Identification and Classification of Conserved RNA Secondary Structures in the Human Genome

DSpace/Manakin Repository

Identification and Classification of Conserved RNA Secondary Structures in the Human Genome

Citable link to this page

. . . . . .

Title: Identification and Classification of Conserved RNA Secondary Structures in the Human Genome
Author: Pedersen, Jakob Skou; Bejerano, Gill; Siepel, Adam; Rosenbloom, Kate; Lindblad-Toh, Kerstin; Lander, Eric Steven; Kent, Jim; Webb, Miller; Haussler, David

Note: Order does not necessarily reflect citation order of authors.

Citation: Pedersen, Jakob Skou, Gill Bejerano, Adam Siepel, Kate Rosenbloom, Kerstin Lindblad-Toh, Eric S. Lander, Jim Kent, Webb Miller, and David Haussler. 2006. Identification and classification of conserved RNA secondary structures in the human genome. PLoS Computational Biology 2(4): e33.
Full Text & Related Files:
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.
Published Version: doi:10.1371/journal.pcbi.0020033
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1440920/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:4732394

Show full Dublin Core record

This item appears in the following Collection(s)

 
 

Search DASH


Advanced Search
 
 

Submitters