Table 1.

Nuclear proteins identified by affinity chromatography in both the TATA-stem loop and PE sequences of the antisense lncRNA

Cellular process	PlasmoDB ID	Annotation	Enrichment
			IntPE	TATA
DNA/RNA binding	PF3D7_0919000	Nucleosome assembly protein	*	*
	PF3D7_1006200	DNA/RNA-binding protein Alba 3	*	*
	PF3D7_1011800	PRE-binding protein	*	*
	PF3D7_1105100	Histone H2B	63-fold	55-fold
	PF3D7_1202900	High mobility group protein B1	*	*
	PF3D7_1224300	Polyadenylate-binding protein 1, putative	*	*
	PF3D7_1347500	DNA/RNA-binding protein Alba 4	*	*
	PF3D7_1426100	Transcription factor BTF3, putative	*	*
	PF3D7_1438900	Thioredoxin peroxidase 1	50-fold	42-fold
Metabolism	PF3D7_0513300	Purine nucleoside phosphorylase	*	*
	PF3D7_0608800	Ornithine aminotransferase	*	*
	PF3D7_0922500	Phosphoglycerate kinase	*	*
	PF3D7_1324900	L-lactate dehydrogenase	*	*
	PF3D7_1444800	Fructose-bisphosphate aldolase	*	*
	PF3D7_1462800	Glyceraldehyde-3-phosphate dehydrogenase	*	*
Translation	PF3D7_0309600	60S acidic ribosomal protein P2	*	*
	PF3D7_0517000	60S ribosomal protein L12, putative	*	*
	PF3D7_0913200	Elongation factor 1-β	*	*
	PF3D7_1357100	Elongation factor 1-α	22-fold	12-fold
	PF3D7_1451100	Elongation factor 2	*	*
Conserved unknown function	PF3D7_0721100	Conserved protein, unknown function	*	*
	PF3D7_0813300	Conserved protein, unknown function	*	*
	PF3D7_1115800	Conserved Plasmodium protein, unknown function	*	*
Other	PF3D7_0505800	Small ubiquitin-related modifier	*	*
	PF3D7_0826700	Receptor for activated c kinase	*	*
	PF3D7_1115600	Peptidyl-prolyl cis-trans isomerase	*	*
	PF3D7_1129100	Parasitophorous vacuolar protein 1	*	*
	PF3D7_1229400	Macrophage migration inhibitory factor	*	*

Proteins were grouped by function. The three proteins shaded in boldface were also identified using the dCHIRP methodology. A full list of proteins identified in each method can be found in SI Appendix, Tables S2, S3, S5, and S6. Asterisks (*) denotes proteins exclusively found in antisense specific versus control probes.