title: Genome-wide characterization of cis-acting DNA targets reveals the transcriptional regulatory framework of opaque2 in maize.
abstract: 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.
authors.affiliation: Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China.
authors.forename: Chaobin
authors.initials: C
authors.lastname: Li
authors.affiliation: Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China.
authors.forename: Zhenyi
authors.initials: Z
authors.lastname: Qiao
authors.affiliation: Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China Coordinated Crop Biology Research Center, Beijing 100193, China.
authors.forename: Weiwei
authors.initials: W
authors.lastname: Qi
authors.affiliation: Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Yuan
authors.affiliation: Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China.
authors.forename: Xi
authors.initials: X
authors.lastname: Yang
authors.affiliation: Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China.
authors.forename: Yuanping
authors.initials: Y
authors.lastname: Tang
authors.affiliation: Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China.
authors.forename: Bing
authors.initials: B
authors.lastname: Mei
authors.affiliation: Institute of Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
authors.forename: Yuanda
authors.initials: Y
authors.lastname: Lv
authors.affiliation: Institute of Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
authors.forename: Han
authors.initials: H
authors.lastname: Zhao
authors.affiliation: National Key Laboratory of Plant Molecular Genetics/CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
authors.forename: Han
authors.initials: H
authors.lastname: Xiao
authors.affiliation: Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China Coordinated Crop Biology Research Center, Beijing 100193, China rentaosong@staff.shu.edu.cn.
authors.forename: Rentao
authors.initials: R
authors.lastname: Song
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D018744:DNA, Plant / Q000235:genetics*; D015536:Down-Regulation / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D017343:Genes, Plant; D018745:Genome, Plant; D008969:Molecular Sequence Data; D009154:Mutation; D009584:Nitrogen / Q000378:metabolism; D059372:Nucleotide Motifs / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D022661:RNA, Untranslated / Q000235:genetics; D017423:Sequence Analysis, RNA; D013312:Stress, Physiological / Q000235:genetics; D014158:Transcription, Genetic; D003313:Zea mays / Q000235:genetics*; D015028:Zein / Q000235:genetics
chemical_list: D018744:DNA, Plant; D010940:Plant Proteins; D012333:RNA, Messenger; D022661:RNA, Untranslated; D015028:Zein; D009584:Nitrogen