Abstract
Diverse bacteria encode RNAs that are not translated into proteins but are instead involved in regulating a wide variety of cellular functions. Computational approaches have proven successful in identifying numerous regulatory RNAs in myriad bacterial species but the difficultly of implementing most of these approaches has limited their accessibility to many researchers. Moreover, few of these approaches provide annotations of predicted loci to guide downstream experimental validation and characterization. Here I describe the implementation of SIPHT, a web-accessible program that enables screens for putative loci encoding regulatory RNAs to be conducted in any of nearly 2,000 sequenced bacterial replicons. SIPHT identifies candidate loci by searching for regions of intergenic sequence conservation upstream of predicted intrinsic transcription terminators. Each locus is then annotated for numerous features that provide clues about its potential function and/or enable the most reliable candidates to be identified.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Altuvia S (2007) Identification of bacterial small non-coding RNAs: experimental approaches. Curr Opin Microbiol 10:257–261
Sorek R, Cossart P (2010) Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat Rev Genet 11:9–16
Weissenmayer BA et al (2011) Sequencing illustrates the transcriptional response of Legionella pneumophila during infection and identifies seventy novel small non-coding RNAs. PLoS One 6:e17570
Liu JM et al (2009) Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing. Nucleic Acids Res 37:e46
Livny J, Waldor MK (2010) Mining regulatory 5′UTRs from cDNA deep sequencing datasets. Nucleic Acids Res 38:1504–1514
Irnov I et al (2010) Identification of regulatory RNAs in Bacillus subtilis. Nucleic Acids Res 38:6637–6651
Sharma CM et al (2010) The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464:250–255
Mraheil MA et al (2011) The intracellular sRNA transcriptome of Listeria monocytogenes during growth in macrophages. Nucleic Acids Res 39:4235–4248
Livny J, Waldor MK (2007) Identification of small RNAs in diverse bacterial species. Curr Opin Microbiol 10:96–101
Lu X et al (2011) Assessing computational tools for the discovery of small RNA genes in bacteria. RNA 17:1635–1647
Livny J et al (2008) High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs. PLoS One 3:e3197
Valverde C et al (2008) Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011. BMC Genomics 9:416
Faucher SP et al (2010) Legionella pneumophila 6S RNA optimizes intracellular multiplication. Proc Natl Acad Sci USA 107:7533–7538
Dichiara JM et al (2010) Multiple small RNAs identified in Mycobacterium bovis BCG are also expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis. Nucleic Acids Res 38:4067–4078
Postic G et al (2010) Identification of small RNAs in Francisella tularensis. BMC Genomics 11:625
Altschul SF et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
Macke TJ et al (2001) RNAMotif, an RNA secondary structure definition and search algorithm. Nucleic Acids Res 29:4724–4735
Kingsford CL et al (2007) Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol 8:R22
Wassarman K et al (2001) Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev 15:1637–1651
Barrick JE, Breaker RR (2007) The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol 8:R239
Gardner PP et al (2011) Rfam: Wikipedia, clans and the “decimal” release. Nucleic Acids Res 39:D141–D145
Hulton CS et al (1991) ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol Microbiol 5:825–834
Rivas E et al (2001) Computational identification of noncoding RNAs in E. coli by comparative genomics. Curr Biol 11:1369–1373
van Helden J (2003) Regulatory sequence analysis tools. Nucleic Acids Res 31:3593–3596
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Livny, J. (2012). Bioinformatic Discovery of Bacterial Regulatory RNAs Using SIPHT. 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_1
Download citation
DOI: https://doi.org/10.1007/978-1-61779-949-5_1
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-61779-948-8
Online ISBN: 978-1-61779-949-5
eBook Packages: Springer Protocols