SEARCH · Search PubMed

Results for “RNA modifications”

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.

SourceResearch connectionFrom yearThrough year

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

At least 271 records · Page 15Linked to original sources

PubMed1979

Mapping of RNA by a modification of the Berk-Sharp procedure: the 5' termini of 15 S beta-globin mRNA precursor and mature 10 s beta-globin mRNA have identical map coordinates.

We have used a modification of the Berk-Sharp technique to determine that the 5' termini of the mouse 15 S beta-globin precursor and the mature mRNA have identical map coordinates. The modification involves the use of 5' (or 3') terminally labeled probes; it allows the detection of the precursor in the presence of excess mature mRNA.

Animals↗

PubMed1997

SnoRNAs as tools for RNA cleavage and modification.

Eukaryotic small nucleolar RNAs (snoRNAs) influence rRNA synthesis at two stages: nucleolytic processing and selection of nucleotides to be ribose methylated (Nm) or converted to pseudouridine (psi). The two modification functions and some processing activities involve direct base pairing of snoRNA with rRNA. In addition to rRNA-targeting sequences, snoRNA function depends on the presence of conserved box elements involved in snoRNA synthesis and localization. The present investigation is directed at using snoRNAs as tools for two purposes: 1) introducing nucleotide modifications into novel sites in rRNA and other snoRNAs, and: 2) targeting nucleolar RNAs for destruction using snoRNA:ribozyme chimers ('snorbozymes'). Early results demonstrate that snoRNAs can be used for both applications.

Cell Nucleolus↗

PubMed1991

Developmental regulation of covalent modification of double-stranded RNA during silkmoth oogenesis.

Follicular cells of the silkmoth Bombyx mori contain an enzymatic activity that modifies RNA duplexes in vitro. The modifying activity converts adenosine residues into inosine in duplex but not single-stranded RNA and mediates the partial unwinding of the complement strands. Because of the modification, the RNA loses its ability to form perfect duplexes with its complement upon reannealing in vitro. The modifying enzyme is localized in the cytoplasm of follicular cells and its activity is modulated in a developmentally regulated manner. In contrast, follicular nuclei contain an activity that inhibits the modification and unwinding of duplex RNA. The modifying activity is also present in the cytoplasm of unfertilized oocytes and its accumulation during oogenesis parallels that of the follicular cells. Examination of an established silkmoth cell line of ovarian origin revealed that, in contrast to the situation with follicular cells, the modifying activity has an exclusive nuclear localization. The cytoplasmic fraction of these cells is not only devoid of modifying activity but, as is the case with the nuclear fraction of follicular cells, contains an activity that inhibits duplex RNA modification and unwinding. We conclude that the modification promoting and inhibiting activities are not restricted to a single cell type and that their compartmentalization is developmentally regulated.

Adenosine↗

PubMed1978

A study of the thermal unfolding of Escherichia coli phenylalanine transfer RNA by chemical modification at elevated temperatures.

Escherichia coli tRNAPhe was modified by 3 M sodium bisulphite pH 6.0 for 24 h in the temperature range 25 degrees C (x 5 degrees C) to 55 degrees C and in the absence of added magnesium ions. The sites and extents of conversion of cytidines to uridine occurring at each temperature were determined by fingerprinting. The new sites of cytidine modification found at higher reaction temperatures were assumed to arise from breakage of secondary and tertiary structure hydrogen bonds involving cytidine residues. From these data, we conclude that hydrogen bonds within the 'complex core' of the tRNA (including the base pairs G-10 . C-25, C-11 . G-24 and C-13 . G-21 within the dihydrouridine stem and the tertiary structure base pair G-15 . C-48 melt at a lower temperature than the tertiary structure hydrogen bonds between G-19 in the dihydrouridine loop and C-56 in the TpsiC loop.

Base Sequence↗

PubMed1985

Effect of cyclosporin A on the early activation of human T helper lymphocytes: inhibition of RNA-synthesis and modification of the expression of activation antigens.

The ability of cyclosporin A (CS-A) to inhibit induced lymphocyte activation and to modify expression of membrane receptors was assessed on human T helper cells. Flow cytometric cell cycle analyses of acridine orange-stained cells showed that CS-A (0.5 micrograms/ml) inhibits the G0-G1 activation process of a substantial proportion of PHA- and Con A-stimulated lymphocytes. The expression of Tac, OKT9 and 4F2 antigens (previously shown to be expressed or increased on activated cells) was investigated by immunofluorescence. Fewer cells expressed the Tac and OKT9 antigens after activation in presence of CS-A, but the percentage of 4F2-positive cells remained unchanged. Analyses of receptor densities measured by fluorescence intensity revealed for all three investigated antigens a decreased receptor density on positive cells in presence of CS-A. Thus, CS-A not only inhibited cell activation (G0-G1 transition) and the expression of Tac, OKT9 and 4F2 antigens, but it also diminished the number of Tac, OKT9 and 4F2 antigens per cell. Assessing specifically the activation of OKT4 (helper) and OKT8 (cytotoxic) cells after 24 h, either by double-fluorescence or by cell fractionation with anti-OKT4 or anti-OKT8 antibodies plus complement, showed that preferentially OKT4 cell activation as well as expression of Tac and OKT9 antigens on those cells was inhibited in the presence of CS-A.

Antibodies, Monoclonal↗

PubMed2007

Optimization of ribonucleic acid detection from archival Guinea pig temporal bone specimens.

HYPOTHESIS: The choice of ribonucleic acid (RNA) isolation protocol coupled with modifications to RNA extraction and detection procedures may result in a more reliable method to detect gene expression in archived temporal bones. BACKGROUND: A large number of archival temporal bones exist. Retrospective analysis of these specimens using techniques of RNA extraction will greatly enrich our understanding of the pathophysiology of specific otologic diseases. However, archival human temporal bones are aged and embedded in paraffin or celloidin, rendering isolation and manipulation of nucleic acid in preserved specimens difficult, especially as it pertains to RNA degradation. Despite some reports of moderate success in the recent past, RNA isolation and gene expression using polymerase chain reaction (PCR) analysis continues to be challenging and unreliable. Archival guinea pig temporal bone specimens were used to develop and optimize a protocol for RNA extraction and gene expression analysis using PCR and quantitative PCR methods. The genes amplified comprise housekeeping genes and genes associated with the glutamate pathway. METHODS: Archival celloidin-embedded guinea pig temporal bones were collected from the senior author's collection of experimental hydropic inner ear specimens. RNA from this tissue was extracted using the protocol described previously in 16animals and using a modified trizol extraction technique in 10 animals. Gene expression analysis was performed on the extracted RNA. Analysis included two housekeeping genes, GAPDH and 18S, as well as three mediators of the glutamate pathway, glutamate aspartate transporter, glutamate synthetase, and inducible nitric oxide synthase. RESULTS: Compared with the standard extraction protocol, the trizol-based extraction technique showed greater reliability and reproducibility of RNA detection. The housekeeping gene GAPDH or 18S was detected in 7 of 36 attempts with the standard protocol versus 9 of 9 using the modified extraction method (P < 0.001). The gene of interest, glutamate aspartate transporter, was detected in 3 of 26 attempts with the standard protocol versus 12 of 13 attempts using the modified extraction method (P < 0.001). Quantification of messenger RNA levels was then achieved using quantitative PCR methods. CONCLUSION: Improved reliability for detection of gene expression and demonstration of reproducibility were accomplished by modification of RNA extraction technique and standard reverse transcriptase PCR protocol. In addition, we also showed that gene expression from archival material can be quantified by real-time PCR.

Animals↗

PubMed1975

Ultrastructural alterations and modifications of nuclear RNA of rat liver by the combined action of thioacetamide and aflatoxin.

When aflatoxin is administered to thioacetamide-treated rats, the synthesis of nuclear RNA not only stops but the RNA that had accumulated in the nuclei by thioacetamide action disappears, probably by degradation "in situ" as none appears in the cytoplasm. Morphologically, the lesions provoked by aflatoxin add to those caused by thioacetamide. In the gigantic nucleoli that develop upon exposure to thioacetamide, aflatoxin provokes atypical segregations that result in the formation of larger and larger spaces in the nucleoli.

Acetamides↗

PubMed1981

Modification in messenger RNA population synthesized in rabbit cerebral cortex in the recovery period following convulsions.

The labeling pattern of microsomal poly(A)-associated messenger RNA was studied in rabbit cerebral cortex during the postconvulsive period. Labeled uridine was injected into the brain 2 hr after a single electroconvulsive shock and the animals sacrificed 1 hr later. Poly(A) RNA was then extracted from cerebral cortex microsomes, and fractionated by gel electrophoresis. The results indicate that the messenger RNA population synthesized in the cortex in the postconvulsive recovery period is clearly different from that synthesized in the normal controls.

Animals↗

PubMed1996

RNA sequence determinants for aminoglycoside binding to an A-site rRNA model oligonucleotide.

The codon-anticodon interaction on the ribosome occurs in the A site of the 30 S subunit. Aminoglycoside antibiotics, which bind to ribosomal RNA in the A site, cause misreading of the genetic code and inhibit translocation. Biochemical studies and nuclear magnetic resonance spectroscopy were used to characterize the interaction between the aminoglycoside antibiotic paromomycin and a small model oligonucleotide that mimics the A site of Escherichia coli 16 S ribosomal RNA. Upon chemical modification, the RNA oligonucleotide exhibits an accessibility pattern similar to that of 16 S rRNA in the 30 S subunit. In addition, the oligonucleotide binds specifically aminoglycoside antibiotics. The antibiotic binding site forms an asymmetric internal loop, caused by non-canonical base-pairs. Nucleotides that are important for binding of paromomycin were identified by performing quantitative footprinting on oligonucleotide sequence variants and include the C1407.G1494 base-pair, and A.U base-pair at positions 1410/1490, and nucleotides A1408, A1493 and U1495. The asymmetry of the internal loop, which requires the presence of a nucleotide in position 1492, is also crucial for antibiotic binding. Introduction into the oligonucleotide of base changes that are known to confer aminoglycoside resistance in 16 S rRNA result in weaker binding of paromomycin to the oligonucleotide. Oligonucleotides homologous to eukaryotic rRNA sequences show reduced binding of paromomycin, suggesting a physical origin for the species-specific action of aminoglycosides.

Aminoglycosides↗

PubMed1967