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

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 ide...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Jakob Skou Pedersen, Gill Bejerano, Adam Siepel, Kate Rosenbloom, Kerstin Lindblad-Toh, Eric S Lander, Jim Kent, Webb Miller, David Haussler
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2006
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/610c8207089841ca86ee090b5f3685f7
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:610c8207089841ca86ee090b5f3685f7
record_format	dspace
spelling	oai:doaj.org-article:610c8207089841ca86ee090b5f3685f72021-11-25T05:41:07ZIdentification and classification of conserved RNA secondary structures in the human genome.1553-734X1553-735810.1371/journal.pcbi.0020033https://doaj.org/article/610c8207089841ca86ee090b5f3685f72006-04-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.0020033https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The 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.Jakob Skou PedersenGill BejeranoAdam SiepelKate RosenbloomKerstin Lindblad-TohEric S LanderJim KentWebb MillerDavid HausslerPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 2, Iss 4, p e33 (2006)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Jakob Skou Pedersen Gill Bejerano Adam Siepel Kate Rosenbloom Kerstin Lindblad-Toh Eric S Lander Jim Kent Webb Miller David Haussler Identification and classification of conserved RNA secondary structures in the human genome.
description	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.
format	article
author	Jakob Skou Pedersen Gill Bejerano Adam Siepel Kate Rosenbloom Kerstin Lindblad-Toh Eric S Lander Jim Kent Webb Miller David Haussler
author_facet	Jakob Skou Pedersen Gill Bejerano Adam Siepel Kate Rosenbloom Kerstin Lindblad-Toh Eric S Lander Jim Kent Webb Miller David Haussler
author_sort	Jakob Skou Pedersen
title	Identification and classification of conserved RNA secondary structures in the human genome.
title_short	Identification and classification of conserved RNA secondary structures in the human genome.
title_full	Identification and classification of conserved RNA secondary structures in the human genome.
title_fullStr	Identification and classification of conserved RNA secondary structures in the human genome.
title_full_unstemmed	Identification and classification of conserved RNA secondary structures in the human genome.
title_sort	identification and classification of conserved rna secondary structures in the human genome.
publisher	Public Library of Science (PLoS)
publishDate	2006
url	https://doaj.org/article/610c8207089841ca86ee090b5f3685f7
work_keys_str_mv	AT jakobskoupedersen identificationandclassificationofconservedrnasecondarystructuresinthehumangenome AT gillbejerano identificationandclassificationofconservedrnasecondarystructuresinthehumangenome AT adamsiepel identificationandclassificationofconservedrnasecondarystructuresinthehumangenome AT katerosenbloom identificationandclassificationofconservedrnasecondarystructuresinthehumangenome AT kerstinlindbladtoh identificationandclassificationofconservedrnasecondarystructuresinthehumangenome AT ericslander identificationandclassificationofconservedrnasecondarystructuresinthehumangenome AT jimkent identificationandclassificationofconservedrnasecondarystructuresinthehumangenome AT webbmiller identificationandclassificationofconservedrnasecondarystructuresinthehumangenome AT davidhaussler identificationandclassificationofconservedrnasecondarystructuresinthehumangenome
_version_	1718414519455186944

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

Ejemplares similares