Transcriptome Analysis of Duck Liver and Identification of Differentially Expressed Transcripts in Response to Duck Hepatitis A Virus Genotype C Infection

PLoS ONE

Volumn 8, Issue 7, 2013, Pages

  Tang, Cheng ^a   Lan, Daoliang ^a   Zhang, Huanrong ^a   Ma, Jing ^a   Yue, Hua ^a  

^a SOUTHWEST UNIVERSITY FOR NATIONALITIES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ADAM32 GENE; AICL LIKE 2 PROTEIN; ARTICLE; AVIHEPADNAVIRUS; BIRD DISEASE; CHAC1 GENE; CRP GENE; CYB26A1 GENE; DOWN REGULATION; DUCK; DUCK HEPATITIS A; DUCK HEPATITIS A VIRUS; GENE; GENE EXPRESSION; GENE FUNCTION; GENE REPLICATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC DATABASE; GENETIC RECOMBINATION; GENETIC TRANSCRIPTION; GENOTYPE; L1CAM GENE; LRRC3B GENE; MOLECULAR MECHANICS; NONHUMAN; ORTHOLOGY; PCK1 GENE; REAL TIME POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; UPREGULATION; VIRUS CELL INTERACTION;

ANIMALS; DUCKS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENOTYPE; HEPATITIS VIRUS, DUCK; HEPATITIS, VIRAL, ANIMAL; IMMUNITY, INNATE; LIVER; MOLECULAR SEQUENCE ANNOTATION; PICORNAVIRIDAE INFECTIONS; TRANSCRIPTOME;

EID: 84880802089     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0071051     Document Type: Article

References (60)

1. Summers J, (1981) Three recently described animal virus models for human hepatitis B virus. Hepatology 1: 179-183.
2. Cova L, Zoulim F, (2004) Duck hepatitis B virus model in the study of hepatitis B virus. Methods Mol Med 96: 261-268.
3. Schultz U, Grgacic E, Nassal M, (2004) Duck hepatitis B virus: an invaluable model system for HBV infection. Adv Virus Res 63: 1-70.
4. Wang L, Pan M, Fu Y, Zhang D, (2008) Classification of duck hepatitis virus into three genotypes based on molecular evolutionary analysis. Virus Genes 37: 52-59.
5. Kim MC, Kwon YK, Joh SJ, Lindberg AM, Kwon JH, et al. (2006) Molecular analysis of duck hepatitis virus type 1 reveals a novel lineage close to the genus Parechovirus in the family Picornaviridae. J Gen Virol 87: 3307-3316.
6. Tseng CH, Knowles NJ, Tsai HJ, (2007) Molecular analysis of duck hepatitis virus type 1 indicates that it should be assigned to a new genus. Virus Res 123: 190-203.
7. Fu Y, Pan M, Wang X, Xu Y, Yang H, et al. (2008) Molecular detection and typing of duck hepatitis A virus directly from clinical specimens. Vet Microbiol 131: 247-257.
8. Huang Q, Yue H, Zhang B, Nie P, Tang C, (2012) Development of a real-time quantitative PCR for detecting duck hepatitis a virus genotype C. J Clin Microbiol. 50: 3318-3323.
9. Zhang H, Pi J, Tang C, Yue H, Yang F, (2012) An experimental study of the pathogenicity of a duck hepatitis A virus genotype C isolate in specific pathogen free ducklings. Avian Pathol 41: 613-620.
10. Xiao S, Jia J, Mo D, Wang Q, Qin L, et al. (2010) Understanding PRRSV infection in porcine lung based on genome-wide transcriptome response identified by deep sequencing. PLoS One 5: e11377.
11. Huang Y, Huang X, Yan Y, Cai J, Ouyang Z, et al. (2011) Transcriptome analysis of orange-spotted grouper (Epinephelus coioides) spleen in response to Singapore grouper iridovirus. BMC Genomics 12: 556.
12. Li S, Zhang X, Sun Z, Li F, Xiang J, (2013) Transcriptome Analysis on Chinese Shrimp Fenneropenaeus chinensis during WSSV Acute Infection. PLoS One 8: e58627.
13. Tariq MA, Kim HJ, Jejelowo O, Pourmand N, (2011) Whole-transcriptome RNAseq analysis from minute amount of total RNA. Nucleic Acids Res 39: e120.
14. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, et al. (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321: 956-960.
15. Richard H, Schulz MH, Sultan M, Nurnberger A, Schrinner S, et al. (2010) Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. Nucleic Acids Res 38: e112.
16. Radford AD, Chapman D, Dixon L, Chantrey J, Darby AC, et al. (2012) Application of next-generation sequencing technologies in virology. J Gen Virol 93: 1853-1868.
17. Luciani F, Bull RA, Lloyd AR, (2012) Next generation deep sequencing and vaccine design: today and tomorrow. Trends Biotechnol 30: 443-452.
18. Rismani-Yazdi H, Haznedaroglu BZ, Bibby K, Peccia J, (2011) Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: pathway description and gene discovery for production of next-generation biofuels. BMC Genomics 12: 148.
19. Hsu JC, Chien TY, Hu CC, Chen MJ, Wu WJ, et al. (2012) Discovery of genes related to insecticide resistance in Bactrocera dorsalis by functional genomic analysis of a de novo assembled transcriptome. PLoS One 7: e40950.
20. Li S, Wang C, Yu W, Zhao S, Gong Y, (2012) Identification of genes related to white and black plumage formation by RNA-Seq from white and black feather bulbs in ducks. PLoS One 7: e36592.
21. Yang D, Liu Q, Yang M, Wu H, Wang Q, et al. (2012) RNA-seq liver transcriptome analysis reveals an activated MHC-I pathway and an inhibited MHC-II pathway at the early stage of vaccine immunization in zebrafish. BMC Genomics 13: 319.
22. Li B, Dewey CN, (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12: 323.
23. Robinson MD, McCarthy DJ, Smyth GK, (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140.
24. Robinson MD, Oshlack A, (2010) A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11: R25.
25. Yue H, Lei XW, Yang FL, Li MY, Tang C, (2010) Reference gene selection for normalization of PCR analysis in chicken embryo fibroblast infected with H5N1 AIV. Virol Sin 25: 425-431.
26. Zanotto PM, Gibbs MJ, Gould EA, Holmes EC, (1996) A reevaluation of the higher taxonomy of viruses based on RNA polymerases. J Virol 70: 6083-6096.
27. Kao CC, Singh P, Ecker DJ, (2001) De novo initiation of viral RNA-dependent RNA synthesis. Virology 287: 251-260.
28. Barber GN, (2001) Host defense, viruses and apoptosis. Cell Death Differ 8: 113-126.
29. Gillet G, Brun G, (1996) Viral inhibition of apoptosis. Trends Microbiol 4: 312-317.
30. Thomson BJ, (2001) Viruses and apoptosis. Int J Exp Pathol 82: 65-76.
31. Brune W, (2011) Inhibition of programmed cell death by cytomegaloviruses. Virus Res 157: 144-150.
32. Goebel G, Berger R, Strasak AM, Egle D, Muller-Holzner E, et al. (2012) Elevated mRNA expression of CHAC1 splicing variants is associated with poor outcome for breast and ovarian cancer patients. Br J Cancer 106: 189-198.
33. Mungrue IN, Pagnon J, Kohannim O, Gargalovic PS, Lusis AJ, (2009) CHAC1/MGC4504 is a novel proapoptotic component of the unfolded protein response, downstream of the ATF4-ATF3-CHOP cascade. J Immunol 182: 466-476.
34. Li J, Hu P, Li K, Zhao Q, (2012) Identification and characterization of a novel retinoic acid response element in zebrafish cyp26a1 promoter. Anat Rec (Hoboken) 295: 268-277.
35. Thatcher JE, Buttrick B, Shaffer SA, Shimshoni JA, Goodlett DR, et al. (2011) Substrate specificity and ligand interactions of CYP26A1, the human liver retinoic acid hydroxylase. Mol Pharmacol 80: 228-239.
36. Osanai M, Petkovich M, (2005) Expression of the retinoic acid-metabolizing enzyme CYP26A1 limits programmed cell death. Mol Pharmacol 67: 1808-1817.
37. Hamann J, Montgomery KT, Lau S, Kucherlapati R, van Lier RA, (1997) AICL: a new activation-induced antigen encoded by the human NK gene complex. Immunogenetics 45: 295-300.
38. Cambi A, Koopman M, Figdor CG, (2005) How C-type lectins detect pathogens. Cell Microbiol 7: 481-488.
39. Takada A, Fujioka K, Tsuiji M, Morikawa A, Higashi N, et al. (2004) Human macrophage C-type lectin specific for galactose and N-acetylgalactosamine promotes filovirus entry. J Virol 78: 2943-2947.
40. Chaipan C, Soilleux EJ, Simpson P, Hofmann H, Gramberg T, et al. (2006) DC-SIGN and CLEC-2 mediate human immunodeficiency virus type 1 capture by platelets. J Virol 80: 8951-8960.
41. Thomas M, Wills M, Lehner PJ, (2008) Natural killer cell evasion by an E3 ubiquitin ligase from Kaposi's sarcoma-associated herpesvirus. Biochem Soc Trans 36: 459-463.
42. Thomas M, Boname JM, Field S, Nejentsev S, Salio M, et al. (2008) Down-regulation of NKG2D and NKp80 ligands by Kaposi's sarcoma-associated herpesvirus K5 protects against NK cell cytotoxicity. Proc Natl Acad Sci U S A 105: 1656-1661.
43. Xu ZM, Yu L, Lu XC, Han WD, Li XJ, et al. (2003) [Cloning of the full length cDNA for a novel leukemia relapse-associated candidate gene LRP15]. Zhongguo Shi Yan Xue Ye Xue Za Zhi 11: 22-26.
44. Dou LP, Wang C, Xu ZM, Kang HY, Fan H, et al. (2007) Methylation pattern of LRP15 gene in leukemia. Chin Med Sci J 22: 187-191.
45. Xu ZM, Gao WR, Mei Q, Chen J, Lu J, (2008) The novel gene LRP15 is regulated by DNA methylation and confers increased efficiency of DNA repair of ultraviolet-induced DNA damage. BMB Rep 41: 230-235.
46. Kondratov AG, Stoliar LA, Kvasha SM, Gordiyuk VV, Zgonnyk YM, et al. (2012) Methylation pattern of the putative tumor-suppressor gene LRRC3B promoter in clear cell renal cell carcinomas. Mol Med Report 5: 509-512.
47. Kim M, Kim JH, Jang HR, Kim HM, Lee CW, et al. (2008) LRRC3B, encoding a leucine-rich repeat-containing protein, is a putative tumor suppressor gene in gastric cancer. Cancer Res 68: 7147-7155.
48. Gambino R, (1997) C-reactive protein - undervalued, underutilized. Clin Chem 43: 2017-2018.
49. Atono Y, Sata M, Tanikawa K, (1989) Kinetics of C-reactive protein in acute viral hepatitis. Gastroenterol Jpn 24: 655-662.
50. Shima M, Nakao K, Kato Y, Nakata K, Ishii N, et al. (1996) Comparative study of C-reactive protein in chronic hepatitis B and chronic hepatitis C. Tohoku J Exp Med. 178: 287-297.
51. Cho SY, Choi SH, Park JH, Chung JW, (2011) Initial laboratory predictors of severe hepatitis and acute kidney injury in patients with acute hepatitis A. Diagn Microbiol Infect Dis. 69: 400-404.
52. Che W, Zhang B, Liu W, Wei Y, Xu Y, et al. (2012) Association between high-sensitivity C-reactive protein and N-Terminal Pro-B-Type Natriuretic Peptide in patients with hepatitis C virus infection. Mediators Inflamm 2012: 730923.
53. Nascimento MM, Bruchfeld A, Suliman ME, Hayashi SY, Pecoits-Filho R, et al. (2005) Effect of hepatitis C serology on C-reactive protein in a cohort of Brazilian hemodialysis patients. Braz J Med Biol Res 38: 783-788.
54. Maddaluno L, Verbrugge SE, Martinoli C, Matteoli G, Chiavelli A, et al. (2009) The adhesion molecule L1 regulates transendothelial migration and trafficking of dendritic cells. J Exp Med 206: 623-635.
55. Edwards DR, Handsley MM, Pennington CJ, (2008) The ADAM metalloproteinases. Mol Aspects Med 29: 258-289.
56. Keating DT, Sadlier DM, Patricelli A, Smith SM, Walls D, et al. (2006) Microarray identifies ADAM family members as key responders to TGF-beta1 in alveolar epithelial cells. Respir Res 7: 114.
57. Brocker CN, Vasiliou V, Nebert DW, (2009) Evolutionary divergence and functions of the ADAM and ADAMTS gene families. Hum Genomics 4: 43-55.
58. Ting CN, Burgess DL, Chamberlain JS, Keith TP, Falls K, et al. (1993) Phosphoenolpyruvate carboxykinase (GTP): characterization of the human PCK1 gene and localization distal to MODY on chromosome 20. Genomics 16: 698-706.
59. Lecube A, Hernandez C, Genesca J, Simo R, (2006) Glucose abnormalities in patients with hepatitis C virus infection: Epidemiology and pathogenesis. Diabetes Care 29: 1140-1149.
60. Qadri I, Choudhury M, Rahman SM, Knotts TA, Janssen RC, et al. (2012) Increased phosphoenolpyruvate carboxykinase gene expression and steatosis during hepatitis C virus subgenome replication: role of nonstructural component 5A and CCAAT/enhancer-binding protein beta. J Biol Chem 287: 37340-37351.