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Journal articles on the topic 'Small Untranslated RNA'

Author: Grafiati

Published: 4 June 2021

Last updated: 29 January 2023

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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 (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 g

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Skryabin, Boris V., Valentina Sukonina, Ursula Jordan, et al. "Neuronal Untranslated BC1 RNA: Targeted Gene Elimination in Mice." Molecular and Cellular Biology 23, no. 18 (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 distribu

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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 (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 t

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Hartmann, Claudia, Corinna Benz, Stefanie Brems, 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 (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 sever

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5

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 (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

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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 (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

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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 (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 det

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8

Waldminghaus, Torsten, Anja Fippinger, Juliane Alfsmann та Franz Narberhaus. "RNA thermometers are common in α- and γ-proteobacteria". Biological Chemistry 386, № 12 (2005): 1279–86. http://dx.doi.org/10.1515/bc.2005.145.

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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 potentia

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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 (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

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10

Booy, Evan P., Ryan Howard, Oksana Marushchak, et al. "The RNA helicase RHAU (DHX36) suppresses expression of the transcription factor PITX1." Nucleic Acids Research 42, no. 5 (2013): 3346–61. http://dx.doi.org/10.1093/nar/gkt1340.

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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,

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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 (2019): 465–71. http://dx.doi.org/10.2217/fvl-2019-0037.

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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

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12

Lin, Kuo-Chih, Huei-Lan Chang, and Ruey-Yi Chang. "Accumulation of a 3′-Terminal Genome Fragment in Japanese Encephalitis Virus-Infected Mammalian and Mosquito Cells." Journal of Virology 78, no. 10 (2004): 5133–38. http://dx.doi.org/10.1128/jvi.78.10.5133-5138.2004.

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ABSTRACT Japanese encephalitis virus (JEV) contains a single positive-strand RNA genome nearly 11 kb in length and is not formally thought to generate subgenomic RNA molecules during replication. Here, we report the abundant accumulation of a 3′-terminal 521- to 523-nucleotide (nt) genome fragment, representing a major portion of the 585-nt 3′ untranslated region, in both mammalian (BHK-21) and mosquito (C6/36) cells infected with any of nine strains of JEV. In BHK-21 cells, the viral genome was detected as early as 24 h postinfection, the small RNA was detected as early as 28 h postinfection,

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13

Szczesniak, Izabela, Agnieszka Baliga-Gil, Aleksandra Jarmolowicz, Marta Soszynska-Jozwiak, and Elzbieta Kierzek. "Structural and Functional RNA Motifs of SARS-CoV-2 and Influenza A Virus as a Target of Viral Inhibitors." International Journal of Molecular Sciences 24, no. 2 (2023): 1232. http://dx.doi.org/10.3390/ijms24021232.

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the COVID-19 pandemic, whereas the influenza A virus (IAV) causes seasonal epidemics and occasional pandemics. Both viruses lead to widespread infection and death. SARS-CoV-2 and the influenza virus are RNA viruses. The SARS-CoV-2 genome is an approximately 30 kb, positive sense, 5′ capped single-stranded RNA molecule. The influenza A virus genome possesses eight single-stranded negative-sense segments. The RNA secondary structure in the untranslated and coding regions is crucial in the viral replication cycle. The

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14

Hendrickson, Emily N., Marna E. Ericson, and Lynne T. Bemis. "Host tRNA-Derived RNAs Target the 3′Untranslated Region of SARS-CoV-2." Pathogens 11, no. 12 (2022): 1479. http://dx.doi.org/10.3390/pathogens11121479.

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The COVID-19 pandemic revealed a need for new understanding of the mechanisms regulating host–pathogen interactions during viral infection. Transfer RNA-derived RNAs (tDRs), previously called transfer RNA fragments (tRFs), have recently emerged as potential regulators of viral pathogenesis. Many predictive studies using bioinformatic approaches have been conducted providing a repertoire of potential small RNA candidates for further analyses; however, few targets have been validated to directly bind to SARS-CoV-2 sequences. In this study, we used available data sets to identify host tDR express

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15

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 (2006): 520–36. http://dx.doi.org/10.1111/j.1365-2958.2006.05384.x.

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16

Yao, Shiyi, and David H. Bechhofer. "Processing and Stability of Inducibly Expressed rpsO mRNA Derivatives in Bacillus subtilis." Journal of Bacteriology 191, no. 18 (2009): 5680–89. http://dx.doi.org/10.1128/jb.00740-09.

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ABSTRACT The Bacillus subtilis rpsO gene specifies a small (388-nucleotide), monocistronic mRNA that encodes ribosomal protein S15. We showed earlier that rpsO mRNA decay intermediates accumulated to a high level in a strain lacking polynucleotide phosphorylase. Here, we used inducibly expressed derivatives of rpsO, encoding smaller RNAs that had the complex 5′ region deleted, to study aspects of mRNA processing in B. subtilis. An IPTG (isopropyl-β-d-thiogalactopyranoside)-inducible rpsO transcript that contained lac sequences at the 5′ end, called lac-rpsO RNA, was shown to undergo processing

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17

Wang, Huidong, Anna Iacoangeli, Daisy Lin, et al. "Dendritic BC1 RNA in translational control mechanisms." Journal of Cell Biology 171, no. 5 (2005): 811–21. http://dx.doi.org/10.1083/jcb.200506006.

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Translational control at the synapse is thought to be a key determinant of neuronal plasticity. How is such control implemented? We report that small untranslated BC1 RNA is a specific effector of translational control both in vitro and in vivo. BC1 RNA, expressed in neurons and germ cells, inhibits a rate-limiting step in the assembly of translation initiation complexes. A translational repression element is contained within the unique 3′ domain of BC1 RNA. Interactions of this domain with eukaryotic initiation factor 4A and poly(A) binding protein mediate repression, indicating that the 3′ B

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18

Hann, L. E., A. C. Webb, J. M. Cai, and L. Gehrke. "Identification of a competitive translation determinant in the 3' untranslated region of alfalfa mosaic virus coat protein mRNA." Molecular and Cellular Biology 17, no. 4 (1997): 2005–13. http://dx.doi.org/10.1128/mcb.17.4.2005.

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We report that the competitive translational activity of alfalfa mosaic virus coat protein mRNA (CP RNA), a nonadenylated mRNA, is determined in part by the 3' untranslated region (UTR). Competitive translation was characterized both in vitro, with cotranslation assays, and in vivo, with microinjected Xenopus laevis oocytes. In wheat germ extracts, coat protein synthesis was constant when a fixed amount of full-length CP RNA was cotranslated with increasing concentrations of competitor globin mRNA. However, translation of CP RNA lacking the 3' UTR decreased significantly under competitive cond

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19

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 (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 -&gt; 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 r

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de la Torre, María Eugenia Sánchez, Carmelo López, Oscar Grau, and María Laura García. "RNA 2 of Citrus psorosis virus is of negative polarity and has a single open reading frame in its complementary strand." Journal of General Virology 83, no. 7 (2002): 1777–81. http://dx.doi.org/10.1099/0022-1317-83-7-1777.

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Citrus psorosis virus (CPsV) causes a citrus disease occurring worldwide. Isolate CPV 4 has a genome with three single-stranded RNAs. The complete sequence of RNA 2 (1643 nucleotides) is reported here. Northern blot hybridization with strand-specific probes showed that most of the encapsidated RNA 2 is of negative polarity, although a small amount of the complementary strand may also be present in particles. The RNA 2 complementary strand contained a single open reading frame encoding a protein of 476 amino acids, which includes a motif resembling a nuclear localization signal. The sequence of

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Weaver, Keith E., Erik A. Ehli, Jessica S. Nelson, and Smita Patel. "Antisense RNA Regulation by Stable Complex Formation in the Enterococcus faecalis Plasmid pAD1 par Addiction System." Journal of Bacteriology 186, no. 19 (2004): 6400–6408. http://dx.doi.org/10.1128/jb.186.19.6400-6408.2004.

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ABSTRACT The par stability determinant, encoded by the Enterococcus faecalis plasmid pAD1, is the only antisense RNA regulated postsegregational killing system identified in gram-positive bacteria. Because of the unique organization of the par locus, the par antisense RNA, RNA II, binds to its target, RNA I, at relatively small, interspersed regions of complementarity. The results of this study suggest that, rather than targeting the antisense bound message for rapid degradation, as occurs in most other antisense RNA regulated systems, RNA I and RNA II form a relatively stable, presumably tran

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Opdyke, Jason A., Ju-Gyeong Kang, and Gisela Storz. "GadY, a Small-RNA Regulator of Acid Response Genes in Escherichia coli." Journal of Bacteriology 186, no. 20 (2004): 6698–705. http://dx.doi.org/10.1128/jb.186.20.6698-6705.2004.

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ABSTRACT A previous bioinformatics-based search for small RNAs in Escherichia coli identified a novel RNA named IS183. The gene encoding this small RNA is located between and on the opposite strand of genes encoding two transcriptional regulators of the acid response, gadX (yhiX) and gadW (yhiW). Given that IS183 is encoded in the gad gene cluster and because of its role in regulating acid response genes reported here, this RNA has been renamed GadY. We show that GadY exists in three forms, a long form consisting of 105 nucleotides and two processed forms, consisting of 90 and 59 nucleotides.

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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 (2021): 110. http://dx.doi.org/10.3390/cells10010110.

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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 la

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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 (2021): 110. http://dx.doi.org/10.3390/cells10010110.

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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 la

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Zhu, H., C. G. Duan, W. N. Hou, et al. "Satellite RNA-Derived Small Interfering RNA satsiR-12 Targeting the 3' Untranslated Region of Cucumber Mosaic Virus Triggers Viral RNAs for Degradation." Journal of Virology 85, no. 24 (2011): 13384–97. http://dx.doi.org/10.1128/jvi.05806-11.

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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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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 (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 ge

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Lin, Jing-Yi, Mei-Ling Li, Peng-Nien Huang, Kun-Yi Chien, Jim-Tong Horng, and Shin-Ru Shih. "Heterogeneous nuclear ribonuclear protein K interacts with the enterovirus 71 5′ untranslated region and participates in virus replication." Journal of General Virology 89, no. 10 (2008): 2540–49. http://dx.doi.org/10.1099/vir.0.2008/003673-0.

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Enterovirus 71 (EV71) is a picornavirus that can cause severe neurological complications in children. Like other picornaviruses, the genomic RNA of EV71 contains a long 5′ untranslated region (UTR). Cellular proteins interact with the EV71 5′ UTR, and these interactions are important for virus replication. Using an RNA pull-down assay and proteomics approaches, this study identified the heterogeneous nuclear ribonucleoprotein K (hnRNP K) as one of the EV71 5′ UTR-associated proteins. The interaction between hnRNP K and the 5′ UTR was further confirmed by mapping the interaction regions to stem

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Alonso, Ana, Jaime Larraga, Francisco Javier Loayza, et al. "Stable Episomal Transfectant Leishmania infantum Promastigotes Over-Expressing the DEVH1 RNA Helicase Gene Down-Regulate Parasite Survival Genes." Pathogens 11, no. 7 (2022): 761. http://dx.doi.org/10.3390/pathogens11070761.

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The compartmentalization of untranslated mRNA molecules in granules occurring in many eukaryotic organisms including trypanosomatids involves the formation of complexes between mRNA molecules and RNA-binding proteins (RBPs). The putative ATP-dependent DEAD/H RNA helicase (DEVH1) from Leishmania infantum (Kinetoplastida: Trypanosomatidae) is one such proteins. The objective of this research is finding differentially expressed genes in a stable episomal transfectant L. infantum promastigote line over-expressing DEVH1 in the stationary phase of growth in axenic culture to get insight into the bio

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Funk, Anneke, Katherine Truong, Tomoko Nagasaki, et al. "RNA Structures Required for Production of Subgenomic Flavivirus RNA." Journal of Virology 84, no. 21 (2010): 11407–17. http://dx.doi.org/10.1128/jvi.01159-10.

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ABSTRACT Flaviviruses are a group of single-stranded, positive-sense RNA viruses causing ∼100 million infections per year. We have recently shown that flaviviruses produce a unique, small, noncoding RNA (∼0.5 kb) derived from the 3′ untranslated region (UTR) of the genomic RNA (gRNA), which is required for flavivirus-induced cytopathicity and pathogenicity (G. P. Pijlman et al., Cell Host Microbe, 4: 579-591, 2008). This RNA (subgenomic flavivirus RNA [sfRNA]) is a product of incomplete degradation of gRNA presumably by the cellular 5′-3′ exoribonuclease XRN1, which stalls on the rigid seconda

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Park, Hongmarn, Helen Yakhnin, Michael Connolly, Tony Romeo, and Paul Babitzke. "CsrA Participates in a PNPase Autoregulatory Mechanism by Selectively Repressing Translation ofpnpTranscripts That Have Been Previously Processed by RNase III and PNPase." Journal of Bacteriology 197, no. 24 (2015): 3751–59. http://dx.doi.org/10.1128/jb.00721-15.

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ABSTRACTCsr is a conserved global regulatory system that represses or activates gene expression posttranscriptionally. CsrA ofEscherichia coliis a homodimeric RNA binding protein that regulates transcription elongation, translation initiation, and mRNA stability by binding to the 5′ untranslated leader or initial coding sequence of target transcripts.pnpmRNA, encoding the 3′ to 5′ exoribonuclease polynucleotide phosphorylase (PNPase), was previously identified as a CsrA target by transcriptome sequencing (RNA-seq). Previous studies also showed that RNase III and PNPase participate in apnpautor

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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 (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 rec

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de Morree, Antoine, Julian D. D. Klein, Qiang Gan, et al. "Alternative polyadenylation of Pax3 controls muscle stem cell fate and muscle function." Science 366, no. 6466 (2019): 734–38. http://dx.doi.org/10.1126/science.aax1694.

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Adult stem cells are essential for tissue homeostasis. In skeletal muscle, muscle stem cells (MuSCs) reside in a quiescent state, but little is known about the mechanisms that control homeostatic turnover. Here we show that, in mice, the variation in MuSC activation rate among different muscles (for example, limb versus diaphragm muscles) is determined by the levels of the transcription factor Pax3. We further show that Pax3 levels are controlled by alternative polyadenylation of its transcript, which is regulated by the small nucleolar RNA U1. Isoforms of the Pax3 messenger RNA that differ in

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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 (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

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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 (2000): 856–68. http://dx.doi.org/10.1046/j.1365-2958.2000.02051.x.

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Guan, Lingyu, and Andrey Grigoriev. "Computational meta-analysis of ribosomal RNA fragments: potential targets and interaction mechanisms." Nucleic Acids Research 49, no. 7 (2021): 4085–103. http://dx.doi.org/10.1093/nar/gkab190.

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Abstract The most abundant cellular RNA species, ribosomal RNA (rRNA), appears to be a source of massive amounts of non-randomly generated fragments. We found rRNA fragments (rRFs) in immunoprecipitated Argonaute (Ago-IP) complexes in human and mouse cells and in small RNA sequencing datasets. In human Ago1-IP, guanine-rich rRFs were preferentially cut in single-stranded regions of mature rRNAs between pyrimidines and adenosine, and non-randomly paired with cellular transcripts in crosslinked chimeras. Numerous identical rRFs were found in the cytoplasm and nucleus in mouse Ago2-IP. We report

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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 (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 onrsmYandrsmZexpr

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Mottet-Osman, Geneviève, Frédéric Iseni, Thierry Pelet, Maciej Wiznerowicz, Dominique Garcin, and Laurent Roux. "Suppression of the Sendai Virus M Protein through a Novel Short Interfering RNA Approach Inhibits Viral Particle Production but Does Not Affect Viral RNA Synthesis." Journal of Virology 81, no. 6 (2006): 2861–68. http://dx.doi.org/10.1128/jvi.02291-06.

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ABSTRACT Short RNA interference is more and more widely recognized as an effective method to specifically suppress viral functions in eukaryotic cells. Here, we used an experimental system that allows suppression of the Sendai virus (SeV) M protein by using a target sequence, derived from the green fluorescent protein gene, that was introduced in the 3′ untranslated region of the M protein mRNA. Silencing of the M protein gene was eventually achieved by a small interfering RNA (siRNA) directed against this target sequence. This siRNA was constitutively expressed in a cell line constructed by t

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Fatima, Attia, and Dermot G. Morris. "MicroRNAs in domestic livestock." Physiological Genomics 45, no. 16 (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 poten

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Conrad, R., J. Thomas, J. Spieth, and T. Blumenthal. "Insertion of part of an intron into the 5' untranslated region of a Caenorhabditis elegans gene converts it into a trans-spliced gene." Molecular and Cellular Biology 11, no. 4 (1991): 1921–26. http://dx.doi.org/10.1128/mcb.11.4.1921-1926.1991.

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In nematodes, the RNA products of some genes are trans-spliced to a 22-nucleotide spliced leader (SL), while the RNA products of other genes are not. In Caenorhabditis elegans, there are two SLs, SL1 and SL2, donated by two distinct small nuclear ribonucleoprotein particles in a process functionally quite similar to nuclear intron removal. We demonstrate here that it is possible to convert a non-trans-spliced gene into a trans-spliced gene by placement of an intron missing only the 5' splice site into the 5' untranslated region. Stable transgenic strains were isolated expressing a gene in whic

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Conrad, R., J. Thomas, J. Spieth, and T. Blumenthal. "Insertion of part of an intron into the 5' untranslated region of a Caenorhabditis elegans gene converts it into a trans-spliced gene." Molecular and Cellular Biology 11, no. 4 (1991): 1921–26. http://dx.doi.org/10.1128/mcb.11.4.1921.

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In nematodes, the RNA products of some genes are trans-spliced to a 22-nucleotide spliced leader (SL), while the RNA products of other genes are not. In Caenorhabditis elegans, there are two SLs, SL1 and SL2, donated by two distinct small nuclear ribonucleoprotein particles in a process functionally quite similar to nuclear intron removal. We demonstrate here that it is possible to convert a non-trans-spliced gene into a trans-spliced gene by placement of an intron missing only the 5' splice site into the 5' untranslated region. Stable transgenic strains were isolated expressing a gene in whic

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Lai, M., D. B. Thomason, and N. W. Weisbrodt. "Effect of intestinal bypass on the expression of actin mRNA in ileal smooth muscle." American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 258, no. 1 (1990): R39—R43. http://dx.doi.org/10.1152/ajpregu.1990.258.1.r39.

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In this study, messenger RNAs (mRNAs) for actin isoforms were assessed in longitudinal smooth muscle from the ileum of unoperated rats and from rats that had undergone bypass of the middle 70% of the small intestine. The plasmid clone pGEM 10C, which contains a DNA insert complementary to the 3' untranslated region and the region of mRNA that codes for the synthesis of alpha-smooth muscle actin protein, was used to synthesize two riboprobes. One probe, complementary to the coding region of the insert, hybridizes to most, if not all, actin isoform mRNAs. The second probe, complementary to the 3

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Быков, А. А., and A. A. Bykov. "Bacterial nucleoid protein Dps binds structured RNA molecules." Mathematical Biology and Bioinformatics 11, no. 2 (2016): 311–22. http://dx.doi.org/10.17537/2016.11.311.

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Architectural protein Dps of the bacterial nucleoid employs side groups of lysines at its N-terminal modules for interacting with the sugar-phosphate backbone of the DNA. Electrostatic nature of interaction assumes the potential ability of Dps to bind with any nucleotide sequence including RNA. The available data also indicate that Dps exhibits enhanced affinity to branched DNA structures. In RNA molecules such structures are formed more frequently than in DNA. Hence, the aim of this investigation was studying the ability of purified Dps immobilized on acrylate spheres to bind with short RNAs

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Parsch, John, John M. Braverman, and Wolfgang Stephan. "Comparative Sequence Analysis and Patterns of Covariation in RNA Secondary Structures." Genetics 154, no. 2 (2000): 909–21. http://dx.doi.org/10.1093/genetics/154.2.909.

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Abstract A novel method of RNA secondary structure prediction based on a comparison of nucleotide sequences is described. This method correctly predicts nearly all evolutionarily conserved secondary structures of five different RNAs: tRNA, 5S rRNA, bacterial ribonuclease P (RNase P) RNA, eukaryotic small subunit rRNA, and the 3′ untranslated region (UTR) of the Drosophila bicoid (bcd) mRNA. Furthermore, covariations occurring in the helices of these conserved RNA structures are analyzed. Two physical parameters are found to be important determinants of the evolution of compensatory mutations:

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Smith, Kelly P., Meg Byron, Carol Johnson, Yigong Xing, and Jeanne B. Lawrence. "Defining early steps in mRNA transport: mutant mRNA in myotonic dystrophy type I is blocked at entry into SC-35 domains." Journal of Cell Biology 178, no. 6 (2007): 951–64. http://dx.doi.org/10.1083/jcb.200706048.

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In myotonic dystrophy type 1 (DM1), triplet repeat expansion in the 3′ untranslated region of dystrophia myotonica protein kinase (DMPK) causes the nuclear retention of mutant messenger RNA (mRNA). Although the DMPK gene locus positions precisely at the outer edge of a factor-rich SC-35 domain, the normal mRNA consistently accumulates within the domain, and this RNA is depleted upon transcriptional inhibition. In DM1, mutant transcripts detach from the gene but accumulate in granules that abut but do not enter SC-35 domains, suggesting that RNA entry into the domain is blocked. Despite their e

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Landt, Stephen G., Joseph A. Lesley, Leticia Britos, and Lucy Shapiro. "CrfA, a Small Noncoding RNA Regulator of Adaptation to Carbon Starvation in Caulobacter crescentus." Journal of Bacteriology 192, no. 18 (2010): 4763–75. http://dx.doi.org/10.1128/jb.00343-10.

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ABSTRACT Small noncoding regulatory RNAs (sRNAs) play a key role in the posttranscriptional regulation of many bacterial genes. The genome of Caulobacter crescentus encodes at least 31 sRNAs, and 27 of these sRNAs are of unknown function. An overexpression screen for sRNA-induced growth inhibition along with sequence conservation in a related Caulobacter species led to the identification of a novel sRNA, CrfA, that is specifically induced upon carbon starvation. Twenty-seven genes were found to be strongly activated by CrfA accumulation. One-third of these target genes encode putative TonB-dep

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Rossi, Chiara, Nicola Zadra, Cristina Fevola, et al. "Evolutionary Relationships of Ljungan Virus Variants Circulating in Multi-Host Systems across Europe." Viruses 13, no. 7 (2021): 1317. http://dx.doi.org/10.3390/v13071317.

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The picornavirus named ‘Ljungan virus’ (LV, species Parechovirus B) has been detected in a dozen small mammal species from across Europe, but detailed information on its genetic diversity and host specificity is lacking. Here, we analyze the evolutionary relationships of LV variants circulating in free-living mammal populations by comparing the phylogenetics of the VP1 region (encoding the capsid protein and associated with LV serotype) and the 3Dpol region (encoding the RNA polymerase) from 24 LV RNA-positive animals and a fragment of the 5′ untranslated region (UTR) sequence (used for defini

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Beerens, Nancy, and Eric J. Snijder. "RNA signals in the 3′ terminus of the genome of Equine arteritis virus are required for viral RNA synthesis." Journal of General Virology 87, no. 7 (2006): 1977–83. http://dx.doi.org/10.1099/vir.0.81750-0.

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RNA virus genomes contain cis-acting sequences and structural elements involved in virus replication. Both full-length and subgenomic negative-strand RNA synthesis are initiated at the 3′ terminus of the positive-strand genomic RNA of Equine arteritis virus (EAV). To investigate the molecular mechanism of EAV RNA synthesis, the RNA secondary structure of the 3′-proximal region of the genome was analysed by chemical and enzymic probing. Based on the RNA secondary structure model derived from this analysis, several deletions were engineered in a full-length cDNA copy of the viral genome. Two RNA

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Pandey, Smriti, Chandra M. Gravel, Oliver M. Stockert, et al. "Genetic identification of the functional surface for RNA binding by Escherichia coli ProQ." Nucleic Acids Research 48, no. 8 (2020): 4507–20. http://dx.doi.org/10.1093/nar/gkaa144.

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Abstract The FinO-domain-protein ProQ is an RNA-binding protein that has been known to play a role in osmoregulation in proteobacteria. Recently, ProQ has been shown to act as a global RNA-binding protein in Salmonella and Escherichia coli, binding to dozens of small RNAs (sRNAs) and messenger RNAs (mRNAs) to regulate mRNA-expression levels through interactions with both 5′ and 3′ untranslated regions (UTRs). Despite excitement around ProQ as a novel global RNA-binding protein, and its potential to serve as a matchmaking RNA chaperone, significant gaps remain in our understanding of the molecu

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Koh, Dora Chin-Yen, D. X. Liu, and Sek-Man Wong. "A Six-Nucleotide Segment within the 3′ Untranslated Region of Hibiscus Chlorotic Ringspot Virus Plays an Essential Role in Translational Enhancement." Journal of Virology 76, no. 3 (2002): 1144–53. http://dx.doi.org/10.1128/jvi.76.3.1144-1153.2002.

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ABSTRACT RNA plant viruses use various translational regulatory mechanisms to control their gene expression. Translational enhancement of viral mRNAs that leads to higher levels of protein synthesis from specific genes may be essential for the virus to successfully compete for cellular translational machinery. The control elements have yet to be analyzed for members of the genus Carmovirus, a small group of plant viruses with positive-sense RNA genomes. In this study, we examined the 3′ untranslated region (UTR) of hibiscus chlorotic ringspot virus (HCRSV) genomic RNA (gRNA) and subgenomic RNA

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