SEARCH · PubMed Health

Results for “RNP complex”

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 721 records · Page 40Linked to original sources

PubMed1997

Roles of the influenza virus polymerase and nucleoprotein in forming a functional RNP structure.

Influenza virus transcription and replication is performed by ribonucleoprotein particles (RNPs). They consist of an RNA molecule covered with many copies of nucleoprotein (NP) and carry a trimeric RNA polymerase complex. RNA modification analysis and electron microscopy performed on native RNPs suggest that the polymerase forms a complex with both conserved viral RNA (vRNA) ends, whereas NP binding exposes the RNA bases to the solvent. After chemical removal of the polymerase, the bases at the vRNA extremities become reactive to modification and the vRNPs behave as structures with free ends, as judged from the observation of salt-induced conformational changes by electron microscopy. The vRNA appears to be completely single-stranded in polymerase-free RNPs despite a partial, inverted complementarity of the vRNA ends. The absence of a stable double-stranded panhandle structure in polymerase-free RNPs has important implications for the mechanism of viral transcription and the switch from transcription to replication.

Animals↗

PubMedDate not supplied

[Circular dichroism study of the ribonucleoprotein structure of Sendai virus isolated from infected chick embryo cells].

Thermostability and secondary structure of RNA, a component of ribonucleoprotein (RNP) of Sendai virus isolated from infected chick embryo cells (cRNP) and from virions (vRNP) were studied by the method of circular dichroism. The secondary structure of RNA in cRNP was shown to be practically no different from that of free RNA whereas incorporation of RNA into vRNP was accompanied by a significant decrease in the number of paired bases in it. Comparison of thermodenaturation parameters of cRNP and vRNP also revealed significant differences in their structural organization. Thus, melting of cRNP as well as of free RNA is of markedly non-cooperative nature indicating poor RNA-protein interactions in the complex. In contrast, the process of vRNP thermodenaturation occurs in a step-wise manner in a narrow temperature range indicating a significant role in the maintenance of this RNP structure of both RNA-protein and, apparently, protein-protein interactions.

Animals↗

PubMed1988

Monoclonal autoantibody recognizing a unique set of small nuclear ribonucleoprotein complexes.

A murine IgG2a, kappa-monoclonal autoantibody (mAb) F78 is described that recognizes a novel epitope associated with small nuclear ribonucleoprotein complexes (snRNP). F78 selectively immunoprecipitated a unique pattern of small nuclear RNA (U1, U2, and U4 to U6) characterized by a marked depletion of U1 and an elevated proportion of U2 compared with known patterns immunoprecipitated by previously described anti-RNP (2.73) and anti-Sm (7.13, Y12) mAb. Analysis of immunoprecipitated RNA from extracts previously cleared with mAb F78 and probed with anti-RNP mAb 2.73 further indicated the presence of two distinct subsets of U1. Immunoblots of whole cell extracts separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) without heating showed that F78 selectively bound to a trypsin-sensitive component of apparent m.w. greater than 120,000 which was decreased in size following RNase A treatment. The anti-Sm mAb, but not the anti-RNP mAb, also recognized this component in unheated samples. Heating before SDS-PAGE resulted in abrogation of binding to the F78 epitope. Immunoprecipitation of unlabeled or [35S]methionine-labeled cell extracts with F78 revealed the presence of most snRNP peptides, but the absence of peptide C and the 68,000 m.w. component, known to be selectively associated with U1-specific snRNP. Two-dimensional SDS-PAGE analysis of F78 immunoprecipitates confirmed that the epitope recognized by this mAb resides on a heat-dissociable complex containing snRNP-related peptides B, B', D, E, F, and G, but lacking U1-associated peptides. F78 mAb therefore defines a subset of snRNP which lack anti-RNP associated U1 RNA as well as peptides known to be selectively associated with this RNA species. It apparently recognizes an epitope associated with an assembled form of these particles and may be useful in examining structures involved in RNA processing.

Antibodies, Monoclonal↗

PubMed1992

Prosomes and their multicatalytic proteinase activity.

Prosomes were first described as being mRNA-associated RNP (ribonucleoprotein) particles and subcomponents of repressed mRNPs (messenger ribonucleoprotein). We show here that prosomes isolated from translationally inactive mRNP have a protease activity identical to that described by others for the multicatalytic proteinase complex (MCP, 'proteasome'). By RNase or non-ionic detergent treatment, the MCP activity associated with repressed non-globin mRNP from avian erythroblasts, sedimenting at 35 S, could be quantitatively shifted on sucrose gradients to the 19-S sedimentation zone characteristic of prosomes, which were identified by monoclonal antibodies. The presence of small RNA in the enzymatic complex was shown by immunoprecipitation of the protease activity out of dissociated mRNP using a mixture of anti-prosome monoclonal antibodies; a set of small RNAs 80-120 nucleotides long was isolated from the immunoprecipitate. Furthermore, on CsCl gradients, colocalisation of the MCP activity with prosomal proteins and prosomal RNA was found, and no difference in the prosomal RNA pattern was observed whether the particles were fixed or not prior to centrifugation. These data indicate that the MCP activity is a property of prosomes, shown to be in part RNP and subcomplexes of in vivo untranslated mRNP. A hypothesis for the role of the prosome-MCP particles in maintaining homeostasis of specific protein levels is proposed.

Amino Acid Sequence↗

PubMed1999

Expression of the heterogenous nuclear ribonucleoprotein complex K protein and the prolyl-4-hydroxylase alpha-subunit in atherosclerotic arterial smooth muscle cells.

Smooth muscle cells (SMC) play a major role in the formation of atherosclerotic lesions found on major blood vessels. SMC proliferation, migration, and protein synthesis promote the progression of the early lesion, the fatty streak, into a complex myointimal fibrous plaque. To investigate altered gene expression in SMC during atherogenesis, we characterized differences between SMC from normal rabbits, rabbits fed a 2% cholesterol diet, and Watanabe Heritable Hyperlipidemic rabbits (WHHL). We detected and isolated a 501 bp cDNA fragment representing the A isoform of heterogenous nuclear ribonucleoprotein complex K (hnRNP-K) and a 281 bp cDNA fragment representing the prolyl-4-hydroxylase alpha-subunit (alphaPH) mRNAs. hn-RNP-K was upregulated in SMC from cholesterol-fed rabbits isolated in primary culture, as well as in SMC medial tissue from both the cholesterol-fed and WHHL rabbits. alphaPH was upregulated in SMC from the cholesterol-fed rabbits isolated in primary culture and in the tissue from WHHL rabbits. These data demonstrate genes consistent with increased proliferation and collagen production are upregulated in SMC during atherogenesis and may shed new light on gene expression changes and corresponding phenotype changes in SMC during atherogenesis.

Animals↗

PubMed2002

New components of the spliced leader RNP required for nematode trans-splicing.

Pre-messenger-RNA maturation in nematodes and in several other lower eukaryotic phyla involves spliced leader (SL) addition trans-splicing. In this unusual RNA processing reaction, a short common 5' exon, the SL, is affixed to the 5'-most exon of multiple pre-mRNAs. The nematode SL is derived from a trans-splicing-specific approximately 100-nucleotide RNA (SL RNA) that bears striking similarities to the cis-spliceosomal U small nuclear RNAs U1, U2, U4 and U5 (refs 3, 4); for example, the SL RNA functions only if it is assembled into an Sm small nuclear ribonucleoprotein (snRNP). Here we have purified and characterized the SL RNP and show that it contains two proteins (relative molecular masses 175,000 and 30,000 (M(r) 175K and 30K)) in addition to core Sm proteins. Immunodepletion and reconstitution with recombinant proteins demonstrates that both proteins are essential for SL trans-splicing; however, neither protein is required either for conventional cis-splicing or for bimolecular (trans-) splicing of fragmented cis constructs. The M(r) 175K and 30K SL RNP proteins are the first factors identified that are involved uniquely in SL trans-splicing. Several lines of evidence indicate that the SL RNP proteins function by participating in a trans-splicing specific network of protein protein interactions analogous to the U1 snRNP SF1/BBP U2AF complex that comprises the cross-intron bridge in cis-splicing.

Animals↗

PubMed1995

Major histocompatibility complex class II gene associations with anti-U1 small nuclear ribonucleoprotein antibody. Relationship to immunoreactivity with individual constituent proteins.

OBJECTIVE: To better define immunogenetic associations with the anti-U1 ribonucleoprotein (U1 RNP) autoantibody response. METHODS: HLA class II alleles were determined by genotyping in 49 Japanese rheumatic disease patients with anti-U1 RNP antibody and 43 race-matched healthy controls. Immunoreactivities to U1 RNP constituent proteins (70K, A, B/B', and C) were detected by immunoblots using purified HeLa cell Sm antigen, and antibody titer was determined by passive hemagglutination assay. RESULTS: DQB1*0302 was significantly more frequent in anti-U1 RNP-positive patients than in controls (43% versus 14%; odds ratio [OR] = 4.6, corrected P = 0.03). All anti-U1 RNP-positive patients had either a DQB1*0601, *0602, *0301, *0302, or *0303 allele, which share tyrosine at position 30, and the amino acid sequence Thr, Arg, Ala, Glu, Leu, Asp, and Thr at positions 71-77 in the DQB1 beta 1 domain. In contrast, one of these alleles was found in 81% of the controls (OR = 24, P = 0.002). In addition, anti-U1 RNP antibody was associated with unique DQB1*0302; DRB1*0401 haplotype. Anti-70K reactivity and antibody titer were positively associated with a basic amino acid residue, arginine or histidine, at position 13 (DR2 or DR4) and were negatively associated with the amino acid sequence Ile, Leu, Glu, and Asp at positions 67-70, which was present in some of the DR5-, DR6-, and DR8-associated alleles, in the DRB1 beta 1 domain. Anti-C reactivity was strongly associated with DR2, particularly with DRB1*1502. CONCLUSION: The several shared epitopes located on HLA-DRB1 and DQB1 genes control the anti-U1 RNP autoantibody response.

Amino Acid Sequence↗

PubMed1982

The fourth chromosome of Chironomus tentans Malpighian tubules: an ultrastructural study.

Morphology and banding pattern of the 4th chromosome in Chironomus tentans Malpighian tubules have been investigated by electron microscopy, using the squash and selection technique. The map we composed from our observations shows a remarkable increase (75%) in band numbers as compared to the map previously presented by Beermann for the 4th chromosome from salivary glands. Extrapolation of this increase to the entire genome would result in a total band number of about 3,500. The mean DNA content of bands can thus be calculated to be about 50 kb. Many bands show a complex structure, including the BR2 band. Some bands seem to result from fusion of smaller components. "Minibands" have also been observed. Some interbands contain RNP particles. In our material the interbands appeared to be made up of fibrils with a diameter of about 120 A. On the basis of these results we estimate the DNA in the interbands as amounting to 2% of the entire genome. The results are discussed with respect to the organization of the polytene chromosomes and the functional significance of the banding pattern.

Animals↗

PubMed1996

Structure of the polyadenylation regulatory element of the human U1A pre-mRNA 3'-untranslated region and interaction with the U1A protein.

The N-terminal RNP domain of U1A binds two different RNA substrates with high affinity and specificity: stem-loop II of the U1 snRNA and a complex secondary structure in the 3'-untranslated region (3'-UTR) of the U1A pre-mRNA. Both RNAs contain a single-stranded sequence which is the main site of interaction with the protein, but in completely different structural contexts. Here we describe the solution structure of the free 3'-UTR RNA molecule and the NMR characterization of its complex with the U1A protein N-terminal domain. The structure of the free RNA indicates that the stems are nearly canonical A-form helices and that the single-stranded region contains local stacking interactions in the context of a generally flexible structure. Upon protein binding, the internal loop region folds into an ordered structure containing significant changes in the local stacking interactions. These results demonstrate the role of RNA structure and folding in specific RNA-protein recognition.

Humans↗

PubMed2004

Complementarity, sequence and structural elements within the 3' and 5' non-coding regions of the Bunyamwera orthobunyavirus S segment determine promoter strength.

The genome of Bunyamwera virus (BUN; family Bunyaviridae) consists of three segments of negative-sense, single-stranded RNA that are called L (large), M (medium) and S (small), according to their size. The genomic RNAs are encapsidated by the viral nucleocapsid protein to form ribonucleoprotein complexes (RNPs). The terminal 3' and 5' non-coding sequences are complementary and interact to give a panhandle-like structure to the RNP. Located within these non-coding sequences are elements that control replication and transcription. The sequences of the terminal 11 nt are conserved among the genome segments and are followed by shorter, complementary nucleotide motifs that are conserved on a segment-specific basis. Here, a detailed analysis of the 3' and 5' non-coding regions of the BUN S segment is presented. By using a mini-replicon system, it was shown that a functional BUN S promoter requires complementarity, as well as defined sequences, within the terminal 15 nt of either end. It was also shown that the minimal requirement for transcription is localized within the terminal 32 nt of the S segment. A comparison of known strong BUN promoters led to the prediction of a structural element outside the terminal 15 nt; introduction of this motif into the BUN S sequence resulted in increased antigenome and mRNA levels and increased expression of S segment proteins, as shown by mini-replicon assays, as well as recovery of a recombinant virus.

3' Untranslated Regions↗

PubMed1983

Fragmentation of 'nuclear matrix' on a mica target.

Chromatin depleted nuclei ('nuclear matrix') of Ehrlich ascites cells were characterized and fragmented by glycerol shot technique (particle fragmentation). The preparations reveal that 'nuclear matrix' is entirely composed of granules and fibres. Prominent size classes of granules are 10 to 20 nm and 25 to 40 nm, respectively. Most of the granules remain attached to fibres during the fragmentation process. The diameter of the fibres corresponds with double-stranded DNA visualized under identical conditions. The RNP-like nature of the particles is shown by their proteinase K/RNase sensitivity. Since the 'nuclear matrix' architecture becomes instable in high salt buffer after pretreatment with RNase which changes the RNP-particle-like material it must be inferred that the RNP/DNA interaction is a prerequisite for the high salt stability of the 'nuclear matrix' complex.

Animals↗

PubMed1981

Transcriptionally active chromatin in loops of lampbrush chromosomes at physiological salt concentrations as revealed by electron microscopy of sections.

The structural organization of the transcribed loops of lampbrush chromosomes present in the vegetative nuclei of the green algae, Acetabularia mediterranea and A. crenulata, and in oocyte nuclei of the newt, Pleurodeles waltlii, has been studied by electron microscopy of relatively thick (100--200 nm) and ultrathin sections through chromosomes prepared and fixed at physiological salt concentrations. The procedure allows the direct comparison of the same chromosome or chromosome region by light and electron microscopy, that means identification of the transcriptional arrays in specific loops. After such preparations the loop axis reveals regions that are smoothly-contoured ("non-beaded") and only 4 to 7 nm thick and are clearly different from supranucleosomal forms of inactive chromatin fibrils as well as from extended filaments of nucleosomal granules examined in parallel. This indicates that the chromatin of the loops axis of intensely transcribed regions is in a structural form different from that of non-transcribed chromatin. A similarly thin axis has been identified in loops of chromosomes of nuclei fixed in situ. The lateral ribonucleoprotein (RNP) fibrils associated with transcribed loop regions appear as serial arrays of granules, often of regular size, which are smaller in the chromosomes of Acetabularia (mean diameter 18 nm) than in those of amphibia (mean diameter 28 nm). Discontinuous arrays of lateral RNP fibrils and fibril arrays with different polarity are found in some loops. Certain loops and loop regions are characterized by specific patterns of aggregation of such lateral RNP fibrils which appear to correspond to the "granules" visible in these loops in the light microscope. The observations show that arrays of transcriptional complexes in chromosome loops can be visualized in thin sections of material prepared at physiological ionic strength with similar resolution and clarity as in spread preparations of chromosomal material dispersed in extremely low salts buffers. The results are interpreted to approximate the organization of loop structures in vivo and to show that, at physiological ionic strength, the chromatin of the loop axis is organized in a form different from that characteristic of non-transcribed chromatin.

Chlorophyta↗

PubMed1987

HLA-DR antigens in systemic lupus erythematosus: association with specificity of autoantibody responses to nuclear antigens.

HLA-DR antigens and autoantibodies to the nuclear or cytoplasmic antigens Ro/SSA, La/SSB, Sm, and RNP were determined in North American and Austrian patients with systemic lupus erythematosus (SLE). Analysis of the association of antibodies to these ribonucleic acid (RNA)-protein antigens with HLA-DR antigens showed that HLA-DR3 was related to the presence of anti-Ro/SSA or anti-La/SSB, or both. In contrast, anti-Sm or anti-RNP, or both were associated with HLA-DR4. HLA-DR5 was associated with absence of these autoantibodies. The data extend evidence for the complexity and heterogeneity of SLE. Moreover, they indicate that, in SLE, genes linked to those coding for HLA-DR antigens, are related to the specificity of autoantibody responses rather than to the primary immunological abnormalities of this disorder.

Adolescent↗

PubMedDate not supplied

[Ribonucleoproteins containing mRNA in the cytoplasm of mouse plasmacytoma cells].

The rapidly labelled postribosomal ribonucleoprotein (RNP) found in the cytoplasm of mouse plasmacytoma cells were investigated. It has been shown that 45S and 80S particles contain relatively high molecular weight (approximately 12-17S) pulse-labelled RNA similar to the polyribosomal mRNA. No other postribosomal RNP was found which would contain an RNA with similar sedimentation characteristics. In CsC1 density gradients, the postribosomal RNP gives two peaks. One of them, the rapidly labelled component (rho 1.52 g/cm3) is found only in 45S RNP. The other rapidly labelled component (rho 1.36-1.41 g/cm3) is revealed in all investigated regions of sucrose gradients. The latter contains relatively low molecular weight RNA (approximately7-9S). These RNP are supposed to be informosome-like particles. The components with a buoyant density of 1.52 g/cm3 may represent an mRNP-45S subparticles complex. The rapidly labelled mRNA of 80S particles is released after EDTA treatment in the form of mRNP with a buoyant density of 1.45-1.47 g/cm3.

Animals↗

PubMed1996

hTAF(II)68, a novel RNA/ssDNA-binding protein with homology to the pro-oncoproteins TLS/FUS and EWS is associated with both TFIID and RNA polymerase II.

TFIID is the main sequence-specific DNA-binding component of the RNA polymerase II (Pol II) transcriptional machinery. It is a multiprotein complex composed of the TATA-binding protein (TBP) and TBP-associated factors (TAF(II)s). Here we report the cloning and characterization of a novel human TBP-associated factor, hTAF(II)68. It contains a consensus RNA-binding domain (RNP-CS) and binds not only RNA, but also single stranded (ss) DNA. hTAF(II)68 shares extensive sequence similarity with TLS/FUS and EWS, two human nuclear RNA-binding pro-oncoproteins which are products of genes commonly translocated in human sarcomas. Like hTAF(II)68, TLS/FUS is also associated with a sub-population of TFIID complexes chromatographically separable from those containing hTAF(II)68. Therefore, these RNA and/or ssDNA-binding proteins may play specific roles during transcription initiation at distinct promoters. Moreover, we demonstrate that hTAF(II)68 co-purifies also with the human RNA polymerase II and can enter the preinitiation complex together with Pol II.

Amino Acid Sequence↗

PubMed2001

The nucleoporin Nup153 is required for nuclear pore basket formation, nuclear pore complex anchoring and import of a subset of nuclear proteins.

The nuclear pore complex (NPC) is a large proteinaceous structure through which bidirectional transport of macromolecules across the nuclear envelope (NE) takes place. Nup153 is a peripheral NPC component that has been implicated in protein and RNP transport and in the interaction of NPCs with the nuclear lamina. Here, Nup153 is localized by immunogold electron microscopy to a position on the nuclear ring of the NPC. Nuclear reconstitution is used to investigate the role of Nup153 in nucleo- cytoplasmic transport and NPC architecture. NPCs assembled in the absence of Nup153 lacked several nuclear basket components, were unevenly distributed in the NE and, unlike wild-type NPCs, were mobile within the NE. Importin alpha/beta-mediated protein import into the nucleus was strongly reduced in the absence of Nup153, while transportin-mediated import was unaffected. This was due to a reduction in import complex translocation rather than to defective receptor recycling. Our results therefore reveal functions for Nup153 in NPC assembly, in anchoring NPCs within the NE and in mediating specific nuclear import events.

Animals↗

PubMed2002

Analysis of RNA-protein complexes by oligonucleotide-targeted RNase H digestion.

Oligonucleotide-targeted RNase H protection assays are powerful means to analyze protein binding domains in ribonucleoprotein particles (RNPs). In such an assay, the RNA component of a RNP and, in an essential control reaction, the corresponding deproteinized RNA are targeted with an antisense DNA oligonucleotide and RNase H. If the oligonucleotide is able to anneal to the complementary sequence of the RNA, RNase H will cleave the RNA within the double-stranded DNA/RNA region. However, protein binding to a specific RNA sequence may prevent hybridization of the DNA oligonucleotide, thereby protecting the RNA molecule from endonucleolytic cleavage. An RNase H protection analysis can usually be carried out with crude cell extract and does not require further RNP purification. On the other hand, purified RNP fractions are preferable when a crude extract contains RNase activity or a heterogenous RNP population of a specific RNA. The cleavage pattern of RNase H digestion can be analyzed by Northern blotting or primer-extension assays. In addition, the investigation of RNP fragments, for example, by native gel electrophoresis, may reveal important structural information about a RNP. In this article, we describe procedures for RNP and RNA preparation, the oligonucleotide-targeted RNase H protection assay, and methods for the analysis of RNA and RNP cleavage products. As an example, we show oligonucleotide-targeted RNase H protection of the Trypanosoma brucei U1 small nuclear RNP.

Biotinylation↗

PubMed1984

Antibody profiles of sera giving different nuclear staining patterns.

Antibodies to three major antigens of the non-histone or saline-extractable nuclear antigen (ENA) complex were sought by counterimmunoelectrophoresis (CEP) in three groups of sera which gave different patterns in the immunofluorescence test for antinuclear antibodies (ANA). Precipitins, mainly anti RNP and anti SS-B, were found most commonly (61%) in 70 sera with a speckled ANA pattern but were less frequent (8%) in 61 sera with a homogeneous ANA pattern and exceptional (1%) in 72 sera which showed fibrillar ANA staining. Rim staining was an insensitive indicator of nDNA antibody. An enzyme immunoassay (EIA), specific for anti-SS-B was more sensitive than CEP and identified this antibody in 28 sera, compared with 18 for CEP.

Adult↗