Genome-wide DNase I-hypersensitive site assay reveals distinct genomic distributions and functional features of open chromatin in autopolyploid sugarcane

文献类型： 外文期刊

第一作者： Yu, Guangrun

作者： Yu, Guangrun;Sun, Bo;Zhu, Zhiying;Teng, Ailing;Han, Jinlei;Zhang, Hui;Wang, Kai;Sun, Bo;Zhu, Zhiying;Mehareb, Eid M.;Liu, Jiayong;Liu, Xinlong;Zhang, Yuebin;Raza, Ghulam;Zhang, Baohong

作者机构：

关键词： sugarcane; open chromatin; DNase I-hypersensitive site; cis-regulatory DNA element; tissue-specific promoter

期刊名称：PLANT JOURNAL （ 影响因子：7.2； 五年影响因子：7.9 ）

ISSN： 0960-7412

年卷期： 2023 年

页码：

收录情况： SCI

摘要： The characterization of cis-regulatory DNA elements (CREs) is essential for deciphering the regulation of gene expression in eukaryotes. Although there have been endeavors to identify CREs in plants, the properties of CREs in polyploid genomes are still largely unknown. Here, we conducted the genome-wide identification of DNase I-hypersensitive sites (DHSs) in leaf and stem tissues of the auto-octoploid species Saccharum officinarum. We revealed that DHSs showed highly similar distributions in the genomes of these two S. officinarum tissues. Notably, we observed that approximately 74% of DHSs were located in distal intergenic regions, suggesting considerable differences in the abundance of distal CREs between S. officinarum and other plants. Leaf- and stem-dependent transcriptional regulatory networks were also developed by mining the binding motifs of transcription factors (TFs) from tissue-specific DHSs. Four TEOSINTE BRANCHED 1, CYCLOIDEA, and PCF1 (TCP) TFs (TCP2, TCP4, TCP7, and TCP14) and two ethylene-responsive factors (ERFs) (ERF109 and ERF03) showed strong causal connections with short binding distances from each other, pointing to their possible roles in the regulatory networks of leaf and stem development. Through functional validation in transiently transgenic protoplasts, we isolate a set of tissue-specific promoters. Overall, the DHS maps presented here offer a global view of the potential transcriptional regulatory elements in polyploid sugarcane and can be expected to serve as a valuable resource for both transcriptional network elucidation and genome editing in sugarcane breeding.

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