title: Revealing natural antisense transcripts from Plasmodium vivax isolates: evidence of genome regulation in complicated malaria.
abstract: Plasmodium vivax is the most geographically widespread human malaria parasite causing approximately 130-435 million infections annually. It is an economic burden in many parts of the world and poses a public health challenge along with the other Plasmodium sp. The biology of this parasite is less studied and poorly understood, in spite of these facts. Emerging evidence of severe complications due to infections by this parasite provides an impetus to focus research on the same. Investigating the parasite directly from infected patients is the best way to study its biology and pathogenic mechanisms. Gene expression studies of this parasite directly obtained from the patients has provided evidence of gene regulation resulting in varying amount of transcript levels in the different blood stages. The mechanisms regulating gene expression in malaria parasites are not well understood. Discovery of Natural Antisense Transcripts (NATs) in Plasmodium falciparum has suggested that these might play an important role in regulating gene expression. We report here the genome-wide occurrence of NATs in P. vivax parasites from patients with differing clinical symptoms. A total of 1348 NATs against annotated gene loci have been detected using a custom designed microarray with strand specific probes. Majority of NATs identified from this study shows positive correlation with the expression pattern of the sense (S) transcript. Our data also shows condition specific expression patterns of varying S and antisense (AS) transcript levels. Genes with AS transcripts enrich to various biological processes. To our knowledge this is the first report on the presence of NATs from P. vivax obtained from infected patients with different disease complications. The data suggests differential regulation of gene expression in diverse clinical conditions, as shown by differing sense/antisense ratios and would lead to future detailed investigations of gene regulation.
authors.affiliation: Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India. Electronic address: boopathiarunachalam@gmail.com.
authors.forename: P A
authors.initials: PA
authors.lastname: Boopathi
authors.forename: Amit Kumar
authors.initials: AK
authors.lastname: Subudhi
authors.forename: Shilpi
authors.initials: S
authors.lastname: Garg
authors.forename: Sheetal
authors.initials: S
authors.lastname: Middha
authors.forename: Jyoti
authors.initials: J
authors.lastname: Acharya
authors.forename: Deepak
authors.initials: D
authors.lastname: Pakalapati
authors.forename: Vishal
authors.initials: V
authors.lastname: Saxena
authors.forename: Mohammed
authors.initials: M
authors.lastname: Aiyaz
authors.forename: Bipin
authors.initials: B
authors.lastname: Chand
authors.forename: Raja C
authors.initials: RC
authors.lastname: Mugasimangalam
authors.forename: Sanjay K
authors.initials: SK
authors.lastname: Kochar
authors.forename: Parmendra
authors.initials: P
authors.lastname: Sirohi
authors.forename: Dhanpat K
authors.initials: DK
authors.lastname: Kochar
authors.forename: Ashis
authors.initials: A
authors.lastname: Das
mesh_terms: D000293:Adolescent; D000328:Adult; D016375:Antisense Elements (Genetics) / Q000235:genetics*; D002874:Chromosome Mapping; D005260:Female; D005786:Gene Expression Regulation / Q000235:genetics*; D006801:Humans; D016780:Malaria, Vivax / Q000235:genetics* / Q000469:parasitology; D008297:Male; D010966:Plasmodium vivax / Q000235:genetics* / Q000302:isolation & purification; D016372:RNA, Antisense / Q000235:genetics*; D016053:RNA, Protozoan / Q000097:blood / Q000235:genetics; D014158:Transcription, Genetic; D055815:Young Adult
chemical_list: D016375:Antisense Elements (Genetics); D016372:RNA, Antisense; D016053:RNA, Protozoan
keywords: 1,3 BPG; 1,3-biphosphoglycerate; 2-Oxaloglutarate; 2-phophoglycerate; 2OG; 2PG; 3-phosphoglycerate; 3PG; 6-phophogluconate; 6-phosphoglucono-δ-lactone, 6PGNT, 6-phophogluconate; 6PGNL; 6PGNT; AC-COA; ACON-C; ASP; CIT; Complicated malaria; DHAP; DR1P; DR5P; E4P; F-6-P; F6P; FBP; FUM; G-6-P; G3P; GAP; GDP-4-oxo-6-deoxy-mannose; GDP-FUC; GDP-Fucose; GDP-L-fucose synthetase; GDP-MAN; GDP-Mannose; GDP-ODM; GLC; GLCN6P; GLCNAC1P; GLCNAC6P; GLN; GLU; GLYC; GLYC3P; ICT; Isocitrate; LAC; MAL; MAN; MAN1P; MAN6P; N-acetyl-glucosamime-6-phosphate; N-acetyl-glucosamine-1-phosphate; Natural antisense transcripts; OXA; PEP; PVX_001945; PVX_080515; PVX_091100; PVX_094915; PVX_099535; PVX_111455; PVX_118255; PVX_118495; PYR; Plasmodium vivax; R5P; RU5P; S7P; SUC; SUC-COA; Strand specific microarray; UDP-GLCNAC; UDP-N-acetyl-glucosamine. Gene coding for protein:PVX_114315, hexokinase, putative; Uncomplicated malaria; X5P; acetyl-CoA; aspartate; cis-aconitate; citrate; deoxyribose-1-phosphate; deoxyribose-5-phosphate; deoxyribose-phosphate aldolase; dihydroxy-acetone-phosphate; erythrose-4-phosphate; fructose 1,6-bis phosphate; fructose 1,6-bisphosphate aldolase; fructose-6-phosphate; fumarate; glucosamine-6-phosphate; glucosamine-fructose-6-phosphate aminotransferase; glucose; glucose-6-phosphate; glutamate; glutamine; glyceraldehyde 3-phosphate; glyceraldehyde-3-phophate; glycerol; glycerol-3-phosphate; lactate; malate; mannose; mannose-1-phosphate; mannose-6-phosphate; oxaloacetate; phosphoenolpyruvate; phosphoglycerate kinase; pyruvate; ribose 5-phosphate epimerase; ribose-5-phosphate; ribulose-5-phosphate; sedoheptulose-7-phosphate, F6P, fructose-6-phosphate; succinate; succinyl-COA; succinyl-CoA synthetase alpha subunit; triosephosphate isomerase; xylulose-5-phosphate, G3P, glyceraldehyde-3-phophate