Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “small RNA”

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 397 records · Page 22Linked to original sources
PubMed1987

Reverse-transcribed pseudogenes of U1 small nuclear RNA presumably amplified in the rat genome together with the flanking region.

We have examined 25 independent rat genomic clones each of which contains a U1 RNA gene or a pseudogene. We have found five clones whose restriction maps are identical with or overlapping one another. These clones contain sequences which are co-linear with that of U1 RNA except for one or two nucleotides (nt). They also contain 21-23-nt poly(A) stretches immediately after U1 RNA homology. In addition, the U1 RNA-poly(A) regions are surrounded by the same direct repeat sequences. Therefore, they seem to be pseudogenes which have been generated by the reverse transcription of poly(A)-tailed U1 RNA followed by the insertion of the transcript into the genome. Furthermore, conservation of the sequences extends over at least 18 kb of the flanking sequences. This suggests a family of conserved reverse-transcribed pseudogenes, which implies amplification of an original pseudogene. It is also suggested that the target sequence without insertion of a U1 RNA sequence has been amplified. The mechanisms for the amplification and sequence conservation are discussed.

Animals↗
PubMed1987

Properties of a distal regulatory element controlling transcription of the U2 small nuclear RNA.

The upstream region of human U2 genes contains a distal transcriptional control element, previously mapped between nucleotide (nt) positions -198 and -258 (Westin et al., 1984b). In the present study we show that it resembles transcriptional enhancers in being active even from a distance of 1.4 kb. However, in contrast to most other enhancers it functions unidirectionally in Xenopus laevis oocytes. The distal control element was further mapped by construction of truncated templates for U2 RNA transcription. The results showed that templates, which extended to either of nt positions -214 and -218, were inactive. Templates comprising sequences to nt positions -225 or -226 displayed an intermediate level of activity whereas templates which extend to nt -258 were fully active. It has previously been shown that the human U2 enhancer contains binding sites for the so-called octamer binding protein and for transcription factor Sp1 [Janson et al., Nucl. Acids Res. 15 (1987) 4997-5016]. The partially active templates included one binding site for the octamer binding protein, whereas the fully active template included, in addition, two Sp1 binding sites, thus indicating that these transcription factors are of importance for U2 RNA transcription. The structure of the enhancer was also probed by inserting a pair of complementary synthetic oligodeoxynucleotides which represented the region between nt positions -235 and -215 into a truncated template which lacked the enhancer. The oligodeoxynucleotide enhanced transcription to approximately 50% of the level obtained with templates extending to position -258.

Animals↗
PubMed1992

A transcriptional analysis of the gene encoding mouse U7 small nuclear RNA.

Expression of the U7 gene, encoding mouse U7 snRNA, following microinjection into Xenopus oocytes is both accurate and efficient, giving rise to mature U7 snRNA and a precursor with an 8-nucleotide (nt) 3' extension. The mouse U7 gene promoter, which is similar to that of the vertebrate major U genes comprising a DSE, a PSE and a 3' box, with the same spatial arrangement, is as efficient as the Xenopus U2 gene promoter in this assay. A deletion analysis of the mouse U7 gene identified sequences downstream from the 3' box, within the region (nt +74 to +196), which seem to have a negative regulatory effect upon the frequency of transcription initiation and are also required for accurate 3' end formation. Sequences in the nt -1699 to -431 region also seemed to have a negative effect on the level of transcription. In addition, sequences upstream from the PSE, within the nt -65 to -421 region, are necessary for accurate and efficient synthesis of mature U7 snRNA. Finally, the mouse U7 snRNA may not form a functional snRNP in Xenopus oocytes due to defective snRNP assembly and/or nuclear import.

Animals↗
PubMed2005

Modulation of human dUTPase using small interfering RNA.

Deoxyuridine triphosphate nucleotidohydrolase (dUTPase) is responsible for maintaining low intracellular levels of dUTP, thus preventing the incorporation of dUTP into DNA. A 21 bp double-stranded RNA molecule (siRNAdUT3) targeted against motif 3 of human dUTPase resulted in a time- and dose-dependent decrease in dUTPase activity in transfected cells. dUTPase activity was reduced approximately 95+/-5% in all cell lines tested 48 h after transfection with 2 microg siRNAdUT3 and it was maintained at this decreased level for at least 72 h. Down-regulation of dUTPase resulted in a significant increase in intracellular dUTP and a decreased proliferation of the transfected cells. Therefore, we conclude that dUTPase activity/expression can be down-regulated using siRNA specifically targeted to dUTPase mRNA and that this approach can be used to elucidate the role of dUTPase in DNA metabolism, as well as, to determine whether dUTPase is a valid target for drug development.

Cell Line, Tumor↗
PubMed2004

Suppression of human Mnk1 by small interfering RNA increases the eukaryotic initiation factor 4F activity in HEK293T cells.

Short-interfering RNAs (siRNAs) have proved to be a useful tool in studying gene function in plants, invertebrates and mammalian systems. Herein, we report the use of siRNAs for targeting the human MAP kinase-interacting kinase Mnk1 gene. This study demonstrates the efficacy of the designed siRNA in silencing Mnk1 in the human cell line HEK293T and shows that Mnk1 suppression decreases eukaryotic initiation factor 4E phosphorylation without causing any change in global protein synthesis rate and cell proliferation. Interestingly, suppression of Mnk1 results in a significant increase in eukaryotic initiation factor 4F complex formation after 72 h of transfection.

Animals↗
PubMed2004

Suppression of caspase-3-dependent proteolytic activation of protein kinase C delta by small interfering RNA prevents MPP+-induced dopaminergic degeneration.

The cellular mechanisms underlying the neurodegenerative process in Parkinson's disease are not well understood. Using RNA interference (RNAi), we demonstrate that caspase-3-dependent proteolytic activation of protein kinase Cdelta (PKCdelta) contributes to the degenerative process in dopaminergic neurons. The Parkinsonian toxin MPP(+) activated caspase-3 and proteolytically cleaved PKCdelta into catalytic and regulatory subunits, resulting in persistent kinase activation in mesencephalic dopaminergic neuronal cells. The caspase-3 inhibitor Z-DEVD-FMK and the caspase-9 inhibitor Z-LEHD-FMK effectively blocked MPP(+)-induced PKCdelta proteolytic activation. To characterize the functional role of PKCdelta activation in MPP(+)-induced dopaminergic cell death, RNAi-mediated gene knockdown was performed. Among four siRNAs designed against PKCdelta, two specifically suppressed PKCdelta expression. The application of siRNA abolished the MPP(+)-induced PKCdelta activation, DNA fragmentation, and tyrosine hydroxylase (TH)-positive neuronal loss. Together, these results suggest that proteolytic activation of PKCdelta may be a critical downstream event in the degenerative process of Parkinson's disease.

1-Methyl-4-phenylpyridinium↗
PubMed2002

Small interfering RNA and gene silencing in transgenic mice and rats.

After short duplexes of synthetic 21-23 nt RNAs (siRNA) were reported to be effective in silencing specific genes, a vector-based approach for siRNAs was demonstrated in mammalian cultured cell lines. However, the effect of RNA interference (RNAi) on various differentiated cells in live animals remains unknown. In this report, we demonstrate that transgenically supplied siRNA can silence ubiquitously expressed enhanced green fluorescent protein in every part of the mouse and rat body. These results suggest that transgenic RNAi could function as an alternative method of gene silencing by applying homologous recombination to embryonic stem (ES) cells, and should be successful even in species where ES cell lines remain unestablished.

Animals↗
PubMed1985

Sequences required for 3' end formation of human U2 small nuclear RNA.

Xenopus oocytes injected with human U2 snRNA genes synthesize mature U2 as well as a U2 precursor with about 10 extra 3' nucleotides (human pre-U2 RNA). Formation of the pre-U2 3' end requires a downstream element located between position +16 and +37 in the U2 3'-flanking sequence. The distance between this element and the U2 coding region can be increased without affecting formation of the pre-U2 3' end. When the natural sequence surrounding the pre-U2 3' end is changed, novel 3' ends are still generated within a narrow range upstream from the element. The 3' terminal stem-loop of U2 snRNA is not required for pre-U2 3' end formation. A sequence within the 3' element (GTTTN0-3AAAPuNNAGA) is conserved among snRNA genes transcribed by RNA polymerase II. Our results suggest that the 3' ends of pre-U2 RNA and histone mRNA may be generated by related but distinct RNA processing mechanisms.

Animals↗
PubMed2003

Small interfering RNA inhibits hepatitis B virus replication in mice.

Current therapies for chronic hepatitis B virus (HBV) infection are limited in their effect on viral gene expression and replication. Recent reports have shown that RNA interference can be induced in mammalian cells by short interfering RNA duplexes (siRNA). Here we studied the effects of an HBV-specific 21-bp siRNA targeted to the surface antigen region (HBsAg), where three major viral mRNAs overlap, on HBV gene expression and replication both in a cell culture system and in a mouse model for HBV replication. Transfection of siRNA into HepG2.2.15 cells, which constitutively produce HBV particles, caused a significant reduction in viral RNA production that was accompanied by a >80% drop in the secretion of viral HBsAg and HBeAg into the medium. The effect of RNAi was tested in vivo in a mouse model that we have developed for HBV infection, which entails hydrodynamic injection of a plasmid bearing the HBV genome into tail veins of mice. Injection of the HBV plasmid induces viral replication and generation of HBV viral particles detectable in the mouse sera. Co-injection of the HBV plasmid together with siRNA caused a significant inhibition in the level of viral transcripts, viral antigens, and viral DNA detected in the livers and sera of the treated mice relative to control animals. Results suggest that siRNA is capable of inhibiting HBV replication in vivo and thus may constitute a new therapeutic strategy for HBV infection.

Animals↗
PubMed2003

Identification and characterization of U1 small nuclear RNA genes from two crustacean isopod species.

Four different units containing three variants of the U1 snRNA gene have been identified in the genome of Asellus aquaticus and only one unit has been identified in the genome of Proasellus coxalis. All four identified U1 snRNA genes can be folded according to the proper secondary structure and possess the functionally useful conserved sequences. Moreover, in the 3 flanking regions, all genes present both the 3 box, a conserved sequence required for 3 processing of mature snRNA, and a polyadenylation signal which is unusual for these genes. The PCR products were used as probes in fluorescent in-situ hybridization (FISH) experiments to locate them on chromosomes of A. aquaticus and P. coxalis.

Animals↗
PubMedDate not supplied

Compensatory mutations suggest that base-pairing with a small nuclear RNA is required to form the 3' end of H3 messenger RNA.

Processing of the 3' end of sea urchin H3 histone pre-mRNA requires conserved sequence elements and the presence of U7 snRNA. A mutation in the conserved CAAGAAGA sequence of the H3 pre-mRNA that renders 3' processing of this precursor defective is shown to be suppressed by a compensatory change in the U7 snRNA, restoring the base-pairing potential of the two RNAs. RNA-RNA contacts between these two molecules appear to be an essential feature of the 3' processing reaction.

Animals↗
PubMed2005

Small interfering RNA targeting Raf-1 inhibits tumor growth in vitro and in vivo.

Raf-1 is a cytosolic serine-threonine kinase that plays an important role in tumor cell growth, proliferation, and apoptosis. Upregulated Raf-1 activity has also been implicated in tumor angiogenesis and metastasis. In this study, we used a promising new RNA interfering technology that targets Raf-1 mRNA both in vitro and in vivo. We initially found that Raf-1 siRNA markedly reduced Raf-1 mRNA in MDA-MB-435 cells in vitro by approximately 75% compared to control siRNA treatment groups. Raf-1 siRNA also reduced cell number by inducing apoptosis in a number of cell lines including HUVEC, MDA-MB-435, and C6 cells. After screening several histidine-lysine polymers in complex with Raf-1 siRNA to reduce tumor growth, we further evaluated the efficacy of this siRNA in complex with the optimal histidine-lysine carrier to reduce the tumor growth in vivo. MDA-MB-435 xenografts treated by intratumoral injections of Raf-1 siRNA were significantly reduced compared with the control groups. By the fourth measurement, tumor growth was reduced by nearly 60% in the Raf-1 siRNA treatment group compared with the untreated group (P < .02). Taken together, our data provide evidence that Raf-1 siRNA may be an effective strategy for reducing tumor growth.

Animals↗