PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “RNA Caps”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 433 records · Page 24Linked to original sources
PubMed2002

Sequence-specific interaction of U1 snRNA with the SMN complex.

The survival of motor neurons (SMN) protein complex functions in the biogenesis of spliceosomal small nuclear ribonucleoprotein particles (snRNPs) and prob ably other RNPs. All spliceosomal snRNPs have a common core of seven Sm proteins. To mediate the assembly of snRNPs, the SMN complex must be able to bring together Sm proteins with U snRNAs. We showed previously that SMN and other components of the SMN complex interact directly with several Sm proteins. Here, we show that the SMN complex also interacts specifically with U1 snRNA. The stem--loop 1 domain of U1 (SL1) is necessary and sufficient for SMN complex binding in vivo and in vitro. Substitution of three nucleotides in the SL1 loop (SL1A3) abolishes SMN interaction, and the corresponding U1 snRNA (U1A3) is impaired in U1 snRNP biogenesis. Microinjection of excess SL1 but not SL1A3 into Xenopus oocytes inhibits SMN complex binding to U1 snRNA and U1 snRNP assembly. These findings indicate that SMN complex interaction with SL1 is sequence-specific and critical for U1 snRNP biogenesis, further supporting the direct role of the SMN complex in RNP biogenesis.

Animals↗
PubMed2002

Discontinuous and non-discontinuous subgenomic RNA transcription in a nidovirus.

Arteri-, corona-, toro- and roniviruses are evolutionarily related positive-strand RNA viruses, united in the order Nidovirales. The best studied nidoviruses, the corona- and arteriviruses, employ a unique transcription mechanism, which involves discontinuous RNA synthesis, a process resembling similarity-assisted copy-choice RNA recombination. During infection, multiple subgenomic (sg) mRNAs are transcribed from a mirror set of sg negative-strand RNA templates. The sg mRNAs all possess a short 5' common leader sequence, derived from the 5' end of the genomic RNA. The joining of the non-contiguous 'leader' and 'body' sequences presumably occurs during minus-strand synthesis. To study whether toroviruses use a similar transcription mechanism, we characterized the 5' termini of the genome and the four sg mRNAs of Berne virus (BEV). We show that BEV mRNAs 3-5 lack a leader sequence. Surprisingly, however, RNA 2 does contain a leader, identical to the 5'-terminal 18 residues of the genome. Apparently, BEV combines discontinuous and non-discontinuous RNA synthesis to produce its sg mRNAs. Our findings have important implications for the understanding of the mechanism and evolution of nidovirus transcription.

Base Sequence↗
PubMed2003

The proline-rich homeodomain protein, PRH, is a tissue-specific inhibitor of eIF4E-dependent cyclin D1 mRNA transport and growth.

The translation initiation factor eIF4E is involved in the modulation of cellular growth. In the nucleus, where eIF4E is associated with PML nuclear bodies, eIF4E mediates nucleocytoplasmic transport of specific transcripts, and this contributes to its transformation activity. Surprisingly, we found that a trans cription factor, the proline-rich homeodomain protein PRH, is a negative regulator of eIF4E in myeloid cells, interacting with eIF4E through a conserved binding site typically found in translational regulators. Through this interaction, PRH inhibits eIF4E-dependent mRNA transport and subsequent transformation. These activities of PRH are independent of its transcriptional functions. Further, we found that 199 homeodomain proteins contain potential eIF4E-binding sites. Thus, there could be many tissue-specific regulators of eIF4E. These findings provide a model for regulation of a general factor, eIF4E, in tissue- specific contexts, and suggest that its regulation is important in differentiation and development.

Active Transport, Cell Nucleus↗
PubMed1987

Hsp28stl: a P-element insertion mutation that alters the expression of a heat shock gene in Drosophila melanogaster.

We have identified and cloned a mutant allele of the small heat shock gene Hsp28 of Drosophila melanogaster. This allele, which we have called Hsp28stl, produces small amounts of a single aberrantly large, heat-inducible transcript in heat-shocked flies, while a normal-sized Hsp28 transcript is present only in fertile females. No Hsp28 transcript at all is detected in mutant prepupae, a stage when wildtype flies show high levels of Hsp28 RNA. We have cloned the Hsp28stl allele, and have found that a 1.3-kb defective P-element is present 5' to Hsp28 in the mutant line. The site of P-element insertion lies between the Hsp28 "TATA box" sequence and the Hsp28 RNA cap site; in contrast to previously described P-element insertions, the element at Hsp28stl is flanked by a two base pair duplication of the insertional target sequence. The results suggest that this insert may separate elements regulating heat-inducible and developmental expression of Hsp28, leading to the different patterns of transcription observed.

Alleles↗
PubMed2001

Two related proteins, Edc1p and Edc2p, stimulate mRNA decapping in Saccharomyces cerevisiae.

The major mRNA decay pathway in Saccharomyces cerevisiae occurs through deadenylation, decapping, and 5' to 3' degradation of the mRNA. Decapping is a critical control point in this decay pathway. Two proteins, Dcp1p and Dcp2p, are required for mRNA decapping in vivo and for the production of active decapping enzyme. To understand the relationship between Dcp1p and Dcp2p, a combination of both genetic and biochemical approaches were used. First, we demonstrated that when Dcp1p is biochemically separated from Dcp2p, Dcp1p was active for decapping. This observation confirmed that Dcp1p is the decapping enzyme and indicated that Dcp2p functions to allow the production of active Dcp1p. We also identified two related proteins that stimulate decapping, Edc1p and Edc2p (Enhancer of mRNA DeCapping). Overexpression of the EDC1 and EDC2 genes suppressed conditional alleles of dcp1 and dcp2, respectively. Moreover, when mRNA decapping was compromised, deletion of the EDC1 and/or EDC2 genes caused significant mRNA decay defects. The Edc1p also co-immunoprecipitated with Dcp1p and Dcp2p. These results indicated that Edc1p and Edc2p interact with the decapping proteins and function to enhance the decapping rate.

Alleles↗
PubMed1982

Sea urchin small nuclear RNA genes are organized in distinct tandemly repeating units.

The genes coding for the two major small nuclear RNAs in the sea urchin are organized in independent tandem repeating units. The small nuclear RNAs, N1 and N2 were purified from gastrula embryos of Lytechinus variegatus. These RNAs are analogous to the U series of RNA in mammalian cells as judged by their identical 5' termini and the sequence homology of the N1 urchin RNA and U1 mouse RNA. These RNAs were polyadenylated with E. Coli adenylate transferase. A 32PO4 labeled copy of each RNA was made with RNA-dependent DNA polymerase. This copy was used to probe the gene organization of these RNAs by hybridizing to restriction enzyme digests of sperm DNA. Each of these RNAs is coded in a tandemly repeated cluster (at least 30 kb) with a repeat length of 1100-1400 bases. The N1 and N2 clusters are distinct. The N1 repeat has been cloned and the repeating organization confirmed with the cloned gene.

Animals↗
PubMed1985

Affinity electrophoresis for monitoring terminal phosphorylation and the presence of queuosine in RNA. Application of polyacrylamide containing a covalently bound boronic acid.

An affinity electrophoretic method has been developed to study the state of terminal phosphorylation of RNAs and the presence of the hypermodified base Q in tRNA. It is based on the copolymerization of acryloylaminophenylboronic acid into standard polyacrylamide gels and the interaction of this derivative with free cis-diol groups present in the RNA. In the case of terminal phosphorylation, free ribose groups are present either as such, or may be introduced by enzymatic reactions specific for a particular phosphorylation pattern (e.g. using T4 RNA ligase or guanylyltransferase). Additionally, tRNA species containing the Q base may be resolved from Q-lacking tRNAs by boronate affinity electrophoresis. The introduction of a non-destructive, one-step electrophoretic procedure not only offers an alternative to classical analytical methods, but also provides a means of isolating such populations of RNAs for which other methods are unavailable or are less convenient.

Acrylamide↗
PubMed1986

Sequence of 2,617 nucleotides from the 3' end of Newcastle disease virus genome RNA and the predicted amino acid sequence of viral NP protein.

DNA fragments complementary to the Newcastle disease virus genome (strain D26) were cloned and sequenced. The sequence of 2,617 nucleotides from the 3' end of the genome was determined and an open reading frame (OP-1) consisting of 1,467 nucleotides, most likely encoding NP protein, was found in this region. This was followed by a second unfinished open reading frame (OP-2) of at least 729 nucleotides which continued beyond the 2,617th nucleotide. Another relatively short (312 nucleotides long) open reading frame (OP-2') was found overlapping with OP-2, but its significance is still unclear. The amino acid sequence deduced from the nucleotide sequence of OP-1 showed a moderate homology to that of the NP protein of Sendai virus in the central portion of the peptide. The leader sequence of 53 nucleotides was also identified. The 5' end of mRNAs synthesized in the infected cells was analyzed and found to be m7GpppA, suggesting that the transcription of viral mRNAs starts with A, but not with G residue.

Amino Acid Sequence↗
PubMed1986

The control of herpes simplex virus type-1 late gene transcription: a 'TATA-box'/cap site region is sufficient for fully efficient regulated activity.

The transcriptional programme of herpes simplex virus type 1 (HSV-1) is organised into three principle phases; immediate-early (IE), early (E) and late. The appearance of IE gene products provides the switch for E transcription. Abundant expression of late genes requires viral DNA replication. There is some overlap between E and late genes according to their degree of dependence on DNA replication. The pattern of expression of gene US11 is regulated with 'true-late' kinetics (Johnson et al., 1986). In a transient assay system, regulation of a plasmid-borne US11 promoter mimics its viral counterpart, and has a similar dependence on DNA replication for abundant expression. Using plasmids which contain a functional HSV-1 origin of replication (ORIS), we have identified the sequence requirements for the expression of late genes. All DNA sequence elements necessary for fully efficient regulated expression of US11 lie within 31 bp of the RNA cap sites; therefore it appears that a late gene promoter consists only of a proximal 'TATA-box' and cap-site region. We tested this hypothesis by removing the distal upstream region of the gD promoter (which is required for its normal regulation as an early promoter) and linking this truncated promoter to ORIS. This resulted in the conversion of gD promoter regulation to late gene kinetics during virus superinfection. The implications of these results for the mechanisms of HSV gene regulation are discussed.

Base Sequence↗
PubMed1986

Transcription signals for stable RNA genes in Methanococcus.

A previous survey of upstream sequences of tRNA genes from the archaebacterium Methanococcus vannielii has revealed that there are two boxes of sequence homology: A box "A" of about 20 conserved nucleotides at a distance of 30 to 49 basepairs upstream from the gene and a box "B" 18 to 19 nucleotides downstream from box "A" (Wich, G., Sibold, L., and Böck, A. (1985) System. Appl. Microbiol. (in press). Nuclease S1 mapping experiments were carried out with two of these tRNA transcriptional units and with a ribosomal RNA operon, to determine whether these consensus sequences have a function in the initiation of transcription. Use was made of the fact that cells from Methanococcus accumulate primary transcript and processing intermediates of ribosomal RNA under conditions of protein synthesis inhibition. The following results were obtained: (i) Transcription in all three systems starts at the G within the conserved trinucleotide TGC of box "B". Since the box "B" motif, 5'TGCaagT3', also occurs at the site of transcription initiation of protein encoding genes, both in methanogenic and halophilic organisms, it appears to constitute a frequently used transcription start signal within these archaebacterial groups. (ii) The box "A" motif occurs with constant spacing, relative to box "B", in all 10 tRNA and ribosomal RNA transcriptional units investigated from Methanococcus. Since it is not present in the leader region of genes coding for proteins, it seems to function as a specific element which is required for the expression of genes for stable RNA. (iii) Termination of transcription of the ribosomal RNA operon from Methanococcus occurs at a distinct T within an oligo-T stretch immediately downstream from the 3'-terminal 5S RNA gene. This signal occurs in all 3'-flanking regions of transcriptional units for stable RNA from the Methanococcus strains studied. Termination signals for stable RNA genes in Methanococcus appear to be similar with those of stable RNA genes in eukaryotes. (iv) By nuclease S1 mapping a recognition site was identified for a processing enzyme involved in the maturation of preribosomal RNA.

Chromosome Mapping↗
PubMed1986

Homologies of nucleotide sequences in the 5'-end regions of two developmentally regulated genes of Sarcophaga peregrina.

In the previous paper we demonstrated that the storage protein gene and 25-kDa protein gene are expressed sequentially in the fat body of middle third-instar Sarcophaga peregrina larvae. In this paper, we showed that the expressions of these two genes are regulated at the transcriptional level, and searched for homologous nucleotide sequences in the two genes in the vicinity of their 5'-ends, assuming that these two genes are regulated by a common mechanism. We selected 9 homologous sequences and found that most of them were distributed in two clusters located between positions -400 and +1. We identified an SV40 enhancer core segment-like sequence in the nontranslated region of the first exons of both genes, which might explain the efficient transcriptions of these two genes.

Animals↗
PubMed1988

Unusual branch point selection involved in splicing of the alternatively processed Calcitonin/CGRP-I pre-mRNA.

To study splice site selection in alternative RNA processing we used the human Calcitonin/CGRP-I (CALC-I) gene. Expression of the CALC-I gene in thyroid C-cells results predominantly in calcitonin (CT) mRNA (containing exons 1 to 4) whereas CGRP-I mRNA (containing exons 1,2,3,5 and 6) is the exclusive product in particular nerve cells. We previously reported that a model precursor RNA containing the exon 3 to exon 5 region is predominantly processed into CGRP-I mRNA in vitro using nuclear extracts of three different cell types. To study CT specific processing in Hela cell nuclear extracts we have used precursor RNAs corresponding to the exon 3 to exon 4 region containing only CT specific processing signals. The results revealed the usage of a uridine residue 23 nucleotides upstream of the 3' splice site as the major site of lariat formation in CT specific splicing. The implications of this finding for the alternative, tissue specific processing of the CALC-I pre-mRNA and for branch point selection in general are discussed.

Calcitonin↗
PubMed1994

Translation of 2'-modified mRNA in vitro and in vivo.

2'-Fluoro- and 2'-amino-2'-deoxynucleoside triphosphates have been used for in vitro transcription of 2'-modified luciferase mRNA. The 2'-modified deoxynucleoside-containing transcripts were tested for the expression of luciferase in X.Laevis oocytes as well as in rabbit reticulocyte lysate. Only 2'-fluoro-2'-deoxy-adenosine-modified mRNA gave rise to luciferase as shown by SDS gel as well as by enzyme activity measurements in vivo as well as in vitro. 2'-Fluoro-2'-deoxy-pyrimidine nucleoside-modified mRNA did not give rise to luciferase activity. However, they directed incorporation of 35S-labeled methionine into peptide fragments in rabbit reticulocyte lysate indicating premature termination of translation. No or only extremely little of such incorporation could be detected with 2'-amino modified transcripts.

Animals↗
PubMed1996

mRNA turnover in yeast promoted by the MATalpha1 instability element.

The decay rates of eukaryotic transcripts can be determined by sequence elements within an mRNA. One example of this phenomenon is the rapid degradation of the yeast MATalpha1 mRNA, which is promoted by a 65 nt segment of its coding region termed the MATalpha1 instability element (MIE). The MIE is also capable of destabilizing the stable PGK1 transcript. To determine how the MIE accelerates mRNA turnover we examined the mechanism of degradation of the MATalpha1 transcript. These experiments indicated that the MATalpha1 mRNA was degraded by a deadenylation-dependent decapping reaction which exposed the transcript to 5'-->3' exonucleolytic digestion. Deletion of the MIE from the MATalpha1 mRNA decreased the rate at which this mRNA was decapped. In contrast, insertion of the MIE into the PGK1 transcript caused an increase in the rate of deadenylation of the resulting chimeric mRNA. These observations suggest that the MIE promotes rapid mRNA decay by increasing the rates of deadenylation and decapping, with its primary effect on mRNA turnover depending on additional features of a given transcript. These results also strengthen the hypothesis that deadenylation-dependent decapping is a common pathway of mRNA decay in yeast and indicate that an instability element within the coding region of an mRNA can effect nucleolytic events that occur at both the 5'- and 3'-ends of an mRNA.

Adenine↗