RIP assays were implemented as previously described with some modifications [33]. Briefly, RNP complex in mature florets and leaves captured by formaldehyde crosslinking were ground in liquid nitrogen and the supernatant was incubated overnight at 4 °C with 10 μg eIF3h-antibody and further incubated with protein A/G Dynabeads for 2 h at 4 °C. The beads were washed with lysis buffer, high-salt buffer every two times after removing the supernatants. Suspend the beads in fresh elution buffer (50 mM Tris 8.0, 10 mM EDTA and 1% SDS). The RNA was purified with Trizol reagent (Life Technologies, Carlsbad, CA, USA). The cDNA libraries were prepared by the Illumina ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre, Charlotte, NC, USA), according to the manufacturer’s instructions. Finally, the libraries were applied to the Illumina HiSeq X Ten system for 150 nt paired-end sequencing. The seq data have been deposited into the NCBI Short Read Archive (SRA) under accession number PRJNA725322.

The data were analyzed in the pipeline with default settings except for customer parameters. Briefly, the Bowtie2 [39] was run to align the WT and mutant samples’ clean reads to the MUS7 rice reference file [40]. Piranha, a peak-calling tool based on the zero-truncated negative binomial regression model, was used for peak calling with default settings [41]. The parameter of bin size was set to 300 considering the computer configuration. Peaks were considered if FDR < 0.01 and stored in a bed-format file for subsequent annotation. Peaks annotation and plots were utilized in the R/Bioconductor ChIPSeeker package [42]. Gene ontology (GO) enrichment analysis of genes bearing RIP peaks was performed using agriGO online tools [43].

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