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1
Silvaggi, Jessica M., John B. Perkins, and Richard Losick. "Small Untranslated RNA Antitoxin in Bacillus subtilis." Journal of Bacteriology 187, no. 19 (October 1, 2005): 6641–50. http://dx.doi.org/10.1128/jb.187.19.6641-6650.2005.
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ABSTRACT Toxin-antitoxin (TA) modules are pairs of genes in which one member encodes a toxin that is neutralized or whose synthesis is prevented by the action of the product of the second gene, an antitoxin, which is either protein or RNA. We now report the identification of a TA module in the chromosome of Bacillus subtilis in which the antitoxin is an antisense RNA. The antitoxin, which is called RatA (for RNA antitoxin A), is a small (222 nucleotides), untranslated RNA that blocks the accumulation of the mRNA for a toxic peptide TxpA (for toxic peptide A; formerly YqdB). The txpA and ratA genes are in convergent orientation and overlap by ca. 75 nucleotides, such that the 3′ region of ratA is complementary to the 3′ region of txpA. Deletion of ratA led to increased levels of txpA mRNA and lysis of the cells. Overexpression of txpA also caused cell lysis and death, a phenotype that was prevented by simultaneous overexpression of ratA. We propose that the ratA transcript is an antisense RNA that anneals to the 3′ end of the txpA mRNA, thereby triggering its degradation.
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Yamashita, Riu, Yutaka Suzuki, Kenta Nakai, and Sumio Sugano. "Small open reading frames in 5′ untranslated regions of mRNAs." Comptes Rendus Biologies 326, no. 10-11 (October 2003): 987–91. http://dx.doi.org/10.1016/j.crvi.2003.09.028.
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Davis, Brigid M., Mariam Quinones, Jason Pratt, Yanpeng Ding, and Matthew K. Waldor. "Characterization of the Small Untranslated RNA RyhB and Its Regulon in Vibrio cholerae." Journal of Bacteriology 187, no. 12 (June 15, 2005): 4005–14. http://dx.doi.org/10.1128/jb.187.12.4005-4014.2005.
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ABSTRACT Numerous small untranslated RNAs (sRNAs) have been identified in Escherichia coli in recent years, and their roles are gradually being defined. However, few of these sRNAs appear to be conserved in Vibrio cholerae, and both identification and characterization of sRNAs in V. cholerae remain at a preliminary stage. We have characterized one of the few sRNAs conserved between E. coli and V. cholerae: RyhB. Sequence conservation is limited to the central region of the gene, and RyhB in V. cholerae is significantly larger than in E. coli. As in E. coli, V. cholerae RyhB is regulated by the iron-dependent repressor Fur, and it interacts with the RNA-binding protein Hfq. The regulons controlled by RyhB in V. cholerae and E. coli appear to differ, although some overlap is evident. Analysis of gene expression in V. cholerae in the absence of RyhB suggests that the role of this sRNA is not limited to control of iron utilization. Quantitation of RyhB expression in the suckling mouse intestine suggests that iron availability is not limiting in this environment, and RyhB is not required for colonization of this mammalian host by V. cholerae.
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Macdonald, P. M., K. Kerr, J. L. Smith, and A. Leask. "RNA regulatory element BLE1 directs the early steps of bicoid mRNA localization." Development 118, no. 4 (August 1, 1993): 1233–43. http://dx.doi.org/10.1242/dev.118.4.1233.
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Deployment of the bicoid morphogen gradient in early Drosophila embryos requires the prelocalization of bicoid mRNA to the anterior pole of the egg. This anterior localization is mediated by a cis-acting localization signal contained within the 3′ untranslated region of the bicoid mRNA. Here we use a series of bicoid transgenes carrying small deletions in the 3′ untranslated region to survey for functional elements that constitute the localization signal. We identify and characterize one essential element, BLE1, which specifically directs the early steps of localization. In addition, we find that many deletions within the bicoid mRNA 3′ untranslated region impair but do not prevent localization. One such deletion specifically interferes with a later step in localization. Thus the bicoid mRNA localization signal appears to consist of multiple different elements, each responsible for different steps in the localization process.
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Skryabin, Boris V., Valentina Sukonina, Ursula Jordan, Lars Lewejohann, Norbert Sachser, Ilham Muslimov, Henri Tiedge, and Jürgen Brosius. "Neuronal Untranslated BC1 RNA: Targeted Gene Elimination in Mice." Molecular and Cellular Biology 23, no. 18 (September 15, 2003): 6435–41. http://dx.doi.org/10.1128/mcb.23.18.6435-6441.2003.
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ABSTRACT Despite the potentially important roles of untranslated RNAs in cellular form or function, genes encoding such RNAs have until now received surprisingly little attention. One such gene encodes BC1 RNA, a small non-mRNA that is delivered to dendritic microdomains in neurons. We have now eliminated the BC1 RNA gene in mice. Three independent founder lines were established from separate embryonic stem cells. The mutant mice appeared to be healthy and showed no anatomical or neurological abnormalities. The gross brain morphology was unaltered in such mice, as were the subcellular distributions of two prototypical dendritic mRNAs (encoding MAP2 and CaMKIIα). Due to the relatively recent evolutionary origin of the gene, we expected molecular and behavioral consequences to be subtle. Behavioral analyses, to be reported separately, indicate that the lack of BC1 RNA appears to reduce exploratory activity.
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Shirokikh, Nikolay E., Yulia S. Dutikova, Maria A. Staroverova, Ross D. Hannan, and Thomas Preiss. "Migration of Small Ribosomal Subunits on the 5′ Untranslated Regions of Capped Messenger RNA." International Journal of Molecular Sciences 20, no. 18 (September 10, 2019): 4464. http://dx.doi.org/10.3390/ijms20184464.
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Several control mechanisms of eukaryotic gene expression target the initiation step of mRNA translation. The canonical translation initiation pathway begins with cap-dependent attachment of the small ribosomal subunit (SSU) to the messenger ribonucleic acid (mRNA) followed by an energy-dependent, sequential ‘scanning’ of the 5′ untranslated regions (UTRs). Scanning through the 5′UTR requires the adenosine triphosphate (ATP)-dependent RNA helicase eukaryotic initiation factor (eIF) 4A and its efficiency contributes to the specific rate of protein synthesis. Thus, understanding the molecular details of the scanning mechanism remains a priority task for the field. Here, we studied the effects of inhibiting ATP-dependent translation and eIF4A in cell-free translation and reconstituted initiation reactions programmed with capped mRNAs featuring different 5′UTRs. An aptamer that blocks eIF4A in an inactive state away from mRNA inhibited translation of capped mRNA with the moderately structured β-globin sequences in the 5′UTR but not that of an mRNA with a poly(A) sequence as the 5′UTR. By contrast, the nonhydrolysable ATP analogue β,γ-imidoadenosine 5′-triphosphate (AMP-PNP) inhibited translation irrespective of the 5′UTR sequence, suggesting that complexes that contain ATP-binding proteins in their ATP-bound form can obstruct and/or actively block progression of ribosome recruitment and/or scanning on mRNA. Further, using primer extension inhibition to locate SSUs on mRNA (‘toeprinting’), we identify an SSU complex which inhibits primer extension approximately eight nucleotides upstream from the usual toeprinting stop generated by SSUs positioned over the start codon. This ‘−8 nt toeprint’ was seen with mRNA 5′UTRs of different length, sequence and structure potential. Importantly, the ‘−8 nt toeprint’ was strongly stimulated by the presence of the cap on the mRNA, as well as the presence of eIFs 4F, 4A/4B and ATP, implying active scanning. We assembled cell-free translation reactions with capped mRNA featuring an extended 5′UTR and used cycloheximide to arrest elongating ribosomes at the start codon. Impeding scanning through the 5′UTR in this system with elevated magnesium and AMP-PNP (similar to the toeprinting conditions), we visualised assemblies consisting of several SSUs together with one full ribosome by electron microscopy, suggesting direct detection of scanning intermediates. Collectively, our data provide additional biochemical, molecular and physical evidence to underpin the scanning model of translation initiation in eukaryotes.
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MARTIGNETTI, LOREDANA, ANDREI ZINOVYEV, and EMMANUEL BARILLOT. "IDENTIFICATION OF SHORTENED 3′ UNTRANSLATED REGIONS FROM EXPRESSION ARRAYS." Journal of Bioinformatics and Computational Biology 10, no. 02 (April 2012): 1241001. http://dx.doi.org/10.1142/s0219720012410016.
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Cancer cells have been recently shown to express high level of short 3′UTR isoforms that can escape miRNA-mediated regulation. We present here a computational procedure for systematically identifying shortened 3′UTRs by Affymetrix 3′ microarrays. The advantage of this technology compared to more recent and promising ones such as exon arrays and RNA-Seq is that, giving the relatively small cost, already existing datasets in public databases include a considerably higher number of experiments. Moreover, the design of Affymetrix Gene Chips is well-suited for 3′UTR analysis of a large number of genes. Initially, Affymetrix individual probes are regrouped into customized probesets mapping specifically the CDS or the 3′UTR of the transcript, according to RefSeq annotation. Then, candidate 3′UTR shortening events are identified by statistical differential expression analysis of customized probesets in different biological conditions. The procedure has been applied to expression data from two ovarian adenocarcinoma datasets. Selected gene sets are significantly enriched for annotated splice variant genes as well as genes involved in estrogen dependent cancer mechanisms, confirming the validity of the proposed procedure.
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Suess, B. "Engineered riboswitches control gene expression by small molecules." Biochemical Society Transactions 33, no. 3 (June 1, 2005): 474–76. http://dx.doi.org/10.1042/bst0330474.
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We have developed conditional gene expression systems based on engineered small-molecule-binding riboswitches. Tetracycline-dependent regulation can be imposed on an mRNA in yeast by inserting an aptamer in its 5′-untranslated region. Biochemical and genetic analyses determined that binding of the ligand tetracycline leads to a pseudoknot-like linkage within the aptamer structure, thereby inhibiting the initial steps of translation. A second translational control element was designed by combining a theophylline aptamer with a communication module for which a 1 nt slipping mechanism had been proposed. This structural element was inserted close to the bacterial ribosomal binding site at a position just interfering with translation in the non-ligand-bound form. Addition of the ligand then shifts the inhibitory element to a distance that permits efficient translation.
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Hartmann, Claudia, Corinna Benz, Stefanie Brems, Louise Ellis, Van-Duc Luu, Mhairi Stewart, Iván D'Orso, et al. "Small Trypanosome RNA-Binding Proteins TbUBP1 and TbUBP2 Influence Expression of F-Box Protein mRNAs in Bloodstream Trypanosomes." Eukaryotic Cell 6, no. 11 (September 1, 2007): 1964–78. http://dx.doi.org/10.1128/ec.00279-07.
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ABSTRACT In the African trypanosome Trypanosoma brucei nearly all control of gene expression is posttranscriptional; sequences in the 3′-untranslated regions of mRNAs determine the steady-state mRNA levels by regulation of RNA turnover. Here we investigate the roles of two related proteins, TbUBP1 and TbUBP2, containing a single RNA recognition motif, in trypanosome gene expression. TbUBP1 and TbUBP2 are in the cytoplasm and nucleus, comprise ca. 0.1% of the total protein, and are not associated with polysomes or RNA degradation enzymes. Overexpression of TbUBP2 upregulated the levels of several mRNAs potentially involved in cell division, including the CFB1 mRNA, which encodes a protein with a cyclin F-box domain. CFB1 regulation was mediated by the 3′-untranslated region and involved stabilization of the mRNA. Depletion of TbUBP2 and TbUBP1 inhibited growth and downregulated expression of the cyclin F box protein gene CFB2; trans splicing was unaffected. The results of pull-down assays indicated that all tested mRNAs were bound to TbUBP2 or TbUBP1, with some preference for CFB1. We suggest that TbUBP1 and TbUBP2 may be relatively nonspecific RNA-binding proteins and that specific effects of overexpression or depletion could depend on competition between various different proteins for RNA binding.
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Serano, T. L., and R. S. Cohen. "A small predicted stem-loop structure mediates oocyte localization of Drosophila K10 mRNA." Development 121, no. 11 (November 1, 1995): 3809–18. http://dx.doi.org/10.1242/dev.121.11.3809.
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The establishment of dorsoventral polarity in the Drosophila oocyte and future embryo is dependent on the efficient transport of K10 mRNA from nurse cells into the oocyte. To investigate the cis-requirements of K10 mRNA transport, we used a transgenic fly assay to analyze the expression patterns of a series of K10 deletion variants. Such studies identify a 44 nucleotide sequence within the K10 3′ untranslated region that is required and sufficient for K10 mRNA transport and subsequent localization to the oocyte's anterior cortex. An inspection of the 44 nucleotide transport/localization sequence (TLS) reveals a strong potential for the formation of a stem-loop secondary structure. Nucleotide substitutions that interfere with the predicted base-pairing of the TLS block mRNA transport and anterior localization. Conversely, mutations that alter the base composition of the TLS while maintaining predicted base-pairing do not block mRNA transport or anterior localization. We conclude that K10 mRNA transport and anterior localization is mediated by a 44 nucleotide stem-loop structure. A similar putative stem-loop structure is found in the 3′ untranslated region of the Drosophila orb mRNA, suggesting that the same factors mediate the transport and anterior localization of both K10 and orb mRNAs. Apart from orb, the K10 TLS is not found in any other localized mRNA, raising the possibility that the transport and localization of other mRNAs, e.g., bicoid, oskar and gurken, are mediated by novel sets of cis- and trans-acting factors. Moreover, we find that the K10 TLS overrides the activity of oskar cis-regulatory elements that mediate the late stage movement of the mRNA to the posterior pole. We propose the existence of a family of cis-regulatory elements that mediate mRNA transport into the oocyte, only some of which are compatible with the elements that mediate late stage movements.
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Heidrich, Nadja, Alberto Chinali, Ulf Gerth, and Sabine Brantl. "The small untranslated RNA SR1 from theBacillus subtilisgenome is involved in the regulation of arginine catabolism." Molecular Microbiology 62, no. 2 (September 27, 2006): 520–36. http://dx.doi.org/10.1111/j.1365-2958.2006.05384.x.
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Shetty, Sreerama, and Steven Idell. "Posttranscriptional regulation of plasminogen activator inhibitor-1 in human lung carcinoma cells in vitro." American Journal of Physiology-Lung Cellular and Molecular Physiology 278, no. 1 (January 1, 2000): L148—L156. http://dx.doi.org/10.1152/ajplung.2000.278.1.l148.
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Plasminogen activator inhibitor-1 (PAI-1), the major circulating inhibitor of urokinase [urokinase-type plasminogen activator (uPA)], has been linked to the pathogenesis of lung cancer. PAI-1 belongs to the serpin family of inhibitors and inhibits both free urokinase (uPA) and receptor-bound urokinase (uPA receptor). Although PAI-1 has been related to a poor prognosis in lung carcinoma, mechanisms that regulate its expression in human lung cancer cells are not well understood. We used cultured human small cell and non-small cell lung carcinoma cell lines as model systems to elucidate the regulatory mechanisms that control expression of PAI-1. Levels of PAI-1 protein were significantly increased in selected lung carcinoma cells compared with those in normal small-airway epithelial cells. Corresponding steady-state levels of PAI-1 mRNA were similarly increased in these cells. The half-life of PAI-1 mRNA was prolonged in these lung carcinoma cell lines after transcriptional or translational blockade. We identified a 60-kDa protein that binds the 3′-untranslated region of PAI-1, and complex formation of this binding protein with PAI-1 mRNA reciprocally correlates with mRNA stability. The findings demonstrate that expression of PAI-1 is regulated at the posttranscriptional level in small cell- and non-small cell-derived human lung carcinoma cell lines. Altered regulation of PAI-1 at the posttranscriptional level may contribute to relative overexpression by malignant lung epithelial cells. A newly identified regulatory protein that binds to the 3′-untranslated region of PAI-1 mRNA appears to be involved in the posttranscriptional regulation of PAI-1 gene expression by human lung carcinoma cells in vitro.
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Hellwinkel, Olaf José-Carlos, Paul-Martin Holterhus, Dagmar Struve, Christine Marschke, Nicole Homburg, and Olaf Hiort. "A Unique Exonic Splicing Mutation in the Human Androgen Receptor Gene Indicates a Physiologic Relevance of Regular Androgen Receptor Transcript Variants1." Journal of Clinical Endocrinology & Metabolism 86, no. 6 (June 1, 2001): 2569–75. http://dx.doi.org/10.1210/jcem.86.6.7543.
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In a patient with partial androgen insensitivity syndrome (AIS), we identified a single inherited presumably silent nucleotide variation (AGC -> AGT) in exon 8 (codon 888) of the AR gene. However, in the patient’s genital skin fibroblasts, a considerably shortened transcript of 5.5 kb (normal: 10.5 kb) was detected, which misses a part of exon 8 and a prominent portion of the 3′-untranslated region. The translation product includes eight missense amino acids from codon 886 onward followed by a premature stop codon. As shown by in vitro expression analysis, the mutant protein lacks any residual function. However, reverse transcribed PCRs and sequence data indicate the existence of two additional splicing variants of 6.4 kb and 7.8-kb length both in patient and normal control genital skin fibroblasts. These splicing variants comprise the complete coding region but a shortened 3′-untranslated region. Thus, a distinct alternative pre-messegner RNA-processing event leading to two additional transcripts occurs generally in genital skin fibroblasts. In addition, this process partially prevents aberrant splicing in the patient and produces a small fraction of normal, functionally intact AR-protein that could explain the partial masculinization in this patient. This first report of an exonic splicing mutation in the AR-gene indicates a physiologic relevance of the regular AR-messenger RNA variants with shortened 3′-untranslated regions and their functional translation products in human genital development.
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Higgs, David C., Risa S. Shapiro, Karen L. Kindle, and David B. Stern. "Small cis-Acting Sequences That Specify Secondary Structures in a Chloroplast mRNA Are Essential for RNA Stability and Translation." Molecular and Cellular Biology 19, no. 12 (December 1, 1999): 8479–91. http://dx.doi.org/10.1128/mcb.19.12.8479.
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ABSTRACT Nucleus-encoded proteins interact with cis-acting elements in chloroplast transcripts to promote RNA stability and translation. We have analyzed the structure and function of three such elements within the Chlamydomonas petD 5′ untranslated region; petD encodes subunit IV of the cytochromeb 6/f complex. These elements were delineated by linker-scanning mutagenesis, and RNA secondary structures were investigated by mapping nuclease-sensitive sites in vitro and by in vivo dimethyl sulfate RNA modification. Element I spans a maximum of 8 nucleotides (nt) at the 5′ end of the mRNA; it is essential for RNA stability and plays a role in translation. This element appears to form a small stem-loop that may interact with a previously described nucleus-encoded factor to block 5′→3′ exoribonucleolytic degradation. Elements II and III, located in the center and near the 3′ end of the 5′ untranslated region, respectively, are essential for translation, but mutations in these elements do not affect mRNA stability. Element II is a maximum of 16 nt in length, does not form an obvious secondary structure, and appears to bind proteins that protect it from dimethyl sulfate modification. Element III spans a maximum of 14 nt and appears to form a stem-loop in vivo, based on dimethyl sulfate modification and the sequences of intragenic suppressors of element III mutations. Furthermore, mutations in element II result in changes in the RNA structure near element III, consistent with a long-range interaction that may promote translation.
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Khaladkar, Mugdha, Jianghui Liu, Dongrong Wen, Jason TL Wang, and Bin Tian. "Mining small RNA structure elements in untranslated regions of human and mouse mRNAs using structure-based alignment." BMC Genomics 9, no. 1 (2008): 189. http://dx.doi.org/10.1186/1471-2164-9-189.
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Green-Willms, Noelle S., Thomas D. Fox, and Maria C. Costanzo. "Functional Interactions between Yeast Mitochondrial Ribosomes and mRNA 5′ Untranslated Leaders." Molecular and Cellular Biology 18, no. 4 (April 1, 1998): 1826–34. http://dx.doi.org/10.1128/mcb.18.4.1826.
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ABSTRACT Translation of mitochondrial mRNAs in Saccharomyces cerevisiae depends on mRNA-specific translational activators that recognize the 5′ untranslated leaders (5′-UTLs) of their target mRNAs. We have identified mutations in two new nuclear genes that suppress translation defects due to certain alterations in the 5′-UTLs of both the COX2 and COX3 mRNAs, indicating a general function in translational activation. One gene, MRP21, encodes a protein with a domain related to the bacterial ribosomal protein S21 and to unidentified proteins of several animals. The other gene, MRP51, encodes a novel protein whose only known homolog is encoded by an unidentified gene in S. kluyveri. Deletion of either MRP21 or MRP51 completely blocked mitochondrial gene expression. Submitochondrial fractionation showed that both Mrp21p and Mrp51p cosediment with the mitochondrial ribosomal small subunit. The suppressor mutations are missense substitutions, and those affecting Mrp21p alter the region homologous to E. coli S21, which is known to interact with mRNAs. Interactions of the suppressor mutations with leaky mitochondrial initiation codon mutations strongly suggest that the suppressors do not generally increase translational efficiency, since some alleles that strongly suppress 5′-UTL mutations fail to suppress initiation codon mutations. We propose that mitochondrial ribosomes themselves recognize a common feature of mRNA 5′-UTLs which, in conjunction with mRNA-specific translational activation, is required for organellar translation initiation.
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Balsiger, Sylvia, Curdin Ragaz, Christian Baron, and Franz Narberhaus. "Replicon-Specific Regulation of Small Heat Shock Genes in Agrobacterium tumefaciens." Journal of Bacteriology 186, no. 20 (October 15, 2004): 6824–29. http://dx.doi.org/10.1128/jb.186.20.6824-6829.2004.
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ABSTRACT Four genes coding for small heat shock proteins (sHsps) were identified in the genome sequence of Agrobacterium tumefaciens, one on the circular chromosome (hspC), one on the linear chromosome (hspL), and two on the pAT plasmid (hspAT1 and hspAT2). Induction of sHsps at elevated temperatures was revealed by immunoblot analyses. Primer extension experiments and translational lacZ fusions demonstrated that expression of the pAT-derived genes and hspL is controlled by temperature in a regulon-specific manner. While the sHsp gene on the linear chromosome turned out to be regulated by RpoH (σ32), both copies on pAT were under the control of highly conserved ROSE (named for repression of heat shock gene expression) sequences in their 5′ untranslated region. Secondary structure predictions of the corresponding mRNA strongly suggest that it represses translation at low temperatures by masking the Shine-Dalgarno sequence. The hspC gene was barely expressed (if at all) and not temperature responsive.
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Hong, Wenming, Pengying Zhang, Xinming Wang, Jiajie Tu, and Wei Wei. "The Effects of MicroRNAs on Key Signalling Pathways and Epigenetic Modification in Fibroblast-Like Synoviocytes of Rheumatoid Arthritis." Mediators of Inflammation 2018 (2018): 1–8. http://dx.doi.org/10.1155/2018/9013124.
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MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression at the posttranscriptional level via direct binding to the 3′-untranslated region (UTR) of target mRNAs. Emerging evidence shows that miRNAs play crucial roles in controlling and modulating immune system-related diseases. This review focuses on the role played by miRNAs in fibroblast-like synoviocytes (FLS), which is a key cellular component within synovia, during the establishment and maintenance of rheumatoid arthritis (RA), a systemic inflammatory autoimmune disease. It also provides an overview and classification of known functional miRNAs in RA FLS and summarizes the potential uses of these small molecules in RA diagnosis and treatment.
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Blakqori, Gjon, Ingeborg van Knippenberg, and Richard M. Elliott. "Bunyamwera Orthobunyavirus S-Segment Untranslated Regions Mediate Poly(A) Tail-Independent Translation." Journal of Virology 83, no. 8 (February 4, 2009): 3637–46. http://dx.doi.org/10.1128/jvi.02201-08.
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ABSTRACT The mRNAs of Bunyamwera virus (BUNV), the prototype of the Bunyaviridae family, possess a 5′ cap structure but lack a 3′ poly(A) tail, a common feature of eukaryotic mRNAs that greatly enhances translation efficiency. Viral mRNAs also contain untranslated regions (UTRs) that flank the coding sequence. Using model virus-like mRNAs that harbor the Renilla luciferase reporter gene, we found that the 3′ UTR of the BUNV small-segment mRNA mediated efficient translation in the absence of a poly(A) tail. Viral UTRs did not increase RNA stability, and polyadenylation did not significantly enhance reporter activity. Translation of virus-like mRNAs in transfected cells was unaffected by knockdown of poly(A)-binding protein (PABP) but was markedly reduced by depletion of eukaryotic initiation factor 4G, suggesting a PABP-independent process for translation initiation. In BUNV-infected cells, translation of polyadenylated but not virus-like mRNAs was inhibited. Furthermore, we demonstrate that the viral nucleocapsid protein binds to, and colocalizes with, PABP in the cytoplasm early in infection, followed by nuclear retention of PABP. Our results suggest that BUNV corrupts PABP function in order to inhibit translation of polyadenylated cellular mRNAs while its own mRNAs are translated in a PABP-independent process.
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WAHAB, Nadia ABDEL, James GIBBS, and Roger M. MASON. "Regulation of gene expression by alternative polyadenylation and mRNA instability in hyperglycaemic mesangial cells." Biochemical Journal 336, no. 2 (December 1, 1998): 405–11. http://dx.doi.org/10.1042/bj3360405.
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We have used mRNA differential display to identify a novel high-glucose-regulated gene (HGRG-14) in human mesangial cells cultured for up to 21 days in 30 mM d-glucose. The mRNA of HGRG-14 seems to be regulated post-transcriptionally and encodes a small polypeptide of molecular mass 13 kDa. The native protein occurs as a dimer. The recombinant protein is a substrate for casein kinase II kinase. At high glucose concentrations, HGRG-14 protein levels decrease. This correlates with the appearance of a long form of HGRG-14 mRNA under high-glucose conditions. This form has a long 3´ untranslated region containing several ATTTA RNA-destabilizing sequences and has a short half-life. A truncated, more stable mRNA that lacks the long 3´ untranslated region is produced at 4 mM d-glucose. The switch from the truncated to the long-form transcript is detected within 2 h of exposure to 30 mM d-glucose, indicating that hyperglycaemic conditions have an acute effect on HGRG-14 mRNA processing.
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Urbanowski, Mark L., Lorraine T. Stauffer, and George V. Stauffer. "ThegcvBgene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems inEscherichia coli." Molecular Microbiology 37, no. 4 (August 2000): 856–68. http://dx.doi.org/10.1046/j.1365-2958.2000.02051.x.
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Lin, C. S., W. Shen, Z. P. Chen, Y. H. Tu, and P. Matsudaira. "Identification of I-plastin, a human fimbrin isoform expressed in intestine and kidney." Molecular and Cellular Biology 14, no. 4 (April 1994): 2457–67. http://dx.doi.org/10.1128/mcb.14.4.2457.
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The complete cDNA sequence of human intestine-specific plastin (I-plastin) was determined from a clone derived by PCR. It consists of a 97-bp 5' untranslated region, a 1,887-bp coding region, and a 1,655-bp 3' untranslated region. The coding region predicts a 629-residue polypeptide whose sequence displays 86, 75, and 73% identities with chicken intestine fimbrin, human T-plastin, and human L-plastin, respectively. Recombinant I-plastin cross-linked actin filaments into bundles in the absence but not in the presence of calcium. The I-plastin gene was mapped by PCR to human chromosome 3; the L- and T-plastin genes were previously mapped to chromosomes 13 and X, respectively. I-plastin mRNA was detected in the small intestine, colon, and kidneys; relatively lower levels of expression were detected in the lungs and stomach. In contrast, L-plastin expression was restricted to the spleen and other lymph node-containing organs, while T-plastin was expressed in a variety of organs, including muscle, brain, uterus, and esophagus. In contrast to the situation for the intestine, high levels of L- and T-plastin mRNAs were detected in Caco-2, a human colon-derived cell line. Immunofluorescence microscopy detected I-plastin in the brush border of the small intestine and colon. These results identify I-plastin as the human homolog of chicken intestine fimbrin and as a third plastin isoform in humans.
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Lin, C. S., W. Shen, Z. P. Chen, Y. H. Tu, and P. Matsudaira. "Identification of I-plastin, a human fimbrin isoform expressed in intestine and kidney." Molecular and Cellular Biology 14, no. 4 (April 1994): 2457–67. http://dx.doi.org/10.1128/mcb.14.4.2457-2467.1994.
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The complete cDNA sequence of human intestine-specific plastin (I-plastin) was determined from a clone derived by PCR. It consists of a 97-bp 5' untranslated region, a 1,887-bp coding region, and a 1,655-bp 3' untranslated region. The coding region predicts a 629-residue polypeptide whose sequence displays 86, 75, and 73% identities with chicken intestine fimbrin, human T-plastin, and human L-plastin, respectively. Recombinant I-plastin cross-linked actin filaments into bundles in the absence but not in the presence of calcium. The I-plastin gene was mapped by PCR to human chromosome 3; the L- and T-plastin genes were previously mapped to chromosomes 13 and X, respectively. I-plastin mRNA was detected in the small intestine, colon, and kidneys; relatively lower levels of expression were detected in the lungs and stomach. In contrast, L-plastin expression was restricted to the spleen and other lymph node-containing organs, while T-plastin was expressed in a variety of organs, including muscle, brain, uterus, and esophagus. In contrast to the situation for the intestine, high levels of L- and T-plastin mRNAs were detected in Caco-2, a human colon-derived cell line. Immunofluorescence microscopy detected I-plastin in the brush border of the small intestine and colon. These results identify I-plastin as the human homolog of chicken intestine fimbrin and as a third plastin isoform in humans.
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Fatima, Attia, and Dermot G. Morris. "MicroRNAs in domestic livestock." Physiological Genomics 45, no. 16 (August 15, 2013): 685–96. http://dx.doi.org/10.1152/physiolgenomics.00009.2013.
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microRNAs (miRNAs) are a class of small noncoding RNA that bind to complementary sequences in the untranslated regions of multiple target mRNAs resulting in posttranscriptional regulation of gene expression. The recent discovery and expression-profiling studies of miRNAs in domestic livestock have revealed both their tissue-specific and temporal expression pattern. In addition, breed-dependent expression patterns as well as single nucleotide polymorphisms in either the miRNA or in the target mRNA binding site have revealed associations with traits of economic importance and highlight the potential use of miRNAs in future genomic selection programs.
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Jones, T. R., and M. D. Cole. "Rapid cytoplasmic turnover of c-myc mRNA: requirement of the 3' untranslated sequences." Molecular and Cellular Biology 7, no. 12 (December 1987): 4513–21. http://dx.doi.org/10.1128/mcb.7.12.4513.
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Expression of the c-myc gene can be controlled by transcriptional or posttranscriptional mechanisms (or both), depending on the cell type and the growth conditions. An important mechanism of posttranscriptional regulation is modulation of cytoplasmic c-myc mRNA stability; normal human and murine c-myc mRNAs have cytoplasmic half-lives of 30 min or less. To elucidate the c-myc sequences which impart this unusually high rate of cytoplasmic transcript turnover, we have constructed various deletion and hybrid c-myc genes and analyzed the cytoplasmic stability of the mRNAs produced from them in stably transfected murine fibroblasts. The results indicate that sequences contained within the 5' and 3' ends of the c-myc transcript can affect cytoplasmic stability. Specifically, the 3' untranslated sequences of c-myc exon 3 are required for, but do not ensure, a high rate of transcript turnover in the cytoplasm. Exon 2 coding sequences do not seem to be involved, and exon 1 sequences at the 5' end of the transcript have only a small effect on cytoplasmic transcript stability. The sequences that are primarily responsible for the short c-myc RNA half-life were localized to a region of 140 bases in the 3' untranslated region.
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Jones, T. R., and M. D. Cole. "Rapid cytoplasmic turnover of c-myc mRNA: requirement of the 3' untranslated sequences." Molecular and Cellular Biology 7, no. 12 (December 1987): 4513–21. http://dx.doi.org/10.1128/mcb.7.12.4513-4521.1987.
Full textAbstract:
Expression of the c-myc gene can be controlled by transcriptional or posttranscriptional mechanisms (or both), depending on the cell type and the growth conditions. An important mechanism of posttranscriptional regulation is modulation of cytoplasmic c-myc mRNA stability; normal human and murine c-myc mRNAs have cytoplasmic half-lives of 30 min or less. To elucidate the c-myc sequences which impart this unusually high rate of cytoplasmic transcript turnover, we have constructed various deletion and hybrid c-myc genes and analyzed the cytoplasmic stability of the mRNAs produced from them in stably transfected murine fibroblasts. The results indicate that sequences contained within the 5' and 3' ends of the c-myc transcript can affect cytoplasmic stability. Specifically, the 3' untranslated sequences of c-myc exon 3 are required for, but do not ensure, a high rate of transcript turnover in the cytoplasm. Exon 2 coding sequences do not seem to be involved, and exon 1 sequences at the 5' end of the transcript have only a small effect on cytoplasmic transcript stability. The sequences that are primarily responsible for the short c-myc RNA half-life were localized to a region of 140 bases in the 3' untranslated region.
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Zhuo, Manyun, Xiaohong Zhuang, Wenjun Tang, Junnv Xu, Chengsheng Zhang, Xiaoying Qian, Jie Wang, et al. "The Impact of IL-16 3′UTR Polymorphism rs859 on Lung Carcinoma Susceptibility among Chinese Han Individuals." BioMed Research International 2018 (December 24, 2018): 1–10. http://dx.doi.org/10.1155/2018/8305745.
Full textAbstract:
Lung carcinoma is the most common cancer and cause of cancer deaths among both males and females in China. Previously, genetic variants located in gene untranslated region have been well established as interfering factors in mRNA translation and confirmed playing critical roles in lung oncogenesis. However, the correlation between polymorphisms in gene 3′ untranslated region and lung cancer risk is less reported in China Han population. In this study, polymorphisms in 3′-untranslated region of IL-16, CYP24A1, and FBN1 were determined in 322 lung cancer patients and 384 healthy controls with the usage of Sequenom MassARRAY. The correlation between selected variants and lung cancer risk was examined by unconditional logistic regression analysis with or without adjustments for age, gender, smoking status, and alcohol drinking status. Additionally, stratification analysis was applied to detect the associations of SNPs with lung cancer in different subgroups. As the results, significant relationships were found between IL-16 rs859 and lung cancer susceptibility in recessive model (OR= 0.65, 95% CI: 0.44-0.96, P= 0.029) and log-additive model (OR= 0.76, 95% CI: 0.60-0.96, P= 0.019). Moreover, adjusted stratified analysis also revealed the important effects of IL-16 rs859 on lung cancer risk among individuals aged older than 50, males, and nondrinkers. IL-16 rs859 showed statistically significant evidence associated with susceptibility to lung adenocarcinoma and lung small cell carcinoma in Chinese Han population as well. Our research demonstrated that genetic variant rs859 of IL-16 3′UTR was associated with lung cancer risk in Chinese Han population and the result might be exploited as a new biomarker for lung cancer assessment and prevention.
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Zhang, M., Z. Hu, J. Huang, Y. Shu, J. Dai, G. Jin, R. Tang, et al. "A 3'-Untranslated Region Polymorphism in IGF1 Predicts Survival of Non-Small Cell Lung Cancer in a Chinese Population." Clinical Cancer Research 16, no. 4 (February 9, 2010): 1236–44. http://dx.doi.org/10.1158/1078-0432.ccr-09-2719.
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Waldminghaus, Torsten, Anja Fippinger, Juliane Alfsmann, and Franz Narberhaus. "RNA thermometers are common in α- and γ-proteobacteria." Biological Chemistry 386, no. 12 (December 1, 2005): 1279–86. http://dx.doi.org/10.1515/bc.2005.145.
Full textAbstract:
AbstractExpression of many rhizobial small heat-shock genes is controlled by the ROSE element, a thermoresponsive structure in the 5′-untranslated region of the corresponding mRNAs. Using a bioinformatics approach, we found more than 20 new potential ROSE-like RNA thermometers upstream of small heat-shock genes in a wide variety of α- and γ-proteobacteria. Northern blot analyses revealed heat-inducible transcripts of the representative candidateCaulobacter crescentus CC2258,Escherichia coli ibpAandSalmonella typhimurium ibpAgenes. Typical σ32-type promoters were mapped upstream of the potential RNA thermometers by primer extension. Additional translational control was demonstrated in alacZreporter system and by site-directed mutagenesis. RNA secondary structure predictions strongly suggest that the Shine-Dalgarno sequence in the RNA thermometers is masked at low temperatures. Combining two regulatory modules, a σ32promoter and a ROSE-type RNA thermometer, provides a novel stringent mechanism to control expression of small heat-shock genes.
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Goodyer, CG, H. Zheng, and GN Hendy. "Alu elements in human growth hormone receptor gene 5' untranslated region exons." Journal of Molecular Endocrinology 27, no. 3 (December 1, 2001): 357–66. http://dx.doi.org/10.1677/jme.0.0270357.
Full textAbstract:
The human growth hormone receptor (hGHR) is encoded by exons 2-10 of the hGHR gene on chromosome 5p13.1-p12. There are several different 5' untranslated region (5'UTR) variants of hGHR mRNA (V1-V9) that all encode the same protein. We have recently mapped the V1-V9 5'UTR sequences within 40 kb of the 5' flanking region of the hGHR gene. Seven of the exons are clustered within two small modules, module A (V2-V9-V3) and module B (V7-V1-V4-V8), approximately 38 kb and approximately 18 kb respectively upstream of exon 2 of the coding region; V6 lies midway between the two modules and V5 is adjacent to exon 2. We now report the existence of two subvariant V3 exons, one upstream of module A (exon V3b) and one midway between module B and exon 2 (exon V3a/b). Both have sequences homologous to Alu elements. In addition, we determined the alternative splicing mechanisms that produce three different mRNAs from these exons: V3c (from the V3 exon in module A) or V3a and V3b (from a combination of exon V3 and the Alu-containing V3 subvariant exons). hGHR expression is under developmental- and tissue-specific regulation: module A-derived mRNAs are widely expressed in human tissues, while module B-derived mRNAs are only detectable in postnatal liver. Expression of the variant V3 mRNAs is similar to those from module A, being produced ubiquitously in human fetal and postnatal tissues, with V3c always the major variant detected. The Alu-containing mRNAs (V3a and V3b) are also detectable in baboon and rhesus tissues, in accordance with the finding of Alu elements throughout the primate genome. In summary, we have mapped the relative locations of two new 5'UTR exons within the 5' flanking region of the hGHR gene and described the derivation and expression patterns for two variant hGHR mRNAs from these primate-specific exons. The introduction of Alu elements has contributed to the evolution of the primate GHR gene as a highly complex transcriptional unit.
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Huang, Chenxiao, Xiujuan Wang, Shuyi Huang, Linlin Ou, Jianfeng Dai, and Kezhen Wang. "Evasion strategies of Zika virus antagonizing host innate immunity." Future Virology 14, no. 7 (July 2019): 465–71. http://dx.doi.org/10.2217/fvl-2019-0037.
Full textAbstract:
Zika virus is a small enveloped positive-strand RNA virus, which belongs to the Flaviviridae family. The RNA genome of all flaviviruses encodes three structural and seven nonstructural genes, together with 5′- and 3′-untranslated region genes flanking. Accompanying the explosive nature of the Zika outbreak in 2014, there was a devastating congenital neurodevelopmental disease in fetuses. Apart from viral RNA replication, polyprotein cleavage, Zika virus nonstructural proteins also play vital roles in the host's innate immune evasion. In this brief report, we summarize the evasion mechanisms of the viral nonstructural proteins antagonizing host antiviral innate immunity.
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Baou, Maria, Andrew Jewell, and John J. Murphy. "TIS11 Family Proteins and Their Roles in Posttranscriptional Gene Regulation." Journal of Biomedicine and Biotechnology 2009 (2009): 1–11. http://dx.doi.org/10.1155/2009/634520.
Full textAbstract:
Posttranscriptional regulation of gene expression of mRNAs containing adenine-uridine rich elements (AREs) in their untranslated regions is mediated by a number of different proteins that interact with these elements to either stabilise or destabilise them. The present review concerns the TPA-inducible sequence 11 (TIS11) protein family, a small family of proteins, that appears to interact with ARE-containing mRNAs and promote their degradation. This family of proteins has been extensively studied in the past decade. Studies have focussed on determining their biochemical functions, identifying their target mRNAs, and determining their roles in cell functions and diseases.
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Krupitza, G., and G. Thireos. "Translational activation of GCN4 mRNA in a cell-free system is triggered by uncharged tRNAs." Molecular and Cellular Biology 10, no. 8 (August 1990): 4375–78. http://dx.doi.org/10.1128/mcb.10.8.4375.
Full textAbstract:
Translation of GCN4 mRNA is activated when yeast cells are grown under conditions of amino acid limitation. In this study, we established the conditions through which translation of the GCN4 mRNA could be activated in a homologous in vitro system. This activation paralleled the in vivo situation: it required the small open reading frames located in the 5' untranslated region of the GCN4 mRNA, and it was coupled with reduced rates of 43S preinitiation complex formation. Translational derepression in vitro was triggered by uncharged tRNA molecules, demonstrating that deacylated tRNAs are more proximal signals for translational activation of the GCN4 mRNA.
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Krupitza, G., and G. Thireos. "Translational activation of GCN4 mRNA in a cell-free system is triggered by uncharged tRNAs." Molecular and Cellular Biology 10, no. 8 (August 1990): 4375–78. http://dx.doi.org/10.1128/mcb.10.8.4375-4378.1990.
Full textAbstract:
Translation of GCN4 mRNA is activated when yeast cells are grown under conditions of amino acid limitation. In this study, we established the conditions through which translation of the GCN4 mRNA could be activated in a homologous in vitro system. This activation paralleled the in vivo situation: it required the small open reading frames located in the 5' untranslated region of the GCN4 mRNA, and it was coupled with reduced rates of 43S preinitiation complex formation. Translational derepression in vitro was triggered by uncharged tRNA molecules, demonstrating that deacylated tRNAs are more proximal signals for translational activation of the GCN4 mRNA.
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Reza, Abu Musa Md Talimur, and Yu-Guo Yuan. "microRNAs Mediated Regulation of the Ribosomal Proteins and its Consequences on the Global Translation of Proteins." Cells 10, no. 1 (January 8, 2021): 110. http://dx.doi.org/10.3390/cells10010110.
Full textAbstract:
Ribosomal proteins (RPs) are mostly derived from the energy-consuming enzyme families such as ATP-dependent RNA helicases, AAA-ATPases, GTPases and kinases, and are important structural components of the ribosome, which is a supramolecular ribonucleoprotein complex, composed of Ribosomal RNA (rRNA) and RPs, coordinates the translation and synthesis of proteins with the help of transfer RNA (tRNA) and other factors. Not all RPs are indispensable; in other words, the ribosome could be functional and could continue the translation of proteins instead of lacking in some of the RPs. However, the lack of many RPs could result in severe defects in the biogenesis of ribosomes, which could directly influence the overall translation processes and global expression of the proteins leading to the emergence of different diseases including cancer. While microRNAs (miRNAs) are small non-coding RNAs and one of the potent regulators of the post-transcriptional gene expression, miRNAs regulate gene expression by targeting the 3′ untranslated region and/or coding region of the messenger RNAs (mRNAs), and by interacting with the 5′ untranslated region, and eventually finetune the expression of approximately one-third of all mammalian genes. Herein, we highlighted the significance of miRNAs mediated regulation of RPs coding mRNAs in the global protein translation.
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Reza, Abu Musa Md Talimur, and Yu-Guo Yuan. "microRNAs Mediated Regulation of the Ribosomal Proteins and its Consequences on the Global Translation of Proteins." Cells 10, no. 1 (January 8, 2021): 110. http://dx.doi.org/10.3390/cells10010110.
Full textAbstract:
Ribosomal proteins (RPs) are mostly derived from the energy-consuming enzyme families such as ATP-dependent RNA helicases, AAA-ATPases, GTPases and kinases, and are important structural components of the ribosome, which is a supramolecular ribonucleoprotein complex, composed of Ribosomal RNA (rRNA) and RPs, coordinates the translation and synthesis of proteins with the help of transfer RNA (tRNA) and other factors. Not all RPs are indispensable; in other words, the ribosome could be functional and could continue the translation of proteins instead of lacking in some of the RPs. However, the lack of many RPs could result in severe defects in the biogenesis of ribosomes, which could directly influence the overall translation processes and global expression of the proteins leading to the emergence of different diseases including cancer. While microRNAs (miRNAs) are small non-coding RNAs and one of the potent regulators of the post-transcriptional gene expression, miRNAs regulate gene expression by targeting the 3′ untranslated region and/or coding region of the messenger RNAs (mRNAs), and by interacting with the 5′ untranslated region, and eventually finetune the expression of approximately one-third of all mammalian genes. Herein, we highlighted the significance of miRNAs mediated regulation of RPs coding mRNAs in the global protein translation.
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Vera-Otarola, Jorge, Ricardo Soto-Rifo, Emiliano P. Ricci, Théophile Ohlmann, Jean-Luc Darlix, and Marcelo López-Lastra. "The 3′ Untranslated Region of the Andes Hantavirus Small mRNA Functionally Replaces the Poly(A) Tail and Stimulates Cap-Dependent Translation Initiation from the Viral mRNA." Journal of Virology 84, no. 19 (July 21, 2010): 10420–24. http://dx.doi.org/10.1128/jvi.01270-10.
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ABSTRACT In the process of translation of eukaryotic mRNAs, the 5′ cap and the 3′ poly(A) tail interact synergistically to stimulate protein synthesis. Unlike its cellular counterparts, the small mRNA (SmRNA) of Andes hantavirus (ANDV), a member of the Bunyaviridae, lacks a 3′ poly(A) tail. Here we report that the 3′ untranslated region (3′UTR) of the ANDV SmRNA functionally replaces a poly(A) tail and synergistically stimulates cap-dependent translation initiation from the viral mRNA. Stimulation of translation by the 3′UTR of the ANDV SmRNA was found to be independent of viral proteins and of host poly(A)-binding protein.
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Pérez-Martínez, Isabel, and Dieter Haas. "Azithromycin Inhibits Expression of the GacA-Dependent Small RNAs RsmY and RsmZ in Pseudomonas aeruginosa." Antimicrobial Agents and Chemotherapy 55, no. 7 (May 2, 2011): 3399–405. http://dx.doi.org/10.1128/aac.01801-10.
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ABSTRACTAzithromycin at clinically relevant doses does not inhibit planktonic growth of the opportunistic pathogenPseudomonas aeruginosabut causes markedly reduced formation of biofilms and quorum-sensing-regulated extracellular virulence factors. In the Gac/Rsm signal transduction pathway, which acts upstream of the quorum-sensing machinery inP. aeruginosa, the GacA-dependent untranslated small RNAs RsmY and RsmZ are key regulatory elements. As azithromycin treatment and mutational inactivation ofgacAhave strikingly similar phenotypic consequences, the effect of azithromycin onrsmYandrsmZexpression was investigated. In planktonically growing cells, the antibiotic strongly inhibited the expression of both small RNA genes but did not affect the expression of the housekeeping geneproC. The azithromycin treatment resulted in reduced expression ofgacAandrsmA, which are known positive regulators ofrsmYandrsmZ, and of the PA0588-PA0584 gene cluster, which was discovered as a novel positive regulatory element involved inrsmYandrsmZexpression. Deletion of this cluster resulted in diminished ability ofP. aeruginosato produce pyocyanin and to swarm. The results of this study indicate that azithromycin inhibitsrsmYandrsmZtranscription indirectly by lowering the expression of positive regulators of these small RNA genes.
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Connelly, Colleen M., Meryl Thomas, and Alexander Deiters. "High-Throughput Luciferase Reporter Assay for Small-Molecule Inhibitors of MicroRNA Function." Journal of Biomolecular Screening 17, no. 6 (March 12, 2012): 822–28. http://dx.doi.org/10.1177/1087057112439606.
Full textAbstract:
MicroRNAs (miRNAs) are endogenous, single-stranded, noncoding RNAs of 21 to 23 nucleotides that regulate gene expression, typically by binding the 3′ untranslated regions of target messenger RNAs. It is estimated that miRNAs are involved in the regulation of 30% of all genes and almost every genetic pathway. Recently, the misregulation of miRNAs has been linked to various human diseases including cancer and viral infections, identifying miRNAs as potential targets for drug discovery. Thus, small-molecule modifiers of miRNAs could serve as lead structures for the development of new therapeutic agents and be useful tools in the elucidation of detailed mechanisms of miRNA function. As a result, we have developed a high-throughput screen for potential small-molecule regulators of the liver-specific microRNA miR-122, which is involved in hepatocellular carcinoma development and hepatitis C virus infection. Our small-molecule screen employs a Huh7 human hepatoma cell line stably transfected with a Renilla luciferase sensor for endogenous miR-122. The assay was optimized and validated using an miR-122 antisense agent and a previously identified small-molecule miR-122 inhibitor. The described reporter assay will enable the high-throughput screening of small-molecule miR-122 inhibitors and can be readily extended to other miRNAs.
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Bird, R. Curtis, and Bruce H. Sells. "Small cytoplasmic RNAs and their location within the cytoplasm." Biochemistry and Cell Biology 65, no. 6 (June 1, 1987): 582–87. http://dx.doi.org/10.1139/o87-075.
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These studies were designed to establish the location of various species of small RNAs within the subcellular cytoplasmic compartments. Four cytoplasmic RNA-containing compartments were examined: (A) cytoskeleton-bound polyribosomal ribonucleoprotein (RNP) complexes, (B) soluble-phase polyribosomal RNP complexes, (C) cytoskeleton-bound free RNP complexes, (D) soluble-phase free RNP complexes. The presence of the small cytoplasmic RNA (scRNA) population and histone H4 and actin mRNAs in each compartment was examined to determine their spatial distribution within the cytoplasm. The 7S signal recognition RNA and the 5S and 5.8S rRNAs were distributed among all four compartments, while 4S tRNAs were localized largely in fraction D. Fraction C contained a group of seven abundant scRNAs, of approximately 105–348 nucleotides in length, which were localized almost entirely within the cytoskeleton-bound free RNP compartment. Actin mRNAs were localized in fraction A, the actively translating cytoskeleton-bound compartment. Following cytochalasin B treatment, actin mRNAs were released into the soluble phase, implicating a dependence on the integrity of actin filaments in its binding. Such treatment also released several of the scRNAs from their cytoskeleton-bound location. In contrast histone H4 mRNAs were much more widely dispersed, being present in all four cytoskeletal compartments. Approximately 60% of the H4 mRNAs, however, were localized within the soluble-phase polyribosomes in fraction B. Cytochalasin B treatment released only the small portion of untranslated histone H4 mRNA associated with the cytoskeleton in fraction C, suggesting that the binding of these H4 mRNAs was dependent in some manner upon the integrity of actin filaments.
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Feliciano, Andrea, Beatriz Sánchez-Sendra, Hiroshi Kondoh, and Matilde E. LLeonart. "MicroRNAs Regulate Key Effector Pathways of Senescence." Journal of Aging Research 2011 (2011): 1–11. http://dx.doi.org/10.4061/2011/205378.
Full textAbstract:
MicroRNAs (miRNAs) are small (approximately 22 nt) noncoding endogenous RNA molecules that regulate gene expression and protein coding by base pairing with the3′untranslated region (UTR) of target mRNAs. miRNA expression is associated with cancer pathogenesis because miRNAs are intimately linked to cancer development. Senescence blocks cell proliferation, representing an important barrier that cells must bypass to reach malignancy. Importantly, certain miRNAs have been shown to have an important role during cellular senescence, which is also involved in human tumorigenesis. Therefore, therapeutic induction of senescence by drugs or miRNA-based therapies is a potential method to treat cancer by inducing a persistent growth arrest in tumors.
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Guida, M., R. S. Marger, A. C. Papp, P. J. Snyder, M. S. Sedra, J. T. Kissel, J. R. Mendell, and T. W. Prior. "A molecular protocol for diagnosing myotonic dystrophy." Clinical Chemistry 41, no. 1 (January 1, 1995): 69–72. http://dx.doi.org/10.1093/clinchem/41.1.69.
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Abstract Myotonic dystrophy (DM) is an autosomal dominant genetic disease caused by an unstable CTG repeat sequence in the 3' untranslated region of the myotonin protein kinase gene. The CTG repeat is present 5-30 times in the normal population, whereas DM patients have CTG expansions of 50 to several thousand repeats. The age of onset of the disorder and the severity of the phenotype is roughly correlated with the size of the CTG expansion. We developed a molecular protocol for the diagnosis of DM based on an initial polymerase chain reaction screen to detect normal-sized alleles and small expansions, followed by an improved Southern protocol to detect larger expansions.
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Davis, C. Todd, Sareen E. Galbraith, Shuliu Zhang, Melissa C. Whiteman, Li Li, Richard M. Kinney, and Alan D. T. Barrett. "A Combination of Naturally Occurring Mutations in North American West Nile Virus Nonstructural Protein Genes and in the 3′ Untranslated Region Alters Virus Phenotype." Journal of Virology 81, no. 11 (March 21, 2007): 6111–16. http://dx.doi.org/10.1128/jvi.02387-06.
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ABSTRACT We previously reported mutations in North American West Nile viruses (WNVs) with a small-plaque (sp), temperature-sensitive (ts), and/or mouse-attenuated (att) phenotype. Using an infectious clone, site-directed mutations and 3′ untranslated region (3′UTR) exchanges were introduced into the WNV NY99 genome. Characterization of mutants demonstrated that a combination of mutations involving the NS4B protein (E249G) together with either a mutation in the NS5 protein (A804V) or three mutations in the 3′UTR (A10596G, C10774U, A10799G) produced sp, ts, and/or att variants. These results suggested that the discovery of North American WNV-phenotypic variants is rare because of the apparent requirement of concurrent polygenic mutations.
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Standart, N., T. Hunt, and J. V. Ruderman. "Differential accumulation of ribonucleotide reductase subunits in clam oocytes: the large subunit is stored as a polypeptide, the small subunit as untranslated mRNA." Journal of Cell Biology 103, no. 6 (December 1, 1986): 2129–36. http://dx.doi.org/10.1083/jcb.103.6.2129.
Full textAbstract:
Within minutes of fertilization of clam oocytes, translation of a set of maternal mRNAs is activated. One of the most abundant of these stored mRNAs encodes the small subunit of ribonucleotide reductase (Standart, N. M., S. J. Bray, E. L. George, T. Hunt, and J. V. Ruderman, 1985, J. Cell Biol., 100:1968-1976). Unfertilized oocytes do not contain any ribonucleotide reductase activity; such activity begins to appear shortly after fertilization. In virtually all organisms, this enzyme is composed of two dissimilar subunits with molecular masses of approximately 44 and 88 kD, both of which are required for activity. This paper reports the identification of the large subunit of clam ribonucleotide reductase isolated by dATP-Sepharose chromatography as a relatively abundant 86-kD polypeptide which is already present in oocytes, and whose level remains constant during early development. The enzyme activity of this large subunit was established in reconstitution assays using the small subunit isolated from embryos by virtue of its binding to the anti-tubulin antibody YL 1/2. Thus the two components of clam ribonucleotide reductase are differentially stored in the oocyte: the small subunit in the form of untranslated mRNA and the large subunit as protein. When fertilization triggers the activation of translation of the maternal mRNA, the newly synthesized small subunit combines with the preformed large subunit to generate active ribonucleotide reductase.
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Lowen, Anice C., and Richard M. Elliott. "Mutational Analyses of the Nonconserved Sequences in the Bunyamwera Orthobunyavirus S Segment Untranslated Regions." Journal of Virology 79, no. 20 (October 15, 2005): 12861–70. http://dx.doi.org/10.1128/jvi.79.20.12861-12870.2005.
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ABSTRACT Bunyamwera virus (BUNV) is the prototype of the genus Orthobunyavirus and the family Bunyaviridae. BUNV has a tripartite genome of negative-sense RNA composed of small (S), medium (M), and large (L) segments. Partially complementary untranslated regions (UTRs) flank the coding region of each segment. The terminal 11 nucleotides of these UTRs are conserved between the three segments and throughout the genus, while the internal regions are unique to each segment and largely nonconserved between different viruses. To investigate the functions of the UTR sequences, we constructed a series of BUNV S segment cDNA clones with deletions in the 3′ and/or 5′ UTR and then attempted to rescue these segments into recombinant viruses. We found that the genomic 5′ UTR was much more sensitive to mutation than the 3′ UTR and, in general, sequences proximal to the termini were more important than those flanking the coding region. Northern blot analyses of infected-cell RNA showed that the internal, nonconserved sequences of the S segment 3′ UTR play a role in the regulation of transcription and replication and the balance between these two processes. In contrast, deletions in the 5′ UTR caused attenuation of the recombinant virus but did not specifically affect levels of S segment RNAs or the encoded nucleocapsid protein. Thus, the internal regions of both UTRs are functional: most of the 5′ UTR is essential to viral growth, and, while nonessential, the internal 3′ UTR is important to the regulation of viral RNA synthesis.
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Kunden, Rasika D., Sarah Ghezelbash, Juveriya Q. Khan, and Joyce A. Wilson. "Location specific annealing of miR-122 and other small RNAs defines an Hepatitis C Virus 5′ UTR regulatory element with distinct impacts on virus translation and genome stability." Nucleic Acids Research 48, no. 16 (August 18, 2020): 9235–49. http://dx.doi.org/10.1093/nar/gkaa664.
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Abstract Hepatitis C virus (HCV) replication requires annealing of a liver specific small-RNA, miR-122 to 2 sites on 5′ untranslated region (UTR). Annealing has been reported to (a) stabilize the genome, (b) stimulate translation and (c) promote the formation of translationally active Internal Ribosome Entry Site (IRES) RNA structure. In this report, we map the RNA element to which small RNA annealing promotes HCV to nucleotides 1–44 and identify the relative impact of small RNA annealing on virus translation promotion and genome stabilization. We mapped the optimal region on the HCV genome to which small RNA annealing promotes virus replication to nucleotides 19–37 and found the efficiency of viral RNA accumulation decreased as annealing moved away from this region. Then, by using a panel of small RNAs that promote replication with varying efficiencies we link the efficiency of lifecycle promotion with translation stimulation. By contrast small RNA annealing stabilized the viral genome even if they did not promote virus replication. Thus, we propose that miR-122 annealing promotes HCV replication by annealing to an RNA element that activates the HCV IRES and stimulates translation, and that miR-122 induced HCV genome stabilization is insufficient alone but enhances virus replication.
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Varchenko, O. I., B. M. Krasyuk, A. A. Fedchunov, O. V. Zimina, M. F. Parii, and Yu V. Symonenko. "Genetic constructs creation using Golden Gate cloning method." Faktori eksperimental'noi evolucii organizmiv 25 (August 30, 2019): 190–96. http://dx.doi.org/10.7124/feeo.v25.1163.
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Aim. Creation of genetic constructions to study the effects of various regulatory elements, namely promoters, on the expression of GFP reporter protein. Methods. For creation genetic constructs, the method of molecular cloning Golden Gate was used, which allows the rapid creation of genetic vectors using IIS type restriction enzymes and T4 DNA liga-ses. Results. For research six different promoters were selected, namely the 35S CaMV (Cauliflower Mosaic Virus), double 35S CaMV promoter, promoters of the RbcS2B and RbcS1B genes encoding a small subunit of ribulozobisphosphate carboxylase (RuBisCo) isolated from Arabidopsis thaliana (L.) Heynh.; promoters of genes encoding chlorophyll a-b binding proteins (LHB1B1 and LHB1B2) also isolated from A. thaliana (L.) Heynh. All transcription units additionally contained the following elements: the 5'-untranslated region Ω sequence (5’UTR Ω) from the tobacco mosaic virus TMV (Tobacco Mosaic Virus); the coding sequence of the gene gfp (Green Fluorescent Protein) isolated from A. victoria and the 35S Terminator CaMV with the polyadenylation signal and the 3'-untranslated region sequence. As a result, six genetic constructs with different regulatory elements, namely promoters, have been created. Conclusions. To study the effects of various regulatory elements, namely promoters, on the expression of a GFP repor-ter protein in transient or stable genetic transformation of plants the created genetic constructs can be used.Keywords: cloning, genetic constructs, promoters, Green Fluorescent Protein (GFP).
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Booy, Evan P., Ryan Howard, Oksana Marushchak, Emmanuel O. Ariyo, Markus Meier, Stefanie K. Novakowski, Soumya R. Deo, Edis Dzananovic, Jörg Stetefeld, and Sean A. McKenna. "The RNA helicase RHAU (DHX36) suppresses expression of the transcription factor PITX1." Nucleic Acids Research 42, no. 5 (December 24, 2013): 3346–61. http://dx.doi.org/10.1093/nar/gkt1340.
Full textAbstract:
Abstract RNA Helicase associated with AU-rich element (RHAU) (DHX36) is a DEAH (Aspartic acid, Glumatic Acid, Alanine, Histidine)-box RNA helicase that can bind and unwind G4-quadruplexes in DNA and RNA. To detect novel RNA targets of RHAU, we performed an RNA co-immunoprecipitation screen and identified the PITX1 messenger RNA (mRNA) as specifically and highly enriched. PITX1 is a homeobox transcription factor with roles in both development and cancer. Primary sequence analysis identified three probable quadruplexes within the 3′-untranslated region of the PITX1 mRNA. Each of these sequences, when isolated, forms stable quadruplex structures that interact with RHAU. We provide evidence that these quadruplexes exist in the endogenous mRNA; however, we discovered that RHAU is tethered to the mRNA via an alternative non–quadruplex-forming region. RHAU knockdown by small interfering RNA results in significant increases in PITX1 protein levels with only marginal changes in mRNA, suggesting a role for RHAU in translational regulation. Involvement of components of the microRNA machinery is supported by similar and non-additive increases in PITX1 protein expression on Dicer and combined RHAU/Dicer knockdown. We also demonstrate a requirement of argonaute-2, a key RNA-induced silencing complex component, to mediate RHAU-dependent changes in PITX1 protein levels. These results demonstrate a novel role for RHAU in microRNA-mediated translational regulation at a quadruplex-containing 3′-untranslated region.
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Smoak, Kathleen, and John A. Cidlowski. "Glucocorticoids Regulate Tristetraprolin Synthesis and Posttranscriptionally Regulate Tumor Necrosis Factor Alpha Inflammatory Signaling." Molecular and Cellular Biology 26, no. 23 (September 18, 2006): 9126–35. http://dx.doi.org/10.1128/mcb.00679-06.
Full textAbstract:
ABSTRACT Glucocorticoids are used to treat various inflammatory disorders, but the mechanisms underlying these actions are incompletely understood. The zinc finger protein tristetraprolin (TTP) destabilizes several proinflammatory cytokine mRNAs by binding to AU-rich elements within their 3′ untranslated regions, targeting them for degradation. Here we report that glucocorticoids induce the synthesis of TTP mRNA and protein in A549 lung epithelial cells and in rat tissues. Dexamethasone treatment leads to a sustained induction of TTP mRNA expression that is abrogated by RU486. Glucocorticoid induction of TTP mRNA is also blocked by actinomycin D but not by cycloheximide, suggesting a transcriptional mechanism which has been confirmed by transcription run-on experiments. The most widely characterized TTP-regulated gene is the AU-rich tumor necrosis factor alpha (TNF-α) gene. Dexamethasone represses TNF-α mRNA in A549 cells and decreases luciferase expression of a TNF-α 3′ untranslated region reporter plasmid in an orientation-dependent manner. Small interfering RNAs to TTP significantly prevent this effect, and a cell line stably expressing a short-hairpin RNA to TTP conclusively establishes that TTP is critical for dexamethasone inhibition of TNF-α mRNA expression. These studies provide the molecular evidence for glucocorticoid regulation of human TTP and reflect a novel inductive anti-inflammatory signaling pathway for glucocorticoids that acts via posttranscriptional mechanisms.
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Costanzo, M. C., and T. D. Fox. "Suppression of a defect in the 5' untranslated leader of mitochondrial COX3 mRNA by a mutation affecting an mRNA-specific translational activator protein." Molecular and Cellular Biology 13, no. 8 (August 1993): 4806–13. http://dx.doi.org/10.1128/mcb.13.8.4806.
Full textAbstract:
Translation of the Saccharomyces cerevisiae mitochondrial COX3 mRNA, encoding subunit III of cytochrome c oxidase, specifically requires the action of the nuclear gene products PET54, PET122, and PET494 at a site encoded in the 612-base 5' untranslated leader. To identify more precisely the site of action of the translational activators, we constructed two large deletions of the COX3 mRNA 5' untranslated leader. Both deletions blocked translation without affecting mRNA stability. However, one of the large deletions was able to revert to partial function by a small secondary deletion within the remaining 5' leader sequences. Translation of the resulting mutant (cox3-15) mRNA was still dependent on the nuclear-encoded specific activators but was cold sensitive. We selected revertants of this mitochondrial mutant at low temperature to identify genes encoding proteins that might interact with the COX3 mRNA 5' leader. One such revertant carried a missense mutation in the PET122 gene that was a strong and dominant suppressor of the cold-sensitive defect in the mRNA, indicating that the PET122 protein interacts functionally (possibly directly) with the COX3 mRNA 5' leader. The cox3-15 mutation was not suppressed by overproduction of the wild-type PET122 protein but was very weakly suppressed by overproduction of PET494 and slightly better suppressed by co-overproduction of PET494 and PET122.