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Keywords {🔍}

uorfs, genes, utr, gene, utrs, yeast, translational, pubmed, stress, article, uorf, google, scholar, control, data, length, cas, translation, orf, start, figure, regulation, sequences, conserved, codon, general, expression, number, file, conservation, sets, open, conditions, tss, central, phastcons, upstream, sequence, significant, reading, additional, stop, shown, regulated, role, true, species, observed, mrna, addition,

Topics {✒️}

nonsense-mediated mrna decay org/cgi/content/full/0605645103/dc1 open access article article download pdf nonsense mediated decay /pub/yeast/data_download/chromosomal_feature/ hand-curated functional assignments destabilising mrna post-termination central regulatory role post-transcriptional expression regulation transcription start sites open reading frame post-transcriptional control processes post-transcriptional control mechanisms upstream sequence elements recent large-scale datasets experimentally-determined gene set transcriptional start site control initiator-trna binding recent large-scales studies allowing transcriptional factors tiling array definitions genome-wide expression patterns amino acid starvation accession numbers e-mexp-323 triggering mrna decay apparent reading frame post-transcriptional regulation local utr background post-transcriptional control transcriptional regulatory code transcriptional start sites low peroxide concentrations dos reis tiling array studies direct translational control pattern c1-xn-c2 complete reading frame array-based technologies dna binding proteins folding free energies privacy choices/manage cookies full size image utr sequence elements yeast upstream sequences high-resolution map fixed upstream segments article lawless tss-mapped utr set downstream start codon

Questions {❓}

• Brockmann R, Beyer A, Heinisch JJ, Wilhelm T: Posttranscriptional expression regulation: what determines translation rates?
• Rivals I, Personnaz L, Taing L, Potier M: Enrichment or depletion of a GO category within a class of genes: which test?
• Should they be absolutely conserved in UTRs to exert their effects (in position and/or composition), or is merely the presence of one or more uORFs anywhere within the 5' UTR sufficient?

Schema {🗺️}

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         headline:Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast
         description:The control of gene expression in eukaryotic cells occurs both transcriptionally and post-transcriptionally. Although many genes are now known to be regulated at the translational level, in general, the mechanisms are poorly understood. We have previously presented polysomal gradient and array-based evidence that translational control is widespread in a significant number of genes when yeast cells are exposed to a range of stresses. Here we have re-examined these gene sets, considering the role of UTR sequences in the translational responses of these genes using recent large-scale datasets which define 5' and 3' transcriptional ends for many yeast genes. In particular, we highlight the potential role of 5' UTRs and upstream open reading frames (uORFs). We show a highly significant enrichment in specific GO functional classes for genes that are translationally up- and down-regulated under given stresses (e.g. carbohydrate metabolism is up-regulated under amino acid starvation). Cross-referencing these data with the stress response data we show that translationally upregulated genes have longer 5' UTRs, consistent with their role in translational regulation. In the first genome-wide study of uORFs in a set of mapped 5' UTRs, we show that uORFs are rare, being statistically under-represented in UTR sequences. However, they have distinct compositional biases consistent with their putative role in translational control and are more common in genes which are apparently translationally up-regulated. These results demonstrate a central regulatory role for UTR sequences, and 5' UTRs in particular, highlighting the significant role of uORFs in post-transcriptional control in yeast. Yeast uORFs are more highly conserved than has been suggested, lending further weight to their significance as functional elements involved in gene regulation. It also suggests a more complex and novel mechanism of control, whereby uORFs permit genes to escape from a more general attenuation of translation under conditions of stress. However, since uORFs are relatively rare (only ~13% of yeast genes have them) there remain many unanswered questions as to how UTR elements can direct translational control of many hundreds of genes under stress.
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            Tiling Array
            Amino Acid Starvation
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      dateModified:2009-01-07T00:00:00Z
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         Transcriptional Start Site
         Yeast Gene
         Translational Control
         Tiling Array
         Amino Acid Starvation
         Life Sciences
         general
         Microarrays
         Proteomics
         Animal Genetics and Genomics
         Microbial Genetics and Genomics
         Plant Genetics and Genomics
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