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Volumn 7, Issue , 2018, Pages

Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; FEMALE; GENE EXPRESSION; GENETIC TRANSCRIPTION; IMMUNE EVASION; LIFE CYCLE; MALE; MULTIGENE FAMILY; NONHUMAN; PLASMODIUM; RNA SEQUENCE; RODENT; SEXUAL BEHAVIOR; THINKING; ANIMAL; GENE EXPRESSION PROFILING; GENETIC VARIATION; GENETICS; HUMAN; SEQUENCE ANALYSIS; SINGLE CELL ANALYSIS;

EID: 85045640021     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.33105     Document Type: Article
Times cited : (157)

References (79)
  • 1
    • 33745626459 scopus 로고    scopus 로고
    • Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
    • 16606683
    • Alexa A, Rahnenführer J, Lengauer T. 2006. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22:1600–1607. DOI: https://doi.org/10.1093/bioinformatics/btl140, PMID: 16606683
    • (2006) Bioinformatics , vol.22 , pp. 1600-1607
    • Alexa, A.1    Rahnenführer, J.2    Lengauer, T.3
  • 2
    • 84924139017 scopus 로고    scopus 로고
    • Antisense long noncoding RNAs regulate var gene activation in the malaria parasite Plasmodium falciparum
    • 25691743
    • Amit-Avraham I, Pozner G, Eshar S, Fastman Y, Kolevzon N, Yavin E, Dzikowski R. 2015. Antisense long noncoding RNAs regulate var gene activation in the malaria parasite Plasmodium falciparum. PNAS 112:E982– E991. DOI: https://doi.org/10.1073/pnas.1420855112, PMID: 25691743
    • (2015) PNAS , vol.112 , pp. E982-E991
    • Amit-Avraham, I.1    Pozner, G.2    Eshar, S.3    Fastman, Y.4    Kolevzon, N.5    Yavin, E.6    Dzikowski, R.7
  • 3
    • 84928987900 scopus 로고    scopus 로고
    • HTSeq–a Python framework to work with high-throughput sequencing data
    • 25260700
    • Anders S, Pyl PT, Huber W. 2015. HTSeq–a Python framework to work with high-throughput sequencing data. Bioinformatics 31:166–169. DOI: https://doi.org/10.1093/bioinformatics/btu638, PMID: 25260700
    • (2015) Bioinformatics , vol.31 , pp. 166-169
    • Anders, S.1    Pyl, P.T.2    Huber, W.3
  • 7
    • 4243071596 scopus 로고    scopus 로고
    • The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum
    • 12929205
    • Bozdech Z, Llinás M, Pulliam BL, Wong ED, Zhu J, DeRisi JL. 2003a. The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biology 1:E5. DOI: https://doi.org/10.1371/journal.pbio. 0000005, PMID: 12929205
    • (2003) Plos Biology , vol.1 , pp. 5
    • Bozdech, Z.1    Llinás, M.2    Pulliam, B.L.3    Wong, E.D.4    Zhu, J.5    Derisi, J.L.6
  • 8
    • 1342303735 scopus 로고    scopus 로고
    • Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray
    • 12620119
    • Bozdech Z, Zhu J, Joachimiak MP, Cohen FE, Pulliam B, DeRisi JL. 2003b. Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biology 4: R9. DOI: https://doi.org/10.1186/gb-2003-4-2-r9, PMID: 12620119
    • (2003) Genome Biology , vol.4 , pp. 9
    • Bozdech, Z.1    Zhu, J.2    Joachimiak, M.P.3    Cohen, F.E.4    Pulliam, B.5    Derisi, J.L.6
  • 12
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • 15034147
    • Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32:1792–1797. DOI: https://doi.org/10.1093/nar/gkh340, PMID: 15034147
    • (2004) Nucleic Acids Research , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 16
    • 79955424413 scopus 로고    scopus 로고
    • Mitosis in the human malaria parasite Plasmodium falciparum
    • 21317311
    • Gerald N, Mahajan B, Kumar S. 2011. Mitosis in the human malaria parasite Plasmodium falciparum. Eukaryotic Cell 10:474–482. DOI: https://doi.org/10.1128/EC.00314-10, PMID: 21317311
    • (2011) Eukaryotic Cell , vol.10 , pp. 474-482
    • Gerald, N.1    Mahajan, B.2    Kumar, S.3
  • 19
    • 84876342100 scopus 로고    scopus 로고
    • Silence, activate, poise and switch! Mechanisms of antigenic variation in Plasmodium falciparum
    • 23351305
    • Guizetti J, Scherf A. 2013. Silence, activate, poise and switch! Mechanisms of antigenic variation in Plasmodium falciparum. Cellular Microbiology 15:718–726. DOI: https://doi.org/10.1111/cmi.12115, PMID: 23351305
    • (2013) Cellular Microbiology , vol.15 , pp. 718-726
    • Guizetti, J.1    Scherf, A.2
  • 22
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • 1438297
    • Henikoff S, Henikoff JG. 1992. Amino acid substitution matrices from protein blocks. PNAS 89:10915–10919. DOI: https://doi.org/10.1073/pnas.89.22.10915, PMID: 1438297
    • (1992) PNAS , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 26
    • 84888138802 scopus 로고    scopus 로고
    • Standardization in generating and reporting genetically modified rodent malaria parasites: The RMgmDB database
    • PMID 22990775
    • Khan SM, Kroeze H, Franke-Fayard B, Janse CJ. 2013. Standardization in generating and reporting genetically modified rodent malaria parasites: the RMgmDB database. Methods in Molecular Biology 923:139–150. DOI: https://doi.org/10.1007/978-1-62703-026-7_9, PMID: 22990775
    • (2013) Methods in Molecular Biology , vol.923 , pp. 139-150
    • Khan, S.M.1    Kroeze, H.2    Franke-Fayard, B.3    Janse, C.J.4
  • 27
    • 84926519013 scopus 로고    scopus 로고
    • HISAT: A fast spliced aligner with low memory requirements
    • 25751142
    • Kim D, Langmead B, Salzberg SL. 2015. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 12:357–360. DOI: https://doi.org/10.1038/nmeth.3317, PMID: 25751142
    • (2015) Nature Methods , vol.12 , pp. 357-360
    • Kim, D.1    Langmead, B.2    Salzberg, S.L.3
  • 30
    • 84956599311 scopus 로고    scopus 로고
    • Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells
    • 26430063
    • Kowalczyk MS, Tirosh I, Heckl D, Rao TN, Dixit A, Haas BJ, Schneider RK, Wagers AJ, Ebert BL, Regev A. 2015. Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells. Genome Research 25:1860–1872. DOI: https://doi.org/10.1101/gr.192237.115, PMID: 26430063
    • (2015) Genome Research , vol.25 , pp. 1860-1872
    • Kowalczyk, M.S.1    Tirosh, I.2    Heckl, D.3    Rao, T.N.4    Dixit, A.5    Haas, B.J.6    Schneider, R.K.7    Wagers, A.J.8    Ebert, B.L.9    Regev, A.10
  • 31
    • 0022378096 scopus 로고
    • Characterization of permeation pathways in the plasma membrane of human erythrocytes infected with early stages of Plasmodium falciparum: Association with parasite development
    • 2999164
    • Kutner S, Breuer WV, Ginsburg H, Aley SB, Cabantchik ZI. 1985. Characterization of permeation pathways in the plasma membrane of human erythrocytes infected with early stages of Plasmodium falciparum: association with parasite development. Journal of Cellular Physiology 125:521–527. DOI: https://doi.org/10.1002/jcp. 1041250323, PMID: 2999164
    • (1985) Journal of Cellular Physiology , vol.125 , pp. 521-527
    • Kutner, S.1    Breuer, W.V.2    Ginsburg, H.3    Aley, S.B.4    Cabantchik, Z.I.5
  • 32
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • 22388286
    • Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9:357–359. DOI: https://doi.org/10.1038/nmeth.1923, PMID: 22388286
    • (2012) Nature Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 34
    • 84988410148 scopus 로고    scopus 로고
    • A computational lens for sexual-stage transmission, reproduction, fitness and kinetics in Plasmodium falciparum
    • 27653663
    • Lawniczak MK, Eckhoff PA. 2016. A computational lens for sexual-stage transmission, reproduction, fitness and kinetics in Plasmodium falciparum. Malaria Journal 15:487. DOI: https://doi.org/10.1186/s12936-016-1538-5, PMID: 27653663
    • (2016) Malaria Journal , vol.15 , pp. 487
    • Lawniczak, M.K.1    Eckhoff, P.A.2
  • 35
    • 68549104404 scopus 로고    scopus 로고
    • 1000 Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map format and SAMtools
    • 19505943
    • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078–2079. DOI: https://doi.org/10.1093/bioinformatics/btp352, PMID: 19505943
    • Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1    Handsaker, B.2    Wysoker, A.3    Fennell, T.4    Ruan, J.5    Homer, N.6    Marth, G.7    Abecasis, G.8    Durbin, R.9
  • 37
    • 33644854445 scopus 로고    scopus 로고
    • Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains
    • 16493140
    • Llinás M, Bozdech Z, Wong ED, Adai AT, DeRisi JL. 2006. Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains. Nucleic Acids Research 34:1166–1173. DOI: https://doi.org/10.1093/nar/gkj517, PMID: 16493140
    • (2006) Nucleic Acids Research , vol.34 , pp. 1166-1173
    • Llinás, M.1    Bozdech, Z.2    Wong, E.D.3    Adai, A.T.4    Derisi, J.L.5
  • 39
    • 85026452613 scopus 로고    scopus 로고
    • Nascent RNA sequencing reveals mechanisms of gene regulation in the human malaria parasite Plasmodium falciparum
    • 28531310
    • Lu XM, Batugedara G, Lee M, Prudhomme J, Bunnik EM, Le Roch KG. 2017. Nascent RNA sequencing reveals mechanisms of gene regulation in the human malaria parasite Plasmodium falciparum. Nucleic Acids Research 45:7825–7840. DOI: https://doi.org/10.1093/nar/gkx464, PMID: 28531310
    • (2017) Nucleic Acids Research , vol.45 , pp. 7825-7840
    • Lu, X.M.1    Batugedara, G.2    Lee, M.3    Prudhomme, J.4    Bunnik, E.M.5    Le Roch, K.G.6
  • 40
    • 84964556059 scopus 로고    scopus 로고
    • Pooling across cells to normalize single-cell RNA sequencing data with many zero counts
    • 27122128
    • Lun AT, Bach K, Marioni JC. 2016. Pooling across cells to normalize single-cell RNA sequencing data with many zero counts. Genome Biology 17:75. DOI: https://doi.org/10.1186/s13059-016-0947-7, PMID: 27122128
    • (2016) Genome Biology , vol.17 , pp. 75
    • Lun, A.T.1    Bach, K.2    Marioni, J.C.3
  • 44
    • 84961932806 scopus 로고    scopus 로고
    • Genomic epidemiology of artemisinin resistant malaria
    • 26943619
    • Malaria GEN Plasmodium falciparum Community Project. 2016. Genomic epidemiology of artemisinin resistant malaria. eLife 5:e08714. DOI: https://doi.org/10.7554/eLife.08714, PMID: 26943619
    • (2016) Elife , vol.5
    • Malaria, G.E.N.1
  • 49
    • 44349118501 scopus 로고    scopus 로고
    • Default Pathway of var2csa switching and translational repression in Plasmodium falciparum
    • 18431472
    • Mok BW, Ribacke U, Rasti N, Kironde F, Chen Q, Nilsson P, Wahlgren M. 2008. Default Pathway of var2csa switching and translational repression in Plasmodium falciparum. PLoS One 3:e1982. DOI: https://doi.org/10. 1371/journal.pone.0001982, PMID: 18431472
    • (2008) Plos One , vol.3
    • Mok, B.W.1    Ribacke, U.2    Rasti, N.3    Kironde, F.4    Chen, Q.5    Nilsson, P.6    Wahlgren, M.7
  • 50
    • 84857682112 scopus 로고    scopus 로고
    • Plasmodium falciparum 19-kilodalton merozoite surface protein 1 (MSP1)-specific antibodies that interfere with parasite growth in vitro can inhibit MSP1 processing, merozoite invasion, and intracellular parasite development
    • 22202121
    • Moss DK, Remarque EJ, Faber BW, Cavanagh DR, Arnot DE, Thomas AW, Holder AA. 2012. Plasmodium falciparum 19-kilodalton merozoite surface protein 1 (MSP1)-specific antibodies that interfere with parasite growth in vitro can inhibit MSP1 processing, merozoite invasion, and intracellular parasite development. Infection and Immunity 80:1280–1287. DOI: https://doi.org/10.1128/IAI.05887-11, PMID: 22202121
    • (2012) Infection and Immunity , vol.80 , pp. 1280-1287
    • Moss, D.K.1    Remarque, E.J.2    Faber, B.W.3    Cavanagh, D.R.4    Arnot, D.E.5    Thomas, A.W.6    Holder, A.A.7
  • 51
    • 0037197827 scopus 로고    scopus 로고
    • Oligo(DT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription
    • 11972056
    • Nam DK, Lee S, Zhou G, Cao X, Wang C, Clark T, Chen J, Rowley JD, Wang SM. 2002. Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription. PNAS 99:6152–6156. DOI: https://doi.org/10.1073/pnas.092140899, PMID: 11972056
    • (2002) PNAS , vol.99 , pp. 6152-6156
    • Nam, D.K.1    Lee, S.2    Zhou, G.3    Cao, X.4    Wang, C.5    Clark, T.6    Chen, J.7    Rowley, J.D.8    Wang, S.M.9
  • 55
    • 84990992834 scopus 로고    scopus 로고
    • Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
    • 27560171
    • Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. 2016. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nature Protocols 11:1650–1667. DOI: https://doi.org/10. 1038/nprot.2016.095, PMID: 27560171
    • (2016) Nature Protocols , vol.11 , pp. 1650-1667
    • Pertea, M.1    Kim, D.2    Pertea, G.M.3    Leek, J.T.4    Salzberg, S.L.5
  • 56
    • 84887101406 scopus 로고    scopus 로고
    • Smart-seq2 for sensitive full-length transcriptome profiling in single cells
    • 24056875
    • Picelli S, Björklund ÅK, Faridani OR, Sagasser S, Winberg G, Sandberg R. 2013. Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nature Methods 10:1096–1098. DOI: https://doi.org/10.1038/nmeth.2639, PMID: 24056875
    • (2013) Nature Methods , vol.10 , pp. 1096-1098
    • Picelli, S.1    Björklund, Å.K.2    Faridani, O.R.3    Sagasser, S.4    Winberg, G.5    Sandberg, R.6
  • 57
    • 0033821583 scopus 로고    scopus 로고
    • High heterogeneity in the number of Plasmodium falciparum gametocytes in the bloodmeal of mosquitoes fed on the same host
    • 11085230
    • Pichon G, Awono-Ambene HP, Robert V. 2000. High heterogeneity in the number of Plasmodium falciparum gametocytes in the bloodmeal of mosquitoes fed on the same host. Parasitology 121 (Pt 2:115–120. DOI: https://doi.org/10.1017/S0031182099006277, PMID: 11085230
    • (2000) Parasitology , vol.121 , pp. 115-120
    • Pichon, G.1    Awono-Ambene, H.P.2    Robert, V.3
  • 59
    • 0033561460 scopus 로고    scopus 로고
    • A rhoptry-protein-associated mechanism of clonal phenotypic variation in rodent malaria
    • 10217144
    • Preiser PR, Jarra W, Capiod T, Snounou G. 1999. A rhoptry-protein-associated mechanism of clonal phenotypic variation in rodent malaria. Nature 398:618–622. DOI: https://doi.org/10.1038/19309, PMID: 10217144
    • (1999) Nature , vol.398 , pp. 618-622
    • Preiser, P.R.1    Jarra, W.2    Capiod, T.3    Snounou, G.4
  • 60
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • 20110278
    • Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–842. DOI: https://doi.org/10.1093/bioinformatics/btq033, PMID: 20110278
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 61
    • 85045687060 scopus 로고    scopus 로고
    • Adamjamesreid/Plasmodium-single-cell-RNA-seq
    • Reid A. 2018. adamjamesreid/Plasmodium-single-cell-RNA-seq. GitHub. a702505. https://github.com/adamjamesreid/Plasmodium-single-cell-RNA-seq
    • (2018) Github
    • Reid, A.1
  • 62
    • 84911370512 scopus 로고    scopus 로고
    • Large, rapidly evolving gene families are at the forefront of host-parasite interactions in Apicomplexa
    • 25257746
    • Reid AJ. 2015. Large, rapidly evolving gene families are at the forefront of host-parasite interactions in Apicomplexa. Parasitology 142:S57–S70. DOI: https://doi.org/10.1017/S0031182014001528, PMID: 25257746
    • (2015) Parasitology , vol.142 , pp. S57-S70
    • Reid, A.J.1
  • 63
    • 42149152335 scopus 로고    scopus 로고
    • Concentration and purification by magnetic separation of the erythrocytic stages of all human Plasmodium species
    • 18321384
    • Ribaut C, Berry A, Chevalley S, Reybier K, Morlais I, Parzy D, Nepveu F, Benoit-Vical F, Valentin A. 2008. Concentration and purification by magnetic separation of the erythrocytic stages of all human Plasmodium species. Malaria Journal 7:45. DOI: https://doi.org/10.1186/1475-2875-7-45, PMID: 18321384
    • (2008) Malaria Journal , vol.7 , pp. 45
    • Ribaut, C.1    Berry, A.2    Chevalley, S.3    Reybier, K.4    Morlais, I.5    Parzy, D.6    Nepveu, F.7    Benoit-Vical, F.8    Valentin, A.9
  • 64
    • 84871946825 scopus 로고    scopus 로고
    • Streaming fragment assignment for real-time analysis of sequencing experiments
    • 23160280
    • Roberts A, Pachter L. 2013. Streaming fragment assignment for real-time analysis of sequencing experiments. Nature Methods 10:71–73. DOI: https://doi.org/10.1038/nmeth.2251, PMID: 23160280
    • (2013) Nature Methods , vol.10 , pp. 71-73
    • Roberts, A.1    Pachter, L.2
  • 65
    • 75249087100 scopus 로고    scopus 로고
    • EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
    • 19910308
    • Robinson MD, McCarthy DJ, Smyth GK. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140. DOI: https://doi.org/10.1093/bioinformatics/btp616, PMID: 19910308
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 67
    • 84884676244 scopus 로고    scopus 로고
    • Antigenic variation in Plasmodium falciparum
    • 18785843
    • Scherf A, Lopez-Rubio JJ, Riviere L. 2008. Antigenic variation in Plasmodium falciparum. Annual Review of Microbiology 62:445–470. DOI: https://doi.org/10.1146/annurev.micro.61.080706.093134, PMID: 18785843
    • (2008) Annual Review of Microbiology , vol.62 , pp. 445-470
    • Scherf, A.1    Lopez-Rubio, J.J.2    Riviere, L.3
  • 68
    • 38349145774 scopus 로고    scopus 로고
    • Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle
    • 17612404
    • Shock JL, Fischer KF, DeRisi JL. 2007. Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle. Genome Biology 8: R134. DOI: https://doi.org/10.1186/gb-2007-8-7-r134, PMID: 17612404
    • (2007) Genome Biology , vol.8 , pp. 134
    • Shock, J.L.1    Fischer, K.F.2    Derisi, J.L.3
  • 72
    • 77949374916 scopus 로고    scopus 로고
    • A Plasmodium falciparum strain expressing GFP throughout the parasite’s life-cycle
    • 20161781
    • Talman AM, Blagborough AM, Sinden RE. 2010. A Plasmodium falciparum strain expressing GFP throughout the parasite’s life-cycle. PLoS One 5:e9156. DOI: https://doi.org/10.1371/journal.pone.0009156, PMID: 20161781
    • (2010) Plos One , vol.5
    • Talman, A.M.1    Blagborough, A.M.2    Sinden, R.E.3


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