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Results for “Alternative Splicing”

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PubMed2005

Characteristics and regulatory elements defining constitutive splicing and different modes of alternative splicing in human and mouse.

Alternative splicing is a major contributor to genomic complexity, disease, and development. Previous studies have captured some of the characteristics that distinguish alternative splicing from constitutive splicing. However, most published work only focuses on skipped exons and/or a single species. Here we take advantage of the highly curated data in the MAASE database (see related paper in this issue) to analyze features that characterize different modes of splicing. Our analysis confirms previous observations about alternative splicing, including weaker splicing signals at alternative splice sites, higher sequence conservation surrounding orthologous alternative exons, shorter exon length, and more frequent reading frame maintenance in skipped exons. In addition, our study reveals potentially novel regulatory principles underlying distinct modes of alternative splicing and a role of a specific class of repeat elements (transposons) in the origin/evolution of alternative exons. These features suggest diverse regulatory mechanisms and evolutionary paths for different modes of alternative splicing.

Alternative Splicing↗

PubMed2006

Murine leukemia virus regulates alternative splicing through sequences upstream of the 5' splice site.

Alternative splicing of the primary transcript plays a key role in retroviral gene expression. In contrast to all known mechanisms that mediate alternative splicing in retroviruses, we found that in murine leukemia virus, distinct elements located upstream of the 5' splice site either inhibited or activated splicing of the genomic RNA. Detailed analysis of the first untranslated exon showed that the primer binding site (PBS) activates splicing, whereas flanking sequences either downstream or upstream of the PBS are inhibitory. This new function of the PBS was independent of its orientation and primer binding but associated with a particular destabilizing role in a proposed secondary structure. On the contrary, all sequences surrounding the PBS that are involved in stem formation of the first exon were found to suppress splicing. Targeted mutations that destabilized the central stem and compensatory mutations of the counter strand clearly validated the concept that murine leukemia virus attenuates its 5' splice site by forming an inhibitory stem-loop in its first exon. Importantly, this mode of splice regulation was conserved in a complete proviral clone. Some of the mutants that increase splicing revealed an opposite effect on translation, implying that the first exon also regulates this process. Together, these findings suggest that sequences upstream of the 5' splice site play an important role in splice regulation of simple retroviruses, directly or indirectly attenuating the efficiency of splicing.

5' Untranslated Regions↗

PubMed1992

Suboptimal 5' and 3' splice sites regulate alternative splicing of Drosophila melanogaster myosin heavy chain transcripts in vitro.

Using a Drosophila cell-free system, we have analyzed the regulation of alternative splicing of Drosophila muscle myosin heavy chain (MHC) transcripts. Splicing of MHC 3' end transcripts results in exclusion of adult-specific alternative exon 18, as is observed in embryonic and larval muscle in vivo. Mutations that strengthen either the 5' or the 3' splice sites of exon 18 do not promote inclusion of this exon. However, strengthening both splice junctions results in efficient removal of both introns and completely inhibits skip splicing. Our data suggest that the affinity of exons 17 and 19, as well as failure of constitutive splicing factors to recognize exon 18 splice sites, causes the exclusion of exon 18 in wild-type transcripts processed in vitro.

Animals↗

PubMed2005

A genome-wide study of dual coding regions in human alternatively spliced genes.

Alternative splicing is a major mechanism for gene product regulation in many multicellular organisms. By using different exon combinations, some coding regions can encode amino acids in multiple reading frames in different transcripts. Here we performed a systematic search through a set of high-quality human transcripts and show that approximately 7% of alternatively spliced genes contain dual (multiple) coding regions. By using a conservative criterion, we found that in these regions most secondary reading frames evolved recently in mammals, and a significant proportion of them may be specific to primates. Based on the presence of in-frame stop codons in orthologous sequences in other animals, we further classified ancestral and derived reading frames in these regions. Our results indicated that ancestral reading frames are usually under stronger selection than are derived reading frames. Ancestral reading frames mainly influence the coding properties of these dual coding regions. Compared with coding regions of the whole genome, ancestral reading frames largely maintain similar nucleotide composition at each codon position and amino acid usage, while derived reading frames are significantly different. Our results also indicated that prior to acquisition of a new reading frame, the suppression of in-frame stop codons in the ancestral state is mainly achieved by one-step transition substitutions at the first or second codon position. Finally, the selective forces imposed on these dual coding regions will also be discussed.

Alternative Splicing↗

PubMed1998

Specific pregnancy-induced angiotensin II type-1 receptor expression in ovine uterine artery does not involve formation of alternate splice variants or alternate promoter usage.

Recently we reported that pregnancy is associated with a dramatic increase in angiotensin II type-1 receptor (AT1-R; both protein and mRNA) in ovine uterine artery endothelial cells (UAEC), which far exceeds that seen in omental (systemic) arteries. Recent reports also suggest that alternate splicing of AT1-R mRNA may play a role in regulation of AT1-R expression in humans. Herein, we have investigated the possibility of alternate transcript splicing/promoter usage in UAEC from pregnant ewes by 5'-RACE (rapid amplification of cDNA 5'-ends). To provide our control "reference" sequences, we first performed 5'-RACE analysis of AT1-R mRNA transcripts in liver, kidney, and adrenal cortex. Analysis of 17 resultant clones showed exceptional homology, indicating that a single identically spliced mRNA product is observed in all three ovine tissues. Homology of the 5'-untranslated region to that of the human was low (34.2%), but four in-context start/stop codons and the beginning of human exons 1 and 5 were highly conserved. Subsequently we isolated 30 individual clones using UAEC RNA from three pregnant ewes and found no evidence of any sequence formed through unique splicing or promoter usage. We conclude that the pregnancy-induced increase in AT1-R expression unique to UAEC during pregnancy is not mediated by splicing of a unique transcript or unique promoter usage.

Angiotensin II↗

PubMed1999

Reduced stability of regularly spliced but not alternatively spliced p53 protein in PARP-deficient mouse fibroblasts.

The interaction between poly(ADP-ribose) polymerase (PARP) and the product of the tumor suppressor gene p53 has been described previously. Here, we have investigated whether PARP deficiency may affect the expression and regulation of wild-type (wt) p53. For this purpose, we have used immortalized cells derived from wt and PARP knockout mice. We have found a clearly reduced basal level of PAb421 immunoreactive wt p53 protein in PARP-deficient cells. The monoclonal antibody PAb421 is known to recognize an epitope in the COOH terminus of normally spliced p53 protein. Under indirect immunofluorescence, this antibody stained nuclei in normal but not in PARP-deficient cells. Despite marked reduction of wt p53 protein in PARP knockout cells, no significant difference of the p53 transcription rate was observed between wt and PARP-deficient cells. Interestingly, in both cell types, an additional p53 transcript representing the alternatively spliced (AS) p53 form was detected. Because of its reactivity with different specific anti-p53 antibodies, we have determined that the p53 protein present in PARP knockout mouse cells possesses characteristic features of AS p53. Our results clearly show that PARP-deficient cells constitutively express the AS form of wt p53 and indicate that the regularly spliced p53 is extremely unstable in the absence of PARP. Moreover, PARP-/- cells fail to transactivate p53-responsive genes. Treatment of PARP-/- cells with genotoxic agents primarily leads to the activation of AS p53 protein.

Animals↗

PubMed2006

Splice-site contribution in alternative splicing of PLP1 and DM20: molecular studies in oligodendrocytes.

Mutations in the proteolipid protein 1 (PLP1) gene cause the X-linked dysmyelinating diseases Pelizaeus-Merzbacher disease (PMD) and spastic paraplegia 2 (SPG2). We examined the severity of the following mutations that were suspected of affecting levels of PLP1 and DM20 RNA, the alternatively spliced products of PLP1: c.453G>A, c.453G>T, c.453G>C, c.453+2T>C, c.453+4A>G, c.347C>A, and c.453+28_+46del (the old nomenclature did not include the methionine codon: G450A, G450T, G450C, IVS3+2T>C, IVS3+4A>G, C344A, and IVS3+28-+46del). These mutations were evaluated by information theory-based analysis and compared with mRNA expression of the alternatively spliced products. The results are discussed relative to the clinical severity of disease. We conclude that the observed PLP1 and DM20 splicing patterns correlated well with predictions of information theory-based analysis, and that the relative strength of the PLP1 and DM20 donor splice sites plays an important role in PLP1 alternative splicing.

Alternative Splicing↗

PubMed2005

Detection and measurement of alternative splicing using splicing-sensitive microarrays.

Splicing and alternative splicing are major processes in the interpretation and expression of genetic information for metazoan organisms. The study of splicing is moving from focused attention on the regulatory mechanisms of a selected set of paradigmatic alternative splicing events to questions of global integration of splicing regulation with genome and cell function. For this reason, parallel methods for detecting and measuring alternative splicing are necessary. We have adapted the splicing-sensitive oligonucleotide microarrays used to estimate splicing efficiency in yeast to the study of alternative splicing in vertebrate cells and tissues. We use gene models incorporating knowledge about splicing to design oligonucleotides specific for discriminating alternatively spliced mRNAs from each other. Here we present the main strategies for design, application, and analysis of spotted oligonucleotide arrays for detection and measurement of alternative splicing. We demonstrate these strategies using a two-intron yeast gene that has been altered to produce different amounts of alternatively spliced RNAs, as well as by profiling alternative splicing in NCI 60 cancer cell lines.

Alternative Splicing↗

PubMed2007

Plant Gene and Alternatively Spliced Variant Annotator. A plant genome annotation pipeline for rice gene and alternatively spliced variant identification with cross-species expressed sequence tag conservation from seven plant species.

The completion of the rice (Oryza sativa) genome draft has brought unprecedented opportunities for genomic studies of the world's most important food crop. Previous rice gene annotations have relied mainly on ab initio methods, which usually yield a high rate of false-positive predictions and give only limited information regarding alternative splicing in rice genes. Comparative approaches based on expressed sequence tags (ESTs) can compensate for the drawbacks of ab initio methods because they can simultaneously identify experimental data-supported genes and alternatively spliced transcripts. Furthermore, cross-species EST information can be used to not only offset the insufficiency of same-species ESTs but also derive evolutionary implications. In this study, we used ESTs from seven plant species, rice, wheat (Triticum aestivum), maize (Zea mays), barley (Hordeum vulgare), sorghum (Sorghum bicolor), soybean (Glycine max), and Arabidopsis (Arabidopsis thaliana), to annotate the rice genome. We developed a plant genome annotation pipeline, Plant Gene and Alternatively Spliced Variant Annotator (PGAA). Using this approach, we identified 852 genes (931 isoforms) not annotated in other widely used databases (i.e. the Institute for Genomic Research, National Center for Biotechnology Information, and Rice Annotation Project) and found 87% of them supported by both rice and nonrice EST evidence. PGAA also identified more than 44,000 alternatively spliced events, of which approximately 20% are not observed in the other three annotations. These novel annotations represent rich opportunities for rice genome research, because the functions of most of our annotated genes are currently unknown. Also, in the PGAA annotation, the isoforms with non-rice-EST-supported exons are significantly enriched in transporter activity but significantly underrepresented in transcription regulator activity. We have also identified potential lineage-specific and conserved isoforms, which are important markers in evolutionary studies. The data and the Web-based interface, RiceViewer, are available for public access at http://RiceViewer.genomics.sinica.edu.tw/.

Base Sequence↗

PubMed2006

Alternative splicing regulation at tandem 3' splice sites.

Alternative splicing (AS) constitutes a major mechanism creating protein diversity in humans. Previous bioinformatics studies based on expressed sequence tag and mRNA data have identified many AS events that are conserved between humans and mice. Of these events, approximately 25% are related to alternative choices of 3' and 5' splice sites. Surprisingly, half of all these events involve 3' splice sites that are exactly 3 nt apart. These tandem 3' splice sites result from the presence of the NAGNAG motif at the acceptor splice site, recently reported to be widely spread in the human genome. Although the NAGNAG motif is common in human genes, only a small subset of sites with this motif is confirmed to be involved in AS. We examined the NAGNAG motifs and observed specific features such as high sequence conservation of the motif, high conservation of approximately 30 bp at the intronic regions flanking the 3' splice site and overabundance of cis-regulatory elements, which are characteristic of alternatively spliced tandem acceptor sites and can distinguish them from the constitutive sites in which the proximal NAG splice site is selected. Our findings imply that AS at tandem splice sites and constitutive splicing of the distal NAG are highly regulated.

Alternative Splicing↗

PubMed1993

Characterization of multiple transcription initiation sites of the ovine insulin-like growth factor-I gene and expression profiles of three alternatively spliced transcripts.

Alternative splicing of ovine insulin-like growth factor-I (IGF-I) transcripts generates three different mRNAs. Class 1 and class 2 transcripts contain exons 1 and 2 spliced to exon 3, respectively. A novel IGF-I mRNA containing exon W is spliced to exon 3 and has been located upstream of exon 1. No in-frame methionine codon was present in exon W and therefore translation is proposed to initiate at the methionine codon present in exon 3. Using primer extension, transcription initiation sites were found 179, 336, and 368 nucleotides upstream of exon 1 and 86, 96, 131, and approximately 850 nucleotides upstream of exon 2. The locations of these transcription initiation sites are well conserved among mammalian and avian IGF-I genes. Expression of exon 1-, 2-, and W-specific transcripts was examined in brain, heart, kidney, liver, lung, skeletal muscle, and spleen from adult ewes or 75-day fetal lambs using a reverse transcriptase-polymerase chain reaction assay. Exon 1 transcripts were the most abundant and found in all fetal and adult tissues. Exon 2 transcripts were found in all tissues and were generally expressed the highest in adult liver. Exon W transcripts were also found to be expressed in all tissues examined. Thus, the three alternatively spliced ovine IGF-I transcripts were expressed in a variety of fetal and adult tissues.

Amino Acid Sequence↗

PubMed2004

No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions.

BACKGROUND: Alternative splicing is an efficient mechanism for increasing the variety of functions fulfilled by proteins in a living cell. It has been previously demonstrated that alternatively spliced regions often comprise functionally important and conserved sequence motifs. The objective of this work was to test the hypothesis that alternative splicing is correlated with contact regions of protein-protein interactions. RESULTS: Protein sequence spans involved in contacts with an interaction partner were delineated from atomic structures of transient interaction complexes and juxtaposed with the location of alternatively spliced regions detected by comparative genome analysis and spliced alignment. The total of 42 alternatively spliced isoforms were identified in 21 amino acid chains involved in biomolecular interactions. Using this limited dataset and a variety of sophisticated counting procedures we were not able to establish a statistically significant correlation between the positions of protein interaction sites and alternatively spliced regions. CONCLUSIONS: This finding contradicts a naïve hypothesis that alternatively spliced regions would correlate with points of contact. One possible explanation for that could be that all alternative splicing events change the spatial structure of the interacting domain to a sufficient degree to preclude interaction. This is indirectly supported by the observed lack of difference in the behaviour of relatively short regions affected by alternative splicing and cases when large portions of proteins are removed. More structural data on complexes of interacting proteins, including structures of alternative isoforms, are needed to test this conjecture.

Alternative Splicing↗

PubMed2006

Different levels of alternative splicing among eukaryotes.

Alternative splicing increases transcriptome and proteome diversification. Previous analyses aiming at comparing the rate of alternative splicing between different organisms provided contradicting results. These contradicting results were attributed to the fact that both analyses were dependent on the expressed sequence tag (EST) coverage, which varies greatly between the tested organisms. In this study we compare the level of alternative splicing among eight different organisms. By employing an EST independent approach we reveal that the percentage of genes and exons undergoing alternative splicing is higher in vertebrates compared with invertebrates. We also find that alternative exons of the skipping type are flanked by longer introns compared to constitutive ones, whereas alternative 5' and 3' splice sites events are generally not. In addition, although the regulation of alternative splicing and sizes of introns and exons have changed during metazoan evolution, intron retention remained the rarest type of alternative splicing, whereas exon skipping is more prevalent and exhibits a slight increase, from invertebrates to vertebrates. The difference in the level of alternative splicing suggests that alternative splicing may contribute greatly to the mammal higher level of phenotypic complexity, and that accumulation of introns confers an evolutionary advantage as it allows increasing the number of alternative splicing forms.

Algorithms↗

PubMed1995

Two strong 5' splice sites and competing, suboptimal 3' splice sites involved in alternative splicing of human immunodeficiency virus type 1 RNA.

The human immunodeficiency virus type 1 (HIV-1) genome contains 20 exons that are alternatively spliced from 16 splice sites to generate more than 40 different mRNAs, including incompletely spliced and unspliced mRNAs. In contrast to avian retroviral RNA, which has a cis-acting element in gag that negatively regulates splicing (NRS), HIV-1 RNA did not have any NRS sequences in the gag or pol genes detectable by a splicing inhibition assay. However, this assay demonstrated that the HIV-1 first 5' splice site competed with a cellular 5' splice site, suggesting that HIV-1 may have some strong splice sites. To extend this observation, we used a splice site swapping strategy to determine the efficiency of 14 HIV-1 splice sites in human beta globin chimeras tested in transient transfection experiments. While the 1st HIV-1 5' splice site used in all spliced transcripts and the 4th 5' splice site used in most of the 2-kb transcripts were efficient, the other splice sites, including all the 3' splice sites, were less efficient, ranging in use from 25 to 60%. We propose that this range of splice site efficiencies contributes to the regulation of alternative splicing of HIV-1 mRNAs.

Alternative Splicing↗

PubMed2006

Maps, codes, and sequence elements: can we predict the protein output from an alternatively spliced locus?

Alternative splicing choices are governed by splicing regulatory protein interactions with splicing silencer and enhancer elements present in the pre-mRNA. However, the prediction of these choices from genomic sequence is difficult, in part because the regulators can act as either enhancers or silencers. A recent study describes how for a particular neuronal splicing regulatory protein, Nova, the location of its binding sites is highly predictive of the protein's effect on an exon's splicing.

Alternative Splicing↗

PubMed1998

Conserved use of a non-canonical 5' splice site (/GA) in alternative splicing by fibroblast growth factor receptors 1, 2 and 3.

The two classes of sequences for recognition and splicing of pre-mRNA in eukaryotes, GT-AG and AT-AC, are characterized by the nearly invariant dinucleotides present at the extreme 5' (donor) and 3' (acceptor) ends of the intron. Amongst GT-AG introns, which comprise the vast majority, the more extended consensus sequence at the 5' splice site isACAG/GTAGAGT (where / indicates the exon-intron boundary). This sequence is complementary to part of the U1 snRNA and is important in intron recognition. We have determined the genomic structure of the mouse fibroblast growth factor receptor 2 gene (Fgfr2) and identified a divergent 5' splice site (ACA/GAAAGT), conserved in FGFR1 , - 2 and - 3 from humans, mice and Xenopus that is used for alternative splicing of a hexanucleotide sequence, encoding Val-Thr, at the end of exon 10. This is the only example known of the use of /GA in vertebrate splicing. Similarities to a splice site in the Antennapedia gene of Drosophila suggest that this variant motif is involved in alternative splicing of short sequences at the 5' splice site. Inclusion or exclusion of the Val-Thr dipeptide may play an important role in controlling FGFR signalling through the Ras/MAPK pathway.

Alternative Splicing↗

PubMed1998

The rodent alphaA-crystallin gene: mutagenesis of a non-consensus 5'-splice site to study alternative splicing in vivo.

alphaA-Crystallin is a member of the small heat shock protein family that is abundantly expressed as a structural component in the vertebrate eye lens. In lenses of rodents and some other mammals, there occurs a minor variant of alphaA-crystallin, which has an insertion of 23 amino acid residues. This variant, alphaA(ins)-crystallin, results from differential integration of an optional exon into a small fraction of the mRNA. We have studied whether this alternative splicing is caused by a non-consensus cytosine in the 5' splice site adjacent to the optional exon. After replacement of the aberrant cytosine in the hamster alphaA-crystallin gene by a consensus thymine, and transient transfection of this gene in Chinese Hamster Ovary cells, the optional exon is indeed almost completely spliced into the mature mRNA. In contrast, replacement of the cytosine by adenine or guanine completely abolishes the splicing of the optional exon. Our results confirm that alternative splicing of the alphaA-crystallin primary transcript is mainly due to a non-consensus 5' splice site nucleotide. However, we conclude that the small size of the optional exon is probably an additional contributing factor and therefore it seems that the splicing mechanism is based on recognition of exons rather than introns.

Alternative Splicing↗

PubMed2005

MAASE: an alternative splicing database designed for supporting splicing microarray applications.

Alternative splicing is a prominent feature of higher eukaryotes. Understanding of the function of mRNA isoforms and the regulation of alternative splicing is a major challenge in the post-genomic era. The development of mRNA isoform sensitive microarrays, which requires precise splice-junction sequence information, is a promising approach. Despite the availability of a large number of mRNAs and ESTs in various databases and the efforts made to align transcript sequences to genomic sequences, existing alternative splicing databases do not offer adequate information in an appropriate format to aid in splicing array design. Here we describe our effort in constructing the Manually Annotated Alternatively Spliced Events (MAASE) database system, which is specifically designed to support splicing microarray applications. MAASE comprises two components: (1) a manual/computational annotation tool for the efficient extraction of critical sequence and functional information for alternative splicing events and (2) a user-friendly database of annotated events that allows convenient export of information to aid in microarray design and data analysis. We provide a detailed introduction and a step-by-step user guide to the MAASE database system to facilitate future large-scale annotation efforts, integration with other alternative splicing databases, and splicing array fabrication.

Alternative Splicing↗