UTR introns, antisense RNA and differentially spliced transcripts between Plasmodium yoelii subspecies

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• 作者：Jian Li ; Baowei Cai ; Yanwei Qi ; Wenting Zhao ; Jianwen Liu ; Ruixue Xu…
• 关键词：Malaria ; RNA ; seq ; Gene expression ; Single nucleotide polymorphism (SNP) ; Alternative splicing
• 刊名：Malaria Journal
• 出版年：2016
• 出版时间：December 2016
• 年：2016
• 卷：15
• 期：1
• 全文大小：2,253 KB
• 参考文献：1.WHO: Worldmalaria report 2012. World Health Organization. 2014. http://​www.​who.​int/​malaria/​publications/​world_​malaria_​report_​2014/​en/​ . Accessed 15 Jan 2016.
  2.Stephens R, Culleton RL, Lamb TJ. The contribution of Plasmodium chabaudi to our understanding of malaria. Trends Parasitol. 2012;28:73–82.PubMed PubMedCentral CrossRef
  3.Carlton JM, Hayton K, Cravo PV, Walliker D. Of mice and malaria mutants: unravelling the genetics of drug resistance using rodent malaria models. Trends Parasitol. 2001;17:236–42.PubMed CrossRef
  4.Janse CJ, Kroeze H, van Wigcheren A, Mededovic S, Fonager J, Franke-Fayard B, et al. A genotype and phenotype database of genetically modified malaria-parasites. Trends Parasitol. 2011;27:31–9.PubMed CrossRef
  5.Li C, Seixas E, Langhorne J. Rodent malarias: the mouse as a model for understanding immune responses and pathology induced by the erythrocytic stages of the parasite. Med Microbiol Immunol. 2001;189:115–26.PubMed CrossRef
  6.Stevenson M, Lemieux S, Skamene E. Genetic control of resistance to murine malaria. J Cell Biochem. 1984;24:91–102.PubMed CrossRef
  7.Langhorne J, Quin SJ, Sanni LA. Mouse models of blood-stage malaria infections: immune responses and cytokines involved in protection and pathology. Chem Immunol. 2002;80:204–28.PubMed CrossRef
  8.Pattaradilokrat S, Culleton RL, Cheesman SJ, Carter R. Gene encoding erythrocyte binding ligand linked to blood stage multiplication rate phenotype in Plasmodium yoelii yoelii. Proc Natl Acad Sci USA. 2009;106:7161–6.PubMed PubMedCentral CrossRef
  9.Otsuki H, Kaneko O, Thongkukiatkul A, Tachibana M, Iriko H, Takeo S, et al. Single amino acid substitution in Plasmodium yoelii erythrocyte ligand determines its localization and controls parasite virulence. Proc Natl Acad Sci USA. 2009;106:7167–72.PubMed PubMedCentral CrossRef
  10.Li J, Zhang Y, Sullivan M, Hong L, Huang L, Lu F, et al. Typing Plasmodium yoelii microsatellites using a simple and affordable fluorescent labeling method. Mol Biochem Parasitol. 2007;155:94–102.PubMed PubMedCentral CrossRef
  11.Li J, Zhang Y, Liu S, Hong L, Sullivan M, McCutchan TF, et al. Hundreds of microsatellites for genotyping Plasmodium yoelii parasites. Mol Biochem Parasitol. 2009;166:153–8.PubMed PubMedCentral CrossRef
  12.Nair SC, Pattaradilokrat S, Zilversmit MM, Dommer J, Nagarajan V, Stephens MT, et al. Genome-wide polymorphisms and development of a microarray platform to detect genetic variations in Plasmodium yoelii. Mol Biochem Parasitol. 2014;194:9–15.PubMed PubMedCentral CrossRef
  13.Li J, Pattaradilokrat S, Zhu F, Jiang H, Liu S, Hong L, et al. Linkage maps from multiple genetic crosses and loci linked to growth-related virulent phenotype in Plasmodium yoelii. Proc Natl Acad Sci USA. 2011;108:E374–82.PubMed PubMedCentral CrossRef
  14.Pattaradilokrat S, Li J, Wu J, Qi Y, Eastman RT, Zilversmit M, et al. Plasmodium genetic loci linked to host cytokine and chemokine responses. Genes Immun. 2014;15:145–52.PubMed PubMedCentral CrossRef
  15.Pattaradilokrat S, Cheesman SJ, Carter R. Congenicity and genetic polymorphism in cloned lines derived from a single isolate of a rodent malaria parasite. Mol Biochem Parasitol. 2008;157:244–7.PubMed CrossRef
  16.Wu J, Tian L, Yu X, Pattaradilokrat S, Li J, Wang M, et al. Strain-specific innate immune signaling pathways determine malaria parasitemia dynamics and host mortality. Proc Natl Acad Sci USA. 2014;111:E511–20.PubMed PubMedCentral CrossRef
  17.Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC, et al. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature. 2002;419:512–9.PubMed CrossRef
  18.Lindner SE, Mikolajczak SA, Vaughan AM, Moon W, Joyce BR, Sullivan WJ Jr, et al. Perturbations of Plasmodium Puf2 expression and RNA-seq of Puf2-deficient sporozoites reveal a critical role in maintaining RNA homeostasis and parasite transmissibility. Cell Microbiol. 2013;15:1266–83.PubMed CrossRef
  19.Otto TD, Bohme U, Jackson AP, Hunt M, Franke-Fayard B, Hoeijmakers WA, et al. A comprehensive evaluation of rodent malaria parasite genomes and gene expression. BMC Biol. 2014;12:86.PubMed PubMedCentral CrossRef
  20.Lu F, Jiang H, Ding J, Mu J, Valenzuela JG, Ribeiro JM, et al. cDNA sequences reveal considerable gene prediction inaccuracy in the Plasmodium falciparum genome. BMC Genom. 2007;8:255.CrossRef
  21.Lopez-Barragan MJ, Lemieux J, Quinones M, Williamson KC, Molina-Cruz A, Cui K, et al. Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum. BMC Genom. 2011;12:587.CrossRef
  22.Watanabe J, Wakaguri H, Sasaki M, Suzuki Y, Sugano S. Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs. Nucleic Acids Res. 2007;35:D431–8.PubMed PubMedCentral CrossRef
  23.Otto TD, Wilinski D, Assefa S, Keane TM, Sarry LR, Bohme U, et al. New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq. Mol Microbiol. 2010;76:12–24.PubMed PubMedCentral CrossRef
  24.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.PubMed PubMedCentral CrossRef
  25.Bartfai R, Hoeijmakers WA, Salcedo-Amaya AM, Smits AH, Janssen-Megens E, Kaan A, et al. H2A.Z demarcates intergenic regions of the Plasmodium falciparum epigenome that are dynamically marked by H3K9ac and H3K4me3. PLoS Pathog. 2010;6:e1001223.PubMed PubMedCentral CrossRef
  26.MR4: https://​www.​beiresources.​org.​ Accessed 15 Jan 2016.
  27.Peters W, Robinson BL, Mittelholzer ML, Crevoisier C, Sturchler D. The chemotherapy of rodent malaria. LII. Response of Plasmodium yoelii ssp. NS to mefloquine and its enantiomers. Ann Trop Med Parasitol. 1995;89:465–8.PubMed
  28.Tao ZY, Xia H, Cao J, Gao Q. Development and evaluation of a prototype non-woven fabric filter for purification of malaria-infected blood. Malar J. 2011;10:251.PubMed PubMedCentral CrossRef
  29.Read data: accession number SRP066796 http://​www.​ncbi.​nlm.​nih.​gov/​sra/​?​term=​SRP066796 .
  30.Sanger website: YM genome sequence http://​www.​sanger.​ac.​uk/​resources/​downloads/​protozoa/​plasmodium-yoelii.​html .
  31.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.PubMed PubMedCentral CrossRef
  32.Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.PubMed PubMedCentral CrossRef
  33.Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25:1105–11.PubMed PubMedCentral CrossRef
  34.Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7:562–78.PubMed PubMedCentral CrossRef
  35.Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008;5:621–8.PubMed CrossRef
  36.Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11:R106.PubMed PubMedCentral CrossRef
  37.Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28:511–5.PubMed PubMedCentral CrossRef
  38.Florea L, Song L, Salzberg SL: Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues. F1000Res 2013; 2:188.
  39.IGV website : https://​www.​broadinstitute.​org/​igv/​ . Accessed 15 Jan 2016.
  40.TransDecoder: http://​transdecoder.​sourceforge.​net . Accessed 15 Jan 2016.
  41.Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–9.PubMed PubMedCentral CrossRef
  42.GATK2: http://​www.​broadinstitute.​org/​gatk/​ . Accessed 15 Jan 2016.
  43.Carlton J, Silva J, Hall N. The genome of model malaria parasites, and comparative genomics. Curr Issues Mol Biol. 2005;7:23–37.PubMed
  44.Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, et al. Antisense transcription in the mammalian transcriptome. Science. 2005;309:1564–6.PubMed CrossRef
  45.Bicknell AA, Cenik C, Chua HN, Roth FP, Moore MJ. Introns in UTRs: why we should stop ignoring them. BioEssays. 2012;34:1025–34.PubMed CrossRef
  46.Cenik C, Derti A, Mellor JC, Berriz GF, Roth FP. Genome-wide functional analysis of human 5′ untranslated region introns. Genome Biol. 2010;11:R29.PubMed PubMedCentral CrossRef
  47.Chung BY, Simons C, Firth AE, Brown CM, Hellens RP. Effect of 5′ UTR introns on gene expression in Arabidopsis thaliana. BMC Genom. 2006;7:120.CrossRef
  
• 作者单位：Jian Li (1)
  Baowei Cai (1)
  Yanwei Qi (1) (2)
  Wenting Zhao (1)
  Jianwen Liu (1)
  Ruixue Xu (1)
  Qin Pang (1)
  Zhiyong Tao (3)
  Lingxian Hong (1)
  Shengfa Liu (1)
  Maarten Leerkes (4)
  Mariam Quiñones (4)
  Xin-zhuan Su (1) (2)
  
  1. State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, People’s Republic of China
  2. Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
  3. Department of Parasitology, Bengbu Medical College, 2600 Donghai Dadao Road, Bengbu, 233030, People’s Republic of China
  4. Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
  
• 刊物主题：Parasitology; Infectious Diseases; Tropical Medicine;
• 出版者：BioMed Central
• ISSN：1475-2875

文摘

Background The rodent malaria parasite Plasmodium yoelii is an important animal model for studying host-parasite interaction and molecular basis of malaria pathogenesis. Although a draft genome of P. yoelii yoelii YM is available, and RNA sequencing (RNA-seq) data for several rodent malaria species (RMP) were reported recently, variations in coding regions and structure of mRNA transcript are likely present between different parasite strains or subspecies. Sequencing of cDNA libraries from additional parasite strains/subspecies will help improve the gene models and genome annotation.