Abstract
Whole-genome tiling arrays are powerful tools for detecting and characterizing novel RNA transcripts. Here, we describe a complete method combining elements of molecular and computational biology to identify small noncoding RNA (sRNA) transcripts. We focus on the key features of this approach, which include size-fractionation of input RNA, direct detection of array hybridization with antibodies that recognize RNA:DNA hybrids, and correlation-based computational methods for automated sRNA identification and boundary determination.
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References
Sharma CM, Vogel J (2009) Experimental approaches for the discovery and characterization of regulatory sRNA. Curr Opin Microbiol 12:536–546
Waters LS, Storz G (2009) Regulatory RNAs in bacteria. Cell 136:615–628
Zhang A, Wassarman KM, Rosenow C, Tjaden BC, Storz G, Gottesman S (2003) Global analysis of small RNA and mRNA targets of Hfq. Mol Microbiol 50:1111–1124
Hu Z, Zhang A, Storz G, Gottesman S, Leppla SH (2006) An antibody-based microarray assay for small RNA detection. Nucleic Acids Res 34:e52
Gautier L, Cope L, Bolstad BM, Irizarry RA (2004) affy—analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20:307–315
Landt SG, Abeliuk E, McGrath PT, Lesley JA, McAdams HH, Shapiro L (2008) Small non-coding RNAs in Caulobacter crescentus. Mol Microbiol 68:600–614
Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A (2005) Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 33:D121–D124
Delcher AL, Bratke KA, Powers EC, Salzberg SL (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673–679
Lukashin A, Borodovsky M (1998) GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res 26:1107–1115
Kingsford K, Ayanbule K, Salzberg SL (2007) Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol 8:R22
McGrath PT, Lee H, Zhang L, Iniesta AA, Hottes AK, Tan MH et al (2007) High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons. Nat Biotechnol 25:584–592
Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31:e15
Ideker T, Thorsson V, Siegel AF, Hood LE (2001) Testing for differentially expressed genes by maximum-likelihood analysis of microarray data. J Comput Biol 7:805–818
Li C, Wong WH (2001) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci U S A 98:31–36
Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19:185–193
Acknowledgements
This work was supported by NIH grants GM51426 and GM32506, by DOE grants DE-FG03ER63219-A001 and DE-FG02ER63219, and also supported by the Stanford NIH Genome Training Grant (SGL).
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Landt, S.G., Abeliuk, E. (2012). A Strategy for Identifying Noncoding RNAs Using Whole-Genome Tiling Arrays. In: Keiler, K. (eds) Bacterial Regulatory RNA. Methods in Molecular Biology, vol 905. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-949-5_3
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DOI: https://doi.org/10.1007/978-1-61779-949-5_3
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