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Volumn 113, Issue 4, 2014, Pages 1269-1281

Genome-wide identification and functional annotation of Plasmodium falciparum long noncoding RNAs from RNA-seq data

Author keywords

[No Author keywords available]

Indexed keywords

LONG UNTRANSLATED RNA;

EID: 84897023778     PISSN: 09320113     EISSN: 14321955     Source Type: Journal    
DOI: 10.1007/s00436-014-3765-4     Document Type: Article
Times cited : (38)

References (56)
  • 1
    • 38549101265 scopus 로고    scopus 로고
    • The profile of IgG-antibody response against merozoite surface proteins 1 and 2 in severe Plasmodium falciparum malaria in Eastern Sudan
    • doi:10.1007/s00436-007-0777-3
    • A-Elgadir TME, Elbashir MI, Berzins K, Masuadi EM, A-Elbasit IE, ElGhazali G, Giha HA (2008) The profile of IgG-antibody response against merozoite surface proteins 1 and 2 in severe Plasmodium falciparum malaria in Eastern Sudan. Parasitol Res 102(3):401-409. doi:10.1007/s00436-007-0777-3
    • (2008) Parasitol Res , vol.102 , Issue.3 , pp. 401-409
    • A-Elgadir, T.M.E.1    Elbashir, M.I.2    Berzins, K.3    Masuadi, E.M.4    A-Elbasit, I.E.5    ElGhazali, G.6    Giha, H.A.7
  • 2
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • doi:10.1016/S0022-2836(05)80360-2
    • Altschul SF, GishW, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403-410. doi:10.1016/S0022-2836(05) 80360-2
    • (1990) J Mol Biol , vol.215 , Issue.3 , pp. 403-410
    • Altschul, S.F.1    Gish, W.2    Miller, W.3    Myers, E.W.4    Lipman, D.J.5
  • 5
    • 70350238646 scopus 로고    scopus 로고
    • In vitro selection of RNA aptamers against a conserved region of the Plasmodium falciparum erythrocyte membrane protein 1
    • doi:10.1007/s00436-009-1583-x
    • Barfod A, Persson T, Lindh J (2009) In vitro selection of RNA aptamers against a conserved region of the Plasmodium falciparum erythrocyte membrane protein 1. Parasitol Res 105(6):1557-1566. doi:10.1007/s00436-009-1583-x
    • (2009) Parasitol Res , vol.105 , Issue.6 , pp. 1557-1566
    • Barfod, A.1    Persson, T.2    Lindh, J.3
  • 6
    • 58549099716 scopus 로고    scopus 로고
    • Reticulocyte-binding protein homologue 5-an essential adhesin involved in invasion of human erythrocytes by Plasmodium falciparum
    • doi:10.1016/j.ijpara.2008.10.006
    • Baum J, Chen L, Healer J, Lopaticki S, Boyle M, Triglia T, Ehlgen F, Ralph SA, Beeson JG, Cowman AF (2009) Reticulocyte-binding protein homologue 5-an essential adhesin involved in invasion of human erythrocytes by Plasmodium falciparum. Int J Parasitol 39(3):371-380. doi:10.1016/j.ijpara.2008.10.006
    • (2009) Int J Parasitol , vol.39 , Issue.3 , pp. 371-380
    • Baum, J.1    Chen, L.2    Healer, J.3    Lopaticki, S.4    Boyle, M.5    Triglia, T.6    Ehlgen, F.7    Ralph, S.A.8    Beeson, J.G.9    Cowman, A.F.10
  • 7
    • 46449118316 scopus 로고    scopus 로고
    • Plasmodium falciparum STEVOR proteins are highly expressed in patient isolates and located in the surface membranes of infected red blood cells and the apical tips of merozoites
    • doi:10.1128/IAI.01460-07
    • Blythe JE, Yam XY, Kuss C, Bozdech Z, Holder AA, Marsh K, Langhorne J, Preiser PR (2008) Plasmodium falciparum STEVOR proteins are highly expressed in patient isolates and located in the surface membranes of infected red blood cells and the apical tips of merozoites. Infect Immun 76(7):3329 - 3336. doi:10.1128/IAI.01460-07
    • (2008) Infect Immun , vol.76 , Issue.7 , pp. 3329-3336
    • Blythe, J.E.1    Yam, X.Y.2    Kuss, C.3    Bozdech, Z.4    Holder, A.A.5    Marsh, K.6    Langhorne, J.7    Preiser, P.R.8
  • 9
    • 80052978224 scopus 로고    scopus 로고
    • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    • doi:10.1101/gad.17446611
    • CabiliMN, Trapnell C, Goff L, KoziolM, Tazon-Vega B, Regev A, Rinn JL (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25(18):1915-1927. doi:10.1101/gad.17446611
    • (2011) Genes Dev , vol.25 , Issue.18 , pp. 1915-1927
    • Cabili, M.N.1    Trapnell, C.2    Goff, L.3    Koziol, M.4    Tazon-Vega, B.5    Regev, A.6    Rinn, J.L.7
  • 11
    • 35548994539 scopus 로고    scopus 로고
    • Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis
    • DOI 10.1261/rna.751807
    • Chakrabarti K, PearsonM, Grate L, Sterne-Weiler T, Deans J, Donohue JP, Ares M Jr (2007) Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis. RNA 13(11):1923-1939. doi:10.1261/rna.751807 (Pubitemid 350005218)
    • (2007) RNA , vol.13 , Issue.11 , pp. 1923-1939
    • Chakrabarti, K.1    Pearson, M.2    Grate, L.3    Sterne-Weiler, T.4    Deans, J.5    Donohue, J.P.6    Ares Jr., M.7
  • 12
    • 0035191853 scopus 로고    scopus 로고
    • The malaria-infected red blood cell: Structural and functional changes
    • DOI 10.1016/S0065-308X(01)50029-9
    • Cooke BM, Mohandas N, Coppel RL (2001) The malaria-infected red blood cell: structural and functional changes. Adv Parasitol 50:1-86 (Pubitemid 33086301)
    • (2001) Advances in Parasitology , vol.50 , pp. 1-86
    • Cooke, B.M.1    Mohandas, N.2    Coppel, R.L.3
  • 13
    • 80052317455 scopus 로고    scopus 로고
    • Merozoite release from Plasmodium falciparum-infected erythrocytes involves the transfer of DiIC(1)(6) from infected cell membrane to Maurer's clefts
    • doi:10.1007/s00436-011-2314-7
    • Cortes GT, Caldas ML, Rahirant SJ (2011) Merozoite release from Plasmodium falciparum-infected erythrocytes involves the transfer of DiIC(1)(6) from infected cell membrane to Maurer's clefts. Parasitol Res 109(3):941-947. doi:10.1007/s00436-011-2314-7
    • (2011) Parasitol Res , vol.109 , Issue.3 , pp. 941-947
    • Cortes, G.T.1    Caldas, M.L.2    Rahirant, S.J.3
  • 14
    • 33645510456 scopus 로고    scopus 로고
    • Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale
    • doi:10.1101/gr.4573206
    • Date SV, Stoeckert CJ Jr (2006) Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale. Genome Res 16(4):542-549. doi:10.1101/gr.4573206
    • (2006) Genome Res , vol.16 , Issue.4 , pp. 542-549
    • Date, S.V.1    Stoeckert Jr., C.J.2
  • 15
    • 34548588252 scopus 로고    scopus 로고
    • Epidemiology, pathophysiology, management and outcome of renal dysfunction associated with plasmodia infection
    • DOI 10.1007/s00436-007-0650-4
    • Elsheikha HM, Sheashaa HA (2007) Epidemiology, pathophysiology, management and outcome of renal dysfunction associated with plasmodia infection. Parasitol Res 101(5):1183-1190. doi:10.1007/s00436-007-0650-4 (Pubitemid 47389447)
    • (2007) Parasitology Research , vol.101 , Issue.5 , pp. 1183-1190
    • Elsheikha, H.M.1    Sheashaa, H.A.2
  • 16
    • 58149089272 scopus 로고    scopus 로고
    • Chromatin associated sense and antisense noncoding RNAs are transcribed from the var gene family of virulence genes of the malaria parasite Plasmodium falciparum
    • doi:10.1261/rna.1080109
    • Epp C, Li F, Howitt CA, Chookajorn T, Deitsch KW (2009) Chromatin associated sense and antisense noncoding RNAs are transcribed from the var gene family of virulence genes of the malaria parasite Plasmodium falciparum. RNA 15(1):116-127. doi:10.1261/rna.1080109
    • (2009) RNA , vol.15 , Issue.1 , pp. 116-127
    • Epp, C.1    Li, F.2    Howitt, C.A.3    Chookajorn, T.4    Deitsch, K.W.5
  • 22
    • 84870880579 scopus 로고    scopus 로고
    • De novo reconstruction of the Toxoplasma gondii transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs
    • doi:10.1186/1471-2164-13-696
    • Hassan MA, Melo MB, Haas B, Jensen KD, Saeij JP (2012) De novo reconstruction of the Toxoplasma gondii transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs. BMC Genomics 13:696. doi:10.1186/1471-2164-13-696
    • (2012) BMC Genomics , vol.13 , pp. 696
    • Hassan, M.A.1    Melo, M.B.2    Haas, B.3    Jensen, K.D.4    Saeij, J.P.5
  • 23
    • 0028000871 scopus 로고
    • Proteins on the surface of the malaria parasite and cell invasion
    • Holder AA (1994) Proteins on the surface of the malaria parasite and cell invasion. Parasitology 108(Suppl):S5-S18
    • (1994) Parasitology , vol.108 , Issue.SUPPL.
    • Holder, A.A.1
  • 24
    • 57349142137 scopus 로고    scopus 로고
    • Deletion of the Plasmodium falciparum merozoite surface protein 7 gene impairs parasite invasion of erythrocytes
    • doi:10.1128/EC.00274-08
    • Kadekoppala M, O'Donnell RA, Grainger M, Crabb BS, Holder AA (2008) Deletion of the Plasmodium falciparum merozoite surface protein 7 gene impairs parasite invasion of erythrocytes. Eukaryot Cell 7(12):2123-2132. doi:10.1128/EC.00274-08
    • (2008) Eukaryot Cell , vol.7 , Issue.12 , pp. 2123-2132
    • Kadekoppala, M.1    O'Donnell, R.A.2    Grainger, M.3    Crabb, B.S.4    Holder, A.A.5
  • 25
    • 0025898693 scopus 로고
    • Structure and possible function of Plasmodium falciparum proteins exported to the erythrocyte membrane
    • Knapp B, Hundt E, Lingelbach KR (1991) Structure and possible function of Plasmodium falciparum proteins exported to the erythrocyte membrane. Parasitol Res 77(4):277-282
    • (1991) Parasitol Res , vol.77 , Issue.4 , pp. 277-282
    • Knapp, B.1    Hundt, E.2    Lingelbach, K.R.3
  • 26
    • 34547582418 scopus 로고    scopus 로고
    • CPC: Assess the protein-coding potential of transcripts using sequence features and support vector machine
    • doi:10.1093/nar/gkm391
    • Kong L, Zhang Y, Ye ZQ, Liu XQ, Zhao SQ, Wei L, Gao G (2007) CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res 35(Web Server issue):W345-W349. doi:10.1093/nar/gkm391
    • (2007) Nucleic Acids Res , vol.35 , Issue.WEB SERVER ISSUE
    • Kong, L.1    Zhang, Y.2    Ye, Z.Q.3    Liu, X.Q.4    Zhao, S.Q.5    Wei, L.6    Gao, G.7
  • 28
    • 60549111634 scopus 로고    scopus 로고
    • WGCNA: An R package for weighted correlation network analysis
    • doi:10.1186/1471-2105-9-559
    • Langfelder P, Horvath S (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinforma 9:559. doi:10.1186/1471-2105-9-559
    • (2008) BMC Bioinforma , vol.9 , pp. 559
    • Langfelder, P.1    Horvath, S.2
  • 29
    • 41949113248 scopus 로고    scopus 로고
    • Nuclear non-coding RNAs are transcribed from the centromeres of Plasmodium falciparum and are associated with centromeric chromatin
    • doi:10.1074/jbc.M707344200
    • Li F, Sonbuchner L, Kyes SA, Epp C, Deitsch KW (2008) Nuclear non-coding RNAs are transcribed from the centromeres of Plasmodium falciparum and are associated with centromeric chromatin. J Biol Chem 283(9):5692-5698. doi:10.1074/jbc.M707344200
    • (2008) J Biol Chem , vol.283 , Issue.9 , pp. 5692-5698
    • Li, F.1    Sonbuchner, L.2    Kyes, S.A.3    Epp, C.4    Deitsch, K.W.5
  • 33
    • 84870566023 scopus 로고    scopus 로고
    • Long noncoding RNAs in C. Elegans
    • doi:10.1101/gr.140475.112
    • Nam JW, Bartel DP (2012) Long noncoding RNAs in C. elegans. Genome Res 22(12):2529-2540. doi:10.1101/gr.140475.112
    • (2012) Genome Res , vol.22 , Issue.12 , pp. 2529-2540
    • Nam, J.W.1    Bartel, D.P.2
  • 41
    • 0029974952 scopus 로고    scopus 로고
    • Plasmodium falciparum: Surface modifications of infected erythrocytes from clinical isolates. Evidence of antigenic diversity using Venezuelan human malarial sera
    • DOI 10.1007/s004360050151
    • Riggione F, Pulido M, Noya O (1996) Plasmodium falciparum: surface modifications of infected erythrocytes from clinical isolates. Evidence of antigenic diversity using Venezuelan human malarial sera. Parasitol Res 82(6):490-496 (Pubitemid 26228486)
    • (1996) Parasitology Research , vol.82 , Issue.6 , pp. 490-496
    • Riggione, F.1    Pulido, M.2    Noya, O.3
  • 42
    • 22244466784 scopus 로고    scopus 로고
    • Identifying Plasmodium falciparum merozoite surface antigen 3 (MSP3) protein peptides that bind specifically to erythrocytes and inhibit merozoite invasion
    • DOI 10.1110/ps.041304505
    • Rodriguez LE, Curtidor H, Ocampo M, Garcia J, Puentes A, Valbuena J, Vera R, Lopez R, Patarroyo ME (2005) Identifying Plasmodium falciparum merozoite surface antigen 3 (MSP3) protein peptides that bind specifically to erythrocytes and inhibit merozoite invasion. Protein Sci 14(7):1778-1786. doi:10.1110/ps.041304505 (Pubitemid 40994148)
    • (2005) Protein Science , vol.14 , Issue.7 , pp. 1778-1786
    • Rodriguez, L.E.1    Curtidor, H.2    Ocampo, M.3    Garcia, J.4    Puentes, A.5    Valbuena, J.6    Vera, R.7    Lopez, R.8    Patarroyo, M.E.9
  • 43
    • 0037045398 scopus 로고    scopus 로고
    • ORF-FINDER: A vector for high-throughput gene identification
    • DOI 10.1016/S0378-1119(01)00819-8, PII S0378111901008198
    • Rombel IT, Sykes KF, Rayner S, Johnston SA (2002) ORF-FINDER: a vector for high-throughput gene identification. Gene 282(1-2):33-41 (Pubitemid 34117559)
    • (2002) Gene , vol.282 , Issue.1-2 , pp. 33-41
    • Rombel, I.T.1    Sykes, K.F.2    Rayner, S.3    Johnston, S.A.4
  • 45
    • 66049140793 scopus 로고    scopus 로고
    • The role of the Maurer's clefts in protein transport in Plasmodium falciparum
    • doi:10.1016/j.pt.2009.03.009
    • Sam-Yellowe TY (2009) The role of the Maurer's clefts in protein transport in Plasmodium falciparum. Trends Parasitol 25(6):277-284. doi:10.1016/j.pt.2009.03.009
    • (2009) Trends Parasitol , vol.25 , Issue.6 , pp. 277-284
    • Sam-Yellowe, T.Y.1
  • 46
    • 84883755139 scopus 로고    scopus 로고
    • Long non-coding RNAs: A new frontier in the study of human diseases
    • doi:10.1016/j.canlet.2013.06.013
    • Shi X, Sun M, Liu H, Yao Y, Song Y (2013) Long non-coding RNAs: a new frontier in the study of human diseases. Cancer Lett 339(2):159-166. doi:10.1016/j.canlet.2013.06.013
    • (2013) Cancer Lett , vol.339 , Issue.2 , pp. 159-166
    • Shi, X.1    Sun, M.2    Liu, H.3    Yao, Y.4    Song, Y.5
  • 47
    • 9444252845 scopus 로고    scopus 로고
    • The surface of the Plasmodium falciparum-infected erythrocyte
    • Smith JD, Craig AG (2005) The surface of the Plasmodium falciparum-infected erythrocyte. Curr Issues Mol Biol 7(1):81-93
    • (2005) Curr Issues Mol Biol , vol.7 , Issue.1 , pp. 81-93
    • Smith, J.D.1    Craig, A.G.2
  • 48
    • 70149096866 scopus 로고    scopus 로고
    • Virulence and drug resistance in malaria parasites
    • doi:10.1016/j.pt.2009.07.003
    • SteinWD, Sanchez CP, LanzerM(2009)Virulence and drug resistance in malaria parasites. Trends Parasitol 25(10):441-443. doi:10.1016/j.pt.2009.07.003
    • (2009) Trends Parasitol , vol.25 , Issue.10 , pp. 441-443
    • Stein, W.D.1    Sanchez, C.P.2    Lanzer, M.3
  • 49
    • 0029070914 scopus 로고
    • The large diverse gene family var encodes proteins involved in cytoadherence and antigenic variation of Plasmodium falciparum-infected erythrocytes
    • Su XZ, Heatwole VM, Wertheimer SP, Guinet F, Herrfeldt JA, Peterson DS, Ravetch JA, Wellems TE (1995) The large diverse gene family var encodes proteins involved in cytoadherence and antigenic variation of Plasmodium falciparum-infected erythrocytes. Cell 82(1):89-100
    • (1995) Cell , vol.82 , Issue.1 , pp. 89-100
    • Su, X.Z.1    Heatwole, V.M.2    Wertheimer, S.P.3    Guinet, F.4    Herrfeldt, J.A.5    Peterson, D.S.6    Ravetch, J.A.7    Wellems, T.E.8
  • 51
    • 77955237447 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt) in 2010 doi:10.1093/nar/gkp846
    • The Universal Protein Resource (UniProt) in 2010 (2010) Nucleic Acids Res 38(Database issue):D142-D148. doi:10.1093/nar/gkp846
    • (2010) Nucleic Acids Res , vol.38 , Issue.DATABASE ISSUE
  • 52
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • doi:10. 1093/bioinformatics/btp120
    • Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9):1105-1111. doi:10. 1093/bioinformatics/btp120
    • (2009) Bioinformatics , vol.25 , Issue.9 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 53
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • doi:10.1038/nbt.1621
    • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28(5):511-515. doi:10.1038/nbt.1621
    • (2010) Nat Biotechnol , vol.28 , Issue.5 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5    Van Baren, M.J.6    Salzberg, S.L.7    Wold, B.J.8    Pachter, L.9
  • 54
    • 79952634861 scopus 로고    scopus 로고
    • Threonine peptidases as drug targets against malaria
    • doi:10.1517/14728222.2011.555399
    • Tschan S, Mordmuller B, Kun JF (2011) Threonine peptidases as drug targets against malaria. Expert Opin Ther Targets 15(4):365-378. doi:10.1517/14728222.2011.555399
    • (2011) Expert Opin Ther Targets , vol.15 , Issue.4 , pp. 365-378
    • Tschan, S.1    Mordmuller, B.2    Kun, J.F.3
  • 56
    • 67649671961 scopus 로고    scopus 로고
    • Long noncoding RNAs: Functional surprises from the RNA world
    • doi:10.1101/gad.1800909
    • Wilusz JE, Sunwoo H, Spector DL (2009) Long noncoding RNAs: functional surprises from the RNA world. Genes Dev 23(13):1494-1504. doi:10.1101/gad. 1800909
    • (2009) Genes Dev , vol.23 , Issue.13 , pp. 1494-1504
    • Wilusz, J.E.1    Sunwoo, H.2    Spector, D.L.3


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