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Genome-Wide Characterization of cis-Acting DNA Targets Reveals the Transcriptional Regulatory Framework of Opaque2 in Maize

文献类型： 外文期刊

作者： Li, Chaobin 1 ; Qiao, Zhenyi 1 ; Qi, Weiwei 1 ; Wang, Qian 1 ; Yuan, Yue 1 ; Yang, Xi 1 ; Tang, Yuanping 1 ; Mei, Bing 1 ; L 1 ;

作者机构： 1.Shanghai Univ, Sch Life Sci, Shanghai Key Lab Bioenergy Crops, Shanghai 200444, Peoples R China

2.Coordinated Crop Biol Res Ctr, Beijing 100193, Peoples R China

3.Jiangsu Acad Agr Sci, I

期刊名称：PLANT CELL （ 影响因子：11.277； 五年影响因子：12.061 ）

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收录情况： SCI

摘要： Opaque2 (O2) is a transcription factor that plays important roles during maize endosperm development. Mutation of the O2 gene improves the nutritional value of maize seeds but also confers pleiotropic effects that result in reduced agronomic quality. To reveal the transcriptional regulatory framework of O2, we studied the transcriptome of o2 mutants using RNA sequencing (RNA-Seq) and determined O2 DNA binding targets using chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq). The RNA-Seq analysis revealed 1605 differentially expressed genes (DEGs) and 383 differentially expressed long, noncoding RNAs. The DEGs cover a wide range of functions related to nutrient reservoir activity, nitrogen metabolism, stress resistance, etc. ChIP-Seq analysis detected 1686 O2 DNA binding sites distributed over 1143 genes. Overlay of the RNA-Seq and ChIP-Seq results revealed 35 O2-modulated target genes. We identified four O2 binding motifs; among them, TGACGTGG appears to be the most conserved and strongest. We confirmed that, except for the 16- and 18-kD zeins, O2 directly regulates expression of all other zeins. O2 directly regulates two transcription factors, genes linked to carbon and amino acid metabolism and abiotic stress resistance. We built a hierarchical regulatory model for O2 that provides an understanding of its pleiotropic biological effects.

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