研究中，揭示基因组上染色质信号组合模式的染色质谱是检测功能元件及调控活性分类的有力手段。在本文的研究中，作者通过异源六倍体小麦实生苗的开放染色质、DNA甲基化组、7个主要的染色质标记以及转录组数据的综合分析，作者在不同的功能元件周边检测到了不同的染色质结构特征，包括基因、启动子、类增强子元件以及转座子。基于染色质特征的组合模式，作者鉴定了数千个新的基因区及顺式作用元件。作者通过定位高密度染色质开放和组蛋白乙酰化区域、CpG岛富集和低DNA甲基化水平区域，发现基因组上大约1.5%的区域编码一类活性调控元件，包括启动子和类增强子元件。通过亚基因组之间的比较，作者发现基因调控的演化选择主要依赖于序列和染色质特征水平。类增强子序列和启动子之间顺式元件的富集情况差异可能暗示这些功能元件受到了不同转录因子的靶向。因此，作者在本文中报道了育种小麦基因组上顺式调控元件的系统性表观图谱，为异源六倍体小麦中染色质修饰和顺式调控活性之间的关联提供了新的视野。

通讯：张一婧 (http://www.sippe.ac.cn/sourcedb_sippe/zw/zjrc/201812/t20181219_5218231.html)

个人简介：1999-2003年，中国海洋大学，学士；2003-2008年，中科院遗传与发育研究所，硕博；2008-2009年，中国农业大学，博士后；2009-2011年，波士顿大学，博士后。

研究方向：通过大规模数据分析揭示植物表观遗传修饰复合体在控制微观和宏观生物学现象中的机制。

doi: https://doi.org/10.1186/s13059-019-1746-8

Journal: Genome Biology

Published date: July 15, 2019