Fig. 3

In trophozoite stages, a PfAlba1-Ty1 ribonucleoprotein complex interacts with 1665 transcripts. a Schematic representation of the RNA immunoprecipitation protocol. Native lysates prepared from PfAlba1-Ty1 parasites were incubated with rabbit anti-Ty1 antibodies in the presence of protease and RNAse inhibitors to immunoprecipitate (IP) a PfAlba1-Ty1-containing ribonucleoprotein complex. The IPed RNA molecules were identified by strand-specific RNA-seq. RNA IPed from empty vector parasites served as background binding. b Lysates (10 % of the input used for immunoprecipitation) or proteins IPed with anti-Ty1 antibodies from empty vector or PfAlba1-Ty1 transfectants were separated by denaturing gel electrophoresis and analyzed by western blotting with mouse anti-Ty1 antibodies or anti-PfAlba1 antibodies. PfAldolase served as a loading control. The contrasted image clearly shows the presence of PfAlba1 in the anti-PfAlba1-Ty1 co-IPed complex. c A Gaussian density kernel estimate of the distribution of gene ranks according to mRNA abundance of the 1665 transcripts that co-IPed with the PfAlba1-Ty1 complex. The y-axis represents relative density and the x-axis represents gene expression ranks, with 0 being least expressed. d Fourier phase distribution of the normalized RNA-seq data of the 1665 co-IPed transcripts. Top panel: P. falciparum IDC transcriptomic data were obtained from Bozdech et al. [6], where the authors provide a convenient metric, the Fourier phase, to define the hours post-infection (HPI) at which each gene is most abundantly transcribed. Bottom panel: a Gaussian density kernel estimate of the distribution of Fourier phase values of the 1665 transcripts that co-IPed with PfAlba1-Ty1 as sampled from Bozdech et al. [6]