scholarly journals Sequence and Evolutionary Features for the Alternatively Spliced Exons of Eukaryotic Genes

2019 ◽  
Vol 20 (15) ◽  
pp. 3834 ◽  
Author(s):  
Shi-Yi Chen ◽  
Cao Li ◽  
Xianbo Jia ◽  
Song-Jia Lai
Keyword(s):  
Alternative Splicing ◽  
High Throughput Sequencing ◽  
Point Of View ◽  
Sequencing Technologies ◽  
Eukaryotic Genes ◽  
Splicing Pattern ◽  
Evolutionary Features ◽  
Alternatively Spliced ◽  
Alternative Splicing Events ◽  
Alternatively Spliced Exons

Alternative splicing of pre-mRNAs is a crucial mechanism for maintaining protein diversity in eukaryotes without requiring a considerable increase of genes in the number. Due to rapid advances in high-throughput sequencing technologies and computational algorithms, it is anticipated that alternative splicing events will be more intensively studied to address different kinds of biological questions. The occurrences of alternative splicing mean that all exons could be classified to be either constitutively or alternatively spliced depending on whether they are virtually included into all mature mRNAs. From an evolutionary point of view, therefore, the alternatively spliced exons would have been associated with distinctive biological characteristics in comparison with constitutively spliced exons. In this paper, we first outline the representative types of alternative splicing events and exon classification, and then review sequence and evolutionary features for the alternatively spliced exons. The main purpose is to facilitate understanding of the biological implications of alternative splicing in eukaryotes. This knowledge is also helpful to establish computational approaches for predicting the splicing pattern of exons.

scholarly journals Influence of Intron Length on Alternative Splicing of CD44

1998 ◽  
Vol 18 (10) ◽  
pp. 5930-5941 ◽  
Author(s):  
Martyn V. Bell ◽  
Alison E. Cowper ◽  
Marie-Paule Lefranc ◽  
John I. Bell ◽  
Gavin R. Screaton
Keyword(s):  
Alternative Splicing ◽  
Genomic Structure ◽  
Single Gene ◽  
Intron Length ◽  
Protein Isoforms ◽  
Major Influence ◽  
Eukaryotic Genes ◽  
Alternatively Spliced ◽  
Alternatively Spliced Exons

ABSTRACT Although the splicing of transcripts from most eukaryotic genes occurs in a constitutive fashion, some genes can undergo a process of alternative splicing. This is a genetically economical process which allows a single gene to give rise to several protein isoforms by the inclusion or exclusion of sequences into or from the mature mRNA. CD44 provides a unique example; more than 1,000 possible isoforms can be produced by the inclusion or exclusion of a central tandem array of 10 alternatively spliced exons. Certain alternatively spliced exons have been ascribed specific functions; however, independent regulation of the inclusion or skipping of each of these exons would clearly demand an extremely complex regulatory network. Such a network would involve the interaction of many exon-specific trans-acting factors with the pre-mRNA. Therefore, to assess whether the exons are indeed independently regulated, we have examined the alternative exon content of a large number of individual CD44 cDNA isoforms. This analysis shows that the downstream alternatively spliced exons are favored over those lying upstream and that alternative exons are often included in blocks rather than singly. Using a novel in vivo alternative splicing assay, we show that intron length has a major influence upon the alternative splicing of CD44. We propose a kinetic model in which short introns may overcome the poor recognition of alternatively spliced exons. These observations suggest that for CD44, intron length has been exploited in the evolution of the genomic structure to enable tissue-specific patterns of splicing to be maintained.

scholarly journals Trans-acting Factors Required for Inclusion of Regulated Exons in the Ultrabithorax mRNAs of Drosophila melanogaster

Genetics ◽  
1999 ◽  
Vol 151 (4) ◽  
pp. 1517-1529 ◽  
Author(s):  
James M Burnette ◽  
Allyson R Hatton ◽  
A Javier Lopez
Keyword(s):  
Drosophila Melanogaster ◽  
Alternative Splicing ◽  
P Element ◽  
Splicing Factors ◽  
Loss Of Function ◽  
Large Collection ◽  
Splicing Pattern ◽  
Alternatively Spliced ◽  
Hypomorphic Alleles

Abstract Alternatively spliced Ultrabithorax mRNAs differ by the presence of internal exons mI and mII. Two approaches were used to identify trans-acting factors required for inclusion of these cassette exons. First, mutations in a set of genes implicated in the control of other alternative splicing decisions were tested for dominant effects on the Ubx alternative splicing pattern. To identify additional genes involved in regulation of Ubx splicing, a large collection of deficiencies was tested first for dominant enhancement of the haploinsufficient Ubx haltere phenotype and second for effects on the splicing pattern. Inclusion of the cassette exons in Ubx mRNAs was reduced strongly in heterozygotes for hypomorphic alleles of hrp48, which encodes a member of the hnRNP A/B family and is implicated in control of P-element splicing. Significant reductions of mI and mII inclusion were also observed in heterozygotes for loss-of-function alleles of virilizer, fl(2)d, and crooked neck. The products of virilizer and fl(2)d are also required for Sxl autoregulation at the level of splicing; crooked neck encodes a protein with structural similarities to yeast-splicing factors Prp39p and Prp42p. Deletion of at least five other loci caused significant reductions in the inclusion of mI and/or mII. Possible roles of identified factors are discussed in the context of the resplicing strategy for generation of alternative Ubx mRNAs.

scholarly journals The gene structure and hypervariability of the complete Penaeus monodon Dscam gene

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kantamas Apitanyasai ◽  
Shiao-Wei Huang ◽  
Tze Hann Ng ◽  
Shu-Ting He ◽  
Yu-Hsun Huang ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Gene Structure ◽  
Transmembrane Domain ◽  
Stop Codon ◽  
Penaeus Monodon ◽  
Cytoplasmic Tail ◽  
Extracellular Region ◽  
Alternatively Spliced ◽  
Alternatively Spliced Exons ◽  
Selection Of

Abstract Using two advanced sequencing approaches, Illumina and PacBio, we derive the entire Dscam gene from an M2 assembly of the complete Penaeus monodon genome. The P. monodon Dscam (PmDscam) gene is ~266 kbp, with a total of 44 exons, 5 of which are subject to alternative splicing. PmDscam has a conserved architectural structure consisting of an extracellular region with hypervariable Ig domains, a transmembrane domain, and a cytoplasmic tail. We show that, contrary to a previous report, there are in fact 26, 81 and 26 alternative exons in N-terminal Ig2, N-terminal Ig3 and the entirety of Ig7, respectively. We also identified two alternatively spliced exons in the cytoplasmic tail, with transmembrane domains in exon variants 32.1 and 32.2, and stop codons in exon variants 44.1 and 44.2. This means that alternative splicing is involved in the selection of the stop codon. There are also 7 non-constitutive cytoplasmic tail exons that can either be included or skipped. Alternative splicing and the non-constitutive exons together produce more than 21 million isoform combinations from one PmDscam locus in the P. monodon gene. A public-facing database that allows BLAST searches of all 175 exons in the PmDscam gene has been established at http://pmdscam.dbbs.ncku.edu.tw/.

Multiple variants and a differential splicing pattern of kinectin in human hepatocellular carcinoma

2004 ◽  
Vol 82 (2) ◽  
pp. 321-327 ◽  
Author(s):  
Hong-Cheng Wang ◽  
Yan-Rong Su ◽  
Ke-Jun Han ◽  
Xue-Wen Pang ◽  
Ji-Run Peng ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Alternative Splicing ◽  
Tissue Sample ◽  
Cdna Expression Library ◽  
Serological Analysis ◽  
Expression Library ◽  
Humoral Immune ◽  
Cdna Expression ◽  
Splicing Pattern ◽  
Alternatively Spliced

To extend the search for hepatocellular carcinoma (HCC) associated antigens with immunogenicity for clinical applications, we constructed a cDNA expression library using resected human HCC tissue sample and screened it by serological analysis of recombinant cDNA expression library (SEREX) with autologous and allogeneic sera. A total of 24 distinct antigens were isolated and kinectin was the antigen most frequently identified. We found that kinectin was alternatively spliced at four sites and obtained all eight theoretical forms of variant, six by SEREX and two by RT-PCR, from the different splicing combinations of the last three sites. In addition, the splicing patterns of four sites were analyzed. Variant containing D2 was overexpressed in cancerous tissues and this alteration may be tumor associated. The four splicing sites, the variants generated by alternative splicing, and the humoral immune response in HCC patients, may help to analyze the role of kinectin in human HCC cell biology.Key words: alternative splicing, antibody response, hepatocellular carcinoma, kinectin, serological analysis of recombinant cDNA expression library (SEREX).

scholarly journals Targeted RNA-Seq profiling of splicing pattern in the DMD gene: exons are mostly constitutively spliced in human skeletal muscle

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Anne-Laure Bougé ◽  
Eva Murauer ◽  
Emmanuelle Beyne ◽  
Julie Miro ◽  
Jessica Varilh ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Alternative Splicing ◽  
Cdna Sequence ◽  
454 Sequencing ◽  
Exon Skipping ◽  
Rna Seq ◽  
Splicing Pattern ◽  
Alternative Splicing Events ◽  
Diagnostic Research ◽  
Dmd Gene

Abstract We have analysed the splicing pattern of the human Duchenne Muscular Dystrophy (DMD) transcript in normal skeletal muscle. To achieve depth of coverage required for the analysis of this lowly expressed gene in muscle, we designed a targeted RNA-Seq procedure that combines amplification of the full-length 11.3 kb DMD cDNA sequence and 454 sequencing technology. A high and uniform coverage of the cDNA sequence was obtained that allowed to draw up a reliable inventory of the physiological alternative splicing events in the muscular DMD transcript. In contrast to previous assumptions, we evidenced that most of the 79 DMD exons are constitutively spliced in skeletal muscle. Only a limited number of 12 alternative splicing events were identified, all present at a very low level. These include previously known exon skipping events but also newly described pseudoexon inclusions and alternative 3′ splice sites, of which one is the first functional NAGNAG splice site reported in the DMD gene. This study provides the first RNA-Seq-based reference of DMD splicing pattern in skeletal muscle and reports on an experimental procedure well suited to detect condition-specific differences in this low abundance transcript that may prove useful for diagnostic, research or RNA-based therapeutic applications.

scholarly journals Origin, Splicing, and Expression of Rodent Amelogenin Exon 8

2006 ◽  
Vol 85 (10) ◽  
pp. 894-899 ◽  
Author(s):  
J.D. Bartlett ◽  
R. L. Ball ◽  
T. Kawai ◽  
C.E. Tye ◽  
M. Tsuchiya ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Splice Site ◽  
Site Selection ◽  
Proteolytic Processing ◽  
Rt Pcr ◽  
Splice Site Selection ◽  
Rna Transcripts ◽  
Splicing Pattern ◽  
Alternatively Spliced ◽  
Gene Structures

Amelogenin RNA transcripts undergo extensive alternative splicing, and MMP-20 processes the isoforms following their secretion. Since amelogenins have been ascribed cell-signaling activities, we asked if a lack of proteolytic processing by MMP-20 affects amelogenin signaling and consequently alters amelogenin splice site selection. RT-PCR analyses of amelogenin mRNA between control and Mmp20− /−mice revealed no differences in the splicing pattern. We characterized 3 previously unidentified amelogenin alternatively spliced transcripts and demonstrated that exon-8-encoded amelogenin isoforms are processed by MMP-20. Transcripts with exon 8 were expressed approximately five-fold less than those with exon 7. Analyses of the mouse and rat amelogenin gene structures confirmed that exon 8 arose in a duplication of exons 4 through 5, with translocation of the copy downstream of exon 7. No downstream genomic sequences homologous to exons 4–5 were present in the bovine or human amelogenin genes, suggesting that this translocation occurred only in rodents.

scholarly journals Detecting gene subnetworks under selection in biological pathways

2017 ◽  
Author(s):  
Alexandre Gouy ◽  
Joséphine T. Daub ◽  
Laurent Excoffier
Keyword(s):  
Complex Traits ◽  
Gene Networks ◽  
High Throughput Sequencing ◽  
Biological Pathways ◽  
General Idea ◽  
Human Populations ◽  
Sequencing Technologies ◽  
Genetic Components ◽  
Evolutionary Features ◽  
Gene Network Analysis

ABSTRACTAdvances in high throughput sequencing technologies have created a gap between data production and functional data analysis. Indeed, phenotypes result from interactions between numerous genes, but traditional methods treat loci independently, missing important knowledge brought by network-level emerging properties. Therefore, evidencing selection acting on multiple genes affecting the evolution of complex traits remains challenging. In this context, gene network analysis provides a powerful framework to study the evolution of adaptive traits and facilitates the interpretation of genome-wide data. To tackle this problem, we developed a method to analyse gene networks that is suitable to evidence polygenic selection. The general idea is to search biological pathways for subnetworks of genes that directly interact with each other and that present unusual evolutionary features. Subnetwork search is a typical combinatorial optimization problem that we solve using a simulated annealing approach. We have applied our methodology to find signals of adaptation to high-altitude in human populations. We show that this adaptation has a clear polygenic basis and is influenced by many genetic components. Our approach improves on classical tests for selection based on single genes by identifying both new candidate genes and new biological processes involved in adaptation to altitude.

The RNA Environment Of Hematopoietic Stem Cells

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 1171-1171
Author(s):  
George R Wendt ◽  
Motohiko Oshima ◽  
Atsushi Iwama
Keyword(s):  
Stem Cells ◽  
Alternative Splicing ◽  
Hematopoietic Stem Cells ◽  
Rna Editing ◽  
Critical Role ◽  
Hematopoietic Stem ◽  
Rna Biology ◽  
Alternatively Spliced ◽  
Non Coding Rnas ◽  
Alternative Splicing Events

Abstract Recent reports in RNA biology have suggested that long non-coding RNAs, edited RNAs, and alternatively spliced RNAs (henceforth referred to as non-canonical RNAs) play a relatively unclear but critical role in numerous cells, tissues, and diseases. Of interest to hematology, several recent studies have also shown that these non-canonical RNAs all play various roles in both normal and malignant hematopoiesis, but no study yet has comprehensively examined these non-canonical RNAs in hematopoietic stem cells (HSCs). To this end, we conducted microarray and RNAseq analyses of mouse hematopoietic cells at various stages of differentiation. Microarray analysis detected several thousand possible lincRNAs expressed in hematopoietic stem and progenitor cells (HSPCs), several hundred of which were significantly enriched in CD34-LSKs compared to more differentiated populations. RNAseq analysis provided a more detailed look at these non-coding RNAs, as well as a slightly more conservative estimate of the abundance and structure of the long non-coding RNAs expressed and significantly enriched in HSPCs. In addition to examining lincRNAs, RNAseq data allowed us to profile alternative splicing events and RNA editing events in HSPCs. Interestingly, several hundred potentially significant HSC-specific alternative splicing events and RNA editing events were also discovered. In order to test whether these non-canonical RNAs play a functional role in HSPCs we performed shRNA mediated knockdown of several interesting HSC-specific lincRNAs and alternatively-spliced transcripts. We found that knockdown of several of these candidates was incompatible with hematopoiesis, both in vitro and in vivo. To better understand how these particular non-canonical RNAs function in HSCs, we are currently carrying out RNA FISH studies. In this study, we explored the RNA environment of HSCs and compared it to their downstream progenitors. We discovered several hundred novel non-coding transcripts, hundreds of alternative splicing events and hundreds of RNA editing events unique to HSCs. Functional investigation of some of these events revealed that these non-canonical RNAs do indeed play a critical role in HSC maintenance. The data presented here should eventually be an asset to other HSC researchers interested in the RNA biology of HSCs. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Principles and Practical Considerations for the Analysis of Disease-Associated Alternative Splicing Events Using the Gateway Cloning-Based Minigene Vectors pDESTsplice and pSpliceExpress

2021 ◽  
Vol 22 (10) ◽  
pp. 5154
Author(s):  
Elena Putscher ◽  
Michael Hecker ◽  
Brit Fitzner ◽  
Peter Lorenz ◽  
Uwe Klaus Zettl
Keyword(s):  
Alternative Splicing ◽  
Rna Splicing ◽  
Region Of Interest ◽  
Restriction Enzymes ◽  
Genomic Region ◽  
Gateway Cloning ◽  
Splicing Pattern ◽  
Processing Step ◽  
Alternative Splicing Events ◽  
Minigene Assay

Splicing is an important RNA processing step. Genetic variations can alter the splicing process and thereby contribute to the development of various diseases. Alterations of the splicing pattern can be examined by gene expression analyses, by computational tools for predicting the effects of genetic variants on splicing, and by splicing reporter minigene assays for studying alternative splicing events under defined conditions. The minigene assay is based on transient transfection of cells with a vector containing a genomic region of interest cloned between two constitutive exons. Cloning can be accomplished by the use of restriction enzymes or by site-specific recombination using Gateway cloning. The vectors pDESTsplice and pSpliceExpress represent two minigene systems based on Gateway cloning, which are available through the Addgene plasmid repository. In this review, we describe the features of these two splicing reporter minigene systems. Moreover, we provide an overview of studies in which determinants of alternative splicing were investigated by using pDESTsplice or pSpliceExpress. The studies were reviewed with regard to the investigated splicing regulatory events and the experimental strategy to construct and perform a splicing reporter minigene assay. We further elaborate on how analyses on the regulation of RNA splicing offer promising prospects for gaining important insights into disease mechanisms.

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