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General structure of an eukaryotic mRNA illustrating all possible post-transcriptional regulatory elements of gene expression. 5'UTR sequences can mediate regulation through (1) the cap structure made of 7-methyl-guanosine; (2) secondary structures; (3) RNAprotein interactions; (4) upstream open reading frames (ORFs); (5) internal ribosome entry site (IREs). 3'UTR mediated regulation can involve (7) RNAprotein interactions, involving also multi-protein complexes; (8) antisense RNA interactions; (9) cytoplasmic polyadeninylation elements; (10) the poly-A tail and variations of its size
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The crucial role of the non-coding portion of genomes is now widely acknowledged. In particular, mRNA untranslated regions are involved in many post-transcriptional regulatory pathways that control mRNA localisation, stability and translation efficiency. A review is given of the most recent research works on the functional characterisation of eukar...
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... this case, unlike DNA-mediated information (eg promoters, enhancers), which is essentially contained in the primary structure, RNA-mediated information also involves elements of the secondary structure, generally recognised by proteins binding to RNA (RNA binding proteins). Figure 1 shows a schematic representation of the structure of an eukaryotic gene mRNA, marking 5'UTR and 3'UTRs and the different types of post-transcriptional control they are able to implement. The 5'-UTR can also contain functional elements controlling transcription and which, owing to their localisation with respect to canonical promoter elements, are called 'downstream promoter elements'. ...
Citations
... Exon mixte en 3' avec un segment 5' UTR puis une CDS puis un segment 3' UTR 5-3utuexon Mono-exon avec un segment 5' UTR puis une CDS puis un segment 3' UTR iutuexon Exon mixte interne avec un segment 5' UTR puis une CDS puis un segment 3' UTR Tableau 2 -Classification des exons en fonction de leurs caractéristiques de traduction (inspirée de (Zhang, 1998)) Une des particularités des gènes codant pour des protéines est la présence de régions non traduites (UTR pour UnTranslated Region en anglais) qui jouent un rôle dans la régulation, la stabilité et l'efficacité de la traduction des ARNm (Pesole et al., 2000). Ainsi, en raison de la présence des UTR, il ne faut pas considérer les exons comme des séquences codantes uniquement. ...
Les projets de séquençage à haut débit produisent une énorme quantité de données biologiques brutes. Cependant, elles sont difficilement exploitables si elles ne sont pas annotées. Pour traiter ces données, des programmes d’annotation de génomes ont été développés, mais ces derniers sont encore trop sujet aux erreurs de prédiction, faisant de l’annotation des génomes un des défis majeurs en bio-informatique. Dans ce contexte, mes travaux de thèse s’organisent autour d’un trinôme : 1) l’amélioration de la prédiction des gènes eucaryotes codant pour des protéines en se focalisant spécifiquement sur les sites d’épissage 2) en exploitant des algorithmes d’intelligence artificielle (CNN et algorithmes évolutionnaires), 3) entraînés avec des données de haute qualité incluant une forte diversité d’espèces eucaryotes. Notre stratégie consiste à combiner l’ensemble des données validées avec les programmes développés afin d’améliorer la prédiction des gènes en diminuant le taux d’erreurs et éviter qu’elles ne se propagent dans les bases de données. De plus, ces travaux permettront une meilleure compréhension des organismes et de leurs mécanismes biologiques.
... In the literature, we find divergent data about the average/median length of human gene 5 UTRs based on the input data and year of study. Pesole and coworkers [21] constructed the first database focusing on the UTR sequences from different eukaryotic taxa and named it UTRdb. The average length of mRNA 5 UTR in humans was calculated to be 210 nts, maximum length 2803 and minimum 18 [22]. ...
The 12 members of the ABCA subfamily in humans are known for their ability to transport cholesterol and its derivatives, vitamins, and xenobiotics across biomembranes. Several ABCA genes are causatively linked to inborn diseases, and the role in cancer progression and metastasis is studied intensively. The regulation of translation initiation is implicated as the major mechanism in the processes of post-transcriptional modifications determining final protein levels. In the current bioinformatics study, we mapped the features of the 5′ untranslated regions (5′UTR) known to have the potential to regulate translation, such as the length of 5′UTRs, upstream ATG codons, upstream open-reading frames, introns, RNA G-quadruplex-forming sequences, stem loops, and Kozak consensus motifs, in the DNA sequences of all members of the subfamily. Subsequently, the conservation of the features, correlations among them, ribosome profiling data as well as protein levels in normal human tissues were examined. The 5′UTRs of ABCA genes contain above-average numbers of upstream ATGs, open-reading frames and introns, as well as conserved ones, and these elements probably play important biological roles in this subfamily, unlike RG4s. Although we found significant correlations among the features, we did not find any correlation between the numbers of 5′UTR features and protein tissue distribution and expression scores. We showed the existence of single nucleotide variants in relation to the 5′UTR features experimentally in a cohort of 105 breast cancer patients. 5′UTR features presumably prepare a complex playground, in which the other elements such as RNA binding proteins and non-coding RNAs play the major role in the fine-tuning of protein expression.
... UTRs are known to influence translational initiation, elongation, and termination, as well as mRNA stabilization and intracellular localization through their interaction with RNA binding proteins. 35 Depending on the specific motives within the UTR, it can either enhance or decrease mRNA turnover. 21,36 Recently, data on mRNA half lives and the corresponding UTR sequences have been published. ...
Intracellular antigen labeling and manipulation by antibodies have been long-thought goals in the field of cell research and therapy. However, a central limitation for this application is that antibodies are not able to penetrate into the cytosol of living cells. Taking advantages of small sizes and unique structures of the single-domain antibodies, here, we presented a novel approach to rapidly deliver the nanobody/variable domain of heavy chain of heavy-chain antibody (VHH) into living cells via introducing its coding mRNA, which was generated by in vitro transcription. We demonstrated that actin-green fluorescent proteins (GFP) and Golgi-GFP can be recognized by the anti-GFP nanobody/VHH, vimentin can be recognized by the anti-vimentin nanobody/VHH, and histone deacetylase 6 (HDAC6) can be recognized by the anti-HDAC6 nanobody/VHH, respectively. We found that the anti-GFP nanobody expressed via in vitro-transcribed (IVT) mRNA can be detected in 3 h and degraded in 48 h after transfection, whereas the nanobody expressed via plasmid DNA, was not detected until 24 h after transfection. As a result, it is effective in delivering the nanobody through expressing the nanobody/VHH in living cells from its coding mRNA.
... The first reports comparing the average length of whole UTR regions on a whole genome level included species from very distant taxa with a limited number of vertebrates and evaluated hundreds of 5′UTRs sequenced [30][31][32]. Their attention was paid mainly to the length of 3′UTRs, which are strikingly longer and show greater variability between lineages than the average length of 5′UTRs. The increase in average length of 3′UTRs with evolutionary distance, prominent during evolution of vertebrates, was discussed and a possible link to the increase in organism complexity was proposed [30][31][32]. ...
... Their attention was paid mainly to the length of 3′UTRs, which are strikingly longer and show greater variability between lineages than the average length of 5′UTRs. The increase in average length of 3′UTRs with evolutionary distance, prominent during evolution of vertebrates, was discussed and a possible link to the increase in organism complexity was proposed [30][31][32]. Based on the comparison of the average length of 5′UTRs it was concluded that the length of 5′UTRs stays relatively constant during evolution [30][31][32]. ...
... The increase in average length of 3′UTRs with evolutionary distance, prominent during evolution of vertebrates, was discussed and a possible link to the increase in organism complexity was proposed [30][31][32]. Based on the comparison of the average length of 5′UTRs it was concluded that the length of 5′UTRs stays relatively constant during evolution [30][31][32]. colleagues (2003, 2005) [33,34] introduced the idea that the features of 5′UTRs, including the length, in most eukaryotes are largely dictated by random genetic drift and mutational processes that cause stochastic turnover in transcription start sites (TSSs) and premature start codons in relation to the reduced effective population sizes of eukaryotes compared to prokaryotes. For eukaryotes, lengthy 5′UTRs impose a mutational burden on their associated alleles by enhancing the rate of acquisition of a premature start codon. ...
Single nucleotide polymorphisms located in 5′ untranslated regions (5′UTRs) can regulate gene expression and have clinical impact. Recognition of functionally significant sequences within 5′UTRs is crucial in next-generation sequencing applications. Furthermore, information about the behavior of 5′UTRs during gene evolution is scarce. Using the example of the ATP-binding cassette transporter A1 (ABCA1) gene (Tangier disease), we describe our algorithm for functionally significant sequence finding. 5′UTR features (upstream start and stop codons, open reading frames (ORFs), GC content, motifs, and secondary structures) were studied using freely available bioinformatics tools in 55 vertebrate orthologous genes obtained from Ensembl and UCSC. The most conserved sequences were suggested as hot spots. Exon and intron enhancers and silencers (sc35, ighg2 cgamma2, ctnt, gh-1, and fibronectin eda exon), transcription factors (TFIIA, TATA, NFAT1, NFAT4, and HOXA13), some of them cancer related, and microRNA (hsa-miR-4474-3p) were localized to these regions. An upstream ORF, overlapping with the main ORF in primates and possibly coding for a small bioactive peptide, was also detected. Moreover, we showed several features of 5′UTRs, such as GC content variation, hairpin structure conservation or 5′UTR segmentation, which are interesting from a phylogenetic point of view and can stimulate further evolutionary oriented research.
... These mutations were present in exon 3 of SYK gene which is located in 5' untranslated regions (5'UTRs) that contain genetic information for posttranscriptional regulation of gene expression. These regions have important functions in gene regulation and their mutations effecting structure and stability of pre-mRNA is a major factor of regulation and expression [27]. The results of present study are in accordance with previous studies [28,29]. ...
Asthma is a disease marked by inflammation of airways with an increasing incidence rate worldwide especially among Asian population. Spleen tyrosine kinase (Syk) is known to be involved in regulation of such inflammation response and thereby rendering its inevitable importance among asthma patients. DNA extraction followed by PCR and sequencing was performed for genomic analysis, mRNA analysis was done by RT PCR whereas Western blot and ELISA was used for protein study. Image J and UNAFOLD were also used for Bioinformatics analysis.The mean age of patients and controls were 31.1±9.3 and 30.4±6.1 years respectively. Results of sequencing showed nonsense exonic mutations in exon 3 at g.25710G>A and g.25722G>A positions. Substitution mutations in introns were also found at g.25827G>A (intron 3), g.63425C>T (intron 8) and g.63445T>G (intron 8). Significantly increased levels of IgE and significantly decreased expression of Syk at transcriptional level was found in patients compared to controls. The western blot results of asthmatic samples and healthy controls revealed that Syk has comparatively low expression in diseased individual's PBMCs. SYK has been found to be altered in DNA, mRNA and protein expression in asthma patients among Pakistani population therefore patients should be treated according to their Syk status for more effective recovery.
... The whole KU529653 18S sequence was found to be scattered with sequences showing regulatory function on gene expression: five putative upstream open reading frames (uORF) and three conserved motifs of 3' untranslated (UTR) regions of eukaryotic mRNAs. The former are generally found in 5' UTR regions of mRNAs and trigger mRNA decay or regulate translation (Barbosa et al. 2013); the latter act on mRNA stability through post-transcriptional mechanisms for a rapid response to biological and environmental cues (Pesole et al. 2001). ...
This study applies a non-invasive molecular test on common wall lizards (Podarcis muralis)
collected in Northern Italy in order to i) identify protozoan blood parasites using primers targeting a portion
of haemogregarine 18S rRNA; ii) perform a detailed bioinformatic and phylogenetic analysis of amplicons in
a context where sequence analyses data are very scarce. Indeed the corresponding phylum (Apicomplexa)
remains the poorest-studied animal group in spite of its significance for reptile ecology and evolution.
A single genus, i.e., Hepatozoon Miller, 1908 (Apicomplexa: Adeleorina) and an identical infecting genotype
were identified in all positive hosts.
Bioinformatic analyses identified highly conserved sequence patterns, some of which known to be involved in
the host-parasite cross-talk. Phylogenetic analyses evidenced a limited host specificity, in accord with existing
data.
This paper provides the first Hepatozoon sequence from P. muralis and one of the few insights into the
molecular parasitology, sequence analysis and phylogenesis of haemogregarine parasites.
... The whole KU529653 18S sequence was found to be scattered with sequences showing regulatory function on gene expression: five putative upstream open reading frames (uORF) and three conserved motifs of 3' untranslated (UTR) regions of eukaryotic mRNAs. The former are generally found in 5' UTR regions of mRNAs and trigger mRNA decay or regulate translation (Barbosa et al. 2013); the latter act on mRNA stability through post-transcriptional mechanisms for a rapid response to biological and environmental cues (Pesole et al. 2001). ...
... Genes are often regulated at multiple levels, including at the level of transcription, splicing, messenger RNA (mRNA) transport, mRNA stability, translation, protein stability, and post-translational modification [15]. Previous results have demonstrated that the TSP50 promoter region plays a critical role in the regulation of TSP50 expression [16][17][18] and the gene's promoter has become a drug screening tool [14]. ...
While the incidence of cancer continues to increase, the current therapeutic options remain imperfect. Therefore, there is an urgent need to discover new targeted anti-cancer therapies. Testes-specific protease 50 (TSP50) is abnormally expressed in most cancer tissues and downregulation of TSP50 expression can reduce cell proliferation and induce cell apoptosis, which makes it a potential target for cancer therapy. In this study, we constructed a firefly luciferase reporter pGL3-TSP50-3'-UTR as a drug screening model to screen potential candidate compounds that target TSP50 mRNA. We identified the compound 7P3A, which consists of 70 % 25-methoxyl-dammarane-3β, 12β, 20-triol and 30 % artemisinin, as being capable of inhibiting the TSP50-3'-UTR reporter activity, as well as the expression of TSP50. Further investigation revealed that 7P3A could inhibit MDA-MB-231 cell proliferation and induce cell cycle arrest, and over-expression of TSP50 partially reversed the effect of 7P3A. In vivo investigation showed that 7P3A could inhibit tumor growth in a xenograft model of breast cancer. These results suggest that 7P3A exhibits anti-cancer effects, in part, through downregulation of TSP50 expression.
... The UTR of a gene has important biological roles which can influence the half-life, intracellular localization, and differential translational efficiency of the corresponding mRNA (Pesole et al., 2000;Mignone et al., 2002;Mazumder et al., 2003;Chabanon et al., 2004;de Moor et al., 2005). The properties of a transcript are controlled by some features of their UTRs. ...
Soil salinity is one of the most challenging problems that restricts the normal growth and production of rice worldwide. It has therefore become very important to produce more saline tolerant rice varieties. This study shows constitutive over-expression of the vacuolar Na⁺/H⁺ antiporter gene (OsNHX1) from the rice landrace (Pokkali) and attainment of enhanced level of salinity tolerance in transgenic rice plants. It also shows that inclusion of the complete un-translated regions (UTRs) of the alternatively spliced OsNHX1 gene provides a higher level of tolerance to the transgenic rice. Two separate transformation events of the OsNHX1 gene, one with 1.9 kb region containing the 5′ UTR with CDS and the other of 2.3 kb, including 5′ UTR, CDS, and the 3′ UTR regions were performed. The transgenic plants with these two different constructs were advanced to the T3 generation and physiological and molecular screening of homozygous plants was conducted at seedling and reproductive stages under salinity (NaCl) stress. Both transgenic lines were observed to be tolerant compared to WT plants at both physiological stages. However, the transgenic lines containing the CDS with both the 5′ and 3′ UTR were significantly more tolerant compared to the transgenic lines containing OsNHX1 gene without the 3′ UTR. At the seedling stage at 12 dS/m stress, the chlorophyll content was significantly higher (P < 0.05) and the electrolyte leakage significantly lower (P < 0.05) in the order 2.3 kb > 1.9 kb > and WT lines. Yield in g/plant in the best line from the 2.3 kb plants was significantly more (P < 0.01) compared, respectively, to the best 1.9 kb line and WT plants at stress of 6 dS/m. Transformation with the complete transcripts rather than the CDS may therefore provide more durable level of tolerance.
... c Western blot analysis on hiPSCs 1 and DMD hiPSCs 2 EBs from day 0 to day 14 with BMP4 treatment. (Dystrophin antibody: DYS1; BMP4-treated hiPSCs 1 in 2 dimensions (2D) culture (4 days after treatment) was used as control; α-tubulin was used as loading control) translation to begin downstream of the first AUG codon in a cap-independent manner [59,60]. A glucocorticoidresponsive IRES in exon 5 of the DMD gene has already been identified using reporter assays and confirmed in vivo in mice and in vitro using human muscular cells to induce translation initiation in exon 6 [30]. ...
Background:
Duchenne muscular dystrophy (DMD) is a devastating X-linked recessive genetic myopathy. DMD physiopathology is still not fully understood and a prenatal onset is suspected but difficult to address.
Methods:
The bone morphogenetic protein 4 (BMP4) is a critical signaling molecule involved in mesoderm commitment. Human induced pluripotent stem cells (hiPSCs) from DMD and healthy individuals and human embryonic stem cells (hESCs) treated with BMP4 allowed us to model the early steps of myogenesis in normal and DMD contexts.
Results:
Unexpectedly, 72h following BMP4 treatment, a new long DMD transcript was detected in all tested hiPSCs and hESCs, at levels similar to that found in adult skeletal muscle. This novel transcript named "Dp412e" has a specific untranslated first exon which is conserved only in a sub-group of anthropoids including human. The corresponding novel dystrophin protein of 412-kiloDalton (kDa), characterized by an N-terminal-truncated actin-binding domain, was detected in normal BMP4-treated hiPSCs/hESCs and in embryoid bodies. Finally, using a phosphorodiamidate morpholino oligomer (PMO) targeting the DMD exon 53, we demonstrated the feasibility of exon skipping validation with this BMP4-inducible hiPSCs model.
Conclusions:
In this study, the use of hiPSCs to analyze early phases of human development in normal and DMD contexts has led to the discovery of an embryonic 412 kDa dystrophin isoform. Deciphering the regulation process(es) and the function(s) associated to this new isoform can contribute to a better understanding of the DMD physiopathology and potential developmental defects. Moreover, the simple and robust BMP4-inducible model highlighted here, providing large amount of a long DMD transcript and the corresponding protein in only 3 days, is already well-adapted to high-throughput and high-content screening approaches. Therefore, availability of this powerful cell platform can accelerate the development, validation and improvement of DMD genetic therapies.
