Fig. 3

RNA-binding proteins interact with FLAG-BD. A Volcano plots of anti-FLAG immunoprecipitation followed by Mass Spectrometry (IP-MS) of four biological replicates (Rep1-4). The x-axis shows the log2 fold change between each FLAG-IP sample and the mock-IP control, and the y-axis depicts the p-value of Fisher exact test in a negative log scale. The gray shaded region represents the region of statistical significance (fold change ≥ 2, p ≤ 0.05), while the pink shaded region represents proteins that accumulated in the FLAG-IP but did not accumulate in the mock-IP, making their enrichment value infinite. The green point indicates the bait protein BRN1. Red points indicate the significantly enriched proteins. Blue points indicate the proteins significantly enriched in at least 2 of the 4 biological replicates. Gels of the IP protein sample before Mass Spectrometry are shown as Additional file 1: Figure S2. B Stacked bar graph showing the RNA-interaction annotation of the 20 proteins enriched in at least 2 of the 4 biological replicates from part (A ). These are compared to the annotation of the proteins identified in the mock-IP (FLAG-BD mock), the annotation of the entire Arabidopsis genome, or the genes annotated as expressed in rosette or cauline leaves. Bold indicates the percent of genes, with the total number of genes in parentheses. The hypergeometric test results are shown above each bar as fold enrichments (top number) and p-value in parentheses. C Table showing the 11 proteins previously designated as ‘RNA-binding’ enriched in at least 2 of the 4 FLAG-BD IPs from part (B ). The weighted spectral count (number of spectra associated with only a specific protein group plus the apportioned number of spectra shared with other proteins) is indicated for each protein. The total spectral count and total unique peptide count is listed below. Additional results from the IP-MS experiment are shown in Additional file 2: Table S1