Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “RNA guide”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 577 records · Page 32Linked to original sources
PubMed2004

Regulation of relative abundance of arterivirus subgenomic mRNAs.

The subgenomic (sg) mRNAs of arteriviruses (order Nidovirales) form a 5'- and 3'-coterminal nested set with the viral genome. Their 5' common leader sequence is derived from the genomic 5'-proximal region. Fusion of sg RNA leader and "body" segments involves a discontinuous transcription step. Presumably during minus-strand synthesis, the nascent RNA strand is transferred from one site in the genomic template to another, a process guided by conserved transcription-regulating sequences (TRSs) at these template sites. Subgenomic RNA species are produced in different but constant molar ratios, with the smallest RNAs usually being most abundant. Factors thought to influence sg RNA synthesis are size differences between sg RNA species, differences in sequence context between body TRSs, and the mutual influence (or competition) between strand transfer reactions occurring at different body TRSs. Using an Equine arteritis virus infectious cDNA clone, we investigated how body TRS activity affected sg RNA synthesis from neighboring body TRSs. Flanking sequences were standardized by head-to-tail insertion of several copies of an RNA7 body TRS cassette. A perfect gradient of sg RNA abundance, progressively favoring smaller RNA species, was observed. Disruption of body TRS function by mutagenesis did not have a significant effect on the activity of other TRSs. However, deletion of body TRS-containing regions enhanced synthesis of sg RNAs from upstream TRSs but not of those produced from downstream TRSs. The results of this study provide considerable support for the proposed discontinuous extension of minus-strand RNA synthesis as a crucial step in sg RNA synthesis.

Equartevirus↗
PubMed2002

Evidence that siRNAs function as guides, not primers, in the Drosophila and human RNAi pathways.

In Drosophila, two features of small interfering RNA (siRNA) structure--5' phosphates and 3' hydroxyls--are reported to be essential for RNA interference (RNAi). Here, we show that as in Drosophila, a 5' phosphate is required for siRNA function in human HeLa cells. In contrast, we find no evidence in flies or humans for a role in RNAi for the siRNA 3' hydroxyl group. Our in vitro data suggest that in both flies and mammals, each siRNA guides endonucleolytic cleavage of the target RNA at a single site. We conclude that the underlying mechanism of RNAi is conserved between flies and mammals and that RNA-dependent RNA polymerases are not required for RNAi in these organisms.

Animals↗
PubMed2004

A computational search for box C/D snoRNA genes in the Drosophila melanogaster genome.

MOTIVATION: In eukaryotes, the family of non-coding RNA genes includes a number of genes encoding small nucleolar RNAs (mainly C/D and H/ACA snoRNAs), which act as guides in the maturation or post-transcriptional modifications of target RNA molecules. Since in Drosophila melanogaster (Dm) only few examples of snoRNAs have been identified so far by cDNA libraries screening, integration of the molecular data with in silico identification of these types of genes could throw light on their organization in the Dm genome. RESULTS: We have performed a computational screening of the Dm genome for C/D snoRNA genes, followed by experimental validation of the putative candidates. Few of the 26 confirmed snoRNAs had been recognized by cDNA library analysis. Organization of the Dm genome was also found to be more variegated than previously suspected, with snoRNA genes nested in both the introns and exons of protein-coding genes. This finding suggests that the presence of additional mechanisms of snoRNA biogenesis based on the alternative production of overlapping mRNA/snoRNA molecules. AVAILABILITY: Additional information is available at http://www.bioinformatica.unito.it/bioinformatics/snoRNAs.

Animals↗
PubMed2005

Gardening the genome: DNA methylation in Arabidopsis thaliana.

DNA methylation has two essential roles in plants and animals - defending the genome against transposons and regulating gene expression. Recent experiments in Arabidopsis thaliana have begun to address crucial questions about how DNA methylation is established and maintained. One cardinal insight has been the discovery that DNA methylation can be guided by small RNAs produced through RNA-interference pathways. Plants and mammals use a similar suite of DNA methyltransferases to propagate DNA methylation, but plants have also developed a glycosylase-based mechanism for removing DNA methylation, and there are hints that similar processes function in other organisms.

Arabidopsis↗
PubMed2006

Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs.

Small nucleolar RNAs (snoRNAs) and Cajal body-specific RNAs (scaRNAs) are named for their subcellular localization within nucleoli and Cajal bodies (conserved subnuclear organelles present in the nucleoplasm), respectively. They have been found to play important roles in rRNA, tRNA, snRNAs, and even mRNA modification and processing. All snoRNAs fall in two categories, box C/D snoRNAs and box H/ACA snoRNAs, according to their distinct sequence and secondary structure features. Box C/D snoRNAs and box H/ACA snoRNAs mainly function in guiding 2'-O-ribose methylation and pseudouridilation, respectively. ScaRNAs possess both box C/D snoRNA and box H/ACA snoRNA sequence motif features, but guide snRNA modifications that are transcribed by RNA polymerase II. Here we present a Web-based sno/scaRNA database, called sno/scaRNAbase, to facilitate the sno/scaRNA research in terms of providing a more comprehensive knowledge base. Covering 1979 records derived from 85 organisms for the first time, sno/scaRNAbase is not only dedicated to filling gaps between existing organism-specific sno/scaRNA databases that are focused on different sno/scaRNA aspects, but also provides sno/scaRNA scientists with an opportunity to adopt a unified nomenclature for sno/scaRNAs. Derived from a systematic literature curation and annotation effort, the sno/scaRNAbase provides an easy-to-use gateway to important sno/scaRNA features such as sequence motifs, possible functions, homologues, secondary structures, genomics organization, sno/scaRNA gene's chromosome location, and more. Approximate searches, in addition to accurate and straightforward searches, make the database search more flexible. A BLAST search engine is implemented to enable blast of query sequences against all sno/scaRNAbase sequences. Thus our sno/scaRNAbase serves as a more uniform and friendly platform for sno/scaRNA research. The database is free available at http://gene.fudan.sh.cn/snoRNAbase.nsf.

Base Sequence↗
PubMed2001

Regulation of CNS and motor axon guidance in Drosophila by the receptor tyrosine phosphatase DPTP52F.

Receptor-linked protein tyrosine phosphatases (RPTPs) regulate axon guidance and synaptogenesis in Drosophila embryos and larvae. We describe DPTP52F, the sixth RPTP to be discovered in Drosophila. Our genomic analysis indicates that there are likely to be no additional RPTPs encoded in the fly genome. Five of the six Drosophila RPTPs have C. elegans counterparts, and three of the six are also orthologous to human RPTP subfamilies. DPTP52F, however, has no clear orthologs in other organisms. The DPTP52F extracellular domain contains five fibronectin type III repeats and it has a single phosphatase domain. DPTP52F is selectively expressed in the CNS of late embryos, as are DPTP10D, DLAR, DPTP69D and DPTP99A. To define developmental roles of DPTP52F, we used RNA interference (RNAi)-induced phenotypes as a guide to identify Ptp52F alleles among a collection of EMS-induced lethal mutations. Ptp52F single mutant embryos have axon guidance phenotypes that affect CNS longitudinal tracts. This phenotype is suppressed in Dlar Ptp52F double mutants, indicating that DPTP52F and DLAR interact competitively in regulating CNS axon guidance decisions. Ptp52F single mutations also cause motor axon phenotypes that selectively affect the SNa nerve. DPTP52F, DPTP10D and DPTP69D have partially redundant roles in regulation of guidance decisions made by axons within the ISN and ISNb motor nerves.

Amino Acid Sequence↗
PubMed2006

Identification of trans-acting siRNAs in moss and an RNA-dependent RNA polymerase required for their biogenesis.

Trans-acting small interfering RNAs (tasiRNAs) are a class of higher-plant endogenous siRNAs that, like miRNAs, direct the cleavage of non-identical transcripts. tasiRNAs derive from non-coding transcripts (TAS) that are converted into dsRNA by a RNA-dependent RNA polymerase (RDR6), following their initial miRNA-guided cleavage. The dsRNA is then processed by a dicer-like enzyme 4 into phased 21-nucleotide siRNAs. To date, tasiRNAs have been identified only in Arabidopsis, and their identity and function in other land plants are unknown. Here, a set of endogenous small RNAs that correspond in a phased manner to a non-coding transcript (contig13502) were identified in the moss Pyscomitrella patens. Northern analysis suggests that contig13502-derived small RNAs are expressed in the juvenile gametophyte. In addition, miR390-guided cleavage of contig13502 at two sites flanking the small RNAs cluster was validated by 5' RACE. These cleavages are predicted to provide defined termini for the production of phased siRNAs. To elucidate the biogenesis of identified siRNAs, we cloned and generated knock-out mutants for an RDR6 moss homologue (PpRDR6). These mutants exhibited an accelerated transition from juvenile to mature gametophyte. In addition, RNA blots demonstrated that they lacked contig13502-derived siRNAs, suggesting that PpRDR6 is required for siRNA biogenesis. A target gene, which showed homology to an AP2/EREBP transcription factor, for one phased siRNA, was validated, corroborating its identity as a trans-acting siRNA. Taken together, our data indicate that contig13502 is a novel TAS locus and suggest a role for derived tasiRNAs in the regulation of gene expression in moss.

Amino Acid Sequence↗
PubMedDate not supplied

siRNA, miRNA and HIV: promises and challenges.

Small interfering RNA (siRNA) and microRNA (miRNA) are small RNAs of 18-25 nucleotides (nt) in length that play important roles in regulating gene expression. They are incorporated into an RNA-induced silencing complex (RISC) and serve as guides for silencing their corresponding target mRNAs based on complementary base-pairing. The promise of gene silencing has led many researchers to consider siRNA as an anti-viral tool. However, in long-term settings, many viruses appear to escape from this therapeutical strategy. An example of this may be seen in the case of human immunodeficiency virus type-1 (HIV-1) which is able to evade RNA silencing by either mutating the siRNA-targeted sequence or by encoding for a partial suppressor of RNAi (RNA interference). On the other hand, because miRNA targeting does not require absolute complementarity of base-pairing, mutational escape by viruses from miRNA-specified silencing may be more difficult to achieve. In this review, we discuss stratagems used by various viruses to avoid the cells' antiviral si/mi-RNA defenses and notions of how viruses might control and regulate host cell genes by encoding viral miRNAs (vmiRNAs).

HIV↗
PubMed2000

Characterization of Candida albicans RNA triphosphatase and mutational analysis of its active site.

The RNA triphosphatase component (CaCet1p) of the mRNA capping apparatus of the pathogenic fungus Candida albicans differs mechanistically and structurally from the RNA triphosphatase of mammals. Hence, CaCet1p is an attractive antifungal target. Here we identify a C-terminal catalytic domain of CaCet1p from residue 257 to 520 and characterize a manganese-dependent and cobalt-dependent NTPase activity intrinsic to CaCet1p. The NTPase can be exploited to screen in vitro for inhibitors. The amino acids that comprise the active site of CaCet1p were identified by alanine-scanning mutagenesis, which was guided by the crystal structure of the homologous RNA triphosphatase from Saccharomyces cerevisiae (Cet1p). Thirteen residues required for the phosphohydrolase activity of CaCet1p (Glu287, Glu289, Asp363, Arg379, Lys396, Glu420, Arg441, Lys443, Arg445, Asp458, Glu472, Glu474 and Glu476) are located within the hydrophilic interior of an eight-strand beta barrel of Cet1p. Each of the eight strands contributes at least one essential amino acid. The essential CaCet1p residues include all of the side chains that coordinate manganese and sulfate (i.e., gamma phosphate) in the Cet1p product complex. These results suggest that the active site structure and catalytic mechanism are conserved among fungal RNA triphosphatases.

Acid Anhydride Hydrolases↗
PubMed2003

The exon context and distribution of Euascomycetes rRNA spliceosomal introns.

BACKGROUND: We have studied spliceosomal introns in the ribosomal (r)RNA of fungi to discover the forces that guide their insertion and fixation. RESULTS: Comparative analyses of flanking sequences at 49 different spliceosomal intron sites showed that the G - intron - G motif is the conserved flanking sequence at sites of intron insertion. Information analysis showed that these rRNA introns contain significant information in the flanking exons. Analysis of all rDNA introns in the three phylogenetic domains and two organelles showed that group I introns are usually located after the most conserved sites in rRNA, whereas spliceosomal introns occur at less conserved positions. The distribution of spliceosomal and group I introns in the primary structure of small and large subunit rRNAs was tested with simulations using the broken-stick model as the null hypothesis. This analysis suggested that the spliceosomal and group I intron distributions were not produced by a random process. Sequence upstream of rRNA spliceosomal introns was significantly enriched in G nucleotides. We speculate that these G-rich regions may function as exonic splicing enhancers that guide the spliceosome and facilitate splicing. CONCLUSIONS: Our results begin to define some of the rules that guide the distribution of rRNA spliceosomal introns and suggest that the exon context is of fundamental importance in intron fixation.

Ascomycota↗
PubMed2002

RNA cleavage by a mammalian tRNA 3'processing endoribonuclease (3'tRNase) reduces HIV-1 expression.

We examined the suppression of HIV-1 expression by cleavage of the HIV-1 RNA gene, using a mammalian tRNA 3'processing endoribonuclease (3'tRNase) as an External Guide Sequence oligozyme (EGS) in vivo. The enzyme can also recognize and cleave a target RNA that forms a pre-tRNA like complex with a substrate RNA. We designed an EGS to specifically recognize the packaging signal region (p.s.) and the upstream portion of the gag region (g.s.) of HIV-1 mRNA, and constructed EGS expression vectors that used the tRNA(met) promoter as an expression cassette for the EGS. Their cleavage activities were assessed in cell culture, using a transient assay system. The EGS efficiencies were determined by co-transfection of the EGS expression vectors and the HIV-1 gene plasmid vector (pNL-luc) into COS cells. The assay results showed a significant inhibition of the HIV-1 gag p24 antigen expression. In addition, we constructed MLV-based VSV-G pseudotyped retrovirus vectors that express the EGS. They were co-infected into MT-4 cells with the HIV-1 virus (NL4-3). These EGS expression retrovirus vectors exhibited a similar inhibitory effect.

Animals↗
PubMed2005

Highly active antiretroviral therapy (HAART) retreatment in patients on CD4-guided therapy achieved similar virologic suppression compared with patients on continuous HAART: the HIV Netherlands Australia Thailand Research Collaboration 001.4 study.

OBJECTIVE: To assess the safety of 2 intermittent treatment strategies compared with continuous therapy for patients with virologic suppression on highly active antiretroviral therapy (HAART) at baseline. DESIGN: Seventy-four nucleoside reverse transcriptase inhibitor (NRTI) and protease inhibitor (PI) pretreated patients with an HIV RNA level <50 copies at screening were randomized to continuous treatment, CD4-guided treatment, or week-on-week-off treatment with 2 NRTIs plus 1600 mg/100 mg of saquinavir/ritonavir once daily. At week 96 (end of the randomized phase of the study), all patients were given continuous HAART for 12 weeks to week 108. Primary outcomes were the proportion of patients with a CD4 count >350 cells/microL and HIV RNA level <400 copies/mL at week 108. METHODS: Patients were followed up every 12 weeks for CD4 count, HIV RNA level, and clinical and laboratory toxicities. In the CD4-guided arm, treatment was stopped and restarted using a CD4 count threshold (above or below 350 cells/microL or reduction of 30%). RESULTS: Seventy-four patients were enrolled with a median CD4 count of 644 cells/microL before the structured treatment interruption (STI). The week-on-week-off arm (n=26) was discontinued at week 72 because of high rates (46%) of HIV RNA rebound above 50 copies/mL. In the continuous arm, 25 (100%) of 25 patients and 24 (96%) of 25 patients had an HIV RNA level <400 copies/mL and <50 copies/mL, respectively, at week 108, and 96% had a CD4 count above 350 cells/microL, with a median CD4 count of 661 cells/microL. Patients in the CD4-guided arm had a significantly lower median CD4 count (489 cells/microL) than the patients in the continuous arm (P=0.03), but all had a CD4 count above 350 cells/microL and 1 had a new HIV-related illness. At week 108, 21 (91%) of 23 patients and 13 (57%) of 23 patients had an HIV RNA level <400 copies/mL and <50 copies/mL, respectively. Those who did not achieve an HIV RNA level <50 copies/mL had a higher HIV RNA load before retreatment, and 4 of 5 patients subsequently achieved viral suppression after an additional 12 weeks of HAART (week 120). Therefore, 17 (94%) of 18 evaluable CD4-guided arm patients achieved viral suppression after retreatment. Antiretroviral (ARV) side effects were similar in all arms. CD4-guided treatment had a 54% ARV cost savings. CONCLUSIONS: This pilot study suggests that CD4-guided HAART is a well-tolerated and cost-saving treatment strategy for patients with high pre-ARV and pre-STI CD4 counts. Week-on-week-off treatment had a high virologic failure rate and was discontinued. The HIV RNA suppression rate was similar in patients treated with continuous HAART and in those retreated with 12 to 24 weeks of HAART after CD4-guided therapy.

Adult↗
PubMed2005

MicroRNAs: critical regulators of development, cellular physiology and malignancy.

MicroRNAs (miRNAs) are 18-24 nucleotide RNA molecules that regulate the stability or translational efficiency of target mRNAs. These regulatory RNAs function by acting as sequence-specific guides which recruit a large protein complex known as the RNA-induced silencing complex, or RISC, to target mRNAs which are subsequently silenced. Diverse functions have been attributed to miRNAs including the regulation of cellular differentiation, proliferation, and apoptosis. Moreover, significant evidence has accumulated implicating a fundamental role for miRNAs in the development of cancer. We recently demonstrated that the oncogenic transcription factor c-Myc regulates a group of miRNAs known as the mir-17 cluster. This represents the first documented example of a mammalian transcription factor that regulates miRNA expression. Moreover, it was independently demonstrated that the mir-17 cluster accelerates c-Myc-induced lymphomagenesis in an in vivo mouse model. Together, these studies support an important role for this group of miRNAs in c-Myc-mediated tumorigenesis. We have also demonstrated that two miRNAs in this cluster regulate the pro-proliferative, pro-apoptotic transcription factor E2F1. Herein, we propose a model in which the mir-17 cluster prevents excessive E2F1 activity, and thereby apoptosis, in response to activation of c-Myc.

3' Untranslated Regions↗
PubMed2005

RNA interference in vivo: toward synthetic small inhibitory RNA-based therapeutics.

Small interfering RNA (siRNA) mediated inhibition of gene expression has rapidly become a major tool for in vitro analysis of protein function. In vivo gene silencing by siRNAs will play an important role for target validation and is the first step towards the development of siRNA-based therapeutics. This chapter reviews the early and intriguing successes in using siRNAs for in vivo gene silencing. The impact of chemical modification on siRNA efficacy in vitro and the potential for employing such modifications to alter the pharmacokinetic properties of siRNAs is also summarized. A protocol describing siRNA-based gene silencing in tumor models can serve as guide for the design of individual in vivo RNA interference experiments.

Base Sequence↗
PubMed2002

Persistent engrailed expression is required to determine sensory axon trajectory, branching, and target choice.

The transcription factor Engrailed (En) directs, in the cockroach cercal system, the shape of the axonal arborization and the choice of postsynaptic partners of an identified sensory neuron (6m). Knock-out of En using double-stranded RNA interference transforms 6m so that it resembles a neighboring neuron that normally does not express the en gene, has a different arbor anatomy, and makes different connections. We characterized the development of 6m and perturbed en expression at different stages. Our results show that En is not required before birth for 6m to become a neuron, but that it is required in the postmitotic neuron to control axonal arborization and synaptic specificity. Knock-out of En after 6m has entered the CNS does not change the axonal trajectory and has minor effects on axonal branches but causes the formation of synaptic connections typical of an En-negative cell. This suggests that En controls target recognition molecules independently from those guiding the axon. In contrast, double-stranded RNA injection 1 d later does not have any effects on the phenotype of 6m, suggesting that the period of synapse formation is over by the time En levels have fallen or, if synapse turnover occurs, that En is not required to maintain the specificity of synaptic connections. We conclude that persistent en expression is required to determine successive stages in the differentiation of the neuron, suggesting that it is not far upstream from those genes encoding axon guidance and synaptic recognition molecules.

Aging↗
PubMed2005

Small non-coding RNAs in Archaea.

Biochemical and informatics analyses conducted over the past few years have revealed the presence of a plethora of small non-coding RNAs in various species of Archaea. A large proportion of these RNAs contain a common structural motif called the RNA kink turn (K-turn). The best-characterized are the C/D box and the H/ACA box guide small (s)RNAs. Both contain the K-turn fold and require the binding of the L7Ae protein to stabilize the structure of this crucial motif. These sRNAs assemble with L7Ae and several other proteins into complex and dynamic ribonucleoprotein machines that mediate guide-directed ribose methylation or pseudouridylation to specific locations in ribosomal or transfer RNA. Analyses of new archaeal sRNA libraries have identified additional classes of novel sRNAs; many of these contain the RNA K-turn motif and suggest that the RNAs might function as ribonucleoprotein complexes. Some have characteristics of small interfering RNAs or of micro RNAs that have been implicated in the post-transcriptional control of gene expression, whereas others appear to be involved in protein translocation or in ribosomal RNA processing and ribosome assembly. A complete understanding of the structure of the K-turn motif and its contribution to various RNA-RNA and RNA-protein interactions will be absolutely essential to fully elucidate the biological organization, activity and function of these novel archaeal ribonucleoprotein machines.

Archaea↗
PubMed2002

Comparative structure analysis of vertebrate U17 small nucleolar RNA (snoRNA).

Intron-encoded U17 RNA is a member of the H/ACA box class of small nucleolar RNAs (snoRNAs) involved in ribosomal RNA (rRNA) maturation. U17 snoRNA shows typical characteristics of guide RNAs, which specify sites of pseudouridylation on the precursor rRNA (pre-rRNA). However, in spite of the presence of H and ACA boxes and short regions complementary to the pre-rRNA, its secondary structure does not show any evident pseudouridylation pocket. Moreover, its length is larger than the typical one of snoRNAs and it shows a more complex secondary structure compared to the canonical hairpin-hinge-hairpin-tail architecture. Greater knowledge of eukaryotic U17 snoRNA structure is needed to understand its precise function. Comparative molecular studies of this snoRNA with different vertebrates is still limited to a few cases. With the aim of increasing our understanding of the U17 snoRNA secondary structure, we cloned the U17 snoRNA coding sequence from 10 additional vertebrate taxa. On the basis of structure homology derived from sequence comparison and thermodynamic prediction, we propose a vertebrate consensus secondary structure and novel conserved sequence boxes for U17 snoRNA. Host gene localization of U17 coding sequence and its ability to serve as a guide sequence for RNA/RNA interaction has been evolutionarily traced from fish to mammals. It is interesting to note that turtle U17 snoRNAs show a noncanonical ACA box, mainly consisting in the GCA box. Microinjections in X. laevis oocytes of in vitro synthesized turtle transcripts containing the U17 RNA sequence which have canonical ACA, wild-type GCA, and mutated CCA and UCA boxes resulted in efficient production of mature U17 snoRNA.

Animals↗
PubMed2004

Genetic and functional diversification of small RNA pathways in plants.

Multicellular eukaryotes produce small RNA molecules (approximately 21-24 nucleotides) of two general types, microRNA (miRNA) and short interfering RNA (siRNA). They collectively function as sequence-specific guides to silence or regulate genes, transposons, and viruses and to modify chromatin and genome structure. Formation or activity of small RNAs requires factors belonging to gene families that encode DICER (or DICER-LIKE [DCL]) and ARGONAUTE proteins and, in the case of some siRNAs, RNA-dependent RNA polymerase (RDR) proteins. Unlike many animals, plants encode multiple DCL and RDR proteins. Using a series of insertion mutants of Arabidopsis thaliana, unique functions for three DCL proteins in miRNA (DCL1), endogenous siRNA (DCL3), and viral siRNA (DCL2) biogenesis were identified. One RDR protein (RDR2) was required for all endogenous siRNAs analyzed. The loss of endogenous siRNA in dcl3 and rdr2 mutants was associated with loss of heterochromatic marks and increased transcript accumulation at some loci. Defects in siRNA-generation activity in response to turnip crinkle virus in dcl2 mutant plants correlated with increased virus susceptibility. We conclude that proliferation and diversification of DCL and RDR genes during evolution of plants contributed to specialization of small RNA-directed pathways for development, chromatin structure, and defense.

Arabidopsis↗