RNA-Sequencing: A tool to explore new frontiers in animal genetics

Livestock Science

Volumn 166, Issue 1, 2014, Pages 206-216

  Wickramasinghe, Saumya ^a   Cánovas, Angela ^a   Rincón, Gonzalo ^a,b   Medrano, Juan F ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b ZOETIS   (United States)

Author keywords

Gene expression; Next generation sequencing; RNA; SNP discovery

Indexed keywords

ANIMALIA;

EID: 84905585815     PISSN: 18711413     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.livsci.2014.06.015     Document Type: Article

References (98)

1. Alwine J.C., Kemp D.J., Stark G.R. Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes. Proc. Natl. Acad. Sci. USA 1977, 74:5350-5354.
2. Anders S., Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010, 11:R106.
3. Asmann Y., Klee E., Thompson E.A., Perez E., Middha S., Oberg A., Therneau T., Smith D., Poland G., Wieben E., Kocher J.-P. 3' Tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer. BMC Genomics 2009, 10:531.
4. Auer P.L., Doerge R.W. Statistical design and analysis of RNA sequencing data. Genetics 2010, 185:405-416.
5. Babbitt C.C., Tung J., Wray G.A., Alberts S.C. Changes in gene expression associated with reproductive maturation in wild female baboons. Genome Biol. Evol. 2012, 4:102-109.
6. Baldwin R.L., Li R.W., Li C.J., Thomson J.M., Bequette B.J. Characterization of the longissimus lumborum transcriptome response to adding propionate to the diet of growing Angus beef steers. Physiol. Genomics 2012, 44:543-550.
7. Bashir A., Volik S., Collins C., Bafna V., Raphael B.J. Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PLoS Comput. Biol. 2008, 4:e1000051.
8. Becker-André M., Hahlbrock K. Absolute mRNA quantification using the polymerase chain reaction (PCR). A novel approach by a. Nucleic Acids Res. 1989, 17:9437-9446.
9. Bennett S., Solexa Ltd, Pharmacogenomics 5, 2004, 433-438.
10. Busby M.A., Stewart C., Miller C.A., Grzeda K.R., Marth G.T. Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression. Bioinformatics 2013, 29:656-657.
11. Cánovas A., Rincon G., Islas-Trejo A., Wickramasinghe S., Medrano J.F. SNP discovery in the bovine milk transcriptome using RNA-Seq technology. Mamm. Genome 2010, 1-7.
12. Cánovas A., Rincon G., Islas-Trejo A., Jimenez-Flores R., Laubscher A., Medrano J.F. RNA sequencing to study gene expression and single nucleotide polymorphism variation associated with citrate content in cow milk. J. Dairy Sci. 2013, 96:2637-2648.
13. Cánovas A., Rincon G., Bevilacqua C., Islas-Trejo A., Brenaut P., Hovey R.C., Boutinaud M., Morgenthaler C., VanKlompenberg M.K., Martin P., Medrano J.F. Comparison of five different RNA sources to examine the lactating bovine mammary gland transcriptome using RNA-Sequencing. Sci. Rep 2014, 4:5297. 10.1038/srep05297.
14. Capuco A.V., Binelli M., Tucker H.A. Neither bovine somatotropin nor growth hormone-releasing factor alters expression of thyroid hormone receptors in liver and mammary tissues. J. Dairy Sci. 2011, 94:4915-4921.
15. Chen G., Wang C., Shi T. Overview of available methods for diverse RNA-Seq data analyses. Sci. China Life Sci. 2011, 54:1121-1128.
16. Chepelev I., Wei G., Tang Q., Zhao K. Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq. Nucl. Acids Res. 2009, 37:e106.
17. Chitwood J.L., Rincon G., Kaiser G.G., Medrano J.F., Ross P.J. RNA-Seq analysis of single bovine blastocysts. BMC Genomics 2013, 14:350.
18. Cirulli E.T., Singh A., Shianna K.V., Ge D., Smith J.P., Maia J.M., Heinzen E.L., Goedert J.J., Goldstein D.B. Screening the human exome: a comparison of whole genome and whole transcriptome sequencing. Genome Biol. 2010, 11:R57.
19. Cloonan N., Forrest A., Kolle G., Gardiner B., Faulkner G., Brown M., Taylor D., Steptoe A., Wani S., Bethel G., Robertson A., Perkins A., Bruce S., Lee C., Ranade S., Peckham H., Manning J., McKernan K., Grimmond S. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat. Methods 2008, 5:613-619.
20. Cloonan N., Grimmond S. Transcriptome content and dynamics at single-nucleotide resolution. Genome Biol. 2008, 9:234.
21. Coleman S.J., Zeng Z., Hestand M.S., Liu J., Macleod J.N. Analysis of unannotated equine transcripts identified by mRNA sequencing. PLoS One 2013, 8:e70125.
22. Coleman S., Zeng Z., Liu J., MacLeod J. Analysis of equine protein-coding gene structure and expression by RNA-sequencing. BMC Bioinform. 2010, 11:O8.
23. Croucher N.J., Thomson N.R. Studying bacterial transcriptomes using RNA-seq. Curr. Opin. Microbiol. 2010, 13:619-624.
24. de Lima Morais D.A., Fang H., Rackham O.J.L., Wilson D., Pethica R., Chothia C., Gough J. SUPERFAMILY 1.75 including a domain-centric gene ontology method. Nucleic Acids Res. 2011, 39:D427-D434.
25. Djari A., Esquerre D., Weiss B., Martins F., Meersseman C., Boussaha M., Klopp C., Rocha D. Gene-based single nucleotide polymorphism discovery in bovine muscle using next-generation transcriptomic sequencing. BMC Genomics 2013, 14:307.
26. Delseny M., Han B., Hsing Y. High throughput DNA sequencing: The new sequencing revolution. Plant. Sci. 2010, 179:407-422.
27. Denoeud F., Aury J.-M., Da Silva C., Noel B., Rogier O., Delledonne M., Morgante M., Valle G., Wincker P., Scarpelli C., Jaillon O., Artiguenave F. Annotating genomes with massive-scale RNA sequencing. Genome Biol. 2008, 9:R175.
28. Di C.Z., Liang K.Y. Likelihood ratio testing for admixture models with application to genetic linkage analysis. Biometrics 2011, 67:1249-1259.
29. Driver A., Penagaricano F., Huang W., Ahmad K., Hackbart K., Wiltbank M., Khatib H. RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo- and in vitro-derived bovine blastocysts. BMC Genomics 2012, 13:118.
30. Esteve-Codina A., Kofler R., Palmieri N., Bussotti G., Notredame C., Perez-Enciso M. Exploring the gonad transcriptome of two extreme male pigs with RNA-seq. BMC Genomics 2011, 12:552.
31. Filichkin S.A., Priest H.D., Givan S.A., Shen R., Bryant D.W., Fox S.E., Wong W.-K., Mockler T.C. Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res. 2010, 20:45-58.
32. Frias-Lopez J., Shi Y., Tyson G.W., Coleman M.L., Schuster S.C., Chisholm S.W., DeLong E.F. Microbial community gene expression in ocean surface waters. Proc. Natl. Acad. Sci. 2008, 105:3805-3810.
33. Fu X., Fu N., Guo S., Yan Z., Xu Y., Hu H., Menzel C., Chen W., Li Y., Zeng R., Khaitovich P. Estimating accuracy of RNA-Seq and microarrays with proteomics. BMC Genomics 2009, 10:161.
34. Gautier L., Cope L., Bolstad B.M., Irizarry R.A. affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004, 20:307-315.
35. Gowda M., Jantasuriyarat C., Dean R.A., Wang G.-L. Robust-LongSAGE (RL-SAGE): a substantially improved LongSAGE method for gene discovery and transcriptome analysis. Plant Physiol. 2004, 134:890-897.
36. Hanina S.A., Mifsud W., Down T.A., Hayashi K., O'Carroll D., Lao K., Miska E.A., Surani M.A. Genome-wide identification of targets and function of individual microRNAs in mouse embryonic stem cells. PLoS Genet. 2010, 6:e1001163.
37. Holley R.W., Apgar J., Everett G.A., Madison J.T., Marquisee M., Merrill S.H., Penswick J.R., Zamir A. Structure of a ribonucleic acid. Science 1965, 147:1462-1465.
38. Huang W., Yandell B.S., Khatib H. Transcriptomic profiling of bovine IVF embryos revealed candidate genes and pathways involved in early embryonic development. BMC Genomics 2010, 11:23.
39. Huang W., Nadeem A., Zhang B., Babar M., Soller M., Khatib H. Characterization and comparison of the leukocyte transcriptomes of three cattle breeds. PLoS One 2012, 7:e30244.
40. Jager M., Ott C.-E., Grunhagen J., Hecht J., Schell H., Mundlos S., Duda G., Robinson P., Lienau J. Composite transcriptome assembly of RNA-seq data in a sheep model for delayed bone healing. BMC Genomics 2011, 12:158.
41. Jung W.Y., Kwon S.G., Son M., Cho E.S., Lee Y., Kim J.H., Kim B.-W., Park D.H., Hwang J.H., Kim T.W., Park H.C., Park B.Y., Choi J.-S., Cho K.K., Chung K.H., Song Y.M., Kim I.S., Jin S.K., Kim D.H., Lee S.-W., Lee K.W., Bang W.Y., Kim C.W. RNA-Seq approach for genetic improvement of meat quality in pig and evolutionary insight into the substrate specificity of animal carbonyl reductases. PLoS One 2012, 7:e42198.
42. Lamont E.A., Xu W.W., Sreevatsan S. Host-Mycobacterium avium subsp. paratuberculosis interactome reveals a novel iron assimilation mechanism linked to nitric oxide stress during early infection. BMC Genomics 2013, 14:694.
43. Langmead B., Hansen K., Leek J. Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biol. 2010, 11:R83.
44. Li R., Schroeder S. Cytoskeleton remodeling and alterations in smooth muscle contractility in the bovine jejunum during nematode infection. Funct. Integr. Genomics 2012, 12:35-44.
45. Li T., Wang S., Wu R., Zhou X., Zhu D., Zhang Y. Identification of long non-protein coding RNAs in chicken skeletal muscle using next generation sequencing. Genomics 2012, 99:292-298.
46. Loman N.J., Misra R.V., Dallman T.J., Constantinidou C., Gharbia S.E., Wain J., Pallen M.J. Performance comparison of benchtop high-throughput sequencing platforms. Nat. Biotechnol. 2012, 30:434-439.
47. Mamo S., Mehta J.P., Forde N., McGettigan P., Lonergan P. Conceptus-endometrium crosstalk during maternal recognition of pregnancy in cattle. Biol. Reprod. 2012, 87(6):1-9.
48. Mardis E.R. The impact of next-generation sequencing technology on genetics. Trends Genet. 2008, 24:133-141.
49. Marguerat S., Wilhelm B., Bähler J. Next-generation sequencing: applications beyond genomes. Biochem. Soc. Trans. 2008, 36:1091-1096.
50. Marioni J., Mason C., Mane S., Stephens M., Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 2008, 18:1509-1517.
51. Martí E., Pantano L., Bañez-Coronel M., Llorens F., Miñones-Moyano E., Porta S., Sumoy L., Ferrer I., Estivill X. A myriad of miRNA variants in control and Huntington[U+05F3]s disease brain regions detected by massively parallel sequencing. Nucleic Acids Res. 2010, 38:7219-7235.
52. Matsumura H., Ito A., Saitoh H., Winter P., Kahl G., Reuter M., Krüger D.H., Terauchi R. SuperSAGE. Cell. Microbiol. 2005, 7:11-18.
53. McCabe M., Waters S., Morris D., Kenny D., Lynn D., Creevey C. RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balance. BMC Genomics 2012, 13:193.
54. McGivney B., McGettigan P., Browne J., Evans A., Fonseca R., Loftus B., Lohan A., MacHugh D., Murphy B., Katz L., Hill E. Characterization of the equine skeletal muscle transcriptome identifies novel functional responses to exercise training. BMC Genomics 2010, 11:398.
55. Medrano, J.F., Rincon, G., Islas-Trejo, A., 2010. Comparative analysis of bovine milk and mammary gland transcriptome using RNA-Seq. In: Proceedings of the 9th World Congress of Genetics Applied to Livestock Production. Leipzig, Germany, 2010, no. 0852. http://www.kongressband.de/wcgalp2010/assets/pdf/0852.pdf.
56. Meydan H., Yildiz M.A., Dodgson J.B., Cheng H.H. Allele-specific expression analysis reveals CD79B has a cis-acting regulatory element that responds to Marek[U+05F3]s disease virus infection in chickens. Poult. Sci. 2011, 90:1206-1211.
57. Minoche A., Dohm J., Himmelbauer H. Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems. Genome Biol. 2011, 12:R112.
58. Mockler T.C., Ecker J.R. Applications of DNA tiling arrays for whole-genome analysis. Genomics 2005, 85:1-15.
59. Morera D., Roher N., Ribas L., Balasch J.C., Doñate C., Callol A., Boltaña S., Roberts S., Goetz G., Goetz F.W., MacKenzie S.A. RNA-Seq reveals an integrated immune response in nucleated erythrocytes. PLoS One 2011, 6:e26998.
60. Morera L.P., Diaz N.M., Guido M.E. A novel method to prepare highly enriched primary cultures of chicken retinal horizontal cells. Exp. Eye. Res. 2012, 101:44-48.
61. Morozova O., Hirst M., Marra M.A. Applications of new sequencing technologies for transcriptome analysis. Annu. Rev. Genomics Hum. Genet. 2009, 10:135-151.
62. Mortazavi A., Williams B.A., McCue K., Schaeffer L., Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 2008, 5:621-628.
63. Nagalakshmi U., Waern K., Snyder M. RNA-Seq: A Method for Comprehensive Transcriptome Analysis 2001, John Wiley & Sons, Inc.
64. Nalpas N.C., Park S.D., Magee D.A., Taraktsoglou M., Browne J.A., Conlon K.M., Rue-Albrecht K., Killick K.E., Hokamp K., Lohan A.J., Loftus B.J., Gormley E., Gordon S.V., Machugh D.E. Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro. BMC Genomics 2013, 14:230.
65. Oshlack A., Robinson M., Young M. From RNA-seq reads to differential expression results. Genome Biol. 2010, 11:220.
66. Park K.-D., Park J., Ko J., Kim B., Kim H.-S., Ahn K., Do K.-T., Choi H., Kim H.-M., Song S., Lee S., Jho S., Kong H.-S., Yang Y., Jhun B.-H., Kim C., Kim T.-H., Hwang S., Bhak J., Lee H.-K., Cho B.-W. Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq. BMC Genomics 2012, 13:473.
67. Pérez-Montarelo D., Madsen O., Alves E., Rodríguez M.C., Folch J.M., Noguera J.L., Groenen M.A., Fernández A.I. Identification of genes regulating growth and fatness traits in pig through hypothalamic transcriptome analysis. Physiol. Genomics 2014, 46:195-206.
68. Pickrell J.K., Marioni J.C., Pai A.A., Degner J.F., Engelhardt B.E., Nkadori E., Veyrieras J.-B., Stephens M., Gilad Y., Pritchard J.K. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 2010, 464:768-772.
69. Qi M., Wang P., O'Toole N., Barboza P.S., Ungerfeld E., Leigh M.B., Selinger L.B., Butler G., Tsang A., McAllister T.A., Forster R.J. Snapshot of the eukaryotic gene expression in muskoxen rumen-a metatranscriptomic approach. PLoS One 2011, 6:e20521.
70. Reinartz J., Bruyns E., Lin J.-Z., Burcham T., Brenner S., Bowen B., Kramer M., Woychik R. Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organisms. Brief. Funct. Genomics Proteomics 2002, 1:95-104.
71. Robinson M., Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010, 11:R25.
72. Robinson M.D., McCarthy D.J., Smyth G.K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010, 26:139-140.
73. Robles J.A., Qureshi S.E., Stephen S.J., Wilson S.R., Burden C.J., Taylor J.M. Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing. BMC Genomics 2012, 13:484.
74. Saha S., Sparks A.B., Rago C., Akmaev V., Wang C.J., Vogelstein B., Kinzler K.W., Velculescu V.E. Using the transcriptome to annotate the genome. Nat. Biotechnol. 2002, 20:508-512.
75. Salem, M., 2012. Next-generation sequencing and functional genomic analysis in Rainbow Trout. In: Functional Genomics in Aquaculture, (Eds.) M. Saroglia and Z. (John) Liu, Wiley-Blackwell, pp. 321-337.
76. Schena M., Shalon D., Davis R.W., Brown P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270:467-470.
77. Scholey R.A., Evans N.J., Blowey R.W., Massey J.P., Murray R.D., Smith R.F., Ollier W.E., Carter S.D. Identifying host pathogenic pathways in bovine digital dermatitis by RNA-Seq analysis. Vet. J. 2013, 197:699-706.
78. Sengupta S., Bolin J.M., Ruotti V., Nguyen B.K., Thomson J.A., Elwell A.L., Stewart R. Single read and paired end mRNA-Seq Illumina Libraries from 10 nanograms total RNA. J. Vis. Exp. 2011, e3340.
79. Sharma C.M., Hoffmann S., Darfeuille F., Reignier J., Findeisz S., Sittka A., Chabas S., Reiche K., Hackermuller J., Reinhardt R., Stadler P.F., Vogel J. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 2010, 464:250-255.
80. Smith A.M., Heisler L.E., Onge R.P., Farias-Hesson E., Wallace I.M., Bodeau J., Harris A.N., Perry K.M., Giaever G., Pourmand N., Nislow C. Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples. Nucleic Acids Res. 2010, 38:e142.
81. Stefani G., Slack F.J. Small non-coding RNAs in animal development. Nat. Rev. Mol. Cell Biol. 2008, 9:219-230.
82. Stone E.M., Rothblum K.N., Alevy M.C., Kuo T.M., Schwartz R.J. Complete sequence of the chicken glyceraldehyde-3-phosphate dehydrogenase gene. Proc. Natl. Acad. Sci. USA 1985, 82:1628-1632.
83. Sultan M., Schulz M., Richard H., Magen A., Klingenhoff A., Scherf M., Seifert M., Borodina T., Soldatov A., Parkhomchuk D. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 2008, 321:956-960.
84. Tarazona S., Garcia-Alcalde F., Dopazo J., Ferrer A., Conesa A. Differential expression in RNA-seq: a matter of depth. Genome Res. 2011, 21:2213-2223.
85. Trapnell C., Salzberg S.L. How to map billions of short reads onto genomes. Nat. Biotechnol. 2009, 27:455-457.
86. Walsh S.W., Mehta J.P., McGettigan P.A., Browne J.A., Forde N., Alibrahim R.M., Mulligan F.J., Loftus B., Crowe M.A., Matthews D., Diskin M., Mihm M., Evans A.C.O. Effect of the metabolic environment at key stages of follicle development in cattle: focus on steroid biosynthesis. Physiol. Genomics 2012, 44:504-517.
87. Wang E.T., Sandberg R., Luo S., Khrebtukova I., Zhang L., Mayr C., Kingsmore S.F., Schroth G.P., Burge C.B. Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456:470-476.
88. Wang L., Xi Y., Yu J., Dong L., Yen L., Li W. A statistical method for the detection of alternative splicing using RNA-Seq. PLoS One 2010, 5:e8529.
89. Wang X., Sun Q., McGrath S.D., Mardis E.R., Soloway P.D., Clark A.G. Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS One 2008, 3:e3839.
90. Wang Z., Gerstein M., Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009, 10:57-63.
91. Wickramasinghe S., Hua S., Rincon G., Islas-Trejo A., German J.B., Lebrilla C.B., Medrano J.F. Transcriptome profiling of bovine milk oligosaccharide metabolism genes using RNA-Sequencing. PLoS One 2011, 6:e18895.
92. Wickramasinghe S., Rincon G., Islas-Trejo A., Medrano J. Transcriptional profiling of bovine milk using RNA sequencing. BMC Genomics 2012, 13:45.
93. Wilhelm B.T., Landry J.-R. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Methods 2009, 48:249-257.
94. Wurtzel O., Sapra R., Chen F., Zhu Y., Simmons B.A., Sorek R. A single-base resolution map of an archaeal transcriptome. Genome. Res. 2010, 20:133-141.
95. Xie C., Zhang Y.E., Chen J.-Y., Liu C.-J., Zhou W.-Z., Li Y., Zhang M., Zhang R., Wei L., Li C.-Y. Hominoid-specific de novo protein-coding genes originating from long non-coding RNAs. PLoS Genet. 2012, 8:e1002942.
96. Yoder-Himes D.R., Chain P.S., Zhu Y., Wurtzel O., Rubin E.M., Tiedje J.M., Sorek R. Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc. Natl. Acad. Sci 2009, 106:3976-3981.
97. Zhang G., Guo G., Hu X., Zhang Y., Li Q., Li R., Zhuang R., Lu Z., He Z., Fang X., Chen L., Tian W., Tao Y., Kristiansen K., Zhang X., Li S., Yang H., Wang J., Wang J. Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res. 2010, 20:646-654.
98. Zhang S.J., Liu C.J., Shi M., Kong L., Chen J.Y., Zhou W.Z., Zhu X., Yu P., Wang J., Yang X., Hou N., Ye Z., Zhang R., Xiao R., Zhang X., Li C.Y RhesusBase: a knowledgebase for the monkey research community. Nucleic. Acids Res. 2013, 41:D892-D905. (database issue).