Comparative analysis of base correlations in 5′ untranslated regions of various species

Osada, Yuko; Saito, Rintaro; Tomita, Masaru

doi:10.1016/j.gene.2006.02.018

Cited by 7 publications

(5 citation statements)

References 35 publications

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“…The first exon provides the initial binding site for the 40S ribosomal unit which is required to start the translation at an AUG codon of the reading frame [ 28 ]. To have an efficient translation at the AUG codon, the first exon must have an A at three nt upstream of the AUG codon [ 28 , 29 ]. This A was highly conserved across the mammalian species investigated in this experiment.…”

Section: Discussionmentioning

confidence: 99%

Mapping of the transcription start site (TSS) and identification of SNPs in the bovine neuropeptide Y (NPY) gene

Bahar

Sweeney

2008

BMC Genet

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Background: Neuropeptide Y is a key neurotransmitter of the central nervous system which plays a vital role in the feed energy homeostasis in mammals. Mutations in the regulatory and coding regions of the bovine NPY gene can potentially affect the neuronal regulation of appetite and feeding behaviour in cattle. The objectives of this experiment were to: a) fully characterize the bovine NPY gene transcript and b) identify the SNP diversity in both coding and non-coding regions of the NPY gene in a panel of Bos taurus and B. indicus cattle.

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Section: Discussionmentioning

confidence: 99%

Mapping of the transcription start site (TSS) and identification of SNPs in the bovine neuropeptide Y (NPY) gene

Bahar

Sweeney

2008

BMC Genet

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“…Several of these may be species-or kingdom-speci¯c, such as the Kozak and Shine-Dalgarno consensus motifs in Eukaryotes and Bacteria, respectively. 19 In order to identify a species-independent anchor tag suitable for oligonucleotide selection, the importance and role of anchor tags were investigated by examination of Pearson's R 2 correlation with the full 15-mer count, as well as the compute time required for an all-against-all comparison of the set of bacterial genomes ( Table 1).…”

Section: Representative Subsamples Using Conserved Sequence Tagsmentioning

confidence: 99%

A Simple Shortcut to Unsupervised Alignment-Free Phylogenetic Genome Groupings, Even From Unassembled Sequencing Reads

Maurer‐Stroh

Gunalan

Wong

et al. 2013

J. Bioinform. Comput. Biol.

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We propose an extension to alignment-free approaches that can produce reasonably accurate phylogenetic groupings starting from unaligned genomes, for example, as fast as 1 min on a standard desktop computer for 25 bacterial genomes. A 6-fold speed-up and 11-fold reduction in memory requirements compared to previous alignment-free methods is achieved by reducing the comparison space to a representative sample of k-mers of optimal length and with speci¯c tag motifs. This approach was applied to the test case of¯tting the enterohemorrhagic O104:H4 E.coli strain from the 2011 outbreak in Germany into the phylogenetic network of previously known E.coli-related strains and extend the method to allow assigning any new strain to the correct phylogenetic group even directly from unassembled short sequence reads from next generation sequencing data. Hence, this approach is also useful to quickly identify the most suitable reference genome for subsequent assembly steps.

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“…Previous studies have shown that sAUGs tend to have an optimal sequence context to facilitate efficient translation of the main CDS [21], [22]. We reason that selection should have favored a non-optimal context for the uAUGs of VuORFs (termed “VuAUGs”) because an optimal-context VuAUG will potentially aggravate the deleterious effects of the VuORF, leading to a remarkable reduction in fitness and rapid removal of the VuORF.…”

Section: Introductionmentioning

confidence: 98%

Selective Constraint on the Upstream Open Reading Frames That Overlap with Coding Sequences in Animals

Hsu

Chen

2012

PLoS ONE

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Upstream open reading frames (uORFs) are translational regulatory elements located in 5′ untranslated regions. They can significantly repress the translation of the downstream coding sequences (CDS), and participate in the spatio-temporal regulations of protein translation. Notwithstanding this biological significance, the selective constraint on uORFs remains underexplored. Particularly, the uORFs that partially overlap with CDS with a different reading frame (overlapping uORFs, or “VuORFs”) may lead to strong translational inhibition or N-terminal truncation of the peptides encoded by the affected CDS. By analyzing VuORF-containing transcripts (designated as “VuORF transcripts”) in human, mouse, and fruit fly, we demonstrate that VuORFs are in general slightly deleterious - the proportion of genes that encode at least one VuORF transcript is significantly smaller than expected in all of the three examined species. In addition, this proportion is significantly smaller in fruit fly than in mammals, indicating a higher efficiency of removing VuORFs in the former species because of its larger effective population size. Furthermore, the deleterious effect of a VuORF depends on the sequence context of its start codon (VuAUG). VuORFs with an optimal VuAUG context are more strongly disfavored than those with a suboptimal context in all of the three examined species. And the propensity to remove optimal-context VuAUGs is stronger in fruit fly than in mammals. Intriguingly, however, the currently observable optimal-context VuAUGs (but not suboptimal-context VuAUGs) are more conserved than expected. These observations suggest that the regulatory functions of VuORFs may have been gained fortuitously in organisms with a small effective population size because the slightly deleterious effect of these elements can be better tolerated in these organisms, thus allowing opportunities for the development of novel biological functions. Nevertheless, once the functions of VuORFs were established, they became subject to negative selection.

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Comparative analysis of base correlations in 5′ untranslated regions of various species

Cited by 7 publications

References 35 publications

Mapping of the transcription start site (TSS) and identification of SNPs in the bovine neuropeptide Y (NPY) gene

Mapping of the transcription start site (TSS) and identification of SNPs in the bovine neuropeptide Y (NPY) gene

A Simple Shortcut to Unsupervised Alignment-Free Phylogenetic Genome Groupings, Even From Unassembled Sequencing Reads

Selective Constraint on the Upstream Open Reading Frames That Overlap with Coding Sequences in Animals

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