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Results for “RNA Splicing”

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At least 433 records · Page 24Linked to original sources

PubMed1991

Exon amplification: a strategy to isolate mammalian genes based on RNA splicing.

We have developed a method, exon amplification, for fast and efficient isolation of coding sequences from complex mammalian genomic DNA. This method is based on the selection of RNA sequences, exons, which are flanked by functional 5' and 3' splice sites. Fragments of cloned genomic DNA are inserted into an intron, which is flanked by 5' and 3' splice sites of the human immunodeficiency virus 1 tat gene contained within the plasmid pSPL1. COS-7 cells are transfected with these constructs, and the resulting RNA transcripts are processed in vivo. Splice sites of exons contained within the inserted genomic fragment are paired with splice sites of the flanking tat intron. The resulting mature RNA contains the previously unidentified exons, which can then be amplified via RNA-based PCR and cloned. Using this method, we have isolated exon sequences from cloned genomic fragments of the murine Na,K-ATPase alpha 1-subunit gene. We have also screened randomly selected genomic clones known to be derived from a segment of human chromosome 19 and have isolated exon sequences of the DNA repair gene ERCC1. The sensitivity and ease of the exon amplification method permit screening of 20-40 kilobase pairs of genomic DNA in a single transfection. This approach will be extremely useful for rapid identification of mammalian exons and the genes from which they are derived as well as for the generation of chromosomal transcription maps.

Animals↗

PubMed2006

Alternative RNA splicing regulation in the testis.

Alternative splicing regulation has been shown to be critically important for several developmental pathways. It is particularly prevalent in the testis, which is the site of an extensive adult developmental programme. Alternative splicing is controlled by a splicing code, in which transcripts respond to subtle cell type-specific variations in positive and negative trans-acting RNA-binding proteins according to their unique set of binding sites for these proteins. Because of their unique combinations of cis-acting sequence elements, specific transcripts are able to respond individually to this code. In this review, we discuss how this code may be deciphered in germ cells to mediate a splicing response.

Adult↗

PubMed2003

A novel G-to-A mutation in the intron-N of the protein S gene leading to abnormal RNA splicing in a patient with protein S deficiency.

BACKGROUND AND OBJECTIVES: Hereditary protein S (PS) deficiency is a rare autosomal disorder of the coagulation pathway associated with familial thrombophilia. DESIGN AND METHODS: We investigated a young propositus with recurrent deep vein thrombosis, a positive family history for thrombotic episodes, and low plasma concentrations of free, but not total PS antigen (12% and 70%, respectively). RESULTS: Sequence analysis of the PS gene showed a heterozygous G-to-A mutation at the first nucleotide of intron N. The patient's father, who had suffered from deep vein thrombosis and had reduced total and free PS antigen (59% and 28%, respectively) was a heterozygote. The G-to-A change predicts the disappearance of a donor splice site. After transfection with a construct, containing either the wild-type or the mutated sequence, cells with the mutant construct showed an aberrant mRNA, consistent with exclusion of exon 14, but not the expected mRNA. Sequencing of the abnormal mRNA showed the complete absence of exon 14. Exclusion of exon 14 predicts the deletion of the amino acid sequence from residue 508 to residue 582, and the shift of the reading frame of the following 8 amino acids with a premature stop codon within exon 15 at position 591. Thus, the truncated PS gene product would not contain the terminal portion of the sex hormone binding globulin-like domain. INTERPRETATION AND CONCLUSIONS: We have identified a mutation in a highly conserved intronic region of PS gene. The mutation affects in vitro mRNA processing and efficiency of normal splicing.

Adult↗

PubMed1992

The mitochondrial tyrosyl-tRNA synthetase of Podospora anserina is a bifunctional enzyme active in protein synthesis and RNA splicing.

The Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (mt tyrRS), which is encoded by the nuclear gene cyt-18, functions not only in aminoacylation but also in the splicing of group I introns. Here, we isolated the cognate Podospora anserina mt tyrRS gene, designated yts1, by using the N. crassa cyt-18 gene as a hybridization probe. DNA sequencing of the P. anserina gene revealed an open reading frame (ORF) of 641 amino acids which has significant similarity to other tyrRSs. The yts1 ORF is interrupted by two introns, one near its N terminus at the same position as the single intron in the cyt-18 gene and the other downstream in a region corresponding to the nucleotide-binding fold. The P. anserina yts1+ gene transformed the N. crassa cyt-18-2 mutant at a high frequency and rescued both the splicing and protein synthesis defects. Furthermore, the YTS1 protein synthesized in Escherichia coli was capable of splicing the N. crassa mt large rRNA intron in vitro. Together, these results indicate that YTS1 is a bifunctional protein active in both splicing and protein synthesis. The P. anserina YTS1 and N. crassa CYT-18 proteins share three blocks of amino acids that are not conserved in bacterial or yeast mt tyrRSs which do not function in splicing. One of these blocks corresponds to the idiosyncratic N-terminal domain shown previously to be required for splicing activity of the CYT-18 protein. The other two are located in the putative tRNA-binding domain toward the C terminus of the protein and also appear to be required for splicing. Since the E. coli and yeast mt tyrRSs do not function in splicing, the adaptation of the Neurospora and Podospora spp. mt tyrRSs to function in splicing most likely occurred after the divergence of their common ancestor from yeast.

Amino Acid Sequence↗

PubMed2004

A novel RNA splice site mutation in the C1 inhibitor gene of a patient with type I hereditary angioedema.

We describe a patient with type I hereditary angioedema presenting recurrent episodes of skin swelling and abdominal pain. Laboratory examination showed reduced levels of CH50 and C4 with a normal C3 level. The C1 inhibitor was decreased to 7.0 mg/dl (normal, 10-25 mg/dl) with a remarkably reduced activity (<25%; normal, 80-125%). DNA analysis of the C1 inhibitor gene revealed a novel point mutation at the 3' acceptor mRNA splice site of the intron 5 (G-->A at nucleotide 8722). This mutation may abolish the correct splicing of the intron 5 and create unstable mRNA.

Angioedema↗

PubMed1998

RNA secondary structure: an important cis-element in rat calcitonin/CGRP pre-messenger RNA splicing.

The calcitonin/CGRP gene pre-mRNA is alternatively spliced in a tissue-specific manner resulting in the formation of calcitonin mRNA in thyroid C-cells and CGRP mRNA in neurons. Computer analysis of the RNA containing the 3' splice acceptor of the calcitonin-specific exon 4 predicts that this region has the potential to form a thermodynamically stable stem-loop. Data from CD spectroscopy and solution phase structure probing with single-strand specific and double-strand specific RNases indicates that RNA in this region is substantially double stranded. In vitro splicing of chimeric human beta-globin/calcitonin transcripts in HeLa nuclear extract was inhibited by base changes predicted to destabilize the stem, while compensatory base changes resulted in splicing at 50% of wild-type levels. Changing the residue opposite the AG dinucleotide adenosine in the stem from G to U, allowing the formation of an A-U basepair, abolished usage of this splice acceptor in vitro. These results indicate that a thermodynamically stable RNA stem-loop forms in vitro at the 3' splice acceptor of exon 4 of the calcitonin/CGRP gene transcript. This RNA secondary structure acts as a novel cis-element involved in proper splice site selection.

Alternative Splicing↗

PubMed1990

RNA splicing generates alternate forms of germline immunoglobulin alpha heavy chain transcripts.

Emerging evidence implicates germline immunoglobulin heavy chain gene transcription in the targeting of heavy chain genes for switch recombination. In this study, cloned cDNA copies of the major germline alpha heavy chain transcript expressed in the murine B cell lymphoma 1.29 mu, a cell line that switches to IgA in culture, have been used to characterize the germline alpha transcription unit. The 5' end of these transcripts are heterogeneous, being derived from an exon denoted I alpha located approximately 2.2 kb 5' of the alpha switch region. Sequence analysis of cDNA and genomic clones reveals that alternate splice donor sites generate I alpha exons of varying length. While the two smaller spliced forms of I alpha contain stop codons in the open reading frame of the C alpha gene, transcripts utilizing the 3' most splice donor signal may encode a protein in which amino acids derived from the 3' end of the I alpha exon are fused to the C alpha domain.

Animals↗

PubMed2005

RNA splicing capability of live neuronal dendrites.

Dendrites are specialized extensions of the neuronal soma that contain components of the cellular machinery involved in RNA and protein metabolism. Several dendritically localized proteins are associated with the precursor-mRNA (pre-mRNA) splicing complex, or spliceosome. Although some spliceosome-related, RNA-binding proteins are known to subserve separate cytoplasmic functions when moving between the nucleus and cytoplasm, little is known about the pre-mRNA splicing capacity of intact dendrites. Here, we demonstrate the presence and functionality of pre-mRNA-splicing components in dendrites. When isolated dendrites are transfected with a chicken delta-crystallin pre-mRNA or luciferase reporter pre-mRNA, splicing junctions clustered at or near expected splice sites are observed. Additionally, in vitro synaptoneurosome experiments show that this subcellular fraction contains a similar complement of splicing factors that is capable of splicing chicken delta-crystallin pre-mRNA. These observations suggest that pre-mRNA-splicing factors found in the dendroplasm retain the potential to promote pre-mRNA splicing.

Animals↗

PubMed1997

Rapid analysis of distinctive CD44 RNA splicing preferences that characterize colonic tumors.

In normal tissues, the steady-state level of CD44 mRNA is low, and the variety of alternatively spliced transcripts produced by this complex gene is limited. Conversely, increased and disorderly expression of this gene has been observed in a number of types of cancer. This study analyzed the order in which the CD44 variant exons are spliced together in gastrointestinal tumor cell lines and in 20 colonic carcinomas and matched normal mucosa. We used a PCR-based assay to analyze specific exon junctions at the boundary of the standard and variant regions of the CD44 gene transcripts. This revealed characteristically different splicing preferences in colonic tumor and normal tissues. The junction of exon 5 to exon 8 appeared to be the most prevalent in normal mucosa, whereas the presence of junctions between exon 5 and either exon 7, 9, or 11 were increased markedly in tumor samples. These observations demonstrate that the unusual variety of CD44 transcripts in cancer cells results from the fidelity of alternative splicing mechanisms being compromised and are potentially useful as tumor cell markers in diagnostic assays.

Blotting, Southern↗

PubMed1990

Spliced leader RNA sequences can substitute for the essential 5' end of U1 RNA during splicing in a mammalian in vitro system.

L. collosoma or C. elegans SL RNA sequences joined to an adenovirus intron and 3' exon are spliced highly efficiently and accurately in HeLa nuclear extract. After inactivation of U1 snRNPs using RNAase H and a deoxyoligonucleotide complementary to the first 12 nucleotides of U1, splicing of SL RNA-containing constructs continues undiminished, whereas control substrates no longer splice. Since neither binding of U1 snRNPs nor inhibition of splicing is detected using anti-(U1)RNP antibodies, splicing of SL RNA-containing constructs may be entirely U1 snRNP independent. Analyses of altered L. collosoma constructs revealed that the sequence surrounding the 5' splice site is not sufficient to confer U1-independent splicing; the smallest U1-independent region identified so far retains only the first stem-loop of the SL RNA. That sequences responsible for recognition of the 5' splice site can be relocated within the splicing substrate itself reinforces the similarity between group II self-splicing and spliceosome-mediated pre-mRNA splicing.

Animals↗

PubMed2005

New calcium channel mutations predict aberrant RNA splicing in episodic ataxia.

Episodic ataxia type 2 (EA2) is an autosomal dominant channelopathy characterized by paroxysmal cerebellar ataxia. Previous studies suggest that most EA2 cases are associated with mutations in the alpha1A subunit of the P/Q-type voltage-gated calcium channel gene CACNA1A. In a UK national study, the authors analyzed 15 index cases with typical EA2 and identified two unreported intronic mutations that predict aberrant splicing.

Adolescent↗

PubMed1990

Mutations affecting RNA splicing in man are detected more frequently in somatic than in germ cells.

The spectrum of DNA sequence alterations in the hypoxanthine-guanine phosphoribosyltransferase (hprt) gene of HPRTase-deficient T-lymphocytes isolated from the blood of healthy male donors was determined and compared with the spectrum found in patients suffering from genetic diseases (Lesch-Nyhan syndrome or gouty arthritis) associated with a mutation in the same gene. Most of the T-cell mutants still produced hprt mRNA which was converted into cDNA and used for DNA sequence analysis after amplification using the polymerase chain reaction (PCR). In 39% of the 31 analyzed T-cell mutants of normal donors 1 or 2 exons were completely or partially deleted from hprt mRNA, probably because of a mutation in a splice acceptor site. Among patients suffering from the Lesch-Nyhan syndrome or gouty arthritis, the class of splice mutations amounts only to 7%. These data suggest that carriers of splice mutations often do not show the characteristics of HPRTase deficiency associated with these genetic diseases, because correctly spliced hprt mRNA is still produced at a low level.

Arthritis, Gouty↗

PubMed1992

Cell-specific alternative RNA splicing of an FMRFamide gene transcript in the brain.

Individual neurons synthesize different peptide neurotransmitters and neuromodulators. In general, specificity is achieved by transcriptional regulation of neuropeptide-encoding genes. In Lymnaea, the FMRFamide and GDP/SDPFLRFamide neuropeptides are encoded by separate exons. Here we provide evidence that the two exons are part of the same gene and that in neurons expressing the gene the two exons are spliced onto a common upstream exon encoding a hydrophobic leader sequence. In addition, in situ hybridization data show that there is mutually exclusive cytoplasmic expression of each of the neuropeptide-encoding exons. Thus, differential neuropeptide synthesis is likely to be regulated by an alternative splicing mechanism. The cellular specificity of these splicing events is remarkable and suggests that cell-specific alternative splicing may be of major importance in establishing neuronal diversity in this system.

Animals↗

PubMed1994

A new variant of muscle phosphofructokinase deficiency in a Japanese case with abnormal RNA splicing.

A genetic defect was investigated in a newly diagnosed Japanese case with muscle type phosphofructokinase (PFK-M) deficiency. Polymerase chain reaction (PCR) amplification of patient cDNA revealed an in-frame truncation of 165 bases. This was compatible to the complete deletion of exon 19. The rest of the sequence was identical to that of the normal PFK-M cDNA. Sequencing of PCR amplified genomic DNA of the patient revealed a point mutation from G to A at the 5' donor site of intron 19. This mutation resulted in the skipping of exon 19 in the patient mRNA. Homozygosity of this patient was confirmed by allele specific amplification of the genomic DNA. Donor mutations in intron 15 and intron 5 associated with different splicing errors were previously reported to cause this disease. Thus, the human PFK-M gene mutations are heterogeneous, however, the donor mutations and splicing errors would represent one of the frequent causes of this disease.

Adult↗

PubMed1985

Cap-dependent RNA splicing in a HeLa nuclear extract.

We have studied the involvement of the 5' cap structure in the splicing of precursor mRNAs in a HeLa nuclear extract. We show that precursor mRNAs are spliced efficiently only when they possess a cap structure and that preincubation of a HeLa nuclear extract rendered the splicing reaction highly sensitive to inhibition by cap analogues. This sensitization was dependent on exogenous Mg2+ but not exogenous ATP or GTP. These results demonstrate that splicing in a nuclear extract is highly dependent on the cap structure, as was demonstrated for the splicing process in a HeLa whole-cell extract [Konarska, M. M., Padget, R. A. & Sharp, P. A. (1984) Cell 38, 731-736], and thus support the contention that cap recognition is an important feature of eukaryotic mRNA biogenesis.

Adenosine Triphosphate↗

PubMed2004

CDKN1C mutation in Wiedemann-Beckwith syndrome patients reduces RNA splicing efficiency and identifies a splicing enhancer.

Wiedemann-Beckwith syndrome (WBS) is a human overgrowth disorder that is accompanied by an increased risk of embryonal tumors and is associated with dsyregulation of the imprinting of genes in chromosome 11p15.5. Maternally inherited mutations in the imprinted CDKN1C gene are known to be associated with WBS. We have identified a novel mutation in several members of a large family affected by WBS. The mutation is a G --> T change in a run of seven G's near the 5' splice site of intron 3. All obligate carriers and affected individuals carry the mutation, and in each affected case, the allele was inherited maternally, strongly suggesting a role in causing WBS. The mutation is located in a poly-G tract in the intron; intronic G-rich sequences in other genes have been shown to have a role in promoting splicing. In transfected 293HEK cells, we found that the G --> T mutation reduced splicing efficiency. Mutation of all seven G's in the poly-G tract further reduced splicing efficiency, supporting a role for the G-tract as a splicing enhancer. The fibroblasts of one affected patient showed a similar reduction in splicing efficiency. Maternal monoallelic expression of CDKN1C was verified in this patient cell line. However, the total amount of spliced message was not reduced by the mutation in spite of the reduced efficiency of splicing. We discuss the possible role of the splicing defect in the pathogenesis of WBS in this pedigree.

Base Sequence↗

PubMed2024

Effect of the OPHN1 novel variant c.1025+1 G>A on RNA splicing: insights from a minigene assay.

This research analyzes the clinical data, whole-exome sequencing results, and in vitro minigene functional experiments of a child with developmental delay and intellectual disability. The male patient, aged 4, began experiencing epileptic seizures at 3 months post-birth and has shown developmental delay. Rehabilitation training was administered between the ages of one and two. There were no other significant family medical histories. Through comprehensive family exome genetic testing, a hemizygous variant in the 11th exon of the OPHN1 gene was identified in the affected child: c.1025 + 1G > A. Family segregation analysis confirmed the presence of this variant in the patient's mother, which had not been previously reported. According to the ACMG guidelines, this variant was classified as a likely pathogenic variant. In response to this variant, an in vitro minigene functional experiment was designed and conducted, confirming that the mutation affects the normal splicing of the gene's mRNA, resulting in a 56 bp retention on the left side of Intron 11. It was confirmed that OPHN1: c.1025 + 1G > A is the pathogenic cause of X-linked intellectual disabilities in the child, with clinical phenotypes including developmental delay and seizures.

Humans↗

PubMed1983

Alternative RNA splicing of the murine alpha A-crystallin gene: protein-coding information within an intron.

The eye lens contains a structural protein (alpha-crystallin), composed of two homologous primary gene products, alpha A2 and alpha B2. In certain rodents, there is another minor alpha-crystallin polypeptide, alpha Ains, which is identical to alpha A2 except for a 22 amino acid insert between residues 63 and 64 of the alpha A2 chain. Here we show that the mouse contains a single alpha A-crystallin gene, which has a 1376 bp intron separating codons 63 and 64 of the alpha A2-crystallin mRNA. A sequence encoding a 23 amino acid insert peptide was found 266 bp into the intron. The nucleotide borders of this sequence deviate from the AGGT consensus sequence. The DNA sequence encoding the insert peptide hybridizes to a cytoplasmic 14S RNA, demonstrating that it is transcribed in the lens. We propose that the murine alpha A2-crystallin gene generates both the alpha A2 and the alpha Ains mRNAs by alternative splicing.

Amino Acid Sequence↗