Rice(Oryza sativa) is a major crop that feeds billions of people, and its yield is strongly influenced by flowering time(heading date). Loss of RICE INDETERMINATE1(RID1) function causes plants not to flower;thus, RID1...Rice(Oryza sativa) is a major crop that feeds billions of people, and its yield is strongly influenced by flowering time(heading date). Loss of RICE INDETERMINATE1(RID1) function causes plants not to flower;thus, RID1 is considered a master switch among flowering-related genes. However, it remains unclear whether other proteins function together with RID1 to regulate rice floral transition.Here, we revealed that the chromatin accessibilityand H3 K9 ac, H3 K4 me3, and H3 K36 me3 levels at Heading date 3 a(Hd3 a) and RICE FLOWERING LOCUS T1(RFT1) loci were significantly reduced in rid1 mutants. Notably, RID1 interacted with SET DOMAIN GROUP PROTEIN 722(SDG722), a methyltransferase. We determined that SDG722 affects the global level of H3 K4 me2/3 and H3 K36 me2/3, and promotes flowering primarily through the Early heading date1-Hd3 a/RFT1 pathway. We further established that rice DELLA protein SLENDER RICE1(SLR1) interacted with RID1 to inhibit its transactivation activity, that SLR1 suppresses rice flowering, and that messenger RNA and protein levels of SLR1 gradually decrease with plant growth. Furthermore, SLR1 competed with SDG722 for interaction with RID1. Overall, our results establish that interplay between RID1, SLR1, and SDG722 feeds into rice flowering-time control.展开更多
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 large...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 unclear.Here,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 genome-wide.RID1 binding peaks were highly enriched for TTTGTC,the direct binding motif of the INDETERMINATE DOMAIN protein family that includes RID1.Interestingly,CACGTG and GTGGGCCC,two previously uncharacterized indirect binding motifs,were enriched through the interactions of RID1 with the novel floweringpromoting proteins OsPIL12 and OsTCP11,respectively.Moreover,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 pathways.Genetic 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 expression.Overall,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.展开更多
基金funded by the National Natural Science Foundation of China(32070855 and 31821005)the National Key Research and Development Program of China(2016YFD0100903)。
文摘Rice(Oryza sativa) is a major crop that feeds billions of people, and its yield is strongly influenced by flowering time(heading date). Loss of RICE INDETERMINATE1(RID1) function causes plants not to flower;thus, RID1 is considered a master switch among flowering-related genes. However, it remains unclear whether other proteins function together with RID1 to regulate rice floral transition.Here, we revealed that the chromatin accessibilityand H3 K9 ac, H3 K4 me3, and H3 K36 me3 levels at Heading date 3 a(Hd3 a) and RICE FLOWERING LOCUS T1(RFT1) loci were significantly reduced in rid1 mutants. Notably, RID1 interacted with SET DOMAIN GROUP PROTEIN 722(SDG722), a methyltransferase. We determined that SDG722 affects the global level of H3 K4 me2/3 and H3 K36 me2/3, and promotes flowering primarily through the Early heading date1-Hd3 a/RFT1 pathway. We further established that rice DELLA protein SLENDER RICE1(SLR1) interacted with RID1 to inhibit its transactivation activity, that SLR1 suppresses rice flowering, and that messenger RNA and protein levels of SLR1 gradually decrease with plant growth. Furthermore, SLR1 competed with SDG722 for interaction with RID1. Overall, our results establish that interplay between RID1, SLR1, and SDG722 feeds into rice flowering-time control.
基金supported by the National Natural Science Foundation of China(32070855,31821005)the Foundation of Hubei Hongshan Laboratory(2021hszd010)。
文摘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 unclear.Here,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 genome-wide.RID1 binding peaks were highly enriched for TTTGTC,the direct binding motif of the INDETERMINATE DOMAIN protein family that includes RID1.Interestingly,CACGTG and GTGGGCCC,two previously uncharacterized indirect binding motifs,were enriched through the interactions of RID1 with the novel floweringpromoting proteins OsPIL12 and OsTCP11,respectively.Moreover,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 pathways.Genetic 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 expression.Overall,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.
