Rfam: annotating non-coding RNAs in complete genomes

Griffiths-Jones, Sam; Moxon, Simon; Marshall, Mhairi; Khanna, Ajay K.; Eddy, Sean R.; Bateman, Alex

doi:10.1093/nar/gki081

Cited by 1,380 publications

(1,141 citation statements)

References 19 publications

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“…This is useful in particular for the snRNAs of the minor spliceosome for which very few sequences are reported in databases; indeed, the Rfam 7.0 [23] lists only the U11 and U12 families with a meager set of seed sequences from few model organisms. The sequence and secondary structure data compiled in this study provide a substantially improved databasis and set the stage for systematic searches of even more distant homologs.…”

Section: Discussionmentioning

confidence: 99%

“…Known snRNA sequences were retrieved from Genbank [4], Rfam [23], and in some cases extracted directly from the literature. Genomic DNA sequences were downloaded from the websites of ensembl, the Joint Genome Institute, the Sanger Institute, WormBase, the Genome Sequencing Center, UCSC, CAF1, Broad Institute, BGI, and the NCBI trace archive.…”

Section: Sequence Datamentioning

confidence: 99%

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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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Section: Discussionmentioning

confidence: 99%

Section: Sequence Datamentioning

confidence: 99%

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

2008

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“…Rfam [49,50] is a database system that stores covariance models for 503 different ncRNA families (release 7.0) and that uses INFERNAL to identify candidate ncRNAs in an arbitrary input sequence (possibly a whole genome). Since analyzing the input data using all of the 503 models would be too slow, a previous Blast-based filter is applied to select promising models.…”

Section: Comparative Methodsmentioning

confidence: 99%

Computational methods in noncoding RNA research

2007

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Non protein-coding RNAs (ncRNAs) are a research hotspot in bioinformatics. Recent discoveries have revealed new ncRNA families performing a variety of roles, from gene expression regulation to catalytic activities. It is also believed that other families are still to be unveiled. Computational methods developed for protein coding genes often fail when searching for ncRNAs. Noncoding RNAs functionality is often heavily dependent on their secondary structure, which makes gene discovery very different from protein coding RNA genes. This motivated the development of specific methods for ncRNA research. This article reviews the main approaches used to identify ncRNAs and predict secondary structure.

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“…As an example of a potential non-metabolite ligand, levels of intracellular metal ions have been proposed to regulate the expression of the Salmonella enterica mgtA gene via an RNA element located within its 5′ UTR [63]. Additionally, a broadly distributed orphan riboswitch class appears to regulate the expression of an MgtE-family magnesium transporter (ykoK) in Bacillus subtilis as well as many genes responsible for metal uptake in other organisms [64,65], allowing one to wonder whether multiple classes of RNAs could function as metal ion sensors. The utilization of better bioinformatic search algorithms and genetic screens could uncover additional examples of structural noncoding RNAs, including new riboswitches.…”

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confidence: 99%

Structural features of metabolite-sensing riboswitches

Wakeman

Winkler

Dann

2007

Trends in Biochemical Sciences

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Riboswitches, metabolite-sensing RNA elements found in untranslated regions of the transcripts they regulate, possess extensive tertiary structure to couple metabolite binding to genetic control. Herein, we discuss recently published structures from four riboswitch classes and compare these natural RNA structures to those of in vitro selected RNA aptamers, which bind similar ligands to those of the riboswitches. Additionally, we examine the glmS riboswitch, the first example of a ribozyme-based riboswitch. This RNA provides the latest twist in the riboswitch field and portends exciting advances in the coming years. Our knowledge of the mechanisms of genetic regulation by riboswitches has increased mightily in recent years and will continue to grow as new riboswitch classes and ligands are discovered and structurally characterized. KeywordsRNA structure; riboswitch; ribozyme; transcription attenuation; noncoding RNAs; posttranscriptional regulation; crystallography; NMR Riboswitches: Remnants of an ancient mode of genetic regulation?The "central dogma" states that information is stored as DNA, transcribed into RNA, and translated into proteins, which are traditionally thought to satisfy most cellular structural and catalytic requirements. Genetic control of these steps is believed to occur primarily through the action of regulatory proteins; however, the importance of noncoding RNAs in these processes has become increasingly appreciated in recent years [1]. In eubacterial organisms, regulatory RNAs can elicit control of gene expression through regulation of transcription attenuation, translation initiation [reviewed in 2,3], or mRNA stability [4]. These eubacterial regulatory RNAs function via diverse intermolecular (trans) or intramolecular (cis) mechanisms to regulate the target mRNA. Trans-acting regulatory RNAs interact with target mRNAs to control translation, mRNA stability, or transcription termination [reviewed in 5,6, 7], whereas others regulate gene expression through specific sequestration of RNA-binding proteins [8]. Cis-acting RNAs, which are the focus of this review, are located within untranslated regions (UTRs) of the mRNA transcript that they regulate. Genetic control by the latter RNA elements can be accomplished either through the sole action of the RNA molecule or in conjunction with recruited protein factors.A classic example of a cis-acting regulatory RNA is the transcription attenuation control of tryptophan biosynthesis genes in certain Gram-negative bacteria [9]. For this mechanism, the kinetics of translation of a short leader peptide dictates the conformational state of the overall 5′-UTR. Under tryptophan-depleted conditions the translating ribosome stalls at tryptophan codons within the leader peptide thereby allowing for formation of an antiterminator helix and [24-26; reviewed in 27,12]. Given their ability to function as sensitive sentinels for intracellular metabolites in a protein-independent manner, these RNAs are likely to require exquisite structural sophistication....

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Rfam: annotating non-coding RNAs in complete genomes

Cited by 1,380 publications

References 19 publications

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

Computational methods in noncoding RNA research

Structural features of metabolite-sensing riboswitches

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