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

Area of Science:

• Plant Molecular Biology
• Genetics
• Agricultural Science

Background:

• Floral transition in rice (Oryza sativa) is crucial for crop yield.
• The precise molecular mechanisms of RICE INDETERMINATE 1 (RID1) in regulating this process are not fully understood.

Purpose of the Study:

• To elucidate the molecular targets and regulatory network of RID1 in rice.
• To identify novel binding partners and downstream genes controlled by RID1.

Main Methods:

• Genome-wide chromatin immunoprecipitation followed by sequencing (ChIP-seq) to map RID1 binding sites.
• Transcriptome sequencing (RNA-seq) to analyze gene expression changes.
• Genetic analysis to validate regulatory relationships.

Main Results:

• RID1 binds to 2,680 genes, with enrichment of direct (TTTGTC) and novel indirect motifs (CACGTG, GTGGGCCC) via interactions with OsPIL12 and OsTCP11.
• RID1 directly targets key heading date genes including HEADING DATE 1 (HD1) and OsFKF1.
• RID1 directly represses the expression of OsERF#136, a negative regulator of flowering.

Conclusions:

• RID1 acts as a central regulator of rice floral transition through direct and indirect mechanisms.
• OsERF#136 is identified as a novel direct target of RID1, revealing a new layer of regulatory control.