The Alternatively Spliced Isoforms of Key Molecules in the cGAS-STING Signaling Pathway

Alternative splicing of pre-mRNA increases transcriptome and proteome diversity by generating distinct isoforms that encode functionally diverse proteins, thus affecting many biological processes, including innate immunity. cGAS-STING signaling pathway, whose key molecules also undergo alternative splicing, plays a crucial role in regulating innate immunity. Protein isoforms of key components in the cGAS-STING-TBK1-IRF3 axis have been detected in a variety of species. A chain of evidence showed that these protein isoforms exhibit distinct functions compared to their normal counterparts. The mentioned isoforms act as positive or negative modulators in interferon response via distinct mechanisms. Particularly, we highlight that alternative splicing serves a vital function for the host to avoid the overactivation of the cGAS-STING signaling pathway and that viruses can utilize alternative splicing to resist antiviral response by the host. These findings could provide insights for potential alternative splicing-targeting therapeutic applications.

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Influence of Intron Length on Alternative Splicing of CD44

Molecular and Cellular Biology ◽

10.1128/mcb.18.10.5930 ◽

1998 ◽

Vol 18 (10) ◽

pp. 5930-5941 ◽

Cited By ~ 49

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.

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Asian Zika virus isolate significantly changes the transcriptional profile and alternative RNA splicing events in a neuroblastoma cell line

10.1101/660209 ◽

2019 ◽

Author(s):

Gaston Bonenfant ◽

Ryan Meng ◽

Carl Shotwell ◽

J. Andrew Berglund ◽

Cara T. Pager

Keyword(s):

Alternative Splicing ◽

Zika Virus ◽

Rna Splicing ◽

Virus Isolate ◽

Neuroblastoma Cell ◽

Neuroblastoma Cell Line ◽

Transcriptional Profile ◽

Protein Isoforms ◽

And Function ◽

Functionally Diverse

AbstractAlternative splicing of pre-mRNAs expands a single genetic blueprint to encode multiple functionally diverse protein isoforms. Viruses have previously been shown to interact with, depend on, and alter host splicing machinery. The consequences however incited by viral infection on the global alternative slicing (AS) landscape are under appreciated. Here we investigated the transcriptional and alternative splicing profile of neuronal cells infected with a contemporary Puerto Rican Zika virus (ZIKVPR) isolate, the prototypical Ugandan ZIKV (ZIKVMR) isolate and dengue virus 2 (DENV2). Our analyses revealed that ZIKVPRinduced significantly more differential changes in expressed genes compared to ZIKVMRor DENV2, despite all three viruses showing equivalent infectivity and viral RNA levels. Consistent with the transcriptional profile, ZIKVPRinduced a higher number of alternative splicing events compared to ZIKVMRor DENV2, and gene ontology analyses highlighted alternative splicing changes in genes associated with mRNA splicing. All three viruses modulated alternative splicing with ZIKVPRhaving the largest impact on splicing. ZIKV alteration of the transcriptomic landscape during infection caused changes in cellular RNA homeostasis, which might dysregulate neurodevelopment and function leading to neuropathologies such as microcephaly and Guillain-Barré syndrome associated with the ZIKV infection.

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Evolutionary conservation of the structure and expression of alternatively spliced Ultrabithorax isoforms from Drosophila.

Genetics ◽

10.1093/genetics/136.3.965 ◽

1994 ◽

Vol 136 (3) ◽

pp. 965-977

Author(s):

H M Bomze ◽

A J López

Keyword(s):

Alternative Splicing ◽

Protein Function ◽

Developmental Regulation ◽

Expression Patterns ◽

Proximal Region ◽

Amino Acid Sequences ◽

Drosophila Virilis ◽

Protein Isoforms ◽

Developmentally Regulated ◽

Alternatively Spliced

Abstract In Drosophila melanogaster, alternatively spliced mRNAs from the homeotic gene Ultrabithorax (Ubx) encode a family of structurally distinct homeoprotein isoforms. The developmentally regulated expression patterns of these isoforms suggest that they have specialized stage- and tissue-specific functions. To evaluate the functional importance of UBX isoform diversity and gain clues to the mechanism that regulates processing of Ubx RNAs, we have investigated whether the Ubx RNAs of other insects undergo similar alternative splicing. We have isolated and characterized Ubx cDNA fragments from D. melanogaster, Drosophila pseudoobscura, Drosophila hydei and Drosophila virilis, species separated by as much as 60 million years of evolution, and have found that three aspects of Ubx RNA processing have been conserved. (1) These four species exhibit identical patterns of optional exon use in a region adjacent to the homeodomain. (2) These four species produce the same family of UBX protein isoforms with identical amino acid sequences in the optional exons, even though the common amino-proximal region has undergone substantial divergence. The nucleotide sequences of the optional exons, including third positions of rare codons, have also been conserved strongly, suggesting functional constraints that are not limited to coding potential. (3) The tissue- and stage-specific patterns of expression of different UBX isoforms are identical among these Drosophila species, indicating that the developmental regulation of the alternative splicing events has also been conserved. These findings argue for an important role of alternative splicing in Ubx function. We discuss the implications of these results for models of UBX protein function and the mechanism of alternative splicing.

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RNA Interference Knockdown of hU2AF35 Impairs Cell Cycle Progression and Modulates Alternative Splicing of Cdc25 Transcripts

Molecular Biology of the Cell ◽

10.1091/mbc.e06-01-0036 ◽

2006 ◽

Vol 17 (10) ◽

pp. 4187-4199 ◽

Cited By ~ 55

Author(s):

Teresa Raquel Pacheco ◽

Luís Ferreira Moita ◽

Anita Quintal Gomes ◽

Nir Hacohen ◽

Maria Carmo-Fonseca

Keyword(s):

Cell Cycle ◽

Alternative Splicing ◽

Rna Interference ◽

Cell Cycle Progression ◽

Protein Isoforms ◽

Cell Cycle Gene ◽

Mitotic Progression ◽

Cycle Progression ◽

Specific Subset ◽

Alternatively Spliced

U2AF is a heterodimeric splicing factor composed of a large (U2AF65) and a small (U2AF35) subunit. In humans, alternative splicing generates two U2AF35 variants, U2AF35a and U2AF35b. Here, we used RNA interference to specifically ablate the expression of each isoform in HeLa cells. Our results show that knockdown of the major U2AF35a isoform reduced cell viability and impaired mitotic progression, leading to accumulation of cells in prometaphase. Microarray analysis revealed that knockdown of U2AF35a affected the expression level of ∼500 mRNAs, from which >90% were underrepresented relative to the control. Among mRNAs underrepresented in U2AF35a-depleted cells we identified an essential cell cycle gene, Cdc27, for which there was an increase in the ratio between unspliced and spliced RNA and a significant reduction in protein level. Furthermore, we show that depletion of either U2AF35a or U2AF35b altered the ratios of alternatively spliced isoforms of Cdc25B and Cdc25C transcripts. Taken together our results demonstrate that U2AF35a is essential for HeLa cell division and suggest a novel role for both U2AF35 protein isoforms as regulators of alternative splicing of a specific subset of genes.

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A saga of cancer epigenetics: linking epigenetics to alternative splicing

Biochemical Journal ◽

10.1042/bcj20161047 ◽

2017 ◽

Vol 474 (6) ◽

pp. 885-896 ◽

Cited By ~ 18

Author(s):

Sathiya Pandi Narayanan ◽

Smriti Singh ◽

Sanjeev Shukla

Keyword(s):

Alternative Splicing ◽

Rna Polymerase Ii ◽

Cancer Progression ◽

Rna Binding ◽

Rna Binding Proteins ◽

Epigenetic Modifications ◽

Protein Isoforms ◽

Epigenetic Alterations ◽

Cancer Epigenetics ◽

Alternatively Spliced

The discovery of an increasing number of alternative splicing events in the human genome highlighted that ∼94% of genes generate alternatively spliced transcripts that may produce different protein isoforms with diverse functions. It is now well known that several diseases are a direct and indirect consequence of aberrant splicing events in humans. In addition to the conventional mode of alternative splicing regulation by ‘cis’ RNA-binding sites and ‘trans’ RNA-binding proteins, recent literature provides enormous evidence for epigenetic regulation of alternative splicing. The epigenetic modifications may regulate alternative splicing by either influencing the transcription elongation rate of RNA polymerase II or by recruiting a specific splicing regulator via different chromatin adaptors. The epigenetic alterations and aberrant alternative splicing are known to be associated with various diseases individually, but this review discusses/highlights the latest literature on the role of epigenetic alterations in the regulation of alternative splicing and thereby cancer progression. This review also points out the need for further studies to understand the interplay between epigenetic modifications and aberrant alternative splicing in cancer progression.

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The Atypical Kinase RIOK3 Limits RVFV Propagation and Is Regulated by Alternative Splicing

Viruses ◽

10.3390/v13030367 ◽

2021 ◽

Vol 13 (3) ◽

pp. 367

Author(s):

Katherine E. Havranek ◽

Luke Adam White ◽

Thomas C. Bisom ◽

Jean-Marc Lanchy ◽

J. Stephen Lodmell

Keyword(s):

Alternative Splicing ◽

Mammalian Cells ◽

Rift Valley Fever Virus ◽

Critical Role ◽

Fine Tuning ◽

Interferon Response ◽

Type I ◽

Interferon Signaling ◽

Valley Fever ◽

Alternatively Spliced

In recent years, transcriptome profiling studies have identified changes in host splicing patterns caused by viral invasion, yet the functional consequences of the vast majority of these splicing events remain uncharacterized. We recently showed that the host splicing landscape changes during Rift Valley fever virus MP-12 strain (RVFV MP-12) infection of mammalian cells. Of particular interest, we observed that the host mRNA for Rio Kinase 3 (RIOK3) was alternatively spliced during infection. This kinase has been shown to be involved in pattern recognition receptor (PRR) signaling mediated by RIG-I like receptors to produce type-I interferon. Here, we characterize RIOK3 as an important component of the interferon signaling pathway during RVFV infection and demonstrate that RIOK3 mRNA expression is skewed shortly after infection to produce alternatively spliced variants that encode premature termination codons. This splicing event plays a critical role in regulation of the antiviral response. Interestingly, infection with other RNA viruses and transfection with nucleic acid-based RIG-I agonists also stimulated RIOK3 alternative splicing. Finally, we show that specifically stimulating alternative splicing of the RIOK3 transcript using a morpholino oligonucleotide reduced interferon expression. Collectively, these results indicate that RIOK3 is an important component of the mammalian interferon signaling cascade and its splicing is a potent regulatory mechanism capable of fine-tuning the host interferon response.

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Alternative Splicing Programs in Prostate Cancer

International Journal of Cell Biology ◽

10.1155/2013/458727 ◽

2013 ◽

Vol 2013 ◽

pp. 1-10 ◽

Cited By ~ 7

Author(s):

Claudio Sette

Keyword(s):

Prostate Cancer ◽

Alternative Splicing ◽

Protein Isoforms ◽

Splicing Regulation ◽

Therapeutic Approaches ◽

Male Population ◽

Incurable Disease ◽

Prostate Cells ◽

Mrna Variants ◽

Alternatively Spliced

Prostate cancer (PCa) remains one of the most frequent causes of death for cancer in the male population. Although the initial antiandrogenic therapies are efficacious, PCa often evolves into a hormone-resistant, incurable disease. The genetic and phenotypic heterogeneity of this type of cancer renders its diagnosis and cure particularly challenging. Mounting evidence indicates that alternative splicing, the process that allows production of multiple mRNA variants from each gene, contributes to the heterogeneity of the disease. Key genes for the biology of normal and neoplastic prostate cells, such as those encoding for the androgen receptor and cyclin D1, are alternatively spliced to yield protein isoforms with different or even opposing functions. This review illustrates some examples of genes whose alternative splicing regulation is relevant to PCa biology and discusses the possibility to exploit alternative splicing regulation as a novel tool for prognosis, diagnosis, and therapeutic approaches to PCa.

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Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources

Briefings in Bioinformatics ◽

10.1093/bib/bby047 ◽

2019 ◽

Vol 20 (5) ◽

pp. 1754-1768 ◽

Cited By ~ 5

Author(s):

Dinanath Sulakhe ◽

Mark D’Souza ◽

Sheng Wang ◽

Sandhya Balasubramanian ◽

Prashanth Athri ◽

...

Keyword(s):

Alternative Splicing ◽

Contextual Information ◽

Single Gene ◽

Cellular Responses ◽

Protein Isoforms ◽

Modeling And Analysis ◽

The Public ◽

Alternatively Spliced ◽

Cellular Pathways ◽

Genome Analyses

Abstract In recent years, the emphasis of scientific inquiry has shifted from whole-genome analyses to an understanding of cellular responses specific to tissue, developmental stage or environmental conditions. One of the central mechanisms underlying the diversity and adaptability of the contextual responses is alternative splicing (AS). It enables a single gene to encode multiple isoforms with distinct biological functions. However, to date, the functions of the vast majority of differentially spliced protein isoforms are not known. Integration of genomic, proteomic, functional, phenotypic and contextual information is essential for supporting isoform-based modeling and analysis. Such integrative proteogenomics approaches promise to provide insights into the functions of the alternatively spliced protein isoforms and provide high-confidence hypotheses to be validated experimentally. This manuscript provides a survey of the public databases supporting isoform-based biology. It also presents an overview of the potential global impact of AS on the human canonical gene functions, molecular interactions and cellular pathways.

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Asian Zika Virus Isolate Significantly Changes the Transcriptional Profile and Alternative RNA Splicing Events in a Neuroblastoma Cell Line

Viruses ◽

10.3390/v12050510 ◽

2020 ◽

Vol 12 (5) ◽

pp. 510 ◽

Cited By ~ 3

Author(s):

Gaston Bonenfant ◽

Ryan Meng ◽

Carl Shotwell ◽

Pheonah Badu ◽

Anne F. Payne ◽

...

Keyword(s):

Alternative Splicing ◽

Zika Virus ◽

Rna Splicing ◽

Virus Isolate ◽

Neuroblastoma Cell ◽

Neuroblastoma Cell Line ◽

Mrna Splicing ◽

Transcriptional Profile ◽

Protein Isoforms ◽

Functionally Diverse

The alternative splicing of pre-mRNAs expands a single genetic blueprint to encode multiple, functionally diverse protein isoforms. Viruses have previously been shown to interact with, depend on, and alter host splicing machinery. The consequences, however, incited by viral infection on the global alternative slicing (AS) landscape are under-appreciated. Here, we investigated the transcriptional and alternative splicing profile of neuronal cells infected with a contemporary Puerto Rican Zika virus (ZIKVPR) isolate, an isolate of the prototypical Ugandan ZIKV (ZIKVMR), and dengue virus 2 (DENV2). Our analyses revealed that ZIKVPR induced significantly more differential changes in expressed genes compared to ZIKVMR or DENV2, despite all three viruses showing equivalent infectivity and viral RNA levels. Consistent with the transcriptional profile, ZIKVPR induced a higher number of alternative splicing events compared to ZIKVMR or DENV2, and gene ontology analyses highlighted alternative splicing changes in genes associated with mRNA splicing. In summary, we show that ZIKV affects cellular RNA homeostasis not only at the transcriptional levels but also through the alternative splicing of cellular transcripts. These findings could provide new molecular insights into the neuropathologies associated with this virus.

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