scholarly journals An atlas of transposable element-derived alternative splicing in cancer

2020 ◽  
Vol 375 (1795) ◽  
pp. 20190342 ◽  
Author(s):  
Evan A. Clayton ◽  
Lavanya Rishishwar ◽  
Tzu-Chuan Huang ◽  
Saurabh Gulati ◽  
Dongjo Ban ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Transposable Element ◽  
Alternative Splice ◽  
Splice Variants ◽  
Cancer Genes ◽  
Splice Sites ◽  
Transcript Isoforms ◽  
Alternatively Spliced ◽  
Cancer Types ◽  
Cancer Tissues

Transposable element (TE)-derived sequences comprise more than half of the human genome, and their presence has been documented to alter gene expression in a number of different ways, including the generation of alternatively spliced transcript isoforms. Alternative splicing has been associated with tumorigenesis for a number of different cancers. The objective of this study was to broadly characterize the role of human TEs in generating alternatively spliced transcript isoforms in cancer. To do so, we screened for the presence of TE-derived sequences co-located with alternative splice sites that are differentially used in normal versus cancer tissues. We analysed a comprehensive set of alternative splice variants characterized for 614 matched normal-tumour tissue pairs across 13 cancer types, resulting in the discovery of 4820 TE-generated alternative splice events distributed among 723 cancer-associated genes. Short interspersed nuclear elements (Alu) and long interspersed nuclear elements (L1) were found to contribute the majority of TE-generated alternative splice sites in cancer genes. A number of cancer-associated genes, including MYH11 , WHSC1 and CANT1 , were shown to have overexpressed TE-derived isoforms across a range of cancer types. TE-derived isoforms were also linked to cancer-specific fusion transcripts, suggesting a novel mechanism for the generation of transcriptome diversity via trans -splicing mediated by dispersed TE repeats. This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation'.

scholarly journals Amount of RNA secondary structure required to induce an alternative splice.

1987 ◽  
Vol 7 (9) ◽  
pp. 3194-3198 ◽  
Author(s):  
D Solnick ◽  
S I Lee
Keyword(s):  
Alternative Splicing ◽  
Secondary Structure ◽  
Alternative Splice ◽  
Rna Secondary Structure ◽  
Secondary Structures ◽  
Splice Sites ◽  
Perfect Complementarity ◽  
Set Up

We set up an alternative splicing system in vitro in which the relative amounts of two spliced RNAs, one containing and the other lacking a particular exon, were directly proportional to the length of an inverted repeat inserted into the flanking introns. We then used the system to measure the effect of intramolecular complementarity on alternative splicing in vivo. We found that an alternative splice was induced in vivo only when the introns contained more than approximately 50 nucleotides of perfect complementarity, that is, only when the secondary structure was much more stable than most if not all possible secondary structures in natural mRNA precursors. We showed further that intron insertions containing long complements to splice sites and a branch point inhibited splicing in vitro but not in vivo. These results raise the possibility that in cells most pre-mRNA secondary structures either are not maintained long enough to influence splicing choices, or never form at all.

Characterization of three alternative splice variants associated with the Arabidopsis rhomboid protein gene At1g74130

Botany ◽  
2013 ◽  
Vol 91 (12) ◽  
pp. 840-849 ◽  
Author(s):  
Joshua Powles ◽  
Katharine Sedivy-Haley ◽  
Eric Chapman ◽  
Kenton Ko
Keyword(s):  
Alternative Splicing ◽  
Alternative Splice ◽  
Splice Variant ◽  
Serine Proteases ◽  
Transmembrane Domain ◽  
Splice Variants ◽  
Genes Encoding ◽  
Different Characteristics ◽  
Alternative Splice Variants

Rhomboid serine proteases are grouped into three main types — secretases, presenilin-like associated rhomboid-like (PARL) proteases, and “inactive” rhomboid proteins. Although the three rhomboid groups are distinct, the different types are likely to operate within the same cell or compartment, such as observed in the plastids of Arabidopsis. There are four distinct plastid rhomboid genes at play in Arabidopsis plastids, two for active types (At1g25290 and At5g25752) and two for inactive forms (At1g74130 and At1g74140). The number of working plastid rhomboids is further increased by alternative splicing, as reported for At1g25290. To understand how the plastid rhomboid system works, it is necessary to identify all rhomboid forms in play. To this end, this study was designed to examine the alternative splicing activities of At1g74130, one of the two genes encoding proteolytically “inactive” plastid rhomboids. The exon mapping and DNA sequencing results obtained here indicate the presence of three prominent alternative splice variants in the At1g74130 transcript population. The dominant splice variant, L, encodes the full-length protein. The other two splice variants, M and S, produce proteins lacking sections from the carboxyl transmembrane domain region. The splice variants M and S appear to be at levels with functional potential and appear to adjust relative to each other during development and in response to changes in the level of Tic40, a component of the plastid translocon. The splice variant proteins themselves exhibit different characteristics with respect to rhomboid protein–substrate interactions. These differences were observed in bacterial co-expression pull-down assays and in yeast mitochondrial studies. When considered together, the data suggest that the alternative splicing of At1g74130 bears functional significance in Arabidopsis and is likely to be part of a mechanism for diversifying plastid rhomboid function.

scholarly journals Identification of embryo specific human isoforms using a database of predicted alternative splice forms

2006 ◽  
Vol 3 (1) ◽  
pp. 1-10
Author(s):  
Heike Pospisil
Keyword(s):  
Alternative Splice ◽  
Splice Site ◽  
Splice Variants ◽  
Main Idea ◽  
Protein Isoforms ◽  
Unequal Distribution ◽  
Interesting Candidate ◽  
Alternatively Spliced ◽  
Specific Alternative ◽  
Splice Forms

Abstract Alternative splicing is one of the most important mechanisms to generate a large number of mRNA and protein isoforms from a small number of genes. Its study became one of the hot topics in computational genome analysis. The repository EASED (Extended Alternatively Spliced EST Database, http://eased.bioinf.mdc-berlin.de/) stores a large collection of splice variants predicted from comparing the human genome against EST databases. It enables finding new unpublished splice forms that could be interesting candidate genes for stage specific, diseases specific or tissue specific splicing. The main idea behind selecting specific splice forms is to compare the number and the origin of ESTs confirming one isoform with the number and the origin of ESTs confirming the opposite isoform. A measure asDcs is introduced to take into account the unequal distribution of ESTs per splice site on one hand, and the possible uncertainties due to the relatively low quality of EST data on the other hand. First, the number of ESTs per splice site is scaled with a modified Hill function. The measure asDcs computes in the second step the distance of each pair of ESTs from equipartition. Equipartition exists if for every number of adult ESTs the same number of embryonic ESTs. The effect of several input parameters for the scaling of true EST values is analysed and can be reproduced on http://cardigan.zbh.uni-hamburg.de/asDcs. Some of the obtained best scoring hits for selected parameters (transcription factor P65, drebrin, and fetuin) have been already described in literature as been involved in embryonic development. This result shows the plausibility of this approach and looks promising for the identification of unplublished embryo specific alternative splice sites in human.

scholarly journals Myosin light-chain 1/3 gene alternative splicing: cis regulation is based upon a hierarchical compatibility between splice sites.

1990 ◽  
Vol 10 (5) ◽  
pp. 2133-2144 ◽  
Author(s):  
M E Gallego ◽  
B Nadal-Ginard
Keyword(s):  
Alternative Splicing ◽  
Light Chain ◽  
Myosin Light Chain ◽  
Cooperative Interaction ◽  
Splice Sites ◽  
Exon 2 ◽  
Exon 1 ◽  
Alternatively Spliced ◽  
Flanking Sequences ◽  
Exon 4

The mechanisms involved in the selective joining of appropriate 5' and 3' splice sites are still poorly understood in both constitutive and alternatively spliced genes. With two promoters associated with different exons, the myosin light-chain 1/3 gene generates two pre-mRNAs that also differ by the use of a pair of internal exons, 3 and 4, that are spliced in a mutually exclusive fashion. When the promoter upstream from exon 1 is used, only exon 4 is included. If the promoter upstream from exon 2 is used, only exon 3 is included. In an attempt to understand the molecular basis for the mutually exclusive behavior of these two exons and the basis of their specific selection, a number of minigene constructs containing exons 3 and 4 were tested in a variety of homologous or heterologous cis and trans environments. The results demonstrate that the mutually exclusive behavior of myosin light-chain exons 3 and 4 and selection between the two exons are cis regulated and are affected by the nature of the flanking sequences. Both exons competed for the common flanking 5' and 3' splice sites. Flanking exons were found that favored inclusion into mature mRNA of exon 3, exon 4, both, or neither, suggesting a specific cooperative interaction between certain 5' and 3' splice sites. Thus, alternative splicing of myosin light-chain 1/3 pre-mRNAs is regulated in cis by a hierarchy of compatibilities between pairs of 5' and 3' splice sites.

scholarly journals Splice variants’ role in mediating different disease states in tissue requiring ion transduction through calcium channel for function

2017 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Alternative Splicing ◽  
Calcium Channel ◽  
Alternative Splice ◽  
Splice Variant ◽  
Splice Variants ◽  
Energetic Cost ◽  
Hypoxic Stress ◽  
Tissue Samples ◽  
Hek 293 ◽  
Selection Of

Structure informs function, and this may be the evolutionary reason why alternative splicing, which is capable of generating different variants of the same protein, arise. But, given the energetic cost of generating different splice variants for testing their capability at a specific task, which incurs cellular functional uncertainty; as well as the exertion of differing physiological effects on cells that may translate into diseased states, what is the evolutionary advantage of this process? Additionally, what are the factors that select a specific variant for a presented task? Using heart tissue samples exposed to hypoxia stress as model system, this research idea entails the illumination of single nucleotide polymorphisms (SNP) of the calcium channel transporter, Cav 1.2 gene in the population through gene sequencing followed by bioinformatic analysis for alternative splice sites. This would be followed by a scan for alternative splice variants through colony polymerase chain reaction using universal primers for Cav 1.2 gene. Confirmation of splice variant identity through Western blot laid the stage for subsequent efforts at cloning and expressing the variant gene in HEK 293 cells lacking endogenous expression of Cav 1.2, for biophysical characterization of calcium conduction through patch clamp electrophysiology. In parallel, structural elucidation efforts necessitate the purification of the calcium channel via hydrophobic interaction or reversed phase liquid chromatography after its heterologous expression in a bacterial host. But, biophysical and biochemical characterization does not speak of the signaling and metabolic pathways laying the path to generation of the splice variant(s). Hence, discovery approaches such as RNA-seq and mass spectrometry proteomics could uncover the molecular mysteries at the transcript and protein level that help guide the selection of specific splice variant in response to hypoxic stress, where HIF is a candidate pathway. Implementing this approach from the retrospective angle of examining diseased human tissue samples provide one important facet for uncovering possible mechanisms driving the generation of a splice variant. However, the complementary prospective approach of identifying the molecular basis and processes for responding to hypoxia in a cell line such as HEK 293 would help provide confirmatory evidence in understanding the key drivers of physiological response to lack of oxygen at the cellular level. Collectively, this research route would illuminate both the nucleotide informational basis of alternative splicing in calcium channel Cav 1.2 as well as identify the molecular mechanisms enabling the selection of specific splice variants useful for conferring, at the cell and tissue level, ability to withstand hypoxic stress without significant negative effects on cell function. Interested readers can expand on the ideas presented.

The maize transposable Ds1 element is alternatively spliced from exon sequences

1991 ◽  
Vol 11 (12) ◽  
pp. 6192-6196
Author(s):  
S R Wessler
Keyword(s):  
Alternative Splicing ◽  
Mrna Splicing ◽  
Splice Sites ◽  
Ac Element ◽  
Alternatively Spliced ◽  
Wx Gene ◽  
Exon 9

The null wx-ml allele contains a 409-bp Dissociation 1 (Ds1) element in exon 9 of the maize waxy (Wx) gene. In the absence of the autonomous Activator (Ac) element, the Ds1 element cannot transpose, and this allele encodes several Wx transcripts that arise following alternative splicing of Ds1 sequences from Wx pre-mRNA. Splicing involves the utilization of three 5' splice sites and three 3' splice sites. All but one of these splice sites are in Ds1 sequences near the ends of the element. The presence of 5' and 3' splice sites near the Ds1 termini and the element's small size and AT richness are features that distinguish Ds1 elements from all other known Ds elements. It is suggested that these features may enhance the ability of Ds1 to function as a mobile intron.

scholarly journals The Porcine Sodium/Iodide Symporter Gene Exhibits an Uncommon Expression Pattern Related to the Use of Alternative Splice Sites not Present in the Human or Murine Species

Endocrinology ◽  
2003 ◽  
Vol 144 (3) ◽  
pp. 1074-1085 ◽  
Author(s):  
Samia Selmi-Ruby ◽  
Chantal Watrin ◽  
Severine Trouttet-Masson ◽  
Françoise Bernier-Valentin ◽  
Virginie Flachon ◽  
...  
Keyword(s):  
Alternative Splice ◽  
Sodium Iodide ◽  
Transmembrane Domain ◽  
Splice Variants ◽  
Experimental System ◽  
Splice Sites ◽  
Sodium Iodide Symporter ◽  
Iodide Uptake ◽  
Donor And Acceptor ◽  
Nis Gene

The sodium/iodide symporter (NIS) is a membrane protein mediating the active transport of iodide into the thyroid gland. NIS, expressed by human, rat, and mouse thyrocytes, is encoded by a single transcript. We identified NIS mRNA species of 3.5 and 3 kb in porcine thyrocytes. Because porcine thyrocytes in primary culture is a widely used experimental system for thyroid iodide metabolism, we further examined the origin and the function of the porcine NIS (pNIS) transcripts. We generated a porcine thyroid cDNA library from which four different clones, pNIS-D, F, J, and ΔJ were isolated. pNIS-D encodes a protein of 643 amino acids highly homologous to the human, rat, and mouse NIS. pNIS-F and J differ from each other and from pNIS-D in their C-terminal part. pNIS-ΔJ lacks a six-amino-acid segment within the putative transmembrane domain 10. Transiently expressed in Cos-7 cells, the four pNIS-cDNAs led to the synthesis of proteins targeted at the plasma membrane and conferred perchlorate-sensitive iodide uptake activities to Cos-7 cells, except pNIS-ΔJ, which was devoid of activity. PNIS-D probably derives from the 3.5-kb transcript and pNIS-F, J, and ΔJ from the 3-kb transcript. The relative abundance of pNIS-D, F, and J transcripts in porcine thyrocytes was about 60%, 35%, and 5%, respectively; the ΔJ transcript was not present in detectable amount. By comparing porcine NIS genomic and cDNA sequences, splice donor and acceptor sites accounting for the generation of pNIS-F, J, and ΔJ transcripts were identified. None of the combinations of alternative splice sites found in the pig was present in the human, rat or mouse NIS gene. Our data show that porcine NIS gene, contrary to the NIS gene from other species, gives rise to splice variants leading to three active and one inactive NIS proteins.

Alternative splicing landscape of small brown planthopper and different response of JNK2 isoforms to rice stripe virus infection

2021 ◽  
Author(s):  
Lu Tong ◽  
Xiaofang Chen ◽  
Wei Wang ◽  
Yan Xiao ◽  
Jinting Yu ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Brown Planthopper ◽  
Rice Stripe Virus ◽  
Insect Vectors ◽  
Sequencing Technology ◽  
Transcript Isoforms ◽  
Small Brown Planthopper ◽  
Rsv Infection ◽  
Alternatively Spliced ◽  
Complex Relationships

Alternative splicing (AS) is a frequent posttranscriptional regulatory event occurring in response to various endogenous and exogenous stimuli in most eukaryotic organisms. However, little is known about the effects of insect-transmitted viruses on AS events in insect vectors. The present study used third-generation sequencing technology and RNA sequencing (RNA-Seq) to evaluate the AS response in the small brown planthopper Laodelphax striatellus to rice stripe virus (RSV). The full-length transcriptome of L. striatellus was obtained using single-molecule real-time sequencing technology (SMRT). Posttranscriptional regulatory events, including AS, alternative polyadenylation, and fusion transcripts, were analyzed. A total of 28,175 nonredundant transcript isoforms included 24,950 transcripts assigned to 8,500 annotated genes of L. striatellus , and 5,000 of these genes (58.8%) had AS events. RNA-Seq of the gut samples of insects infected by RSV for 8 d identified 3,458 differentially expressed transcripts (DETs); 2,185 of these DETs were transcribed from 1,568 genes that had AS events, indicating that 31.4% of alternatively spliced genes responded to RSV infection of the gut. One of the c-Jun N-terminal kinase ( JNK ) genes, JNK2 , experienced exon skipping, resulting in three transcript isoforms. These three isoforms differentially responded to RSV infection during development and in various organs. Injection of double-stranded RNAs targeting all or two isoforms indicated that three or at least two JNK2 isoforms facilitated RSV accumulation in planthoppers. These results implied that AS events could participate in the regulation of complex relationships between viruses and insect vectors. Importance Alternative splicing (AS) is a regulatory mechanism that occurs after gene transcription. AS events can enrich protein diversity to promote the reactions of the organisms to various endogenous and exogenous stimulations. It is not known how insect vectors exploit AS events to cope with transmitted viruses. The present study used third-generation sequencing technology to obtain the profile of AS events in the small brown planthopper Laodelphax striatellus , which is an efficient vector for rice stripe virus (RSV). The results indicated that 31.4% of alternatively spliced genes responded to RSV infection in the gut of planthoppers. One of the c-Jun N-terminal kinase ( JNK ) genes, JNK2 , produced three transcript isoforms by AS. These three isoforms showed different responses to RSV infection, and at least two isoforms facilitated viral accumulation in planthoppers. These results implied that AS events could participate in the regulation of complex relationships between viruses and insect vectors.

scholarly journals Caffeine Regulates Alternative Splicing in a Subset of Cancer-Associated Genes: a Role for SC35

2007 ◽  
Vol 28 (2) ◽  
pp. 883-895 ◽  
Author(s):  
Jia Shi ◽  
Zhen Hu ◽  
Kirk Pabon ◽  
Kathleen W. Scotto
Keyword(s):  
Alternative Splicing ◽  
Splice Variants ◽  
Disease Onset ◽  
Splice Site Selection ◽  
Response Element ◽  
Disease States ◽  
Large Gene ◽  
Close Proximity ◽  
Alternatively Spliced ◽  
A Cell

ABSTRACT Alternative splicing of pre-mRNA contributes significantly to human proteomic complexity, playing a key role in development, gene expression and, when aberrant, human disease onset. Many of the factors involved in alternative splicing have been identified, but little is known about their regulation. Here we report that caffeine regulates alternative splicing of a subset of cancer-associated genes, including the tumor suppressor KLF6. This regulation is at the level of splice site selection, occurs rapidly and reversibly, and is concentration dependent. We have recapitulated caffeine-induced alternative splicing of KLF6 using a cell-based minigene assay and identified a “caffeine response element” within the KLF6 intronic sequence. Significantly, a chimeric minigene splicing assay demonstrated that this caffeine response element is functional in a heterologous context; similar elements exist within close proximity to caffeine-regulated exons of other genes in the subset. Furthermore, the SR splicing factor, SC35, was shown to be required for induction of the alternatively spliced KLF6 transcript. Importantly, SC35 is markedly induced by caffeine, and overexpression of SC35 is sufficient to mimic the effect of caffeine on KLF6 alternative splicing. Taken together, our data implicate SC35 as a key player in caffeine-mediated splicing regulation. This novel effect of caffeine provides a valuable tool for dissecting the regulation of alternative splicing of a large gene subset and may have implications with respect to splice variants associated with disease states.

scholarly journals Detection of Alternatively Spliced Transcripts in Leukemia Cell Lines by Minisequencing on Microarrays

2006 ◽  
Vol 52 (2) ◽  
pp. 202-211 ◽  
Author(s):  
Lili Milani ◽  
Mona Fredriksson ◽  
Ann-Christine Syvänen
Keyword(s):  
Alternative Splicing ◽  
Cell Lines ◽  
Splice Variants ◽  
Leukemia Cell ◽  
Clinical Diagnostics ◽  
Size Analysis ◽  
Multiplexed Detection ◽  
Leukemia Cell Lines ◽  
Alternatively Spliced ◽  
Splicing Patterns

Abstract Background: Recent genome-wide expression studies suggest that ∼80% of the 25 000 human genes undergo alternative splicing. Alternative splicing may be associated with human diseases, particularly with cancer, but the molecular disease mechanisms are poorly understood. Convenient, novel methods for multiplexed detection of alternatively spliced transcripts are needed. Methods: We devised a new approach for detecting splice variants based on a tag-microarray minisequencing system, originally developed for genotyping single-nucleotide polymorphisms. We established the system for multiplexed detection of 61 alternatively spliced transcripts in a panel of 19 cancer-related genes and used it to dissect the splicing patterns in cancer and endothelial cells. Results: Our microarray system detected 82% of the splice variants screened for, including both simple and complex splice variants, in at least 1 of the leukemia cell types analyzed. The intraassay CV values for our method ranged from 0.01 to 0.34 (mean, 0.13) for 5 replicate measurements. Our system allowed semiquantitative comparison of the splicing patterns between the cell lines. Similar, but not identical, patterns of alternative splicing were observed among the leukemia cell lines. Size analysis of the PCR products subjected to the tag-array minisequencing system and real-time PCR with exon-junction probes verified the results from the microarray system. Conclusions: The microarray-based method is a robust and easily accessible tool for parallel detection of alternatively spliced transcripts of multiple genes. It can be used for studying alternative splicing in cancer progression and for following up drug treatment, and it may be a useful tool in clinical diagnostics for cancer and other disorders.

Sign in / Sign up

Export Citation Format

Share Document