Genome-wide binding analysis of transcription factor Rice Indeterminate 1 reveals a complex network controlling rice floral transition

作     者：Shuo Zhang Li Deng Lun Zhao Changyin Wu Shuo Zhang;Li Deng;Lun Zhao;Changyin Wu

作者机构：National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research(Wuhan)Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan430070 China 

出 版 物：《Journal of Integrative Plant Biology》 (植物学报（英文版）)

年 卷 期：2022年第64卷第9期

页      面：1690-1705页

核心收录：

学科分类：09[农学] 0901[农学-作物学] 

基　　金：supported by the National Natural Science Foundation of China(32070855,31821005) the Foundation of Hubei Hongshan Laboratory(2021hszd010) 

主　　题：ChIP-seq floral transition OsERF#136 rice(Oryza sativa) RID1 RNA-seq 

摘      要：RICE INDETERMINATE 1(RID1)plays a critical role in controlling floral transition in rice(Oryza sativa).However,the molecular basis for this effect,particularly the target genes and regulatory specificity,remains largely ***,we performed chromatin immunoprecipitation followed by sequencing(ChIP-seq)in young leaves at the pre-floral-transition stage to identify the target genes of RID1,identifying 2,680 genes associated with RID1 binding sites ***1 binding peaks were highly enriched for TTTGTC,the direct binding motif of the INDETERMINATE DOMAIN protein family that includes ***,CACGTG and GTGGGCCC,two previously uncharacterized indirect binding motifs,were enriched through the interactions of RID1 with the novel floweringpromoting proteins OsPIL12 and OsTCP11,***,the ChIP-seq data demonstrated that RID1 bound to numerous rice heading-date genes,such as HEADING DATE1(HD1)and FLAVIN-BINDING,KELCH REPEAT,F-BOX 1(OsFKF1).Notably,transcriptome sequencing(RNA-seq)analysis revealed roles of RID1 in diverse developmental *** analysis combined with genome-wide ChIP-seq and RNA-seq results showed that RID1 directly binds to the promoter of OsERF#136(a repressor of rice flowering)and negatively regulates its ***,our findings provide new insights into the molecular and genetic mechanisms underlying rice floral transition and characterize OsERF#136 as a previously unrecognized direct target of RID1.