메뉴 건너뛰기




Volumn 15, Issue 1, 2014, Pages

Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum

Author keywords

3 UTR; Antisense RNA; Directional RNA Seq; Genes; Natural antisense transcripts; ncRNA; Plasmodium falciparum; Polyadenylation sites

Indexed keywords

3' UNTRANSLATED REGION; ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; DEVELOPMENTAL STAGE; DNA LIBRARY; GENE; GENE CLUSTER; GENE EXPRESSION; GENE MAPPING; GENETIC CODE; GENOME; INTRAERYTHROCYTIC DEVELOPMENTAL CYCLE; PLASMODIUM FALCIPARUM; POLYADENYLATION; PROMOTER REGION; RNA SEQUENCE; RNA TRANSCRIPTION; TRANSCRIPTION REGULATION;

EID: 84899100823     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-150     Document Type: Article
Times cited : (81)

References (52)
  • 2
    • 4243071596 scopus 로고    scopus 로고
    • The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum
    • 176545, 12929205
    • 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. 176545, 12929205.
    • (2003) PLoS Biol , vol.1
    • Bozdech, Z.1    Llinas, M.2    Pulliam, B.L.3    Wong, E.D.4    Zhu, J.5    DeRisi, J.L.6
  • 6
    • 79956001876 scopus 로고    scopus 로고
    • RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts
    • 10.1093/nar/gkq1223, 3089446, 21245033
    • 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, 39:3820-3835. 10.1093/nar/gkq1223, 3089446, 21245033.
    • (2011) Nucleic Acids Res , vol.39 , pp. 3820-3835
    • Sorber, K.1    Dimon, M.T.2    Derisi, J.L.3
  • 10
    • 0034633626 scopus 로고    scopus 로고
    • Lineage-specific loss and divergence of functionally linked genes in eukaryotes
    • 10.1073/pnas.200346997, 17198, 11016957
    • Aravind L, Watanabe H, Lipman DJ, Koonin EV. Lineage-specific loss and divergence of functionally linked genes in eukaryotes. Proc Natl Acad Sci U S A 2000, 97:11319-11324. 10.1073/pnas.200346997, 17198, 11016957.
    • (2000) Proc Natl Acad Sci U S A , vol.97 , pp. 11319-11324
    • Aravind, L.1    Watanabe, H.2    Lipman, D.J.3    Koonin, E.V.4
  • 12
    • 36048951040 scopus 로고    scopus 로고
    • Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae
    • 10.1016/j.cell.2007.09.014, 18022365
    • Camblong J, Iglesias N, Fickentscher C, Dieppois G, Stutz F. Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae. Cell 2007, 131:706-717. 10.1016/j.cell.2007.09.014, 18022365.
    • (2007) Cell , vol.131 , pp. 706-717
    • Camblong, J.1    Iglesias, N.2    Fickentscher, C.3    Dieppois, G.4    Stutz, F.5
  • 13
    • 33750814968 scopus 로고    scopus 로고
    • Antisense transcription controls cell fate in Saccharomyces cerevisiae
    • 10.1016/j.cell.2006.09.038, 17110333
    • Hongay CF, Grisafi PL, Galitski T, Fink GR. Antisense transcription controls cell fate in Saccharomyces cerevisiae. Cell 2006, 127:735-745. 10.1016/j.cell.2006.09.038, 17110333.
    • (2006) Cell , vol.127 , pp. 735-745
    • Hongay, C.F.1    Grisafi, P.L.2    Galitski, T.3    Fink, G.R.4
  • 14
    • 69249217649 scopus 로고    scopus 로고
    • Regulatory roles of natural antisense transcripts
    • 10.1038/nrm2738, 2850559, 19638999
    • Faghihi MA, Wahlestedt C. Regulatory roles of natural antisense transcripts. Nat Rev Mol Cell Biol 2009, 10:637-643. 10.1038/nrm2738, 2850559, 19638999.
    • (2009) Nat Rev Mol Cell Biol , vol.10 , pp. 637-643
    • Faghihi, M.A.1    Wahlestedt, C.2
  • 15
    • 0035171634 scopus 로고    scopus 로고
    • 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
    • 10.1091/mbc.12.10.3114, 60160, 11598196
    • 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, 12:3114-3125. 10.1091/mbc.12.10.3114, 60160, 11598196.
    • (2001) Mol Biol Cell , vol.12 , pp. 3114-3125
    • Patankar, S.1    Munasinghe, A.2    Shoaibi, A.3    Cummings, L.M.4    Wirth, D.F.5
  • 20
    • 84865683734 scopus 로고    scopus 로고
    • Strand-specific RNA-seq applied to malaria samples
    • 10.1007/978-1-61779-839-9_4, 22589124
    • Ponts N, Chung DW, Le Roch KG. Strand-specific RNA-seq applied to malaria samples. Methods Mol Biol 2012, 883:59-73. 10.1007/978-1-61779-839-9_4, 22589124.
    • (2012) Methods Mol Biol , vol.883 , pp. 59-73
    • Ponts, N.1    Chung, D.W.2    Le Roch, K.G.3
  • 21
    • 2342452423 scopus 로고    scopus 로고
    • Widespread distribution of antisense transcripts in the Plasmodium falciparum genome
    • 10.1016/j.molbiopara.2004.02.007, 15138065
    • 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. 10.1016/j.molbiopara.2004.02.007, 15138065.
    • (2004) Mol Biochem Parasitol , vol.136 , pp. 35-42
    • Gunasekera, A.M.1    Patankar, S.2    Schug, J.3    Eisen, G.4    Kissinger, J.5    Roos, D.6    Wirth, D.F.7
  • 23
    • 36148972085 scopus 로고    scopus 로고
    • Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D
    • 10.1093/nar/gkm683, 2095812, 17897965
    • Perocchi F, Xu Z, Clauder-Munster S, Steinmetz LM. Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Res 2007, 35:e128. 10.1093/nar/gkm683, 2095812, 17897965.
    • (2007) Nucleic Acids Res , vol.35
    • Perocchi, F.1    Xu, Z.2    Clauder-Munster, S.3    Steinmetz, L.M.4
  • 25
    • 69949159297 scopus 로고    scopus 로고
    • Pervasive transcription constitutes a new level of eukaryotic genome regulation
    • 10.1038/embor.2009.181, 2750061, 19680288
    • Berretta J, Morillon A. Pervasive transcription constitutes a new level of eukaryotic genome regulation. EMBO Rep 2009, 10:973-982. 10.1038/embor.2009.181, 2750061, 19680288.
    • (2009) EMBO Rep , vol.10 , pp. 973-982
    • Berretta, J.1    Morillon, A.2
  • 26
    • 19444377759 scopus 로고    scopus 로고
    • Transcriptional interference-a crash course
    • 10.1016/j.tig.2005.04.009, 2941638, 15922833
    • Shearwin KE, Callen BP, Egan JB. Transcriptional interference-a crash course. Trends Genet 2005, 21:339-345. 10.1016/j.tig.2005.04.009, 2941638, 15922833.
    • (2005) Trends Genet , vol.21 , pp. 339-345
    • Shearwin, K.E.1    Callen, B.P.2    Egan, J.B.3
  • 27
    • 0037173089 scopus 로고    scopus 로고
    • Transcriptional collision between convergent genes in budding yeast
    • 10.1073/pnas.132270899, 124378, 12077310
    • Prescott EM, Proudfoot NJ. Transcriptional collision between convergent genes in budding yeast. Proc Natl Acad Sci U S A 2002, 99:8796-8801. 10.1073/pnas.132270899, 124378, 12077310.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 8796-8801
    • Prescott, E.M.1    Proudfoot, N.J.2
  • 28
    • 41949113248 scopus 로고    scopus 로고
    • Nuclear non-coding RNAs are transcribed from the centromeres of Plasmodium falciparum and are associated with centromeric chromatin
    • 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, 283:5692-5698.
    • (2008) J Biol Chem , vol.283 , pp. 5692-5698
    • Li, F.1    Sonbuchner, L.2    Kyes, S.A.3    Epp, C.4    Deitsch, K.W.5
  • 29
    • 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
    • 2612763, 19037012
    • 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, 15:116-127. 2612763, 19037012.
    • (2009) RNA , vol.15 , pp. 116-127
    • Epp, C.1    Li, F.2    Howitt, C.A.3    Chookajorn, T.4    Deitsch, K.W.5
  • 31
    • 2542618431 scopus 로고    scopus 로고
    • Natural antisense RNA inhibits the expression of BCMA, a tumour necrosis factor receptor homologue
    • 10.1186/1471-2199-3-4, 107798, 11960555
    • Hatzoglou A, Deshayes F, Madry C, Lapree G, Castanas E, Tsapis A. Natural antisense RNA inhibits the expression of BCMA, a tumour necrosis factor receptor homologue. BMC Mol Biol 2002, 3:4. 10.1186/1471-2199-3-4, 107798, 11960555.
    • (2002) BMC Mol Biol , vol.3 , pp. 4
    • Hatzoglou, A.1    Deshayes, F.2    Madry, C.3    Lapree, G.4    Castanas, E.5    Tsapis, A.6
  • 33
    • 42949137973 scopus 로고    scopus 로고
    • Identification of mRNA polyadenylation sites in genomes using cDNA sequences, expressed sequence tags, and trace
    • 10.1007/978-1-59745-033-1_2, 18369973
    • Lee JY, Park JY, Tian B. Identification of mRNA polyadenylation sites in genomes using cDNA sequences, expressed sequence tags, and trace. Methods Mol Biol 2008, 419:23-37. 10.1007/978-1-59745-033-1_2, 18369973.
    • (2008) Methods Mol Biol , vol.419 , pp. 23-37
    • Lee, J.Y.1    Park, J.Y.2    Tian, B.3
  • 34
    • 0035870688 scopus 로고    scopus 로고
    • Heterogeneity in polyadenylation cleavage sites in mammalian mRNA sequences: implications for SAGE analysis
    • 10.1093/nar/29.8.1690, 31324, 11292841
    • Pauws E, van Kampen AH, van de Graaf SA, de Vijlder JJ, Ris-Stalpers C. Heterogeneity in polyadenylation cleavage sites in mammalian mRNA sequences: implications for SAGE analysis. Nucleic Acids Res 2001, 29:1690-1694. 10.1093/nar/29.8.1690, 31324, 11292841.
    • (2001) Nucleic Acids Res , vol.29 , pp. 1690-1694
    • Pauws, E.1    van Kampen, A.H.2    van de Graaf, S.A.3    de Vijlder, J.J.4    Ris-Stalpers, C.5
  • 35
    • 78649910014 scopus 로고    scopus 로고
    • Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation
    • 10.1016/j.cell.2010.11.020, 3022516, 21145465
    • Ozsolak F, Kapranov P, Foissac S, Kim SW, Fishilevich E, Monaghan AP, John B, Milos PM. Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell 2010, 143:1018-1029. 10.1016/j.cell.2010.11.020, 3022516, 21145465.
    • (2010) Cell , vol.143 , pp. 1018-1029
    • Ozsolak, F.1    Kapranov, P.2    Foissac, S.3    Kim, S.W.4    Fishilevich, E.5    Monaghan, A.P.6    John, B.7    Milos, P.M.8
  • 36
    • 15444363650 scopus 로고    scopus 로고
    • RNA polymerase II synthesizes antisense RNA in Plasmodium falciparum
    • 10.1261/rna.7940705, 1370726, 15703443
    • Militello KT, Patel V, Chessler AD, Fisher JK, Kasper JM, Gunasekera A, Wirth DF. RNA polymerase II synthesizes antisense RNA in Plasmodium falciparum. RNA 2005, 11:365-370. 10.1261/rna.7940705, 1370726, 15703443.
    • (2005) RNA , vol.11 , pp. 365-370
    • Militello, K.T.1    Patel, V.2    Chessler, A.D.3    Fisher, J.K.4    Kasper, J.M.5    Gunasekera, A.6    Wirth, D.F.7
  • 37
    • 78249253329 scopus 로고    scopus 로고
    • HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data
    • 10.1371/journal.pone.0013875, 2975632, 21079731
    • Dimon MT, Sorber K, Derisi JL. HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data. PLoS One 2010, 5:e13875. 10.1371/journal.pone.0013875, 2975632, 21079731.
    • (2010) PLoS One , vol.5
    • Dimon, M.T.1    Sorber, K.2    Derisi, J.L.3
  • 39
    • 77955975125 scopus 로고    scopus 로고
    • Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species
    • 10.1186/gb-2010-11-8-r87, 2945789, 20796282
    • Yassour M, Pfiffner J, Levin JZ, Adiconis X, Gnirke A, Nusbaum C, Thompson DA, Friedman N, Regev A. Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species. Genome Biol 2010, 11:R87. 10.1186/gb-2010-11-8-r87, 2945789, 20796282.
    • (2010) Genome Biol , vol.11
    • Yassour, M.1    Pfiffner, J.2    Levin, J.Z.3    Adiconis, X.4    Gnirke, A.5    Nusbaum, C.6    Thompson, D.A.7    Friedman, N.8    Regev, A.9
  • 40
    • 0033828078 scopus 로고    scopus 로고
    • Inhibition of Plasmodium falciparum clag9 gene function by antisense RNA
    • 10.1016/S0166-6851(00)00254-1, 10989143
    • Gardiner DL, Holt DC, Thomas EA, Kemp DJ, Trenholme KR. Inhibition of Plasmodium falciparum clag9 gene function by antisense RNA. Mol Biochem Parasitol 2000, 110:33-41. 10.1016/S0166-6851(00)00254-1, 10989143.
    • (2000) Mol Biochem Parasitol , vol.110 , pp. 33-41
    • Gardiner, D.L.1    Holt, D.C.2    Thomas, E.A.3    Kemp, D.J.4    Trenholme, K.R.5
  • 41
    • 12344305405 scopus 로고    scopus 로고
    • PfMyb1, a Plasmodium falciparum transcription factor, is required for intra-erythrocytic growth and controls key genes for cell cycle regulation
    • 10.1016/j.jmb.2004.11.045, 15663925
    • Gissot M, Briquet S, Refour P, Boschet C, Vaquero C. PfMyb1, a Plasmodium falciparum transcription factor, is required for intra-erythrocytic growth and controls key genes for cell cycle regulation. J Mol Biol 2005, 346:29-42. 10.1016/j.jmb.2004.11.045, 15663925.
    • (2005) J Mol Biol , vol.346 , pp. 29-42
    • Gissot, M.1    Briquet, S.2    Refour, P.3    Boschet, C.4    Vaquero, C.5
  • 42
    • 0036155407 scopus 로고    scopus 로고
    • RNA interference (RNAi) inhibits growth of Plasmodium falciparum
    • 10.1016/S0166-6851(01)00429-7, 11814579
    • McRobert L, McConkey GA. RNA interference (RNAi) inhibits growth of Plasmodium falciparum. Mol Biochem Parasitol 2002, 119:273-278. 10.1016/S0166-6851(01)00429-7, 11814579.
    • (2002) Mol Biochem Parasitol , vol.119 , pp. 273-278
    • McRobert, L.1    McConkey, G.A.2
  • 43
    • 0036049784 scopus 로고    scopus 로고
    • Double-stranded RNA-mediated gene silencing of cysteine proteases (falcipain-1 and -2) of Plasmodium falciparum
    • 10.1046/j.1365-2958.2002.03105.x, 12207693
    • Malhotra P, Dasaradhi PV, Kumar A, Mohmmed A, Agrawal N, Bhatnagar RK, Chauhan VS. Double-stranded RNA-mediated gene silencing of cysteine proteases (falcipain-1 and -2) of Plasmodium falciparum. Mol Microbiol 2002, 45:1245-1254. 10.1046/j.1365-2958.2002.03105.x, 12207693.
    • (2002) Mol Microbiol , vol.45 , pp. 1245-1254
    • Malhotra, P.1    Dasaradhi, P.V.2    Kumar, A.3    Mohmmed, A.4    Agrawal, N.5    Bhatnagar, R.K.6    Chauhan, V.S.7
  • 44
    • 12744262429 scopus 로고    scopus 로고
    • Characterisation and expression of a PP1 serine/threonine protein phosphatase (PfPP1) from the malaria parasite. Plasmodium falciparum: demonstration of its essential role using RNA interference
    • 10.1186/1475-2875-1-5, 111503, 12057017
    • Kumar R, Adams B, Oldenburg A, Musiyenko A, Barik S. Characterisation and expression of a PP1 serine/threonine protein phosphatase (PfPP1) from the malaria parasite. Plasmodium falciparum: demonstration of its essential role using RNA interference. Malar J 2002, 1:5. 10.1186/1475-2875-1-5, 111503, 12057017.
    • (2002) Malar J , vol.1 , pp. 5
    • Kumar, R.1    Adams, B.2    Oldenburg, A.3    Musiyenko, A.4    Barik, S.5
  • 45
    • 33748793116 scopus 로고    scopus 로고
    • Analysis of short RNAs in the malaria parasite and its red blood cell host
    • 10.1016/j.febslet.2006.08.063, 16963026
    • Rathjen T, Nicol C, McConkey G, Dalmay T. Analysis of short RNAs in the malaria parasite and its red blood cell host. FEBS Lett 2006, 580:5185-5188. 10.1016/j.febslet.2006.08.063, 16963026.
    • (2006) FEBS Lett , vol.580 , pp. 5185-5188
    • Rathjen, T.1    Nicol, C.2    McConkey, G.3    Dalmay, T.4
  • 46
    • 69549135202 scopus 로고    scopus 로고
    • To localize or not to localize: mRNA fate is in 3′UTR ends
    • 10.1016/j.tcb.2009.06.001, 19716303
    • Andreassi C, Riccio A. To localize or not to localize: mRNA fate is in 3′UTR ends. Trends Cell Biol 2009, 19:465-474. 10.1016/j.tcb.2009.06.001, 19716303.
    • (2009) Trends Cell Biol , vol.19 , pp. 465-474
    • Andreassi, C.1    Riccio, A.2
  • 48
    • 0037124114 scopus 로고    scopus 로고
    • Plasmodium falciparum possesses a cell cycle-regulated short type replication protein A large subunit encoded by an unusual transcript
    • 10.1074/jbc.M200100200, 11880371
    • Voss TS, Mini T, Jenoe P, Beck HP. Plasmodium falciparum possesses a cell cycle-regulated short type replication protein A large subunit encoded by an unusual transcript. J Biol Chem 2002, 277:17493-17501. 10.1074/jbc.M200100200, 11880371.
    • (2002) J Biol Chem , vol.277 , pp. 17493-17501
    • Voss, T.S.1    Mini, T.2    Jenoe, P.3    Beck, H.P.4
  • 49
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • 10.1186/gb-2009-10-3-r25, 2690996, 19261174
    • Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
    • (2009) Genome Biol , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 50
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq
    • 10.1038/nmeth.1226, 18516045
    • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5:621-628. 10.1038/nmeth.1226, 18516045.
    • (2008) Nat Methods , vol.5 , pp. 621-628
    • Mortazavi, A.1    Williams, B.A.2    McCue, K.3    Schaeffer, L.4    Wold, B.5
  • 51
    • 75249087100 scopus 로고    scopus 로고
    • EdgeR: a bioconductor package for differential expression analysis of digital gene expression data
    • 10.1093/bioinformatics/btp616, 2796818, 19910308
    • Robinson MD, McCarthy DJ, Smyth GK. EdgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010, 26:139-140. 10.1093/bioinformatics/btp616, 2796818, 19910308.
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.