Fig. 4

Notable lncRNAs include multi-exonic and telomere-associated transcripts. (A)/(B) Multi-exonic antisense transcripts span an apicoplast RNA methyltransferase precursor [PlasmoDB:Pf3D7_0218300] and an ETRAMP [PlasmoDB:Pf3D7_0936100] gene, respectively. Annotated gene models are shown in dark green and dark blue, and assembled transcript models are shown in light green and light blue. Reads from each 56-hour time course sample mapping to the (−) strand are shown below each horizontal axis in light green, while reads mapping to the (+) strand are shown above each horizontal axis in light blue. Intron reads are shown in purple. Uniqueness of 100mers is plotted in red as a mappability track. (C)/(D) Pearson correlation between the Pf3D7_0218300 sense-antisense pair and ETRAMP sense-antisense pair during the 56-hour time course was 0.20 and −0.50, respectively. Notably, Pf3D7_0218300 and ETRAMP antisense transcript levels dropped during parasite invasion, while sense transcript levels did not. Expression is plotted in units of log2(FPKM + 1). (E) Multi-exonic lncRNAs are encoded in the PfGDV1 region on chromosome nine, antisense to PfGDV1 and between PfGDV1 and GEXP22. Refer to (A)/(B) for a description of tracks. (F)/(G) Pearson correlation between the PfGDV1 sense-antisense pair was 0.96, while Pearson correlation between the divergent intergenic lncRNA and GEXP22 pair was 0.46 during the 56-hour time course. Expression is plotted in units of log2(FPKM + 1). (H) As we have previously described, the telomere-associated repetitive element (TARE) 2–3 region transcribes a family of lncRNA-TAREs, with transcription always proceeding towards the telomere [41]. For example, lncRNA-TARE-2 L is transcribed on the left arm of chromosome two. Pf3D7_0200100 is a subtelomeric upsB-type PfEMP1-encoding var gene. Boundaries of the telomere, TAREs 1–5, and Rep20 are shown in purple. See (A)/(B) for a further description of tracks. (I) Plotting the expression level of 22 lncRNA-TARE family members showed that lncRNA-TARE expression was co-regulated, with maximal firing coinciding with parasite invasion. Expression is plotted in units of log2(FPKM + 1). (J) Pearson correlation between lncRNA-TARE-2 L and the neighboring PfEMP1-encoding var gene was −0.09 during the 56-hour time course. Expression is plotted in units of log2(FPKM + 1)