Figure 1

Global transcriptional profiling reveals 60 putative P. falciparum long non-coding RNAs under developmental regulation. (a) We identified 1,360 TARs along the P. falciparum genome, of which 1,229, 8, and 123 predicted transcripts exhibit overlap with known protein-coding genes, ribosomal RNA genes, and un-annotated intergenic regions, respectively. Further filtering of un-annotated transcripts for putative lncRNAs eliminated 46 putative small RNAs and 17 putative novel protein-coding genes or pseudogenes, leaving a set of 60 putative lncRNAs for additional characterization. (b,d) Protein-coding and putative lncRNA transcripts follow the global expression cascade expected during the P. falciparum intraerythrocytic developmental cycle. The mean log2 probe hybridization for each transcript is plotted from time-points T18, T24, T30, and T36 ± 3 hpi corresponding to the ring, ring/trophozoite, trophozoite, and trophozoite/schizont intraerythrocytic stages of parasite growth (pictured below each column). Rows are mean centered. (c,e) Housekeeping gene seryl-tRNA synthetase (PF07_0073), early stage marker (PFD0020c), and late stage marker (PFB0275w) exhibit expected differential expression patterns. Examples of putative lncRNAs are also shown, including lncRNA-TARE-4L (***). Positive probe hybridization intensities are plotted from each sample after quantile normalization, log2 transformation, and median centering.