Identification and classification of conserved RNA secondary structures in the human genome

Pedersen, J. S., Bejerano, G., Siepel, A., Rosenbloom, K., Lindblad-Toh, K., Lander, E. S., Kent, J., Miller, W., Haussler, D. (2006) Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol, 2 (4). e33. ISSN 1553-734x

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URL: http://www.ncbi.nlm.nih.gov/pubmed/16628248
DOI: 10.1371/journal.pcbi.0020033

Abstract

The discoveries of microRNAs and riboswitches, among others, have shown functional RNAs to be biologically more important and genomically more prevalent than previously anticipated. We have developed a general comparative genomics method based on phylogenetic stochastic context-free grammars for identifying functional RNAs encoded in the human genome and used it to survey an eight-way genome-wide alignment of the human, chimpanzee, mouse, rat, dog, chicken, zebra-fish, and puffer-fish genomes for deeply conserved functional RNAs. At a loose threshold for acceptance, this search resulted in a set of 48,479 candidate RNA structures. This screen finds a large number of known functional RNAs, including 195 miRNAs, 62 histone 3'UTR stem loops, and various types of known genetic recoding elements. Among the highest-scoring new predictions are 169 new miRNA candidates, as well as new candidate selenocysteine insertion sites, RNA editing hairpins, RNAs involved in transcript auto regulation, and many folds that form singletons or small functional RNA families of completely unknown function. While the rate of false positives in the overall set is difficult to estimate and is likely to be substantial, the results nevertheless provide evidence for many new human functional RNAs and present specific predictions to facilitate their further characterization.

Item Type: Paper
Uncontrolled Keywords: 3' Untranslated Regions Animals Chickens Computational Biology/methods Conserved Sequence Dogs Genome *Genome, Human Humans Mice MicroRNAs/*chemistry *Nucleic Acid Conformation Rats Sequence Analysis, RNA/*methods Tetraodontiformes Zebrafish
Subjects: bioinformatics
bioinformatics > genomics and proteomics
bioinformatics > computational biology
CSHL Authors:
Communities: CSHL labs > Siepel lab
Depositing User: Matt Covey
Date Deposited: 14 Jan 2015 17:18
Last Modified: 14 Jan 2015 17:18
PMCID: PMC1440920
Related URLs:
URI: http://repository.cshl.edu/id/eprint/31087

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