UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs

Abstract

The 5′ and 3′ untranslated regions of eukaryotic mRNAs (UTRs) play crucial roles in the post-transcriptional regulation of gene expression through the modulation of nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization and message stability. UTRdb is a curated database of 5′ and 3′ untranslated sequences of eukaryotic mRNAs, derived from several sources of primary data. Experimentally validated functional motifs are annotated and also collated as the UTRsite database where more specific information on the functional motifs and cross-links to interacting regulatory protein are provided. In the current update, the UTR entries have been organized in a gene-centric structure to better visualize and retrieve 5′ and 3′UTR variants generated by alternative initiation and termination of transcription and alternative splicing. Experimentally validated miRNA targets and conserved sequence elements are also annotated. The integration of UTRdb with genomic data has allowed the implementation of an efficient annotation system and a powerful retrieval resource for the selection and extraction of specific UTR subsets. All internet resources implemented for retrieval and functional analysis of 5′ and 3′ untranslated regions of eukaryotic mRNAs are accessible at http://utrdb.ba.itb.cnr.it/.

Frac-seq reveals isoform-specific recruitment to polyribosomes

“…Given their prominent role in translational control and mRNA stability, we also analyzed alternative events that remodel sequences in 59 and 39 UTRs associated with isoform-specific polyribosome association. We exploited a list of predicted functional elements annotated in the UTR database (UTRdb) (Grillo et al 2009) and intersected these annotations with the set of alternative events exhibiting a change in polyribosome association (see Methods). Included in this list are well-annotated 59 and 39 UTR specific regulatory elements such as upstream ORFs (uORFs) and internal ribosomal entry site (IRES), as well as microRNA target sites and Alu elements, respectively.…”

“…Included in this list are well-annotated 59 and 39 UTR specific regulatory elements such as upstream ORFs (uORFs) and internal ribosomal entry site (IRES), as well as microRNA target sites and Alu elements, respectively. These element classes are well characterized for their roles in translational control and mRNA stability (Grillo et al 2009;Gong and Maquat 2011a,b;Ramani et al 2011). Our analysis demonstrates that uORFs and IRES elements are associated with an increase in polyribosome association for element-harboring isoforms compared to the element-deficient isoform (P-value < 3.79 3 10 À3 and <1.15 3 10 À3 , respectively) (Fig.…”

Analysis of the 5′ untranslated region (5′UTR) of the alcohol oxidase 1 (AOX1) gene in recombinant protein expression in Pichia pastoris

“…The ΔG of this structure, which is approximately −30 kcal/mol, suggests that it is a moderately stable structure, but it would not be expected to stall the migration of the 40S ribosomal subunit, which would require a ΔG of at least −50 kcal/mol (Mignone et al, 2002). Although such moderately stable motifs can be targets for RNA binding proteins, a bioinformatic analysis of the AOX1 5′UTR found no significant similarity to any known RNA regulatory sequences or potential IRES sites (Grillo et al, 2010). …”

“…Along with an incremental deletion analysis, we also used predicted secondary structures based on an RNA fold program (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi) to explore which regions could influence structure and presumably the function of the 5′UTR in protein production (Bagga, 2008; Grillo et al, 2010). As described above, this analysis suggested the 5′UTR folded into a structure with three hairpins radiating from a central loop region (Fig.…”

“…Our second goal was to comprehend how increases in the length of 5′UTR affect expression of heterologous proteins. Often when investigators are inserting their coding sequences into expression vectors, they may add a large amount of foreign sequence upstream of the ATG or use a restriction site located in the 3′ region of a polylinker (Bagga, 2008; Grillo et al, 2010). Both of these actions lengthen the 5′UTR.…”