Prediction of Small, Noncoding RNAs in Bacteria Using Heterogeneous Data

Overview

Journal J Math Biol

Date 2007 Mar 14

PMID 17354017

Citations 16

Authors

Brian Tjaden

Affiliations

Soon will be listed here.

Abstract

sRNAFinder is a new gene prediction system for systematic identification of noncoding genes in bacteria. Most noncoding RNAs in prokaryotes belong to a class of genes denoted as small RNAs (sRNAs). In the model organism Escherichia coli, over 70 sRNA genes have been identified, and the existence of many more has been hypothesized. While various sources of information have proven useful for prediction of novel sRNA genes, most computational approaches do not take advantage of the disparate sources of data available for identifying these noncoding RNA genes. We present a general probabilistic method for predicting sRNA genes in bacteria. The method, based on a general Markov model, is implemented in the computational tool sRNAFinder. sRNAFinder incorporates heterogeneous data sources for gene prediction, including primary sequence data, transcript expression data from microarray experiments, and conserved RNA structure information as determined from comparative genomics analysis. We demonstrate that sRNAFinder improves upon current tools for identifying small, noncoding genes in bacteria.

Citing Articles

Devising Isolation Forest-Based Method to Investigate the sRNAome of Using sRNA-seq Data.

Maity U, Aggarwal R, Balasubramanian R, Venkatraman D, Hegde S Bioinform Biol Insights. 2024; 18:11779322241263674.

PMID: 39091283 PMC: 11292719. DOI: 10.1177/11779322241263674.

PresRAT: a server for identification of bacterial small-RNA sequences and their targets with probable binding region.

Kumar K, Chakraborty A, Chakrabarti S RNA Biol. 2020; 18(8):1152-1159.

PMID: 33103602 PMC: 8244778. DOI: 10.1080/15476286.2020.1836455.

Sequence-based bacterial small RNAs prediction using ensemble learning strategies.

Tang G, Shi J, Wu W, Yue X, Zhang W BMC Bioinformatics. 2018; 19(Suppl 20):503.

PMID: 30577759 PMC: 6302447. DOI: 10.1186/s12859-018-2535-1.

Improving E. coli growth performance by manipulating small RNA expression.

Negrete A, Shiloach J Microb Cell Fact. 2017; 16(1):198.

PMID: 29137641 PMC: 5686845. DOI: 10.1186/s12934-017-0810-x.

Identification and validation of sRNAs in Edwardsiella tarda S08.

Sun Y, Zhang J, Qin L, Yan C, Zhang X, Liu D PLoS One. 2017; 12(3):e0172783.

PMID: 28267754 PMC: 5340389. DOI: 10.1371/journal.pone.0172783.

References

Carter R, Dubchak I, Holbrook S . A computational approach to identify genes for functional RNAs in genomic sequences. Nucleic Acids Res. 2001; 29(19):3928-38. PMC: 60242. DOI: 10.1093/nar/29.19.3928. View

Selinger D, Cheung K, Mei R, Johansson E, Richmond C, Blattner F . RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat Biotechnol. 2000; 18(12):1262-8. DOI: 10.1038/82367. View

Ermolaeva M, Khalak H, White O, Smith H, Salzberg S . Prediction of transcription terminators in bacterial genomes. J Mol Biol. 2000; 301(1):27-33. DOI: 10.1006/jmbi.2000.3836. View

Hershberg R, Altuvia S, Margalit H . A survey of small RNA-encoding genes in Escherichia coli. Nucleic Acids Res. 2003; 31(7):1813-20. PMC: 152812. DOI: 10.1093/nar/gkg297. View

Lenz D, Mok K, Lilley B, Kulkarni R, Wingreen N, Bassler B . The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell. 2004; 118(1):69-82. DOI: 10.1016/j.cell.2004.06.009. View

Gottesman S . The small RNA regulators of Escherichia coli: roles and mechanisms*. Annu Rev Microbiol. 2004; 58:303-28. DOI: 10.1146/annurev.micro.58.030603.123841. View

Howe K, Chothia T, Durbin R . GAZE: a generic framework for the integration of gene-prediction data by dynamic programming. Genome Res. 2002; 12(9):1418-27. PMC: 186661. DOI: 10.1101/gr.149502. View

Workman C, KROGH A . No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution. Nucleic Acids Res. 1999; 27(24):4816-22. PMC: 148783. DOI: 10.1093/nar/27.24.4816. View

Washietl S, Hofacker I, Stadler P . Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci U S A. 2005; 102(7):2454-9. PMC: 548974. DOI: 10.1073/pnas.0409169102. View

10.

Staden R . Computer methods to locate signals in nucleic acid sequences. Nucleic Acids Res. 1984; 12(1 Pt 2):505-19. PMC: 321067. DOI: 10.1093/nar/12.1part2.505. View

11.

Flicek P, Keibler E, Hu P, Korf I, Brent M . Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map. Genome Res. 2003; 13(1):46-54. PMC: 430948. DOI: 10.1101/gr.830003. View

12.

Brejova B, Brown D, Li M, Vinar T . ExonHunter: a comprehensive approach to gene finding. Bioinformatics. 2005; 21 Suppl 1:i57-65. DOI: 10.1093/bioinformatics/bti1040. View

13.

Livny J, Fogel M, Davis B, Waldor M . sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes. Nucleic Acids Res. 2005; 33(13):4096-105. PMC: 1180744. DOI: 10.1093/nar/gki715. View

14.

Tjaden B, Saxena R, Stolyar S, Haynor D, Kolker E, Rosenow C . Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays. Nucleic Acids Res. 2002; 30(17):3732-8. PMC: 137427. DOI: 10.1093/nar/gkf505. View

15.

Zhang A, Wassarman K, Rosenow C, Tjaden B, Storz G, Gottesman S . Global analysis of small RNA and mRNA targets of Hfq. Mol Microbiol. 2003; 50(4):1111-24. DOI: 10.1046/j.1365-2958.2003.03734.x. View

16.

Yeh R, Lim L, Burge C . Computational inference of homologous gene structures in the human genome. Genome Res. 2001; 11(5):803-16. PMC: 311055. DOI: 10.1101/gr.175701. View

17.

Rivas E, Eddy S . Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics. 2002; 2:8. PMC: 64605. DOI: 10.1186/1471-2105-2-8. View

18.

Masse E, Majdalani N, Gottesman S . Regulatory roles for small RNAs in bacteria. Curr Opin Microbiol. 2003; 6(2):120-4. DOI: 10.1016/s1369-5274(03)00027-4. View

19.

Chen S, Lesnik E, Hall T, Sampath R, Griffey R, Ecker D . A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome. Biosystems. 2002; 65(2-3):157-77. DOI: 10.1016/s0303-2647(02)00013-8. View

20.

Burge C, Karlin S . Prediction of complete gene structures in human genomic DNA. J Mol Biol. 1997; 268(1):78-94. DOI: 10.1006/jmbi.1997.0951. View