ETOPE: evolutionary test of predicted exons

Nekrutenko, Anton; Chung, Wen Yu; Li, Wen-Hsiung

doi:10.1093/nar/gkg597

Cited by 18 publications

(12 citation statements)

References 13 publications

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“…We computed the Ks rate and Ka͞Ks ratio between orthologous exon pairs following the approach of Li and colleagues (30). Briefly, orthologous exon sequences from human and mouse were translated in all possible reading frames.…”

Section: Methodsmentioning

confidence: 99%

Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences

Xing

Lee

2005

Proc. Natl. Acad. Sci. U.S.A.

125

146

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Recently, it was proposed that alternative splicing may act as a mechanism for opening accelerated paths of evolution, by reducing negative selection pressure, but there has been little evidence so far that this mechanism could produce adaptive benefit. Here, we use metrics of very different types of selection pressures [e.g., against amino acid mutations (Ka͞Ks), against mutations at synonymous sites (Ks), and for protein reading-frame preservation] to address this question by genomewide analyses of human, chimpanzee, mouse, and rat. These data show that alternative splicing relaxes Ka͞Ks selection pressure up to 7-fold, but intriguingly this effect is accompanied by a strong increase in selection pressure against synonymous mutations, which propagates into the adjacent intron, and correlates strongly with the alternative splicing level observed for each exon. These effects are highly local to the alternatively spliced exon. Comparisons of these four genomes consistently show an increase in the density of amino acid mutations (Ka) in alternatively spliced exons and a decrease in the density of synonymous mutations (Ks). This selection pressure against synonymous mutations in alternatively spliced exons was accompanied in all four genomes by a striking increase in selection pressure for protein reading-frame preservation, and both increased markedly with increasing evolutionary age. Restricting our analysis to a subset of exons with strong evidence for biologically functional alternative splicing produced identical results. Thus alternative splicing apparently can create evolutionary ''hotspots'' within a protein sequence, and these events have evidently been selected for during mammalian evolution.bioinformatics ͉ exon ͉ comparative genomics ͉ Ka͞Ks ͉ RNA splicing A lternative splicing recently has emerged as a major mechanism of functional regulation in the human genome and in other organisms (1-3), with up to 80% of human genes reported to be alternatively spliced (4). One area that has attracted much interest is comparing alternative splicing in different genomes. Several groups have sought to assess whether alternative splicing is more abundant in the human genome vs. other genomes (5-7). Another major focus has been to use sequence conservation (regions of high-percent identity) to discover motifs that are important for regulation and alternative splicing (8-11). These data indicate that such regulatory motifs are clustered near splice sites, in both exonic sequence and the flanking introns. For example, measurements of conservation by percent identity between human and mouse show an Ϸ20% increase in the 30 nt of intron sequence immediately adjacent to alternatively spliced exons, relative to that for constitutive exons (8). The sequence of alternatively spliced exons also appears to have slightly higher conservation than constitutive exons, perhaps by a few percentage points of identity in comparisons of human vs. mouse (11).It has also been proposed that alternative splicing can greatly increase the rate...

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Section: Methodsmentioning

confidence: 99%

Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences

Xing

Lee

2005

Proc. Natl. Acad. Sci. U.S.A.

125

146

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“…A low dN/dS ratio indicates negative selection, which was found to be a reliable way to detect coding regions in pairwise (Nekrutenko et al 2003) and multiple alignments (Lin et al 2008). The structure of the genetic code leads to a periodic pattern of evolutionary rates (Bofkin and Goldman 2007), another characteristic of protein-coding regions that was applied, for example, to assess the coding potential of unannotated transcripts in S. cerevisiae (David et al 2006) and in human in the ENCODE pilot project (The ENCODE Project Consortium 2007).…”

Section: Comparison To Other Comparative Metricsmentioning

confidence: 99%

“…Various algorithms have been developed to predict coding potential in pairwise alignments (Badger and Olsen 1999;Rivas and Eddy 2001;Mignone et al 2003;Nekrutenko et al 2003), and the power of multi-species comparison for the purpose of coding region prediction was demonstrated impressively in yeast (Kellis et al 2003), human (Clamp et al 2007), and more recently in 12 drosophilid genomes (Stark et al 2007;Lin et al 2008). There is no doubt that these types of analysis are powerful and useful additions to classical gene finders.…”

Section: Introductionmentioning

confidence: 99%

RNAcode: Robust discrimination of coding and noncoding regions in comparative sequence data

Washietl¹,

Findeiß²,

Müller³

et al. 2011

RNA

190

225

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With the availability of genome-wide transcription data and massive comparative sequencing, the discrimination of coding from noncoding RNAs and the assessment of coding potential in evolutionarily conserved regions arose as a core analysis task. Here we present RNAcode, a program to detect coding regions in multiple sequence alignments that is optimized for emerging applications not covered by current protein gene-finding software. Our algorithm combines information from nucleotide substitution and gap patterns in a unified framework and also deals with real-life issues such as alignment and sequencing errors. It uses an explicit statistical model with no machine learning component and can therefore be applied ''out of the box,'' without any training, to data from all domains of life. We describe the RNAcode method and apply it in combination with mass spectrometry experiments to predict and confirm seven novel short peptides in Escherichia coli and to analyze the coding potential of RNAs previously annotated as ''noncoding.'' RNAcode is open source software and available for all major platforms at http://wash.github.com/rnacode.

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“…Following a previously described approach [4,10], the protein alignment generated to identify orthologous exons was used to realign the two nucleotide sequences of each orthologous exon pair. Gaps were removed.…”

Section: Calculation Of Synonymous and Non-synonymous Mutation Ratesmentioning

confidence: 99%

Evolutionary impact of limited splicing fidelity in mammalian genes

2007

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Methods Human and mouse transcript-confirmed exonsHuman and mouse transcript (mRNA and/or EST)-confirmed exons were extracted from the Alternative Splicing Database (ASD) (Release 2, April 2005) [1]. The AltSplice database in ASD is a computationally derived collection of alternative splicing (AS) events of human and mouse based on alignment of EST and mRNA sequences to the corresponding genomic sequences with high quality and minimal redundancy. In ASD, all transcript-genome alignments with ambiguities were removed. A confirmed intron is defined by an alignment gap of genomic sequence flanked by two splice sites of known types. A confirmed exon is defined by an alignment match flanked by two confirmed introns; therefore, only internal exons are considered as being confirmed. Confirmed introns and exons that overlap with each other indicate AS events. In human, AltSplice has 16 293 genes, including 9945 (61%) with one or more alternative splicing events. In mouse, AltSplice has 16 352 genes, including 8211 (50%) alternatively spliced ones. The higher percentage of alternatively spliced genes in human is probably due to the higher EST coverage.In this study, we considered only splicing events involving GT-AG intron boundaries. In total, 133 926 and 121 202 exons, plus 200 nucleotides of flanking intronic sequences, were extracted for human and mouse, respectively. Cassette exons are those included in some transcripts but skipped in others, without affecting the two neighboring exons (denoted as SCE, for simple cassette exons, in ASD). We extracted 10 196 and 5992 cassette exons for human and mouse, respectively. We also compiled a set of 30 892 and 37 313 exons that appear to be constitutively spliced in human and mouse, respectively. These exons were extracted from genes without AS events.A summary of frame-preserving preference and human-mouse conservation (see below) is given in Table S1 and Figure S1. We also compared other features, such as intron phase bias (data not shown). All these general statistics are similar to and consistent to those reported previously (e.g. [2][3][4]). Exon inclusion/skipping levelFor each cassette exon, the number of supporting transcripts for the inclusion and the skipping isoforms was also extracted from ASD [1]. The number of supporting transcripts was used as an approximate measure of the abundance of the exon inclusion/skipping isoform, as done previously [5,6]. The ratio of the skipping to inclusion isoform or the ratio of the minor to major isoform (RMM) was used to estimate the relative abundance of the two isoforms.Previous studies (e.g. [5,7]) have shown that newly evolved splicing isoforms usually have low abundance, whereas original ancestral isoforms remain dominant to minimize the deleterious effects of new isoforms to the organism. During evolution, the new minor isoform becomes more abundant if it has adaptive benefits and is positively selected. Therefore, RMM represents an approximate measure of the evolutionary age and fitness of an AS event. Frame-preserving p...

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ETOPE: evolutionary test of predicted exons

Cited by 18 publications

References 13 publications

Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences

Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences

RNAcode: Robust discrimination of coding and noncoding regions in comparative sequence data

Evolutionary impact of limited splicing fidelity in mammalian genes

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