The utility of shallow RNA-Seq for documenting differential gene expression in genes with high and low levels of expression

PLoS ONE

Volumn 8, Issue 12, 2013, Pages

  Atallah, Joel ^a   Plachetzki, David C ^a   Jasper, W Cameron ^a   Johnson, Brian R ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA; TRANSCRIPTION FACTOR;

ANIMAL STRUCTURES; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DIFFERENTIAL GENE EXPRESSION; DIGESTIVE SYSTEM; GENE EXPRESSION; GENETIC ANALYSIS; HONEYBEE; NONHUMAN; RNA SEQUENCE; SHALLOW RNA SEQUENCE; STING GLAND; TISSUE SPECIFICITY;

ANIMALS; BEES; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION FACTORS; TRANSCRIPTOME;

EID: 84892657766     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0084160     Document Type: Article

References (46)

1. Denoeud F, Aury JM, Da Silva C, Noel B, Rogier O et al. (2008) Annotating genomes with massive-scale RNA sequencing. Genome Biol 9: 12. doi:10.1186/gb-2008-9-1-r12. PubMed: 19087247.
2. Stapley J, Reger J, Feulner PGD, Smadja C, Galindo J et al. (2010) Adaptation genomics: the next generation. Trends Ecol Evol 25: 705-712. doi:10.1016/j.tree.2010.09.002. PubMed: 20952088.
3. Raha D, Wang Z, Moqtaderi Z, Wu LF, Zhong GN et al. (2010) Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci U S A 107: 3639-3644. doi:10.1073/pnas.0911315106. PubMed: 20139302.
4. Xiong YY, Chen XS, Chen ZD, Wang XZ, Shi SH et al. (2010) RNA sequencing shows no dosage compensation of the active X-chromosome. Nat Genet 42: 1043-U1029. doi:10.1038/ng.711.PubMed: 21102464.
5. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628. doi:10.1038/nmeth.1226. PubMed: 18516045.
6. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63. doi:10.1038/nrg2484. PubMed: 19015660.
7. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y (2008) RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18: 1509-1517. doi:10.1101/gr.079558.108. PubMed: 18550803.
8. Hawkins RD, Hon GC, Ren B (2010) Next-generation genomics: an integrative approach. Nat Rev Genet 11: 476-486. PubMed: 20531367.
9. van Bakel H, Nislow C, Blencowe BJ, Hughes TR (2010) Most "Dark Matter" Transcripts Are Associated With Known Genes. PLOS Biology 8: 21.
10. Hallegger M, Llorian M, Smith CWJ (2010) Alternative splicing: global insights. FEBS J 277: 856-866. doi:10.1111/j.1742-4658.2009.07521.x. PubMed: 20082635.
11. Pepke S, Wold B, Mortazavi A (2009) Computation for ChIP-seq and RNA-seq studies. Nat Methods 6: S22-S32. doi:10.1038/nmeth.1371. PubMed: 19844228.
12. Ouyang ZQ, Zhou Q, Wong WH (2009) ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc Natl Acad Sci U S A 106: 21521-21526. doi:10.1073/pnas.0904863106. PubMed: 19995984.
13. Sharma CM, Vogel J (2009) Experimental approaches for the discovery anal characterization of regulatory small. RNA - Current Opinion in Microbiology 12: 536-546. doi:10.1016/j.mib.2009.07.006.
14. Boyle AP, Song LY, Lee BK, London D, Keefe D et al. (2011) High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res 21: 456-464. doi:10.1101/gr.112656.110. PubMed: 21106903.
15. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111. doi:10.1093/ bioinformatics/btp120. PubMed: 19289445.
16. Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106-. PubMed: 20979621.
17. Goecks J, Nekrutenko A, Taylor J, Galaxy T (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11: R86-. PubMed: 20738864.
18. Tarazona S, García-Alcalde F, Dopazo J, Ferrer A, Conesa A (2011) Differential expression in RNA-seq: A matter of depth. Genome Res 21: 2213-2223. doi:10.1101/gr.124321.111. PubMed: 21903743.
19. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D et al. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349. doi:10.1126/science.1158441. PubMed: 18451266.
20. Ramsköld D, Wang ET, Burge CB, Sandberg R (2009) An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data. PLoS Comput Biol 5: 11. PubMed: 20011106.
21. Perkins TT, Kingsley RA, Fookes MC, Gardner PP, James KD et al. (2009) A Strand-Specific RNA-Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi. PLOS Genetics 5.
22. Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y (2010) Sex-specific and lineage-specific alternative splicing in primates. Genome Res 20: 180-189. doi:10.1101/gr.099226.109. PubMed: 20009012.
23. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B et al. (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25: 1915-1927. doi:10.1101/gad.17446611. PubMed: 21890647.
24. Li H, Lovci MT, Kwon YS, Rosenfeld MG, Fu XD et al. (2008) Determination of tag density required for digital transcriptome analysis: Application to an androgen-sensitive prostate cancer model. Proc Natl Acad Sci U S A 105: 20179-20184. doi:10.1073/pnas.0807121105. PubMed: 19088194.
25. Blencowe BJ, Ahmad S, Lee LJ (2009) Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes. Genes Dev 23: 1379-1386. doi:10.1101/gad.1788009. PubMed: 19528315.
26. Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM (2009) A census of human transcription factors: function, expression and evolution. Nat Rev Genet 10: 252-263. doi:10.1038/nrg2538. PubMed: 19274049.
27. Farnham PJ (2009) Insights from genomic profiling of transcription factors. Nat Rev Genet 10: 605-616. doi:10.1038/nrg2636. PubMed: 19668247.
28. Hudson NJ, Reverter A, Wang YH, Greenwood PL, Dalrymple BP (2009) Inferring the Transcriptional Landscape of Bovine Skeletal Muscle by Integrating Co-Expression. Networks - PLOS ONE 4: 14.
29. King TP, Spangfort MD (2000) Structure and biology of stinging insect venom allergens. Int Arch Allergy Immunol 123: 99-106. doi:10.1159/000024440. PubMed: 11060481.
30. Hoffman DR (2006) Hymenoptera venom allergens. Clinical Reviews in Allergy and Immunology 30: 109-128. doi:10.1385/CRIAI:30:2:109.
31. Peiren N, de Graaf DC, Vanrobaeys F, Danneels EL, Devreese B et al. (2008) Proteomic analysis of the honey bee worker venom gland focusing on the mechanisms of protection against tissue damage. Toxicon 52: 72-83. doi:10.1016/j.toxicon.2008.05.003. PubMed: 18573272.
32. Owen MD, Bridges AR (1976) Aging in venom glands of queen and worker honey bees (Apis mellifera L): some morphological and chemical observations. Toxicon 14: 1-&
33. Roat TC, Nocelli RCF, de Moraes R, Cruz-Landim C (2004) Juvenile hormone effect on the venom gland secretory cycle in workers of Apis mellifera (Hymenoptera, apidae). Sociobiology 43: 193-199.
34. Owen MD, Pfaff LA (1995) Melittin synthesis in the venom system of the honey bee (Apis mellifera L.) Toxicon 33: 1181-1188
35. Kliebenstein DJ (2012) Exploring the shallow end: estimating information content in transcriptomics studies. Frontiers in Plant Science 3: 213. PubMed: 22973290.
36. Kumar R, Ichihashi Y, Kimura S, Chitwood DH, Headland LR et al. (2012) A high-throughput method for illumina RNA-Seq library preparation. Front - Plant Sci 3: 202. PubMed: 22973283.
37. Whitfield CW, Ben-Shahar Y, Brillet C, Leoncini I, Crauser D et al. (2006) Genomic dissection of behavioral maturation in the honey bee. Proc Natl Acad Sci U S A 103: 16068-16075. doi:10.1073/pnas.0606909103. PubMed: 17065327.
38. Johnson BR (2008) Within-nest temporal polyethism in the honey bee. Behavioral Ecology and Sociobiology 62: 777-784. doi:10.1007/s00265-007-0503-2.
39. Wegener J, Lorenz MW, Bienefeld K (2009) Physiological consequences of prolonged nursing in the honey bee. Insects Sociaux 56: 85-93. doi:10.1007/s00040-008-1042-1.
40. Johnson BR (2010) Division of labor in honeybees: form, function, and proximate mechanisms. Behav Ecol Sociobiol 64: 305-316. doi: 10.1007/s00265-009-0874-7. PubMed: 20119486.
41. Martin M.Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, North America, 17, May 2011. Available at: http://journal.embnet.org/index.php/embnetjournal/article/view/200.
42. Lourenço AP, Mackert A, Cristino A, dos S, Simões ZLP (2008) Validation of reference genes for gene expression studies in the honey bee, Apis mellifera, by quantitative real-time RT-PCR. Apidologie 39: 372-385. doi:10.1051/apido:2008015.
43. Bullard JH, Purdom E, Hansen KD, Dudoit S (2010) Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. Bmc Bioinformatics 11: 13. doi: 10.1186/1471-2105-11-S6-S13. PubMed: 20055994.
44. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676. doi:10.1093/ bioinformatics/bti610. PubMed: 16081474.
45. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402. doi:10.1093/nar/25.17.3389. PubMed: 9254694.
46. Shpigler H, Patch HM, Cohen M, Fan Y, Grozinger CM et al. (2010) The transcription factor Kruppel homolog 1 is linked to hormone mediated social organization in bees. Bmc. Evolutionary Biology 10.