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At least 217 records · Page 12Linked to original sources
PubMed1990

Multiple proteins are produced from the dec-1 eggshell gene in Drosophila by alternative RNA splicing and proteolytic cleavage events.

The defective chorion-1 gene (dec-1) in Drosophila encodes follicle cell proteins necessary for proper eggshell assembly. A distinctive feature of the gene is the production of multiple products by both alternative RNA splicing and proteolytic processing events. DNA and protein sequencing studies have revealed several dec-1 protein products. The predominant translation product, fc106, has a vitelline membrane-like N-terminal domain followed by a glutamine, methionine-rich central region, largely in the form of 26 amino acid repeats. During late stage 10 the N-terminal portion of fc106 is cleaved, yielding s80, a major eggshell protein. Conceptual translation of the DNA sequence as well as molecular analyses of several dec-1 mutants suggest that the less abundant alternatively spliced RNAs encode primary translation products with different carboxy terminal ends. These results are discussed with respect to previous genetic analyses of dec-1 mutants as well as with respect to potential protein-protein interactions which may underlie stabilization of this complex extracellular structure.

Amino Acid Sequence↗
PubMed1999

Magnesium-dependent folding of self-splicing RNA: exploring the link between cooperativity, thermodynamics, and kinetics.

Folding of the Tetrahymena self-splicing RNA into its active conformation involves a set of discrete intermediate states. The Mg2+-dependent equilibrium transition from the intermediates to the native structure is more cooperative than the formation of the intermediates from the unfolded states. We show that the degree of cooperativity is linked to the free energy of each transition and that the rate of the slow transition from the intermediates to the native state decreases exponentially with increasing Mg2+ concentration. Monovalent salts, which stabilize the folded RNA nonspecifically, induce states that fold in less than 30 s after Mg2+ is added to the RNA. A simple model is proposed that predicts the folding kinetics from the Mg2+-dependent change in the relative stabilities of the intermediate and native states.

Ammonium Sulfate↗
PubMed1987

A combination of RNase H and S1 nuclease circumvents an artefact inherent to conventional S1 analysis of RNA splicing.

S1 nuclease mapping is commonly used to analyze transcription and processing of unlabelled RNAs. However, the S1 protocol that appears best suited to demonstrate splicing of a particular RNA (using an intronless probe that is 5' end-labelled in the downstream exon) is not diagnostic as expected. Rather, both intron-containing RNA and intronless RNA confer protection of probe across the splice juncture. To unambiguously demonstrate correctly spliced RNAs that begin at a specific initiation site, we present a procedure in which unspliced RNA molecules are first cleaved by RNase H following annealing to an intronic DNA fragment and the remaining RNA is then subjected to S1 analysis using an intronless probe present in vast excess. Only spliced, correctly initiated transcripts can protect the probe across the splice junction and up to residue +1. This RNase H/S1 method provides a broadly applicable technique with which to demonstrate splicing and initiation of a variety of transcripts, especially ones from transfected genes that can arise both from the normal and from activated cryptic initiation sites.

Endonucleases↗
PubMed1989

Immunological evidence for the role of phosphoprotein p68/pI = 7.3 in premessenger RNA splicing.

A 68 kDa (pI = 7.3) nuclear phosphoprotein has been previously characterized as a component of transcriptionally active chromatin. Two-dimensional PAGE Western blotting and radioimmunoassay with monoclonal antibodies have identified this protein in nuclear extracts used for in vitro RNA splicing. In vitro splicing activity could be quantitatively inhibited by preincubating nuclear extracts with the antibodies, but the assembly of 60 S spliceosomes could not.

Antibodies, Monoclonal↗
PubMed2000

In vivo expression of a new hepatitis B virus protein encoded by a spliced RNA.

Hepatitis B virus (HBV) is a small DNA virus with a compact genomic organization. All HBV proteins identified to date have been encoded by unspliced HBV RNAs. Spliced HBV RNAs have been described, but their functions are unknown. We show here that a singly spliced HBV RNA encodes a novel HBV protein in vivo. This HBV splice-generated protein (HBSP) corresponds to the fusion of a part of the viral polymerase and a new open reading frame that is created by the splicing event. In vivo, HBSP protein was found in HBV-infected liver samples, and anti-HBSP antibodies occurred in one-third of sera samples collected from chronic HBV carriers. In vitro, the ectopic expression of HBSP had no effect on viral DNA replication or transcription but induced cell apoptosis without a cell-cycle block. Overall, our results suggest that HBV has evolved a mechanism that directly modulates virus-cell interaction through RNA splicing.

Cells, Cultured↗
PubMed2005

A cross-talk between RNA splicing and signaling pathway alters Fas gene expression at post-transcriptional level: alternative splicing of Fas mRNA in the leukemic U937 cells.

It is now widely accepted that alternative splicing is a mechanism that is responsible for generating protein complexity at low genetic cost. However, little is known about molecular mechanisms that govern alternative splicing of key apoptotic regulators. Here we investigate the effect of pro-apoptotic stimuli on alternative splicing of Fas mRNA by means of reverse transcription-polymerase chain reaction (RT-PCR). Exposure of U937 cells to etoposide, staurosporine, pacritaxel, or cyclohexamide promoted the appearance of the splice variant, which retained the 152-base-pair intron 5. Pretreatment with calyculin A, an inhibitor of protein phosphatase-1 (PP-1) as well as fumonisin B1, an inhibitor of ceramide synthase, prevented etoposide-induced alternative splicing of Fas mRNA. Our data demonstrate that cross-talk between RNA splicing and signaling pathways through endogenous ceramide synthesis and subsequent phosphatase activation is a mechanism that modifies Fas gene expression at the posttranscriptional level.

Alternative Splicing↗
PubMed1993

Polymorphic expression of CD46 protein isoforms due to tissue-specific RNA splicing.

CD46 is a member of the regulators of complement activation (RCA) family and serves to protect autologous cells from complement mediated lysis. The CD46 gene consists of 14 exons and extensive RNA splicing produces protein isoforms of different molecular weight. Predominant protein isoforms of 66 and 56 kDa arise from splicing in or out of exon 8 which encodes a region rich in serine, threonine and proline residues known to be heavily O-glycosylated. An inherited allelic polymorphism controls the relative expression of these isoforms in PBL and other tissues. This study has analysed an independent and overriding tissue specific regulation of CD46 splicing. Salivary gland and kidney produce RNA transcripts that preferentially include exon 8, giving rise to the 66 kDa protein species, while exon 8 is spliced out in brain tissue to give the 56 kDa protein. The cytoplasmic tail of CD46 is encoded by either exon 13 (CYT 1) or exon 14 (CYT 2). There is a preferential deletion of exon 13 from transcripts in salivary gland, kidney and brain to encode a protein containing cytoplasmic tail CYT 2. This preferential production of the CYT 2 tail is contrary to that seen on peripheral blood lymphocytes where equivalent expression of both CYT 1 and CYT 2 is observed. Our results suggest that while the splicing of exons within most cells is controlled by nucleotide sequences within or close to the CD46 gene (i.e. cis-regulation), splicing in tissues such as salivary gland, kidney and brain is regulated by trans-splicing factors encoded by another gene(s).

Alternative Splicing↗
PubMed1993

An alternative Pit-1 RNA splicing product reveals modular binding and nonmodular transcriptional activities of the POU-specific domain.

We have identified a form of the pituitary-specific POU protein Pit-1 that results from deletion of the POU-specific (POUs) domain by alternative RNA splicing. This natural variant of Pit-1 (called delta 4Pit-1) has revealed several aspects of the function of the POUs domain. The delta 4Pit-1 protein was characterized using a delta 4Pit-1-specific antiserum. Further, selection assays of random oligonucleotide pools identified binding site preferences for both wild type and delta 4Pit-1. Methylation interference, copper phenanthrolene, and missing contact analyses were used to compare the binding characteristics of the two forms of Pit-1 on a selected site. DNA binding affinity assays on several DNA elements revealed that the POUs domain contains a modular DNA binding activity affecting the DNA binding affinity of the entire POU domain on some, but not on other, DNA sites. Functional analysis on such DNA elements has revealed that the POUs domain is an essential, but nonmodular, component of the Pit-1 trans-activation domain dependent on its natural context within the Pit-1 protein.

Amino Acid Sequence↗
PubMed1986

Yeast pre-messenger RNA splicing efficiency depends on critical spacing requirements between the branch point and 3' splice site.

In the yeast Saccharomyces cerevisiae the 5' and 3' splice junctions and the internal branch acceptor site (TACTAAC box) are highly conserved intron elements. Analyses of mutants have demonstrated the importance of each of these elements in the splicing process. In the present report we show by three different analytical approaches (splicing-dependent beta-galactosidase expression, in vitro splicing assays and in vivo RNA analyses) that at least two of these elements (the TACTAAC and 3' splice signals) also have to fulfill certain spacing requirements to allow efficient splicing to occur. In particular, the spacing of the 3' splice site from the 2'-5' branch site is a critical factor in determining the efficiency for completion of the final reactions of splicing, intron release and exon-exon joining. Whereas insertions within this region have little or no effect on the first reactions in splicing (the 5' cleavage and 2'-5' branch formation), they dramatically affect the efficiency of the final reactions. In contrast, a 15-base deletion between these two sites has no detectable effect on splicing efficiency. We also show that the 5' cleavage and branch formation can take place, albeit inefficiently, in transcripts in which all of the yeast sequences downstream of the branch site have been replaced by Escherichia coli sequences. We conclude from these studies that, in yeast, the 5' and 3' splice sites are recognized independently from one another, but always in conjunction with the TACTAAC signal.

Base Sequence↗
PubMed1996

Pararetro- and retrovirus RNA: splicing and the control of nuclear export.

Splicing and nuclear export of RNA are obligatory steps in gene expression by eukaryotic cells. Not only have novel splicing events been identified during the replication cycle of retro- and pararetroviruses, but the resulting combination of spliced and unspliced products requires specialized mechanisms for nuclear export, which in turn is a key regulatory step for virus replication.

Animals↗
PubMed1996

Increased levels of spliced RNA account for augmented expression from the MFG retroviral vector in hematopoietic cells.

A persistent obstacle in the use of vector systems for gene therapy has been the inability to attain high-level expression of the target gene in primary cells in vivo. The MFG retroviral vector was designed to yield improved expression over the widely used N2 or LN vectors; however, the molecular basis for this effect has not been examined. Using the human glucocerebrosidase (GC) enzyme as a reporter, we compared expression from the MFG and N2 vector backbones in transduced murine hematopoietic cells after syngeneic bone marrow transplantation. Reporter enzyme activities in primary spleen colonies of transplanted mice were seven-fold higher per vector copy in cells transduced with the (MFG-based) MGC vector than in cells bearing the (N2-based) G2 vector. In spleen colonies harboring the MGC vector, the ratio of spliced to unspliced vector RNA was increased four-fold relative to the G2 vector transcripts in Northern blot analyses. Further analyses indicated that MGC-transduced cells contained five-fold higher levels of spliced RNA per vector copy. Since translation of spliced RNA species (in which the complex secondary structure of the packaging signal has been excised) is likely to proceed with enhanced efficiency, the augmented levels of spliced RNA produced by MFG may represent the key element of increased protein expression from this vector. These findings suggest that the MFG retroviral vector may provide higher level expression of target genes used in human gene therapy.

Animals↗
PubMed1984

Messenger RNA splicing in vitro: an excised intervening sequence and a potential intermediate.

Four RNA products have been characterized from a soluble system that accurately splices purified substrate RNA. The labeled substrate RNA contained the first and second exons of the major late transcription unit of adenovirus 2 and a shortened form of the first intervening sequence. One of these RNA products was the excised intervening sequence which accumulated quantitatively with the level of splicing. This RNA species has an unusual structure and is modified at internal sites. A potential intermediate in the splicing pathway which is cleaved at the 5' splice site of the first exon has been isolated. This RNA species is also modified at sites within the first intervening sequence. These results suggest that the splicing of mRNA precursors may involve sites in the intervening sequence, cleavage at the 5' splice site, cleavage at the 3' splice site, and ligation of the two exons.

Adenoviruses, Human↗
PubMed2003

Computational analysis and experimental validation of tumor-associated alternative RNA splicing in human cancer.

A genome-wide computational screen was performed to identify tumor-associated alternative RNA splicing isoforms. A BLAST algorithm was used to compare 11,014 genes from RefSeq with 3,471,822 human expressed sequence tag sequences. The screen identified 26,258 alternative splicing isoforms of which 845 were significantly associated with human cancer, and 54 were specifically associated with liver cancer. Furthermore, canonical GT-AG splice junctions were used significantly less frequently in the alternative splicing isoforms in tumors. Reverse transcription-PCR experiments confirmed association of the alternative splicing isoforms with tumors. These results suggest that alternative splicing may have potential as a diagnostic marker for cancer.

Algorithms↗
PubMed1986

Secretion of HLA-A and -B antigens via an alternative RNA splicing pathway.

Human class I major histocompatibility antigens (HLA-A, -B and -C) are integral membrane protein heterodimers, which are anchored in the membrane via a stretch of hydrophobic amino acids near the carboxyl terminus of the heavy chain. It has previously been shown that a mutagenized cell line secretes a water soluble form of the HLA-A2 antigen, due to a pattern of RNA splicing that removes exon 5 (encoding the transmembrane hydrophobic amino acids) from mature, HLA-A2--encoding transcripts. The present study was undertaken to assess whether a similar process might be operative in nonmutagenized cells. It is shown that water soluble class I molecules (primarily HLA-A24) are secreted by the T leukemic cell line HPB-ALL, and that alternative splicing removes exon 5 from a fraction of HLA-A24--encoding transcripts. It is further shown that class I molecules are secreted, possibly in an allele-specific fashion, from a variety of tumor cells and normal cells. The possible relationship between these findings and previous reports of HLA-A and -B antigens in human serum is discussed.

Amino Acid Sequence↗
PubMed1992

The sequence of porcine alpha s1-casein cDNA: evidence for protein variants generated by altered RNA splicing.

A cDNA library was constructed from mRNA isolated from lactating porcine mammary gland and screened with a bovine alpha s1-casein cDNA clone. Three classes of cDNA isolated varied in the number of bases within the coding region. The full length porcine alpha s1-casein cDNA is 1124bp and codes a preprotein of 206 amino acids. The other two classes of alpha s1-casein cDNA lacked 18bp and 60bp respectively when compared to the 1124-bp cDNA sequence. PCR amplification confirmed the presence of these sequences in total RNA. These differences appear to be due to altered RNA splicing.

Amino Acid Sequence↗
PubMed1987

RNA splicing permits expression of a maize gene with a defective Suppressor-mutator transposable element insertion in an exon.

The bz-m13CS9 allele of the bronze-1 gene in maize contains a 902-base-pair defective Suppressor-mutator (dSpm) transposable element in the second exon. Nevertheless, 40-50% of the enzymatic activity conditioned by a nonmutant allele at the bronze-1 locus is routinely recovered in crude extracts prepared from plants carrying bz-m13CS9 in the absence of an autonomous Suppressor-mutator element. Analyses of RNAs produced by such plants show that transcription proceeds through the dSpm. The dSpm sequence of the messenger RNA precursor is then removed by RNA splicing using the donor site of the single bronze-1 intron and an acceptor site within the inverted terminal repeat of the dSpm. This results in a messenger RNA with the proper reading frame that could produce a functional enzyme. These data demonstrate that this dSpm insertion in an exon of a structural gene has produced a functional allele with a novel intron consisting, in part, of the dSpm. This mechanism appears to allow dSpm elements to reduce the impact of their insertions on gene expression.

Alleles↗
PubMed1983

RNA splicing in neurospora mitochondria: structure of the unspliced 35S precursor ribosomal RNA detected by psoralen cross-linking.

The structure of the unspliced 35S precursor rRNA of Neurospora mitochondria was studied by psoralen photochemical cross-linking. The results show that when the 35S RNA is cross-linked in ribonucleoprotein particles (RNPs) under appropriate conditions, the predominant configuration is a 2.2 kb intron loop which brings opposite splice sites into proximity; that the predominant secondary structural feature in the free RNA is a relatively large hairpin (length = 0.105 kb) in the center of the molecule at or near the 5' splice site; that the intron loop and the central hairpin are different configurations of sequences at or near the 5' splice site; and that the intron loop is stabilized by protein components of RNPs. Based on the structures detected by psoralen photochemical cross-linking, we propose a mechanism for the splicing of the Neurospora mitochondrial precursor rRNA. We propose further that certain features of this mechanism may be relevant to the splicing of other RNAs, including eucaryotic mRNAs.

Base Sequence↗