Identification of a putative quantitative trait nucleotide in guanylate binding protein 5 for host response to PRRS virus infection

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Koltes, James E ^a   Fritz Waters, Eric ^a   Eisley, Chris J ^a,b   Choi, Igseo ^c   Bao, Hua ^d   Kommadath, Arun ^d   Serão, Nick V L ^a   Boddicker, Nicholas J ^e   Abrams, Sam M ^c   Schroyen, Martine ^a   Loyd, Hyelee ^a   Tuggle, Chris K ^a   Plastow, Graham S ^d   Guan, Leluo ^d   Stothard, Paul ^d   Lunney, Joan K ^c   Liu, Peng ^b   Carpenter, Susan ^a   Rowland, Robert R R ^f   Dekkers, Jack C M ^a   Reecy, James M ^a   more..

^a IOWA STATE UNIVERSITY   (United States)

^b Iowa State University   (United States)

^c AGRICULTURAL RESEARCH SERVICE   (United States)

^d UNIVERSITY OF ALBERTA   (Canada)

^e GENESUS INC   (Canada)

^f KANSAS STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GUANINE NUCLEOTIDE BINDING PROTEIN; GUANYLATE BINDING PROTEIN 5; INFLAMMASOME; UNCLASSIFIED DRUG; RNA SPLICING;

ANIMAL EXPERIMENT; ARTERIVIRUS INFECTION; ARTICLE; BARROW (SWINE); CAPILLARY ELECTROPHORESIS; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; GBP5 GENE; GENE INSERTION; GENE LINKAGE DISEQUILIBRIUM; GENETIC LINKAGE; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HAPLOTYPE; HETEROZYGOSITY; HOMOZYGOSITY; IMMUNE RESPONSE; INTRON; NONHUMAN; PORCINE REPRODUCTIVE AND RESPIRATORY SYNDROME VIRUS; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN LOCALIZATION; QUANTITATIVE ANALYSIS; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM; ALTERNATIVE RNA SPLICING; ANIMAL; BLOOD; CHEMISTRY; GENE EXPRESSION REGULATION; GENETICS; GENOTYPE; IMMUNOLOGY; PIG; PORCINE REPRODUCTIVE AND RESPIRATORY SYNDROME; RNA SPLICING; VIROLOGY;

PORCINE RESPIRATORY AND REPRODUCTIVE SYNDROME VIRUS; SUIDAE; SUS SCROFA;

ALTERNATIVE SPLICING; ANIMALS; GENE EXPRESSION REGULATION; GENOTYPE; GTP-BINDING PROTEINS; POLYMORPHISM, SINGLE NUCLEOTIDE; PORCINE REPRODUCTIVE AND RESPIRATORY SYNDROME; PORCINE RESPIRATORY AND REPRODUCTIVE SYNDROME VIRUS; QUANTITATIVE TRAIT LOCI; RNA SPLICE SITES; SUS SCROFA; SWINE;

EID: 85019170930     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-1635-9     Document Type: Article

References (36)

1. Boddicker N, Waide EH, Rowland RR, Lunney JK, Garrick DJ, Reecy JM, et al. Evidence for a major QTL associated with host response to porcine reproductive and respiratory syndrome virus challenge. J Anim Sci. 2012;90(6):1733-46.
2. Boddicker NJ, Bjorkquist A, Rowland RR, Lunney JK, Reecy JM, Dekkers JC. Genome-wide association and genomic prediction for host response to porcine reproductive and respiratory syndrome virus infection. Genet Sel Evol. 2014;46:18.
3. Nordmann A, Wixler L, Boergeling Y, Wixler V, Ludwig S. A new splice variant of the human guanylate-binding protein 3 mediates anti-influenza activity through inhibition of viral transcription and replication. FASEB J. 2012;26(3):1290-300.
4. Pilla DM, Hagar JA, Haldar AK, Mason AK, Degrandi D, Pfeffer K, et al. Guanylate binding proteins promote caspase-11-dependent pyroptosis in response to cytoplasmic LPS. Proc Natl Acad Sci U S A. 2014;111(16):6046-51.
5. Bergsbaken T, Fink SL, Cookson BT. Pyroptosis: host cell death and inflammation. Nat Rev Microbiol. 2009;7(2):99-109.
6. Degrandi D, Kravets E, Konermann C, Beuter-Gunia C, Klumpers V, Lahme S, et al. Murine guanylate binding protein 2 (mGBP2) controls Toxoplasma gondii replication. Proc Natl Acad Sci U S A. 2013;110(1):294-9.
7. Shenoy AR, Wellington DA, Kumar P, Kassa H, Booth CJ, Cresswell P, et al. GBP5 promotes NLRP3 inflammasome assembly and immunity in mammals. Science. 2012;336(6080):481-5.
8. Ito Y, Shibata-Watanabe Y, Ushijima Y, Kawada J, Nishiyama Y, Kojima S, et al. Oligonucleotide microarray analysis of gene expression profiles followed by real-time reverse-transcriptase polymerase chain reaction assay in chronic active Epstein-Barr virus infection. J Infect Dis. 2008;197(5):663-6.
9. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22(22):4673-80.
10. Rowland RR, Lunney J, Dekkers J. Control of porcine reproductive and respiratory syndrome (PRRS) through genetic improvements in disease resistance and tolerance. Front Genet. 2012;3:260.
11. Holtkamp D, Kliebenstein J, Zimmerman J, Neumann E, Rotto H, Yoder T, et al. Assessment of the economic impact of porcine reproductive and respiratory syndrome virus on United States pork production. J Swine Health Production. 2013;21:72-84.
12. Benfield DA, Nelson E, Collins JE, Harris L, Goyal SM, Robison D, et al. Characterization of swine infertility and respiratory syndrome (Sirs) Virus (Isolate Atcc Vr-2332). J Vet Diagn Invest. 1992;4(2):127-33.
13. Wensvoort G, Terpstra C, Pol JMA, Terlaak EA, Bloemraad M, Dekluyver EP, et al. Mystery swine disease in the Netherlands - the isolation of lelystad virus. Vet Q. 1991;13(3):121-30.
14. Zimmerman J, Benfield DA, Murtaugh MP, Osorio F, Stevenson GW, Torremorell M. Porcine reproductive and respiratory syndrom virus (porcine arterivirus), in Diseases of Swine. eds Straw B, Taylor D, Zimmeran J, D'Allaire S, editors. West Sussex, UK: Wiley-Blackwell, 2006.
15. Gillespie J, Opriessnig T, Meng XJ, Pelzer K, Buechner-Maxwell V. Porcine circovirus type 2 and porcine circovirus-associated disease. J Vet Intern Med. 2009;23(6):1151-63.
16. Hansen MS, Pors SE, Jensen HE, Bille-Hansen V, Bisgaard M, Flachs EM, et al. An investigation of the pathology and pathogens associated with porcine respiratory disease complex in Denmark. J Comp Pathol. 2010;143(2-3):120-31.
17. Kimman TG, Cornelissen LA, Moormann RJ, Rebel JMJ, Stochofe-Zurwieden N. Challenges for porcine reproductive and respiratory syndrome virus (PRRSV) vaccinology. Vaccine. 2009;27(28):3704-18.
18. Lewis CR, Ait-Ali T, Clapperton M, Archibald AL, Bishop S. Genetic perspectives on host responses to porcine reproductive and respiratory syndrome (PRRS). Viral Immunol. 2007;20(3):343-58.
19. Lewis CR, Torremorell M, Galina-Pantoja L, Bishop SC. Genetic parameters for performance traits in commercial sows estimated before and after an outbreak of porcine reproductive and respiratory syndrome. J Anim Sci. 2009;87(3):876-84.
20. Serao NV, Matika O, Kemp RA, Harding JC, Bishop SC, Plastow GS, et al. Genetic analysis of reproductive traits and antibody response in a PRRS outbreak herd. J Anim Sci. 2014;92(7):2905-21.
21. Boddicker NJ, Garrick DJ, Rowland RR, Lunney JK, Reecy JM, Dekkers JC. Validation and further characterization of a major quantitative trait locus associated with host response to experimental infection with porcine reproductive and respiratory syndrome virus. Anim Genet. 2014;45(1):48-58.
22. Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, et al. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. 2014;42(Web Server issue):W252-8.
23. Choi I, Bao H, Kommadath A, Hosseini A, Sun X, Meng Y, et al. Increasing gene discovery and coverage using RNA-seq of globin RNA reduced porcine blood samples. BMC Genomics. 2014;15:954.
24. Joshi NA, Fass JN. Sickle: a sliding-window, adaptive, quality-based trimming tool for FastQ files. 1.29 edn. https://github.com/najoshi/sickle ; 2011.
25. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18(5):821-9.
26. Schulz MH, Zerbino DR, Vingron M, Birney E. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics. 2012;28(8):1086-92.
27. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14(4):R36.
28. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357-9.
29. 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(5):511-5.
30. Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11(10):R106.
31. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078-9.
32. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297-303.
33. Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010;11(3):R25.
34. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139-40.
35. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B. 1995;57:289-300.
36. Wangkumhang P, Chaichoompu K, Ngamphiw C, Ruangrit U, Chanprasert J, Assawamakin A, et al. WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations. BMC Genomics. 2007;8:275.