Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “noncoding RNAs”

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 649 records · Page 36Linked to original sources
PubMed1998

Functional significance of three basic N-terminal amino acids of alfalfa mosaic virus coat protein.

Infection of tobacco protoplasts with mutant alfalfa mosaic virus (AMV) RNAs indicated that three basic amino acids in the N-terminus of AMV coat protein are important for the biological activity of the coat protein in the beginning of infection. Substitution of alanines for lysines at position 14 or 17 in the coat protein resulted in a 5- or 10-fold reduction in the activity of the protein, respectively. However, substitution of alanine for arginine at position 18 entirely abolished activity. Arginine 18 was also required for the coat protein to bind to the 3' noncoding region of the virus RNA in vitro, whereas lysine 14 or 17 was not required. Thus, these results indicate that arginine 18 is essential for the activity of the coat protein in early infection and that binding of the coat protein to AMV RNA correlates with activity.

Alfalfa mosaic virus↗
PubMed1981

In vitro translation of the intermediate filament proteins desmin and vimentin.

Polyadenylated ribonucleic acid (RNA) was isolated from chicken skeletal and smooth muscle and translated in a cell-free rabbit reticulocyte system. Both types of muscle tissue contain messenger RNAs that code for the intermediate filament proteins desmin and vimentin, and the relative concentrations of the two translation products reflect the prevalence of the two proteins in vivo. Desmin synthesis represents a greater proportion of the total protein synthesis from smooth muscle RNA than from skeletal muscle RNA, whereas the converse is true of vimentin synthesis. Fractionation of the RNA on formamide-containing sucrose gradients before translation indicates that the desmin messenger RNA is larger than the vimentin messenger RNA and contains an extensive noncoding segment. The desmin and vimentin messages code predominantly for the non-phosphorylated forms of desmin and vimentin. However, the ratio of phosphorylated to unphosphorylated forms of the proteins could be increased by adding cyclic adenosine monophosphate-dependent kinase activity to the translation mixtures. These results suggest that desmin and vimentin are each synthesized from a single messenger RNA species and that posttranslational phosphorylation generates the additional isoelectric variants of each which are observed in vivo.

Animals↗
PubMed2006

Gene silencing in vitro and in vivo using intronic microRNAs.

MicroRNAs (miRNAs), small single-stranded regulatory RNAs capable of interfering with intracellular messenger RNAs (mRNAs) that contain either complete or partial complementarity, are useful for the design of new therapies against cancer polymorphism and viral mutation. Numerous miRNAs have been reported to induce RNA interference (RNAi), a posttranscriptional gene-silencing mechanism. Recent evidence also indicates that they are involved in the transcriptional regulation of genome activities. They were first discovered in Caenorhabditis elegans as native RNA fragments that modulate a wide range of genetic regulatory pathways during embryonic development, and are now recognized as small gene silencers transcribed from the noncoding regions of a genome. In humans, nearly 97% of the genome is noncoding DNA, which varies from one individual to another, and changes in these sequences are frequently noted to manifest clinical and circumstantial malfunction. Type 2 myotonic dystrophy and fragile X syndrome were found to be associated with miRNAs derived from introns. Intronic miRNA is a new class of miRNAs derived from the processing of nonproteincoding regions of gene transcripts. The intronic miRNAs differ uniquely from previously described intergenic miRNAs in the requirement of RNA polymerase (Pol)-II and spliceosomal components for its biogenesis. Several kinds of intronic miRNAs have been identified in C. elegans, mouse, and human cells; however, neither function nor application has been reported. Here, we show for the first time that intron-derived miRNA is not only able to induce RNAi in mammalian cells but also in fish, chicken embryos, and adult mice, demonstrating the evolutionary preservation of this gene regulation system in vivo. These miRNA-mediated animal models provide artificial means to reproduce the mechanisms of miRNA-induced disease in vivo and will shed further light on miRNA-related therapies.

Animals↗
PubMed1994

cDNA-derived hypovirus RNA in transformed chestnut blight fungus is spliced and trimmed of vector nucleotides.

Unencapsidated double-stranded viral RNAs belonging to the genus Hypovirus attenuate virulence of the chestnut blight fungus, Cryphonectria parasitica. A full-length cDNA clone of hypovirus CHV1-713 double-stranded RNA was recently shown to be infectious when introduced into the C. parasitica genome by DNA-mediated transformation. In this study, we show that the viral RNA derived from the chromosomally integrated cDNA copy is trimmed of extraneous vector nucleotide sequences. The cDNA-derived viral RNA was also found to contain a 73-bp deletion located within the 5'-noncoding leader sequence as a result of a pre-mRNA splicing event. Implications of these results are discussed in terms of hypovirus RNA replication and anticipated field studies involving engineered hypovirulent C. parasitica strains.

Base Sequence↗
PubMed1986

Discrimination among multiple AATAAA sequences correlates with interspecies conservation of select 3' untranslated nucleotides.

The DNA sequence corresponding to the 1.3 kb 3' untranslated region of the 6.5 kb human procollagen alpha 1(IV) mRNA was determined and compared with the mouse sequence obtained from 3' cDNA and genomic clones overlapping the reported 5' half (Oberbaumer et al., 1985, Eur. J. Biochem. 147:217). Although four AAUAAA hexanucleotides are found in the human and seven in the mouse RNAs, Northern blot hybridization showed almost exclusive utilization of the most 3' sequence, in contrast to the pattern seen when using alpha 1(I), alpha 2(I), alpha 1(III) and alpha 2(V) procollagen probes. Moreover, the ninety nucleotides 5' to the poly A tail in the major alpha 1(IV) mRNAs exhibit a much greater degree of interspecies homology than those encompassing the other three shared AAUAAA recognition signals. Further examination of this highly conserved area revealed the presence of two "consensus sequences" found in the 3' noncoding region of a number of RNA polymerase II transcribed genes (Mattaj and Zeller, 1983, Embo J. 2:1883) and, unexpectedly, some similarity with the nucleotides 5' to the poly A attachment signals in other procollagen mRNAs.

Animals↗
PubMed1986

Analysis of the genome structure of tobacco rattle virus strain PSG.

The sequence of the 3'-terminal 2077 nucleotides of genomic RNA 1 and the complete sequence of genomic RNA 2 of tobacco rattle virus (TRV, strain PSG) has been deduced. RNA 2 (1905 nucleotides) contains a single open reading frame for the viral coat protein (209 amino acids), flanked by 5'- and 3'-noncoding regions of 570 and 708 nucleotides, respectively. A subgenomic RNA (RNA 4) was found to lack the 5'-terminal 474 nucleotides of RNA 2 and is the putative messenger for coat protein. The deduced RNA 1 sequence contains the 3'-terminal part of a reading frame that probably corresponds to the TRV 170K protein and reading frames for a 29K protein and a 16K protein. Proteins encoded by the first two reading frames show significant amino acid sequence homology with corresponding proteins encoded by tobacco mosaic virus. Subgenomic RNAs 3 (1.6 kb) and 5 (0.7 kb) were identified as the putative messengers for the 29K and 16K proteins, respectively. At their 3'-termini all PSG-RNAs have an identical sequence of 497 nucleotides; at the 5'-termini homology is limited to 5 to 10 bases.

Amino Acid Sequence↗
PubMed1981

Primary sequence of the 5' flanking regions of the Drosophila heat shock genes in chromosome subdivision 67B.

The 5' flanking regions of the four small heat shock genes of Drosophila melanogaster from cytological locus 67B have been characterized. Approximately 500 bp of the primary sequence upstream from the proposed site of initiation of translation has been determined and the 5' end of the messenger RNAs have been localized for each gene. Each of the four genes contains an A-T rich sequence, either TATAAATA or TATAAAAG, which is flanked by a G-C rich region. This A-T rich sequence, which ends about 23 bp upstream from the proposed site of initiation of transcription, is similar to those found in most eukaryotic genes. Novel features of these four genes include a region of homology beginning near the proposed site of initiation of transcription and extending about 20 bp into the 5' noncoding region of the genes. This sequence is also found in the gene for the major heat shock protein, hsp 70. The leaders of these five heat shock genes are long, from 111 to 253 bases in length, as well as unusually A rich, from 46% to 51% A. In addition, each of the four small genes contains the sequence ACTTTNA, 195 +/- 12 bp from the proposed site of initiation of transcription.

Animals↗
PubMed2005

Complete cure of persistent virus infections by antiviral siRNAs.

Small interfering RNAs (siRNAs) have been developed as antiviral agents for mammalian cells. The capacity of specific siRNAs to prevent virus infections has been demonstrated, and there is evidence that these new antiviral agents could have a partial therapeutic effect a few days after infection. We investigated the possibility of curing a persistent infection, several months after becoming established, using an in vitro model of persistent poliovirus (PV) infection in HEp-2 cells. Despite high virus titers and the presence of PV mutants, repeated treatment with a mixture of two siRNAs targeting both noncoding and coding regions, one of them in a highly conserved region, resulted in the complete cure of the majority of persistently infected cultures. No escape mutants emerged in treated cultures. The antiviral effect of specific siRNAs, consistent with a mechanism of RNA interference, correlated with a decrease in the amount of viral RNA, until its complete disappearance, resulting in cultures cured of virions and viral RNA.

Animals↗
PubMed1989

Molecular identification of diabetogenic viral gene.

The best evidence that viruses have a causative role in the pathogenesis of insulin-dependent diabetes mellitus comes from experiments in mice infected with encephalomyocarditis (EMC) virus. When SJL/J male mice were inoculated with a highly diabetogenic EMC-D virus, diabetes developed in 95% of the animals. In contrast, none of the mice inoculated with a nondiabetogenic EMC-B virus became diabetic. Tissue culture experiments showed that EMC-B induces considerable amounts of interferon, whereas EMC-D does not. Despite these differences, EMC-D and EMC-B could not be distinguished antigenically by a sensitive plaque-neutralization assay. Furthermore, the buoyant density in CsCl density gradients and the capsid proteins of these two variants on polyacrylamide gels could not be distinguished. Molecular-hybridization studies with radiolabeled DNA complementary to EMC-D and EMC-B RNAs failed to distinguish them. Determination of complete nucleotide sequences of EMC-D and EMC-B revealed that EMC-D (7829 bases) differs from EMC-B (7825 bases) by only 14 nucleotides. The differences consist of two deletions of five nucleotides, one base insertion, and eight point mutations. The first deletion of three nucleotides and the second deletion of two nucleotides are located in the 5'-poly(C) tract and the 3'-end polyadenylation site, respectively. One base insertion in EMC-B occurs in the 5'-noncoding region. The eight point mutations are located in the polyprotein-coding region. Two of them are silent, whereas the other six mutations, one located on the L gene and five on the VP1 gene, introduce amino acid changes.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1989

Avian retroviral vectors derived from avian defective leukemia virus: role of the translational context of the inserted gene on efficiency of the vectors.

We have constructed retroviral vectors derived from the genome of avian erythroblastosis virus ES4 (AEV ES4). The neo selectable gene was substituted for the original v-erbA or v-erbB oncogenes of AEV, either in the same or in a different reading frames. Recombinant retrovirus were rescued and used to infect chicken embryo fibroblasts or quail QT6 cells. When the neo gene was inserted in the same reading frame as the original oncogene, we obtained (1) a high level of expression of the neo gene, (2) a balanced ration of both genomic and subgenomic RNAs, and (3) high titer recombinant viruses. Conversely, when the neo gene was inserted in a reading frame different from that of the original oncogene, we observed (1) a very low level of expression of the neo protein, (2) a predominance of the viral transcript used as translational template for the neo protein synthesis, and (3) low titer recombinant viruses. One of the vectors was used to transfer a human delta-globin gene into avian cells in culture without detectable rearrangement of this gene, but exhibited a deletion within the conserved noncoding region located between the two original oncogenes. Our data provide information for further construction of double expression vectors. Furthermore, three of the vectors would provide helpful tools to identify genetic elements of the virus genome involved in splicing regulation.

Alpharetrovirus↗
PubMed1992

The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum.

The nucleotide sequences of the mitochondrial DNA (mtDNA) molecules of two nematodes, Caenorhabditis elegans [13,794 nucleotide pairs (ntp)], and Ascaris suum (14,284 ntp) are presented and compared. Each molecule contains the genes for two ribosomal RNAs (s-rRNA and l-rRNA), 22 transfer RNAs (tRNAs) and 12 proteins, all of which are transcribed in the same direction. The protein genes are the same as 12 of the 13 protein genes found in other metazoan mtDNAs: Cyt b, cytochrome b; COI-III, cytochrome c oxidase subunits I-III; ATPase6, Fo ATPase subunit 6; ND1-6 and 4L, NADH dehydrogenase subunits 1-6 and 4L: a gene for ATPase subunit 8, common to other metazoan mtDNAs, has not been identified in nematode mtDNAs. The C. elegans and A. suum mtDNA molecules both include an apparently noncoding sequence that contains runs of AT dinucleotides, and direct and inverted repeats (the AT region: 466 and 886 ntp, respectively). A second, apparently noncoding sequence in the C. elegans and A. suum mtDNA molecules (109 and 117 ntp, respectively) includes a single, hairpin-forming structure. There are only 38 and 89 other intergenic nucleotides in the C. elegans and A. suum mtDNAs, and no introns. Gene arrangements are identical in the C. elegans and A. suum mtDNA molecules except that the AT regions have different relative locations. However, the arrangement of genes in the two nematode mtDNAs differs extensively from gene arrangements in all other sequenced metazoan mtDNAs. Unusual features regarding nematode mitochondrial tRNA genes and mitochondrial protein gene initiation codons, previously described by us, are reviewed. In the C. elegans and A. suum mt-genetic codes, AGA and AGG specify serine, TGA specifies tryptophan and ATA specifies methionine. From considerations of amino acid and nucleotide sequence similarities it appears likely that the C. elegans and A. suum ancestral lines diverged close to the time of divergence of the cow and human ancestral lines, about 80 million years ago.

Amino Acid Sequence↗
PubMed2003

Identification of new human coding steroid receptor RNA activator isoforms.

SRA is a steroid receptor co-activator which acts as a functional RNA and is classified as belonging to the growing family of functional non-coding RNAs. None of the different SRA transcripts described to date encode a detectable SRA protein following in vitro and in vivo translation experiments. We have identified three new SRA-RNA isoforms differing mainly from the originally cloned SRA by an extended 5(') extremity. These long SRA isoforms, able to encode a stable protein in vitro, led to the production in vivo of a nuclear protein when transfected into the MCF-7 human breast cancer cell line. Reverse-transcription polymerase chain reaction and Western blot analysis of RNA and protein extracts from different breast cancer cell lines confirmed the presence of endogenous coding SRA isoforms and their corresponding proteins. Our results demonstrate that full-length SRA-RNAs likely to encode stable proteins are widely expressed in breast cancer cell lines.

5' Flanking Region↗
PubMed1986

Primary structures of canine pancreatic lipase and phospholipase A2 messenger RNAs.

cDNA clones coding for phospholipase A2 and lipase mRNA have been identified in a full-length cDNA library constructed from canine pancreatic poly (A) + mRNA. Phospholipase A2 mRNA contains 562 nucleotides and codes for a preproenzyme of 146 amino acids (Mr = 16,251) containing a 15 residue signal peptide (MetLysPheLeuValLeuAlaAlaLeuLeuThrValAlaAlaAla), a seven residue activation peptide (GluGlyGlyIleSerProArg), and a 124 residue mature enzyme, phospholipase A2 (79.2% homology with the porcine enzyme). The 5' nontranslated sequence contains a region where eight of nine bases show potential hybridization to the 3' end of 18S ribosomal RNA. Lipase mRNA contains 1,493 nucleotides and codes for a preenzyme with 467 amino acids (Mr = 51,489) which contains a 17 residue signal peptide (MetValSerIleTrpThrIleAlaLeuPheLeuLeuGlyAlaAlaLysAla) and a 450 residue mature enzyme, lipase (75.6% homology with porcine lipase). The 5' noncoding sequences for phospholipase A2 (28 bases) and lipase (34 bases) mRNAs both have an adenosine base three positions preceding the AUG initiation codon but otherwise demonstrate no homology.

Amino Acid Sequence↗
PubMed1986

Complementarity of sequences in low molecular weight RNAs to regions of messenger and ribosomal RNAs.

Total low molecular weight nuclear RNAs of mouse ascites cells have been labeled in vitro and used as probes to search for complementary sequences contained in nuclear or cytoplasmic RNA. From a subset of hybridizing lmw RNAs, two major species of 58,000 and 35,000 mol. wt. have been identified as mouse 5 and 5.8S ribosomal RNA. Mouse 5 and 5.8S rRNA hybridize not only to 18 and 28S rRNA, respectively, but also to nuclear and cytoplasmic poly(A+) RNA. Northern blot analysis and oligo-dT cellulose chromatography have confirmed the intermolecular base-pairing of these two small rRNA sequences to total poly(A+) RNA as well as to purified rabbit globin mRNA. 5 and 5.8S rRNA also hybridize with positive (coding) but not negative (noncoding) strands of viral RNA. Temperature melting experiments have demonstrated that their hybrid stability with mRNA sequences is comparable to that observed for the 5S:18S and 5.8S:28S hybrids. The functional significance of 5 and 5.8S rRNA base-pairing with mRNAs and larger rRNAs is unknown, but these interactions could play important coordinating roles in ribosome structure, subunit interaction, and mRNA binding during translation.

Animals↗
PubMed2002

Molecular phylogenetics and mitochondrial genomic evolution in the chamaeleonidae (Reptilia, Squamata).

A phylogenetic hypothesis for the lizard family Chamaeleonidae is generated from 1503 aligned base positions (883 parsimony-informative) of mitochondrial DNA for specimens representing 59 species (57 ingroup and two outgroup). Sequences are reported for a genomic segment encoding eight transfer RNAs, NADH dehydrogenase component 2 (ND2), and portions of NADH dehydrogenase component 1 (ND1) and cytochrome c oxidase subunit 1 (COI). Newly reported genomic rearrangements and duplications support the hypothesis that mitochondrial gene order and content are destabilized by phylogenetic loss of a functional origin for light-strand replication between the genes encoding tRNA(Asn) and tRNA(Cys). A novel gene order characterizes all sampled Brookesia except B. nasus. Brookesia nasus, the apparent sister taxon of a clade formed by all other Brookesia, has the ancestral gene order but contains a large tandem duplication. An apparently noncoding 220 base pair insertion between the genes encoding ND2 and tRNA(Trp) is reported for Bradypodion tavetanum. Phylogenetic analysis identifies nine clades whose ancestral lineages diverged early in chamaeleonid evolutionary history: (1) Brookesia (possibly excluding B. nasus), (2) Chamaeleo subgenus Chamaeleo (excluding C. namaquensis), (3) Chamaeleo subgenus Trioceros, (4) viviparous Bradypodion, (5) oviparous Bradypodion, (6) genus Furcifer (except F. balteatus), and (7-9) three distinct clades of Calumma. Chamaeleo namaquensis, Brookesia nasus, Furcifer balteatus, Rhampholeon brevicaudatus, and R. spectrum represent ancient lineages dating to approximately the same time. Multiple independent losses and a possible secondary gain of horns are inferred for Trioceros. Viviparity has at least two separate origins in chameleons, one in Bradypodion and

Animals↗
PubMed2005

The generation of recombinant influenza A viruses expressing a PB2 fusion protein requires the conservation of a packaging signal overlapping the coding and noncoding regions at the 5' end of the PB2 segment.

We generated recombinant A/WSN/33 influenza A viruses expressing a PB2 protein fused to a Flag epitope at the N- (Flag-PB2) or C-terminus (PB2-Flag), which replicated efficiently and proved to be stable upon serial passage in vitro on MDCK cells. Rescue of PB2-Flag viruses required that the 5' end of the PB2 segment was kept identical to the wild-type beyond the 34 noncoding terminal nucleotides. This feature was achieved by a duplication of the 109 last nucleotides encoding PB2 between the Flag sequence and the 5'NCR. In PB2 mini-genomes rescue experiments, both the 5' and 3' coding ends of the PB2 segment were found to promote the incorporation of mini-genomes into virions. However, the presence of the Flag sequence at the junction between the 3'NCR and the coding sequence did not prevent the rescue of Flag-PB2 viruses. Our observations define requirements that may be useful for the purpose of engineering influenza RNAs.

Animals↗
PubMed1994

enod40, a gene expressed during nodule organogenesis, codes for a non-translatable RNA involved in plant growth.

Rhizobium meliloti can interact symbiotically with Medicago plants, thereby inducing root nodules. However, certain Medicago plants can form nodules spontaneously, in the absence of rhizobia. A differential screening was performed using spontaneous nodule versus root cDNAs from Medicago sativa ssp. varia. Transcripts of a differentially expressed clone, Msenod40, were detected in all differentiating cells of nodule primordia and spontaneous nodules, but were absent in fully differentiated cells. Msenod40 showed homology to a soybean early nodulin gene, Gmenod40, although no significant open reading frame (ORF) or coding capacity was found in the Medicago sequence. Furthermore, in the sequences of cDNAs and a genomic clone (Mtenod40) isolated from Medicago truncatula, a species containing a unique copy of this gene, no ORFs were found either. In vitro translation of purified Mtenod40 transcripts did not reveal any protein product. Evaluation of the RNA secondary structure indicated that both msenod40 and Gmenod40 transcripts showed a high degree of stability, a property shared with known non-coding RNAs. The Mtenod40 RNA was localized in the cytoplasm of cells in the nodule primordium. Infection with Agrobacterium tumefaciens strains bearing antisense constructs of Mtenod40 arrested callus growth of Medicago explants, while overexpressing Mtenod40 embryos developed into teratomas. These data suggest that the enod40 genes might have a role in plant development, acting as 'riboregulators', a novel class of untranslated RNAs associated with growth control and differentiation.

Amino Acid Sequence↗
PubMed1999

Specific in vitro association between the hepatitis C viral genome and core protein.

Little is known about the molecular interactions required for hepatitis C virion assembly. The 5' noncoding region (5'NCR) of the RNA genome is highly conserved and has extensive secondary structure. The highly basic core protein is rich in arginine and lysine residues. We postulate that a specific interaction between these structures may be important for virion assembly. Using an RNA gel mobility shift assay, a specific interaction has been demonstrated between the RNA of the 5'NCR and recombinant core protein. Proteins from other regions of the virus do not interact with the viral RNA. The interaction is inhibited competitively by unlabelled sense polarity RNA, but antisense 5'NCR RNA and nonspecific RNAs compete only at much higher concentrations. These data suggest that there is a specific interaction between the 5'NCR of the hepatitis C virus (HCV) genome and HCV core protein. This interaction may be important for the specific encapsidation of the viral genome during HCV replication.

5' Untranslated Regions↗