Fig. 3

Capturing the mRNA interactome of P. falciparum. a Schematic overview of the experimental procedure, described in detail in the Methods section. b Non-RNA-interacting protein histone H3 is not detected in the capture sample, indicating that the capture methodology results in depletion of proteins that do not interact with poly-adenylated RNA. c Depletion of 18S ribosomal RNA and enrichment of mRNA transcripts in the capture sample, indicating that our approach to capture of poly-adenylated RNA is successful. No RNA was detected in the RNase-digested sample. d Selection of most highly enriched GO terms among the 199 proteins that were captured in two or more experiments. The vertical dashed line indicates a p value of 0.01. e Fraction of candidate RBPs identified by HMM search that were experimentally captured in one, two, three, or four individual experiments. The numbers to the right of the chart indicate the number of proteins with an RBD out of the total number of proteins captured experimentally. f Overlap between the mRBPs identified by HMM search (n = 388) and RBPs captured in one or more experiment (n = 713). The overlap between these two groups of proteins was assessed using the hypergeometric test. g Fold enrichment of RNA-binding domains in captured proteins as compared to the full proteome. mRBDs that are enriched among the mRNA interactome are indicated in orange (p < 0.05, FDR <5 %, hypergeometric test), while non-enriched and depleted mRBDs are shown in blue. h Correlation in abundance between 199 proteins captured at the trophozoite and schizont stages. Proteins are color-coded according to the number of experiments in which they were detected: in two (green), three (magenta), or four (blue) experiments. Highly abundant proteins are encircled and are listed on the right. i Average normalized spectral abundance factor (dNSAF) values of proteins captured at the trophozoite and schizont stages. Proteins absent at a particular stage are indicated in dark blue. The bar on the right indicates the stage at which a higher enrichment of the protein was observed