title: Genome-wide binding analysis of the transcription activator ideal plant architecture1 reveals a complex network regulating rice plant architecture.
abstract: Ideal plant architecture1 (IPA1) is critical in regulating rice (Oryza sativa) plant architecture and substantially enhances grain yield. To elucidate its molecular basis, we first confirmed IPA1 as a functional transcription activator and then identified 1067 and 2185 genes associated with IPA1 binding sites in shoot apices and young panicles, respectively, through chromatin immunoprecipitation sequencing assays. The Squamosa promoter binding protein-box direct binding core motif GTAC was highly enriched in IPA1 binding peaks; interestingly, a previously uncharacterized indirect binding motif TGGGCC/T was found to be significantly enriched through the interaction of IPA1 with proliferating cell nuclear antigen promoter binding factor1 or promoter binding factor2. Genome-wide expression profiling by RNA sequencing revealed IPA1 roles in diverse pathways. Moreover, our results demonstrated that IPA1 could directly bind to the promoter of rice teosinte branched1, a negative regulator of tiller bud outgrowth, to suppress rice tillering, and directly and positively regulate dense and erect panicle1, an important gene regulating panicle architecture, to influence plant height and panicle length. The elucidation of target genes of IPA1 genome-wide will contribute to understanding the molecular mechanisms underlying plant architecture and to facilitating the breeding of elite varieties with ideal plant architecture.
authors.affiliation: State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Zefu
authors.initials: Z
authors.lastname: Lu
authors.forename: Hong
authors.initials: H
authors.lastname: Yu
authors.forename: Guosheng
authors.initials: G
authors.lastname: Xiong
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.forename: Yongqing
authors.initials: Y
authors.lastname: Jiao
authors.forename: Guifu
authors.initials: G
authors.lastname: Liu
authors.forename: Yanhui
authors.initials: Y
authors.lastname: Jing
authors.forename: Xiangbing
authors.initials: X
authors.lastname: Meng
authors.forename: Xingming
authors.initials: X
authors.lastname: Hu
authors.forename: Qian
authors.initials: Q
authors.lastname: Qian
authors.forename: Xiangdong
authors.initials: X
authors.lastname: Fu
authors.forename: Yonghong
authors.initials: Y
authors.lastname: Wang
authors.forename: Jiayang
authors.initials: J
authors.lastname: Li
mesh_terms: D001665:Binding Sites; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D012275:Oryza / Q000235:genetics* / Q000254:growth & development; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D030821:Plants, Genetically Modified / Q000235:genetics / Q000254:growth & development; D011401:Promoter Regions, Genetic; D054730:Protein Interaction Domains and Motifs; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D015533:Transcriptional Activation; D059467:Transcriptome
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors