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Limited By:	Subject = Messenger RNAs;

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Displaying Results 1 - 3 of 3 on page 1 of 1

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Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences (2011)

Ivanov, Ivaylo P.; Firth, Andrew E.; Michel, Audrey M.; Atkins, John F.; Baranov, Pavel V.

Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences (2011)

Ivanov, Ivaylo P.; Firth, Andrew E.; Michel, Audrey M.; Atkins, John F.; Baranov, Pavel V.

Abstract:

In eukaryotes, it is generally assumed that translation initiation occurs at the AUG codon closest to the messenger RNA 5' cap. However, in certain cases, initiation can occur at codons differing from AUG by a single nucleotide, especially the codons CUG, UUG, GUG, ACG, AUA and AUU. While non-AUG initiation has been experimentally verified for a handful of human genes, the full extent to which this phenomenon is utilized-both for increased coding capacity and potentially also for novel regulatory mechanisms-remains unclear. To address this issue, and hence to improve the quality of existing coding sequence annotations, we developed a methodology based on phylogenetic analysis of predicted 5' untranslated regions from orthologous genes. We use evolutionary signatures of protein-coding sequences as an indicator of translation initiation upstream of annotated coding sequences. Our search identified novel conserved potential non-AUG-initiated N-terminal extensions in 42 human ...

http://hdl.handle.net/10468/5024

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Recode-2: new design, new search tools, and many more genes (2010)

Bekaert, Michael; Firth, Andrew E.; Zhang, Yan; Gladyshev, Vadim N.; Atkins, John F.; B...

Recode-2: new design, new search tools, and many more genes (2010)

Bekaert, Michael; Firth, Andrew E.; Zhang, Yan; Gladyshev, Vadim N.; Atkins, John F.; Baranov, Pavel V.

Abstract:

Recoding' is a term used to describe non-standard read-out of the genetic code, and encompasses such phenomena as programmed ribosomal frame-shifting, stop codon readthrough, selenocysteine insertion and translational bypassing. Although only a small proportion of genes utilize recoding in protein synthesis, accurate annotation of 'recoded' genes lags far behind annotation of 'standard' genes. In order to address this issue, provide a service to researchers in the field, and offer training data for developers of gene-annotation software, we have gathered together known cases of recoding within the Recode database. Recode-2 is an improved and updated version of the database. It provides access to detailed information on genes known to utilize translational recoding and allows complex search queries, browsing of recoding data and enhanced visualization of annotated sequence elements. At present, the Recode-2 database stores information on approximately 1500 ge...

http://hdl.handle.net/10468/5029

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Stringency of start codon selection modulates autoregulation of translation initiation factor eIF5 (2012)

Loughran, Gary; Sachs, Matthew S.; Atkins, John F.; Ivanov, Ivaylo P.

Stringency of start codon selection modulates autoregulation of translation initiation factor eIF5 (2012)

Loughran, Gary; Sachs, Matthew S.; Atkins, John F.; Ivanov, Ivaylo P.

Abstract:

An AUG in an optimal nucleotide context is the preferred translation initiation site in eukaryotic cells. Interactions among translation initiation factors, including eIF1 and eIF5, govern start codon selection. Experiments described here showed that high intracellular eIF5 levels reduced the stringency of start codon selection in human cells. In contrast, high intracellular eIF1 levels increased stringency. High levels of eIF5 induced translation of inhibitory upstream open reading frames (uORFs) in eIF5 mRNA that initiate with AUG codons in conserved poor contexts. This resulted in reduced translation from the downstream eIF5 start codon, indicating that eIF5 autoregulates its own synthesis. As with eIF1, which is also autoregulated through translation initiation, features contributing to eIF5 autoregulation show deep evolutionary conservation. The results obtained provide the basis for a model in which auto- and cross-regulation of eIF5 and eIF1 translation establish a regulatory...

http://hdl.handle.net/10468/5022

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