Non-coding RNAs in <i>Ciona intestinalis</i>

Missal, Kristin; Rose, Dominic; Stadler, Peter F.

doi:10.1093/bioinformatics/bti1113

Cited by 49 publications

(44 citation statements)

References 9 publications

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“…An RNAz survey based on the most conserved parts of the vertebrate genomes estimates that the ncRNA content of mammalian genomes is comparable to their protein coding genes (Washietl et al, 2005b), and hence at least an order magnitude larger than in nematodes. In contrast, the predicted number of structured RNAs in the urochordate Ciona intestinalis is comparable to our results for the nematodes (Missal et al, 2005). This indicates that higher vertebrates have dramatically expanded their ncRNA inventory relative to their complement of protein coding genes.…”

Section: Discussionsupporting

confidence: 76%

“…A similar analysis of the genomes of urochordates (Missal et al, 2005), on the other hand, identified only a few thousand putative structured RNAs, consistent with the hypothesis that ncRNAs form the basis of a complex cellular regulation system that has been vastly expanded in vertebrates (Mattick, 2004;Bartel and Chen, 2004). Here we extend the phylogenetic range of systematic surveys for ncRNAs to nematodes.…”

Section: Introductionsupporting

confidence: 66%

“…It is accepted as a pre-miRNA candidate provided (1) it forms a stem-loop structure with a total length between 40 and 130 and (2) its z-score is below z = −3.0. This threshold value was identified by assessing pairwise alignments of random chosen homologous sequences from the Rfam database (Missal et al, 2005). Fig.…”

Section: Novel Microrna Candidatesmentioning

confidence: 99%

See 2 more Smart Citations

Prediction of structured non-coding RNAs in the genomes of the nematodesCaenorhabditis elegans andCaenorhabditis briggsae

Missal¹,

Zhu²,

Rose³

et al. 2006

J. Exp. Zool.

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We present a survey for non-coding RNAs and other structured RNA motifs in the genomes of C. elegans and C. briggsae using the RNAz program. This approach explicitly evaluates comparative sequence information to detect stabilizing selection acting on RNA secondary structure.We detect 3672 structured RNA motifs, of which only 678 are known ncRNAs or clear homologs of known C. elegans ncRNAs. Most of these signals are located in introns or at a distance from known protein-coding genes. With an estimated false positive rate of about 50% and a sensitivity on the order of 50% we estimate that the nematode genomes contain between 3000 and 4000 RNAs with evolutionary conserved secondary structures. Only a small fraction of these belongs to the known RNA classes, including tRNAs, snoRNAs, snRNAs, or microRNAs. A relatively small class of ncRNA candidates is associated with previously observed RNA-specific upstream elements.

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Section: Discussionsupporting

confidence: 76%

Section: Introductionsupporting

confidence: 66%

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Prediction of structured non-coding RNAs in the genomes of the nematodesCaenorhabditis elegans andCaenorhabditis briggsae

Missal¹,

Zhu²,

Rose³

et al. 2006

J. Exp. Zool.

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“…Furthermore, we come close the results of a comparative genomics screen for non-coding RNAs in C. elegans [49], which reported 12 U1, 19 U2, 5 U4, 13 U5, and 23 U6, i.e., only a few more candidates than our present purely homology-based approach. A comparative screen of the two Ciona species for evolutionary conserved structured RNAs [48] missed a small number of snRNA genes that we indentified as most likely functional ones.…”

Section: Homology Searchmentioning

confidence: 93%

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

2008

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While studies of the evolutionary histories of protein families are common place, little is known on noncoding RNAs beyond microRNAs and some snoRNAs. Here we investigate in detail the evolutionary history of the 9 spliceosomal snRNA families (U1, U2, U4, U5, U6, U11, U12, U4atac, and U6atac) across the completely or partially sequenced genomes of metazoan animals. Representatives of the five major spliceosomal snRNAs were found in all genomes. None of the minor splicesomal snRNAs was detected in Nematodes and in the shotgun traces of Oikopleura dioica, while in all other animal genomes at most one of them is missing. Although snRNAs are present in multiple copies in most genomes, distinguishable paralog groups are not stable over long evolutionary times, although they appear independently in several clades. In general, animal snRNA secondary structures are highly conserved, albeit in particular U11 and U12 in insects exhibit dramatic variations. An analysis of genomic context of snRNAs reveals that they behave like mobile elements, exhibiting very little syntenic conservation.

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“…Although a number of studies have successfully identified ncRNAs in several animal (Missal et al 2005;Washietl et al 2007) and microbial genomes (Altuvia 2007), the pace at which such studies are performed and published lags far behind the rate of genome sequence output. Most of the complete genomes sequenced to date have escaped the scrutiny of RNA experts, and their potential for novel RNA functions lies unexplored.…”

mentioning

confidence: 99%

Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles

Marchais¹,

Naville²,

Bohn³

et al. 2009

Genome Res.

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Identification and characterization of functional elements in the noncoding regions of genomes is an elusive and timeconsuming activity whose output does not keep up with the pace of genome sequencing. Hundreds of bacterial genomes lay unexploited in terms of noncoding sequence analysis, although they may conceal a wide diversity of novel RNA genes, riboswitches, or other regulatory elements. We describe a strategy that exploits the entirety of available bacterial genomes to classify all noncoding elements of a selected reference species in a single pass. This method clusters noncoding elements based on their profile of presence among species. Most noncoding RNAs (ncRNAs) display specific signatures that enable their grouping in distinct clusters, away from sequence conservation noise and other elements such as promoters. We submitted 24 ncRNA candidates from Staphylococcus aureus to experimental validation and confirmed the presence of seven novel small RNAs or riboswitches. Besides offering a powerful method for de novo ncRNA identification, the analysis of phylogenetic profiles opens a new path toward the identification of functional relationships between co-evolving coding and noncoding elements.[Supplemental material is available online at www.genome.org.]In all living organisms, the genome regions located between protein-coding sequences are home to a wide diversity of functional elements that include noncoding RNA (ncRNA) genes, DNA regulatory elements, untranslated regions (UTRs) of genes, transposable and self-replicating elements, and a variety of other transcribed or nontranscribed functional sequences. As these elements are often key players in gene regulation and thus in the global cell interaction network, their systematic identification and characterization has become a major challenge in biology.Computational protocols developed to collect and characterize noncoding elements in genomic sequences rely, to a large extent, on comparative genomics. The most common strategies involve, first, collecting sequences under selective pressure and, second, analyzing the aligned sequences using various classifiers that exploit criteria such as nucleotide composition, folding potential, fold conservation, or covariation between distant positions (Rivas and Eddy 2001;Washietl et al. 2005;Pedersen et al. 2006;Torarinsson et al. 2006). In general, such classifiers are designed to detect structured RNAs among noncoding elements with no further distinction between regulatory elements, repeats, or artifacts produced by sequence comparison algorithms.Comparative genomics entails a significant amount of expert intervention, especially in obtaining the right genome set to optimize the specificity and sensitivity of RNA detection. Although a number of studies have successfully identified ncRNAs in several animal (Missal et al. 2005;Washietl et al. 2007) and microbial genomes (Altuvia 2007), the pace at which such studies are performed and published lags far behind the rate of genome sequence output. Most of the complete...

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Non-coding RNAs in Ciona intestinalis

Abstract: www.bioinf.uni-leipzig.de/Publications/SUPPLEMENTS/05-008/

Cited by 49 publications

References 9 publications

Prediction of structured non-coding RNAs in the genomes of the nematodesCaenorhabditis elegans andCaenorhabditis briggsae

Prediction of structured non-coding RNAs in the genomes of the nematodesCaenorhabditis elegans andCaenorhabditis briggsae

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles

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