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Fig. 4 | Genome Biology

Fig. 4

From: Widespread occurrence of microRNA-mediated target cleavage on membrane-bound polysomes

Fig. 4

Widespread occurrence of miRNA-mediated target cleavage on membrane-bound polysomes in maize and rice. a, b Number (left panels) and overlap of identified miRNA target genes (right panels) in input (Total), TP, and MBP samples from maize immature tassels (a) and rice immature panicles (b). Cleavage sites that are classified as category 0 with P value ≤ 0.05 in at least two biological repeats were filtered as miRNA target sites. Category 0 means that the 3′ cleavage fragments with the maximum read count (> 1) are mapped to only one indicated position on the transcript. In the left panels of (a) and (b), the number of miRNA target genes is displayed as mean ± standard deviation (SD) of three biological repeats, and comparisons between Total, TP, and MBP were performed by two-tailed unpaired t-test and P values are displayed above the corresponding comparisons. c PolyA RNA-seq read (top panel) and PARE 3′ cleavage fragment (bottom panel) coverage for Zm00001d018024, an identified MBP-unique target transcript cleaved by miR529-5p in Total, TP and MBP samples from maize immature tassels. d PolyA RNA-seq read (top panel) and PARE 3′ cleavage fragment (bottom panel) coverage for LOC_Os06g03920, an identified MBP-unique target transcript cleaved by miR396c-5p, in Total, TP, and MBP samples from rice immature panicles. The gene models are shown below the RNA-seq panels, with the thicker rectangles, lines, and thinner rectangles representing exons, introns, and UTR regions, respectively. In the PARE panels, the red dots indicate the cleavage sites on the transcripts targeted by miRNAs. The sequences of the target sites and the miRNAs are shown below the PARE panels. “PARE” and “RPM” are short for “parallel analysis of RNA ends” and “reads per million mapped reads,” respectively

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