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Encyclopedia of Malaria pp 1–17Cite as

RNA

  • Living reference work entry
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Synonyms

Antisense RNA (asRNA); Housekeeping RNA; Long noncoding RNA (lncRNA); Messenger RNA (mRNA); Micro RNA (miRNA); Noncoding RNA (ncRNA); Ribosomal RNA (rRNA); RNA-binding proteins (RBPs); RNA machines; RNAse P RNA; Spliceosomal RNAs (snRNAs); SRP RNA; Structural RNA; Telomerase RNA; Transcripts

Definition

RNA molecules are polymers of nucleotides with a ribose and phosphate backbone that can, like proteins, fold into three-dimensional structures to perform versatile function. In recent years, RNA has emerged as a central regulator of gene expression in both prokaryotes and eukaryotes. In malaria parasite of the genus Plasmodium, RNAs are synthesized from monocistronic transcription units by conserved eukaryotic homologs of RNA polymerases. In addition to protein-coding mRNAs, many different RNA species have been discovered in malaria parasites over the past decade, including the known homologs of the housekeeping eukaryotic RNAs such as ribosomal RNAs, spliceosomal RNAs,...

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References

  • Amaral PP, Dinger ME, Mercer TR, Mattick JS. The eukaryotic genome as an RNA machine. Science. 2008;319:1787–9.

    Article  CAS  PubMed  Google Scholar 

  • Amit-Avraham I, Pozner G, Eshar S, Fastman Y, Kolevzon N, Yavin E, Dzikowski R. Antisense long noncoding RNAs regulate var gene activation in the malaria parasite Plasmodium falciparum. Proc Natl Acad Sci U S A. 2015;112:E982–91.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Ares Jr M, Weiser B. Rearrangement of snRNA structure during assembly and function of the spliceosome. Prog Nucleic Acid Res Mol Biol. 1995;50:131–59.

    Article  CAS  PubMed  Google Scholar 

  • Aviran S, Trapnell C, Lucks JB, Mortimer SA, Luo S, Schroth GP, Doudna JA, Arkin AP, Pachter L. Modeling and automation of sequencing-based characterization of RNA structure. Proc Natl Acad Sci U S A. 2011;108:11069–74.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Azzalin CM, Reichenbach P, Khoriauli L, Giulotto E, Lingner J. Telomeric repeat containing RNA and RNA surveillance factors at mammalian chromosome ends. Science. 2007;318:798–801.

    Article  CAS  PubMed  Google Scholar 

  • Balaji S, Babu MM, Iyer LM, Aravind L. Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains. Nucleic Acids Res. 2005;33:3994–4006.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Baum J, Papenfuss AT, Mair GR, Janse CJ, Vlachou D, Waters AP, Cowman AF, Crabb BS, de Koning-Ward TF. Molecular genetics and comparative genomics reveal RNAi is not functional in malaria parasites. Nucleic Acids Res. 2009;37:3788–98.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Bawankar P, Shaw PJ, Sardana R, Babar PH, Patankar S. 5′ and 3′ end modifications of spliceosomal RNAs in Plasmodium falciparum. Mol Biol Rep. 2010;37:2125–33.

    Article  CAS  PubMed  Google Scholar 

  • Blackburn EH. Telomerases. Annu Rev Biochem. 1992;61:113–29.

    Article  CAS  PubMed  Google Scholar 

  • Bottius E, Bakhsis N, Scherf A. Plasmodium falciparum telomerase: de novo telomere addition to telomeric and nontelomeric sequences and role in chromosome healing. Mol Cell Biol. 1998;18:919–25.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL. The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol. 2003;1:E5.

    Article  PubMed Central  PubMed  Google Scholar 

  • Broadbent KM, Park D, Wolf AR, Van Tyne D, Sims JS, Ribacke U, Volkman S, Duraisingh M, Wirth D, Sabeti PC, et al. A global transcriptional analysis of Plasmodium falciparum malaria reveals a novel family of telomere-associated lncRNAs. Genome Biol. 2011;12:R56.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Broadbent KM, Broadbent JC, Ribacke U, Wirth D, Rinn JL, Sabeti PC. Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA. BMC Genomics. 2015;16:454.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Bunnik EM, Chung DW, Hamilton M, Ponts N, Saraf A, Prudhomme J, Florens L, Le Roch KG. Polysome profiling reveals translational control of gene expression in the human malaria parasite Plasmodium falciparum. Genome Biol. 2013;14:R128.

    Article  PubMed Central  PubMed  Google Scholar 

  • Caro F, Ahyong V, Betegon M, DeRisi JL. Genome-wide regulatory dynamics of translation in the asexual blood stages. eLife. 2014;3.

    Google Scholar 

  • Cech TR. Beginning to understand the end of the chromosome. Cell. 2004;116:273–9.

    Article  CAS  PubMed  Google Scholar 

  • Cech TR. The RNA worlds in context. Cold Spring Harb Perspect Biol. 2012;4:a006742.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP, Ares Jr M. Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis. RNA. 2007;13:1923–39.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Collins K. Forms and functions of telomerase RNA. In: Walter NG et al., editors. Non-protein coding RNAs. Berlin/Heidelberg: Springer; 2009.

    Google Scholar 

  • Coulson RM, Hall N, Ouzounis CA. Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum. Genome Res. 2004;14:1548–54.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Davila Lopez M, Rosenblad MA, Samuelsson T. Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of major and minor spliceosomal components. Nucleic Acids Res. 2008;36:3001–10.

    Article  PubMed  CAS  Google Scholar 

  • De Silva EK, Gehrke AR, Olszewski K, Leon I, Chahal JS, Bulyk ML, Llinas M. Specific DNA-binding by apicomplexan AP2 transcription factors. Proc Natl Acad Sci U S A. 2008;105:8393–8.

    Article  PubMed Central  PubMed  Google Scholar 

  • Dreesen O, Li B, Cross GA. Telomere structure and function in trypanosomes: a proposal. Nat Rev Microbiol. 2007;5:70–5.

    Article  CAS  PubMed  Google Scholar 

  • Epp C, Li F, Howitt CA, Chookajorn T, Deitsch KW. Chromatin associated sense and antisense noncoding RNAs are transcribed from the var gene family of virulence genes of the malaria parasite Plasmodium falciparum. RNA. 2009;15:116–27.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Eshar S, Altenhofen L, Rabner A, Ross P, Fastman Y, Mandel-Gutfreund Y, Karni R, Llinas M, Dzikowski R. PfSR1 controls alternative splicing and steady-state RNA levels in Plasmodium falciparum through preferential recognition of specific RNA motifs. Mol Microbiol. 2015;96:1283–97.

    Article  CAS  PubMed  Google Scholar 

  • Feagin JE, Harrell MI, Lee JC, Coe KJ, Sands BH, Cannone JJ, Tami G, Schnare MN, Gutell RR. The fragmented mitochondrial ribosomal RNAs of Plasmodium falciparum. PLoS One. 2012;7:e38320.

    Article  PubMed Central  PubMed  Google Scholar 

  • Figueiredo LM, Rocha EP, Mancio-Silva L, Prevost C, Hernandez-Verdun D, Scherf A. The unusually large Plasmodium telomerase reverse-transcriptase localizes in a discrete compartment associated with the nucleolus. Nucleic Acids Res. 2005;33:1111–22.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Filisetti D, Theobald-Dietrich A, Mahmoudi N, Rudinger-Thirion J, Candolfi E, Frugier M. Aminoacylation of Plasmodium falciparum tRNA(Asn) and insights in the synthesis of asparagine repeats. J Biol Chem. 2013;288:36361–71.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Fonager J, Cunningham D, Jarra W, Koernig S, Henneman AA, Langhorne J, Preiser P. Transcription and alternative splicing in the yir multigene family of the malaria parasite Plasmodium y. yoelii: identification of motifs suggesting epigenetic and post-transcriptional control of RNA expression. Mol Biochem Parasitol. 2007;156:1–11.

    Article  CAS  PubMed  Google Scholar 

  • Fouser LA, Friesen JD. Mutations in a yeast intron demonstrate the importance of specific conserved nucleotides for the two stages of nuclear mRNA splicing. Cell. 1986;45:81–93.

    Article  CAS  PubMed  Google Scholar 

  • Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature. 2002;419:498–511.

    Article  CAS  PubMed  Google Scholar 

  • Ghorbal M, Gorman M, Macpherson CR, Martins RM, Scherf A, Lopez-Rubio JJ. Genome editing in the human malaria parasite Plasmodium falciparum using the CRISPR-Cas9 system. Nat Biotechnol. 2014;32:819–21.

    Article  CAS  PubMed  Google Scholar 

  • Giovannini D, Spath S, Lacroix C, Perazzi A, Bargieri D, Lagal V, Lebugle C, Combe A, Thiberge S, Baldacci P, et al. Independent roles of apical membrane antigen 1 and rhoptry neck proteins during host cell invasion by apicomplexa. Cell Host Microbe. 2011;10:591–602.

    Article  CAS  PubMed  Google Scholar 

  • Golightly LM, Mbacham W, Daily J, Wirth DF. 3′ UTR elements enhance expression of Pgs28, an ookinete protein of Plasmodium gallinaceum. Mol Biochem Parasitol. 2000;105:61–70.

    Article  CAS  PubMed  Google Scholar 

  • Gong C, Maquat LE. Affinity purification of long noncoding RNA-protein complexes from formaldehyde cross-linked mammalian cells. Methods Mol Biol. 2015;1206:81–6.

    Article  PubMed  CAS  Google Scholar 

  • Gopalakrishnan AM, Nyindodo LA, Ross Fergus M, Lopez-Estrano C. Plasmodium falciparum: Preinitiation complex occupancy of active and inactive promoters during erythrocytic stage. Exp Parasitol. 2009;121:46–54.

    Article  CAS  PubMed  Google Scholar 

  • Greider CW. Telomerase is processive. Mol Cell Biol. 1991;11:4572–80.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Gunasekera AM, Patankar S, Schug J, Eisen G, Kissinger J, Roos D, Wirth DF. Widespread distribution of antisense transcripts in the Plasmodium falciparum genome. Mol Biochem Parasitol. 2004;136:35–42.

    Article  CAS  PubMed  Google Scholar 

  • Gunderson JH, Sogin ML, Wollett G, Hollingdale M, de la Cruz VF, Waters AP, McCutchan TF. Structurally distinct, stage-specific ribosomes occur in Plasmodium. Science. 1987;238:933–7.

    Article  CAS  PubMed  Google Scholar 

  • Haile S, Papadopoulou B. Developmental regulation of gene expression in trypanosomatid parasitic protozoa. Curr Opin Microbiol. 2007;10:569–77.

    Article  CAS  PubMed  Google Scholar 

  • Ho CK, Shuman S. A yeast-like mRNA capping apparatus in Plasmodium falciparum. Proc Natl Acad Sci U S A. 2001;98:3050–5.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Hossain M, Sharma S, Korde R, Kanodia S, Chugh M, Rawat K, Malhotra P. Organization of Plasmodium falciparum spliceosomal core complex and role of arginine methylation in its assembly. Malar J. 2013;12:333.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Hussain T, Yogavel M, Sharma A. Inhibition of protein synthesis and malaria parasite development by drug targeting of methionyl-tRNA synthetases. Antimicrob Agents Chemother. 2015;59:1856–67.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Iriko H, Jin L, Kaneko O, Takeo S, Han ET, Tachibana M, Otsuki H, Torii M, Tsuboi T. A small-scale systematic analysis of alternative splicing in Plasmodium falciparum. Parasitol Int. 2009;58:196–9.

    Article  CAS  PubMed  Google Scholar 

  • Jarrous N, Gopalan V. Archaeal/eukaryal RNase P: subunits, functions and RNA diversification. Nucleic Acids Res. 2010;38:7885–94.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kishore S, Stamm S. The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science. 2006;311:230–2.

    Article  CAS  PubMed  Google Scholar 

  • Kiss T. Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs. Embo J. 2001;20:3617–22.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Knapp B, Nau U, Hundt E, Kupper HA. Demonstration of alternative splicing of a pre-mRNA expressed in the blood stage form of Plasmodium falciparum. J Biol Chem. 1991;266:7148–54.

    CAS  PubMed  Google Scholar 

  • Le Roch KG, Zhou Y, Blair PL, Grainger M, Moch JK, Haynes JD, De La Vega P, Holder AA, Batalov S, Carucci DJ, et al. Discovery of gene function by expression profiling of the malaria parasite life cycle. Science. 2003;301:1503–8.

    Article  PubMed  Google Scholar 

  • Le Roch KG, Johnson JR, Florens L, Zhou Y, Santrosyan A, Grainger M, Yan SF, Williamson KC, Holder AA, Carucci DJ, et al. Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res. 2004;14:2308–18.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Lesser CF, Guthrie C. Mutations in U6 snRNA that alter splice site specificity: implications for the active site. Science. 1993;262:1982–8.

    Article  CAS  PubMed  Google Scholar 

  • Li J, Gutell RR, Damberger SH, Wirtz RA, Kissinger JC, Rogers MJ, Sattabongkot J, McCutchan TF. Regulation and trafficking of three distinct 18 S ribosomal RNAs during development of the malaria parasite. J Mol Biol. 1997;269:203–13.

    Article  CAS  PubMed  Google Scholar 

  • Li F, Sonbuchner L, Kyes SA, Epp C, Deitsch KW. Nuclear non-coding RNAs are transcribed from the centromeres of Plasmodium falciparum and are associated with centromeric chromatin. J Biol Chem. 2008;283:5692–8.

    Article  CAS  PubMed  Google Scholar 

  • Lopez-Barragan MJ, Lemieux J, Quinones M, Williamson KC, Molina-Cruz A, Cui K, Barillas-Mury C, Zhao K, Su XZ. Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum. BMC Genomics. 2011;12:587.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Lundblad EW, Altman S. Inhibition of gene expression by RNase P. N Biotechnol. 2010;27:212–21.

    Article  CAS  PubMed  Google Scholar 

  • Lunde BM, Moore C, Varani G. RNA-binding proteins: modular design for efficient function. Nat Rev Mol Cell Biol. 2007;8:479–90.

    Article  CAS  PubMed  Google Scholar 

  • Mair GR, Lasonder E, Garver LS, Franke-Fayard BM, Carret CK, Wiegant JC, Dirks RW, Dimopoulos G, Janse CJ, Waters AP. Universal features of post-transcriptional gene regulation are critical for Plasmodium zygote development. PLoS Pathog. 2010;6:e1000767.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Mancio-Silva L, Lopez-Rubio JJ, Claes A, Scherf A. Sir2a regulates rDNA transcription and multiplication rate in the human malaria parasite Plasmodium falciparum. Nat Commun. 2013;4:1530.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Mantel PY, Hoang AN, Goldowitz I, Potashnikova D, Hamza B, Vorobjev I, Ghiran I, Toner M, Irimia D, Ivanov AR, et al. Malaria-infected erythrocyte-derived microvesicles mediate cellular communication within the parasite population and with the host immune system. Cell Host Microbe. 2013;13:521–34.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • McCutchan TF. The ribosomal genes of Plasmodium. Int Rev Cytol. 1986;99:295–309.

    Article  CAS  PubMed  Google Scholar 

  • Mishra PC, Kumar A, Sharma A. Analysis of small nucleolar RNAs reveals unique genetic features in malaria parasites. BMC Genomics. 2009;10:68.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Mourier T, Carret C, Kyes S, Christodoulou Z, Gardner PP, Jeffares DC, Pinches R, Barrell B, Berriman M, Griffiths-Jones S, et al. Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum. Genome Res. 2008;18:281–92.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Mourier T, Pain A, Barrell B, Griffiths-Jones S. A selenocysteine tRNA and SECIS element in Plasmodium falciparum. RNA 2005;11:119–122.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Muhia DK, Swales CA, Eckstein-Ludwig U, Saran S, Polley SD, Kelly JM, Schaap P, Krishna S, Baker DA. Multiple splice variants encode a novel adenylyl cyclase of possible plastid origin expressed in the sexual stage of the malaria parasite Plasmodium falciparum. J Biol Chem. 2003;278:22014–22.

    Article  CAS  PubMed  Google Scholar 

  • Munding EM, Shiue L, Katzman S, Donohue JP, Ares Jr M. Competition between pre-mRNAs for the splicing machinery drives global regulation of splicing. Mol Cell. 2013;51:338–48.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Newman AJ, Norman C. U5 snRNA interacts with exon sequences at 5′ and 3′ splice sites. Cell. 1992;68:743–54.

    Article  CAS  PubMed  Google Scholar 

  • Novoa EM, Camacho N, Tor A, Wilkinson B, Moss S, Marin-Garcia P, Azcarate IG, Bautista JM, Mirando AC, Francklyn CS, et al. Analogs of natural aminoacyl-tRNA synthetase inhibitors clear malaria in vivo. Proc Natl Acad Sci U S A. 2014;111:E5508–17.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Oguariri RM, Dunn JM, Golightly LM. 3′ gene regulatory elements required for expression of the Plasmodium falciparum developmental protein, Pfs25. Mol Biochem Parasitol. 2006;146:163–72.

    Article  CAS  PubMed  Google Scholar 

  • Otto TD, Wilinski D, Assefa S, Keane TM, Sarry LR, Bohme U, Lemieux J, Barrell B, Pain A, Berriman M, et al. New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq. Mol Microbiol. 2010;76:12–24.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Painter HJ, Campbell TL, Llinas M. The Apicomplexan AP2 family: integral factors regulating Plasmodium development. Mol Biochem Parasitol. 2011;176:1–7.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Panchal M, Rawat K, Kumar G, Kibria KM, Singh S, Kalamuddin M, Mohmmed A, Malhotra P, Tuteja R. Plasmodium falciparum signal recognition particle components and anti-parasitic effect of ivermectin in blocking nucleo-cytoplasmic shuttling of SRP. Cell Death Dis. 2014;5:e994.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Patankar S, Munasinghe A, Shoaibi A, Cummings LM, Wirth DF. Serial analysis of gene expression in Plasmodium falciparum reveals the global expression profile of erythrocytic stages and the presence of anti-sense transcripts in the malarial parasite. Mol Biol Cell. 2001;12:3114–25.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Perriman RJ, Ares Jr M. Rearrangement of competing U2 RNA helices within the spliceosome promotes multiple steps in splicing. Genes Dev. 2007;21:811–20.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Pham JS, Sakaguchi R, Yeoh LM, De Silva NS, McFadden GI, Hou YM, Ralph SA. A dual-targeted aminoacyl-tRNA synthetase in Plasmodium falciparum charges cytosolic and apicoplast tRNACys. Biochem J. 2014;458:513–23.

    Article  CAS  PubMed  Google Scholar 

  • Piccinelli P, Rosenblad MA, Samuelsson T. Identification and analysis of ribonuclease P and MRP RNA in a broad range of eukaryotes. Nucleic Acids Res. 2005;33:4485–95.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Podlevsky JD, Chen JJ. It all comes together at the ends: telomerase structure, function, and biogenesis. Mutat Res. 2012;730:3–11.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Preiser P, Renia L, Singh N, Balu B, Jarra W, Voza T, Kaneko O, Blair P, Torii M, Landau I, et al. Antibodies against MAEBL ligand domains M1 and M2 inhibit sporozoite development in vitro. Infect Immun. 2004;72:3604–8.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Raabe CA, Sanchez CP, Randau G, Robeck T, Skryabin BV, Chinni SV, Kube M, Reinhardt R, Ng GH, Manickam R, et al. A global view of the nonprotein-coding transcriptome in Plasmodium falciparum. Nucleic Acids Res. 2010;38:608–17.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Rai R, Zhu L, Chen H, Gupta AP, Sze SK, Zheng J, Ruedl C, Bozdech Z, Featherstone M. Genome-wide analysis in Plasmodium falciparum reveals early and late phases of RNA polymerase II occupancy during the infectious cycle. BMC Genomics. 2014;15:959.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Regev-Rudzki N, Wilson DW, Carvalho TG, Sisquella X, Coleman BM, Rug M, Bursac D, Angrisano F, Gee M, Hill AF, et al. Cell-cell communication between malaria-infected red blood cells via exosome-like vesicles. Cell. 2013;153:1120–33.

    Article  CAS  PubMed  Google Scholar 

  • Religa AA, Ramesar J, Janse CJ, Scherf A, Waters AP. P. berghei telomerase subunit TERT is essential for parasite survival. PLoS One. 2014;9:e108930.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Rosenblad MA, Zwieb C, Samuelsson T. Identification and comparative analysis of components from the signal recognition particle in protozoa and fungi. BMC Genomics. 2004;5:5.

    Article  PubMed Central  PubMed  Google Scholar 

  • Sandhu R, Sanford S, Basu S, Park M, Pandya UM, Li B, Chakrabarti K. A trans-spliced telomerase RNA dictates telomere synthesis in Trypanosoma brucei. Cell Res. 2013;23:537–51.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Sawhney B, Chopra K, Misra R, Ranjan A. Identification of Plasmodium falciparum apicoplast-targeted tRNA-guanine transglycosylase and its potential inhibitors using comparative genomics, molecular modelling, docking and simulation studies. J Biomol Struct Dyn. 2015;33:1–17.

    Google Scholar 

  • Schwentke A, Krepstakies M, Mueller AK, Hammerschmidt-Kamper C, Motaal BA, Bernhard T, Hauber J, Kaiser A. In vitro and in vivo silencing of plasmodial dhs and eIf-5a genes in a putative, non-canonical RNAi-related pathway. BMC Microbiol. 2012;12:107.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Shankar J, Pradhan A, Tuteja R. Isolation and characterization of Plasmodium falciparum UAP56 homolog: evidence for the coupling of RNA binding and splicing activity by site-directed mutations. Arch Biochem Biophys. 2008;478:143–53.

    Article  CAS  PubMed  Google Scholar 

  • Shaw PJ, Ponmee N, Karoonuthaisiri N, Kamchonwongpaisan S, Yuthavong Y. Characterization of human malaria parasite Plasmodium falciparum eIF4E homologue and mRNA 5′ cap status. Mol Biochem Parasitol. 2007;155:146–55.

    Google Scholar 

  • Shock JL, Fischer KF, DeRisi JL. Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle. Genome Biol. 2007;8:R134.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Siegel TN, Hon CC, Zhang Q, Lopez-Rubio JJ, Scheidig-Benatar C, Martins RM, Sismeiro O, Coppee JY, Scherf A. Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum. BMC Genomics. 2014;15:150.

    Article  PubMed Central  PubMed  Google Scholar 

  • Sierra-Miranda M, Delgadillo DM, Mancio-Silva L, Vargas M, Villegas-Sepulveda N, Martinez-Calvillo S, Scherf A, Hernandez-Rivas R. Two long non-coding RNAs generated from subtelomeric regions accumulate in a novel perinuclear compartment in Plasmodium falciparum. Mol Biochem Parasitol. 2012;185:36–47.

    Article  CAS  PubMed  Google Scholar 

  • Sims JS, Militello KT, Sims PA, Patel VP, Kasper JM, Wirth DF. Patterns of gene-specific and total transcriptional activity during the Plasmodium falciparum intraerythrocytic developmental cycle. Eukaryot Cell. 2009;8:327–38.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Singh N, Preiser P, Renia L, Balu B, Barnwell J, Blair P, Jarra W, Voza T, Landau I, Adams JH. Conservation and developmental control of alternative splicing in maebl among malaria parasites. J Mol Biol. 2004;343:589–99.

    Article  CAS  PubMed  Google Scholar 

  • Singh PK, Kanodia S, Dandin CJ, Vijayraghavan U, Malhotra P. Plasmodium falciparum Prp16 homologue and its role in splicing. Biochim Biophys Acta. 2012;1819:1186–99.

    Article  CAS  PubMed  Google Scholar 

  • Sorber K, Dimon MT, DeRisi JL. RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts. Nucleic Acids Res. 2011;39:3820–35.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Staley JP, Guthrie C. Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell. 1998;92:315–26.

    Article  CAS  PubMed  Google Scholar 

  • Subudhi AK, Boopathi PA, Garg S, Middha S, Acharya J, Pakalapati D, Saxena V, Aiyaz M, Orekondy HB, Mugasimangalam RC, et al. Natural antisense transcripts in Plasmodium falciparum isolates from patients with complicated malaria. Exp Parasitol. 2014;141:39–54.

    Article  CAS  PubMed  Google Scholar 

  • Tuteja R. Unraveling the components of protein translocation pathway in human malaria parasite Plasmodium falciparum. Arch Biochem Biophys. 2007;467:249–60.

    Article  CAS  PubMed  Google Scholar 

  • Tuteja R, Mehta J. A genomic glance at the components of the mRNA export machinery in Plasmodium falciparum. Commun Integr Biol. 2010;3:318–26.

    Article  PubMed Central  PubMed  Google Scholar 

  • Upadhyay R, Bawankar P, Malhotra D, Patankar S. A screen for conserved sequences with biased base composition identifies noncoding RNAs in the A-T rich genome of Plasmodium falciparum. Mol Biochem Parasitol. 2005;144:149–58.

    Article  CAS  PubMed  Google Scholar 

  • Vaidya AB, Mather MW. Mitochondrial evolution and functions in malaria parasites. Annu Rev Microbiol. 2009;63:249–67.

    Article  CAS  PubMed  Google Scholar 

  • Velichutina IV, Rogers MJ, McCutchan TF, Liebman SW. Chimeric rRNAs containing the GTPase centers of the developmentally regulated ribosomal rRNAs of Plasmodium falciparum are functionally distinct. RNA. 1998;4:594–602.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Wagner JC, Platt RJ, Goldfless SJ, Zhang F, Niles JC. Efficient CRISPR-Cas9-mediated genome editing in Plasmodium falciparum. Nat Methods. 2014;11:915–8.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Watanabe J, Sasaki M, Suzuki Y, Sugano S. Analysis of transcriptomes of human malaria parasite Plasmodium falciparum using full-length enriched library: identification of novel genes and diverse transcription start sites of messenger RNAs. Gene. 2002;291:105–13.

    Article  CAS  PubMed  Google Scholar 

  • Wei C, Xiao T, Zhang P, Wang Z, Chen X, Zhang L, Yao M, Chen R, Wang H. Deep profiling of the novel intermediate-size noncoding RNAs in intraerythrocytic Plasmodium falciparum. PLoS One. 2014;9:e92946.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Wongsombat C, Aroonsri A, Kamchonwongpaisan S, Morgan HP, Walkinshaw MD, Yuthavong Y, Shaw PJ. Molecular characterization of Plasmodium falciparum Bruno/CELF RNA binding proteins. Mol Biochem Parasitol. 2014;198:1–10.

    Article  CAS  PubMed  Google Scholar 

  • Xie J, Zhang M, Zhou T, Hua X, Tang L, Wu W. Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs. Nucleic Acids Res. 2007;35:D183–7.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Xue X, Zhang Q, Huang Y, Feng L, Pan W. No miRNA were found in Plasmodium and the ones identified in erythrocytes could not be correlated with infection. Malar J. 2008;7:47.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Yang X, Figueiredo LM, Espinal A, Okubo E, Li B. RAP1 is essential for silencing telomeric variant surface glycoprotein genes in Trypanosoma brucei. Cell. 2009;137:99–109.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Yeoh S, O’Donnell RA, Koussis K, Dluzewski AR, Ansell KH, Osborne SA, Hackett F, Withers-Martinez C, Mitchell GH, Bannister LH, et al. Subcellular discharge of a serine protease mediates release of invasive malaria parasites from host erythrocytes. Cell. 2007;131:1072–83.

    Article  CAS  PubMed  Google Scholar 

  • Zhang Q, Siegel TN, Martins RM, Wang F, Cao J, Gao Q, Cheng X, Jiang L, Hon CC, Scheidig-Benatar C, et al. Exonuclease-mediated degradation of nascent RNA silences genes linked to severe malaria. Nature. 2014a;513:431–5.

    Article  CAS  PubMed  Google Scholar 

  • Zhang Y, Yang L, Chen LL. Life without A tail: new formats of long noncoding RNAs. Int J Biochem Cell Biol. 2014b;54:338–49.

    Article  CAS  PubMed  Google Scholar 

  • Zwieb C, van Nues RW, Rosenblad MA, Brown JD, Samuelsson T. A nomenclature for all signal recognition particle RNAs. RNA. 2005;11:7–13.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Department of Chemistry, Center for Nucleic Acid Science & Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA

    Kausik Chakrabarti

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  1. Kausik Chakrabarti
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Correspondence to Kausik Chakrabarti .

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  1. Heswall, United Kingdom

    Marcel Hommel

  2. Institut für Tropenmedizin, Universität Tübingen, Tübingen, Germany

    Peter G. Kremsner

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Chakrabarti, K. (2015). RNA. In: Hommel, M., Kremsner, P. (eds) Encyclopedia of Malaria. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-8757-9_53-1

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  • DOI: https://doi.org/10.1007/978-1-4614-8757-9_53-1

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