Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development [RNA-seq]

Development of wheat (Triticum aestivum L.) grain mainly depends on the processes of starch synthesis and storage protein accumulation, which are critical for grain yield and quality. However, the regulatory network underlying the transcriptional and physiological changes of grain development is still not clear. Here, we combined ATAC-seq and RNA-seq to discover the chromatin accessibility and gene expression dynamics during these processes. We found that the chromatin accessibility changes are tightly associated with differential expressions and the proportion of distal ACRs were increased gradually during grain development. Specific transcription factor (TF) binding sites were enriched at different stages, and were diversified among the 3 subgenomes. We further predicted the potential interactions between key TFs and genes related with starch and storage protein biosynthesis and found different copies of some key TFs played diversified roles. Overall, our findings have provided numerous resources and illustrated the regulatory network during wheat grain development, which would shed lights on the improvement of wheat yields and qualities. Overall design: It is reported that the CRE variants are associated with many important agronomic traits. In this study, we unravelling the transcriptional network underlying wheat grain development by combing ATAC-seq (Assay for Transposase Accessible Chromatin sequencing) and RNA-seq with samples from a series of time points.

普通小麦（Triticum aestivum L.）籽粒的发育主要依赖淀粉合成与贮藏蛋白积累过程，二者对籽粒产量与品质均具有关键作用。然而，籽粒发育过程中转录与生理变化背后的调控网络仍未明确。本研究结合ATAC-seq（转座酶可及性染色质测序，Assay for Transposase Accessible Chromatin sequencing）与RNA-seq技术，解析该过程中的染色质可及性与基因表达动态变化。研究发现，染色质可及性变化与基因差异表达紧密关联，且远端染色质可及性区域（ACRs）的占比在籽粒发育进程中逐渐升高。不同发育阶段富集有特异性转录因子（TF）结合位点，且这些位点在小麦的三个亚基因组间存在功能分化。我们进一步预测了关键转录因子与淀粉、贮藏蛋白生物合成相关基因间的潜在调控互作，发现部分关键转录因子的不同拷贝发挥着差异化的功能。综上，本研究的发现为小麦籽粒发育调控网络提供了丰富的研究资源，并阐明了其调控机制，可为小麦产量与品质的改良提供理论支撑。
实验设计概述：已有研究表明，顺式调控元件（CRE）变异与诸多重要农艺性状密切相关。本研究通过采集一系列时间节点的小麦籽粒样本，结合ATAC-seq与RNA-seq技术，解析了小麦籽粒发育背后的转录调控网络。