RNA-seq of human reference RNA samples using a thermostable group II intron reverse transcriptase

RNA

Volumn 22, Issue 4, 2016, Pages 597-613

  Nottingham, Ryan M ^a   Wu, Douglas C ^a   Qin, Yidan ^a   Yao, Jun ^a   Hunicke Smith, Scott ^a   Lambowitz, Alan M ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

Diagnostics; High throughput sequencing; Small noncoding RNA; Transcriptome; TRNA; TruSeq

Indexed keywords

MESSENGER RNA; RNA; RNA DIRECTED DNA POLYMERASE; THERMOSTABLE GROUP II INTRON REVERSE TRANSCRIPTASE; UNCLASSIFIED DRUG; RNA SPLICING; SMALL UNTRANSLATED RNA;

ARTICLE; GENE; GENE EXPRESSION; PRIORITY JOURNAL; RNA SEQUENCE; RNA SPLICING; RNA TRANSCRIPTION; CHEMISTRY; GENE EXPRESSION PROFILING; GENETICS; HUMAN; METABOLISM; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS; STANDARD; STANDARDS;

BASE SEQUENCE; GENE EXPRESSION PROFILING; HUMANS; REFERENCE STANDARDS; RNA SPLICE SITES; RNA, MESSENGER; RNA, SMALL UNTRANSLATED; RNA-DIRECTED DNA POLYMERASE; SEQUENCE ANALYSIS, RNA;

EID: 84962533351     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.055558.115     Document Type: Article

References (55)

1. Auffinger P, Westhof E. 1998. Appendix 5: location and distribution of modified nucleotides in tRNA. In Modification and editing of RNA (ed. Grosjean H, Benne R), pp. 569-576. American Society of Microbiology Press, Washington, DC.
2. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120.
3. Burroughs AM, Ando Y, de Hoon MJ, Tomaru Y, Nishibu T, Ukekawa R, Funakoshi T, Kurokawa T, Suzuki H, Hayashizaki Y, et al. 2010. A comprehensive survey of 3′ animal miRNA modification events and a possible role for 3′ adenylation in modulating miRNA targeting effectiveness. Genome Res 20: 1398-1410.
4. Cocquet J, Chong A, Zhang G, Veitia RA. 2006. Reverse transcriptase template switching and false alternative transcripts. Genomics 88: 127-131.
5. DeLuca DS, Levin JZ, Sivachenko A, Fennell T, Nazaire MD, Williams C, Reich M, Winckler W, Getz G. 2012. RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics 28: 1530-1532.
6. Hafner M, Renwick N, Brown M, Mihailović A, Holoch D, Lin C, Pena JTG, Nusbaum JD, Morozov P, Ludwig J, et al. 2011. RNA-ligase- dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries. RNA 17: 1697-1712.
7. Hansen KD, Brenner SE, Dudoit S. 2010. Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res 38: e131.
8. Harrison GP, Mayo MS, Hunter E, Lever AM. 1998. Pausing of reverse transcriptase on retroviral RNA templates is influenced by secondary structures both 5′ and 3′ of the catalytic site. Nucleic Acids Res 26: 3433-3442.
9. Jackson TJ, Spriggs RV, Burgoyne NJ, Jones C, Willis AE. 2014. Evaluating bias-reducing protocols for RNA sequencing library preparation. BMC Genomics 15: 569.
10. Jiang L, Schlesinger F, Davis CA, Zhang Y, Li R, Salit M, Gingeras TR, Oliver B. 2011. Synthetic spike-in standards for RNA-seq experiments. Genome Res 21: 1543-1551.
11. Katibah GE, Qin Y, Sidote DJ, Yao J, Lambowitz AM, Collins K. 2014. Broad and adaptable RNA structure recognition by the human interferon- induced tetratricopeptide repeat protein IFIT5. Proc Natl Acad Sci 111: 12025-12030.
12. Katz Y, Wang ET, Airoldi EM, Burge CB. 2010. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods 7: 1009-1015.
13. Kim D, Salzberg SL. 2011. TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol 12: R72.
14. Kim D, Langmead B, Salzberg SL. 2015. HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12: 357-360.
15. Kirino Y, Mourelatos Z. 2007. Mouse Piwi-interacting RNAs are 2′-Omethylated at their 3′ termini. Nat Struct Mol Biol 14: 347-348.
16. Koppers-Lalic D, Hackenberg M, Bjinsdorp IV, van Eijndhoven MAJ, Sadek P, Sie D, Zini N, Middeldorp JM, Ylstra B, de Menezes RX, et al. 2014. Nontemplated nucleotide additions distinguish the small RNA composition in cells from exosomes. Cell Rep 8: 1649-1658.
17. Kozomara A, Griffiths-Jones S. 2014. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res 42: D68-D73.
18. Kwok CK, Ding Y, Sherlock ME, Assmann SM, Bevilacqua PC. 2013. A hybridization-based approach for quantitative and low-bias singlestranded DNA ligation. Anal Biochem 435: 181-186.
19. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357-359.
20. Lee C, Harris RA, Wall JK, Mayfield RD, Wilke CO. 2013. RNase III and T4 polynucleotide kinase sequence bias and solutions during RNAseq library construction. Biol Direct 8: 16.
21. Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, Gnirke A, Regev A. 2010. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods 7: 709-715.
22. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078-2079.
23. Li S, Tighe SW, Nicolet CM, Grove D, Levy S, Farmerie W, Viale A, Wright C, Schweitzer PA, Gao Y, et al. 2014. Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF nextgeneration sequencing study. Nat Biotechnol 32: 915-925.
24. Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15: 550.
25. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964.
26. Mader RM, Schmidt WM, Sedivy R, Rizovski B, Braun J, Kalipciyan M, Exner M, Steger GG, Mueller MW. 2001. Reverse transcriptase template switching during reverse transcriptase-polymerase chain reaction: artificial generation of deletions in ribonucleotide reductase mRNA. J Lab Clin Med 137: 422-428.
27. Malboeuf CM, Isaacs SJ, Tran NH, Kim B. 2001. Thermal effects on reverse transcription: improvement of accuracy and processivity in cDNA synthesis. Biotechniques 30: 1074-1078.
28. MAQC Consortium, Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, et al. 2006. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24: 1151-1161.
29. Mohr S, Ghanem E, SmithW, Sheeter D, Qin Y, King O, Polioudakis D, Iyer VR, Hunicke-Smith S, Swamy S, et al. 2013. Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing. RNA 19: 958-970.
30. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNAseq. Nat Methods 5: 621-628.
31. Oshlack A, Wakefield MJ. 2009. Transcript length bias in RNA-seq data confounds systems biology. Biol Direct 4: 14.
32. Ouhammouch M, Brody EN. 1992. Temperature-dependent template switching during in vitro cDNA synthesis by the AMV-reverse transcriptase. Nucleic Acids Res 20: 5443-5450.
33. Ozsolak F, Milos PM. 2011. RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 12: 87-98.
34. Parkhomchuk D, Borodina T, Amstislavskly V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A. 2009. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 37: e123.
35. Pelechano V, Steinmetz LM. 2014. Gene regulation by antisense transcription. Nat Rev Genet 14: 880-893.
36. Perocchi F, Xu Z, Clauder-Münster S, Steinmetz LM. 2007. Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Res 35: e128.
37. Qin Y, Yao J, Wu DC, Nottingham RM, Mohr S, Hunicke-Smith S, Lambowitz AM. 2016. High-throughput sequencing of human plasma RNA by using thermostable group II intron reverse transcriptases. RNA 22: 111-128.
38. Quinlan AR, Hall IM. 2010. BEDtools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
39. Raabe CA, Tang T-H, Brosius J, Rozhdestvensky TS. 2014. Biases in small RNA deep sequencing data. Nucleic Acids Res 42: 1414-1426.
40. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. 2011. Integrative genomics viewer. Nat Biotechnol 29: 24-26.
41. Ruprecht RM, Goodman NC, Spiegelman S. 1973. Conditions for the selective synthesis of DNA complementary to template RNA. Biochim Biophys Acta 294: 192-203.
42. Sai Lakshmi S, Agrawal S. 2008. piRNABank: a web resource on classified and clustered Piwi-interacting RNAs. Nucleic Acids Res 36: D173-D177.
43. SEQC/MAQC-III Consortium, Su Z, Łabaj PP, Li S, Thierry-Mieg J, Thierry-Mieg D, Shi W, Wang C, Schroth GP, Setterquist RA, et al. 2014. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat Biotechnol 32: 903-914.
44. Shen PS, Park J, Qin Y, Li X, Parsawar K, Larson MH, Cox J, Cheng Y, Lambowitz AM, Weissman JS, et al. 2015. Protein synthesis. Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains. Science 347: 75-78.
45. Shirley MD, Ma Z, Pedersen BS, Wheelan SJ. 2015. Efficient "pythonic" access to FASTA files using pyfaidx. PeerJ PrePrints 3: e1196.
46. Thorvaldsdóttir H, Robinson JT, Mesirov JP. 2013. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14: 178-192.
47. Vikman P, Fadista J, Oskolkov N. 2014. RNA sequencing: current and prospective uses in metabolic research. J Mol Endocrinol 53: R93-R101.
48. Wang Z, Gerstein M, Snyder M. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63.
49. Wery M, Descrimes M, Thermes C, Gautheret D, Morillon A. 2013. Zinc-mediated RNA fragmentation allows robust transcript reassembly upon whole transcriptome RNA-Seq. Methods 63: 25-31.
50. Westermann AJ, Gorski SA, Vogel J. 2012. Dual RNA-seq of pathogen and host. Nat Rev Microbiol 10: 618-630.
51. Wu W, Henderson LE, Copeland TD, Gorelick RJ, Bosche WJ, Rein A, Levin JG. 1996. Human immunodeficiency virus type 1 nucleocapsid protein reduces reverse transcriptase pausing at a secondary structure near the murine leukemia virus polypurine tract. J Virol 70: 7132-7142.
52. Wyman SK, Knouf EC, Parkin RK, Fritz BR, Lin DW, Dennis LM, Krouse MA, Webster PJ, Tewari M. 2011. Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity. Genome Res 21: 1450-1461.
53. Zajac P, Islam S, Hochgerner H, Lönnerberg P, Linnarsson S. 2013. Base preferences in non-templated nucleotide incorporation by MMLVderived reverse transcriptases. PLOS One 8: e85270.
54. Zheng G, Qin Y, Clark WC, Dai Q, Yi C, He C, Lambowitz AM, Pan T. 2015. Efficient and quantitative high-throughput tRNA sequencing. Nat Methods 12: 835-837.
55. Zhuang F, Fuchs RT, Sun Z, Zheng Y, Robb GB. 2012. Structural bias in T4RNA ligase-mediated 3′ adapter ligation. Nucleic Acids Res 40: e54.