Alternative RNA splicing that is spatially regulated: generation of transcripts from the Antennapedia gene of Drosophila melanogaster with different protein-coding regions

We have shown previously that transcription of the Drosophila homeotic gene Antennapedia results in four major RNA species which differ in long 5'- and 3'-untranslated sequences. The protein-coding portion of these transcripts, however, is located in exons common to all. Using RNase protection assays and further cDNA clone isolation, we have now detected two alternative splicing events between exons of this region. These result in four RNA variations which, if translated, would encode a family of Antennapedia proteins. By analyzing transcripts from various developmental stages and isolated tissues, we show that alternative splicing is under strict temporal and spatial regulation. For example, while similar patterns of splicing were found for all wild-type thoracic imaginal disks examined, these differed distinctly from the patterns observed in neural tissues. Our results suggest that individual RNAs may be associated with different biological roles, and provide molecular evidence that the Antennapedia gene is involved in multiple functions.

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Anguillid Herpesvirus 1 Transcriptome

Journal of Virology ◽

10.1128/jvi.01271-12 ◽

2012 ◽

Vol 86 (18) ◽

pp. 10150-10161 ◽

Cited By ~ 12

Author(s):

Steven J. van Beurden ◽

Derek Gatherer ◽

Karen Kerr ◽

Julie Galbraith ◽

Pawel Herzyk ◽

...

Keyword(s):

Deep Sequencing ◽

Rna Splicing ◽

Direct Repeat ◽

Antisense Transcription ◽

Protein Coding ◽

Coding Regions ◽

Genome Map ◽

Herpesvirus 1 ◽

Rapid Amplification ◽

Splice Junctions

We used deep sequencing of poly(A) RNA to characterize the transcriptome of an economically important eel virus, anguillid herpesvirus 1 (AngHV1), at a stage during the lytic life cycle when infectious virus was being produced. In contrast to the transcription of mammalian herpesviruses, the overall level of antisense transcription from the 248,526-bp genome was low, amounting to only 1.5% of transcription in predicted protein-coding regions, and no abundant, nonoverlapping, noncoding RNAs were identified. RNA splicing was found to be more common than had been anticipated previously. Counting the 10,634-bp terminal direct repeat once, 100 splice junctions were identified, of which 58 were considered likely to be involved in the expression of functional proteins because they represent splicing between protein-coding exons or between 5′ untranslated regions and protein-coding exons. Each of the 30 most highly represented of these 58 splice junctions was confirmed by RT-PCR. We also used deep sequencing to identify numerous putative 5′ and 3′ ends of AngHV1 transcripts, confirming some and adding others by rapid amplification of cDNA ends (RACE). The findings prompted a revision of the AngHV1 genome map to include a total of 129 protein-coding genes, 5 of which are duplicated in the terminal direct repeat. Not counting duplicates, 11 genes contain integral, spliced protein-coding exons, and 9 contain 5′ untranslated exons or, because of alternative splicing, 5′ untranslated and 5′ translated exons. The results of this study sharpen our understanding of AngHV1 genomics and provide the first detailed view of a fish herpesvirus transcriptome.

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Evolutionary Analysis of DNA-Protein-Coding Regions Based on a Genetic Code Cube Metric

Current Topics in Medicinal Chemistry ◽

10.2174/1568026613666131204110022 ◽

2014 ◽

Vol 14 (3) ◽

pp. 407-417

Author(s):

Robersy Sanchez

Keyword(s):

Genetic Code ◽

Evolutionary Analysis ◽

Protein Coding ◽

Coding Regions

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The open targets post-GWAS analysis pipeline

Bioinformatics ◽

10.1093/bioinformatics/btaa020 ◽

2020 ◽

Vol 36 (9) ◽

pp. 2936-2937 ◽

Cited By ~ 4

Author(s):

Gareth Peat ◽

William Jones ◽

Michael Nuhn ◽

José Carlos Marugán ◽

William Newell ◽

...

Keyword(s):

Drug Targets ◽

Gene Expression Regulation ◽

Association Studies ◽

Genome Wide Association Studies ◽

Protein Coding ◽

Data Resource ◽

Coding Regions ◽

Genome Wide ◽

Causal Genes ◽

Interactive Data

Abstract Motivation Genome-wide association studies (GWAS) are a powerful method to detect even weak associations between variants and phenotypes; however, many of the identified associated variants are in non-coding regions, and presumably influence gene expression regulation. Identifying potential drug targets, i.e. causal protein-coding genes, therefore, requires crossing the genetics results with functional data. Results We present a novel data integration pipeline that analyses GWAS results in the light of experimental epigenetic and cis-regulatory datasets, such as ChIP-Seq, Promoter-Capture Hi-C or eQTL, and presents them in a single report, which can be used for inferring likely causal genes. This pipeline was then fed into an interactive data resource. Availability and implementation The analysis code is available at www.github.com/Ensembl/postgap and the interactive data browser at postgwas.opentargets.io.

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Role of Alternative Splicing in Regulating Host Response to Viral Infection

Cells ◽

10.3390/cells10071720 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1720

Author(s):

Kuo-Chieh Liao ◽

Mariano A. Garcia-Blanco

Keyword(s):

Innate Immunity ◽

Alternative Splicing ◽

Immune Responses ◽

Viral Infection ◽

Rna Splicing ◽

Type I ◽

Host Immune Responses ◽

Transcriptional Regulatory Mechanisms ◽

Host Virus Interactions

The importance of transcriptional regulation of host genes in innate immunity against viral infection has been widely recognized. More recently, post-transcriptional regulatory mechanisms have gained appreciation as an additional and important layer of regulation to fine-tune host immune responses. Here, we review the functional significance of alternative splicing in innate immune responses to viral infection. We describe how several central components of the Type I and III interferon pathways encode spliced isoforms to regulate IFN activation and function. Additionally, the functional roles of splicing factors and modulators in antiviral immunity are discussed. Lastly, we discuss how cell death pathways are regulated by alternative splicing as well as the potential role of this regulation on host immunity and viral infection. Altogether, these studies highlight the importance of RNA splicing in regulating host–virus interactions and suggest a role in downregulating antiviral innate immunity; this may be critical to prevent pathological inflammation.

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Profiling PRMT methylome reveals roles of hnRNPA1 arginine methylation in RNA splicing and cell growth

Nature Communications ◽

10.1038/s41467-021-21963-1 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Wen-juan Li ◽

Yao-hui He ◽

Jing-jing Yang ◽

Guo-sheng Hu ◽

Yi-an Lin ◽

...

Keyword(s):

Alternative Splicing ◽

Cell Growth ◽

Rna Splicing ◽

Synergistic Effects ◽

Arginine Methylation ◽

Type I ◽

Prostate Cancer Cells ◽

Cancer Cell Growth ◽

Cancer Mutations ◽

Substrate Spectrum

AbstractNumerous substrates have been identified for Type I and II arginine methyltransferases (PRMTs). However, the full substrate spectrum of the only type III PRMT, PRMT7, and its connection to type I and II PRMT substrates remains unknown. Here, we use mass spectrometry to reveal features of PRMT7-regulated methylation. We find that PRMT7 predominantly methylates a glycine and arginine motif; multiple PRMT7-regulated arginine methylation sites are close to phosphorylations sites; methylation sites and proximal sequences are vulnerable to cancer mutations; and methylation is enriched in proteins associated with spliceosome and RNA-related pathways. We show that PRMT4/5/7-mediated arginine methylation regulates hnRNPA1 binding to RNA and several alternative splicing events. In breast, colorectal and prostate cancer cells, PRMT4/5/7 are upregulated and associated with high levels of hnRNPA1 arginine methylation and aberrant alternative splicing. Pharmacological inhibition of PRMT4/5/7 suppresses cancer cell growth and their co-inhibition shows synergistic effects, suggesting them as targets for cancer therapy.

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Regulation of CD44 Alternative Splicing by SRm160 and Its Potential Role in Tumor Cell Invasion

Molecular and Cellular Biology ◽

10.1128/mcb.26.1.362-370.2006 ◽

2006 ◽

Vol 26 (1) ◽

pp. 362-370 ◽

Cited By ~ 134

Author(s):

Chonghui Cheng ◽

Phillip A. Sharp

Keyword(s):

Alternative Splicing ◽

Tumor Cell ◽

Cell Invasion ◽

Rna Splicing ◽

Tumor Cell Invasion ◽

Dependent Manner ◽

Cd44 Isoforms ◽

Transmembrane Glycoprotein ◽

Cell Invasiveness ◽

Interfering Rna

ABSTRACT The multiple isoforms of the transmembrane glycoprotein CD44 are produced by alternative RNA splicing. Expression of CD44 isoforms containing variable 5 exon (v5) correlates with enhanced malignancy and invasiveness of some tumors. Here we demonstrate that SRm160, a splicing coactivator, regulates CD44 alternative splicing in a Ras-dependent manner. Overexpression of SRm160 stimulates inclusion of CD44 v5 when Ras is activated. Conversely, small interfering RNA (siRNA)-mediated silencing of SRm160 significantly reduces v5 inclusion. Immunoprecipitation shows association of SRm160 with Sam68, a protein that also stimulates v5 inclusion in a Ras-dependent manner, suggesting that these two proteins interact to regulate CD44 splicing. Importantly, siRNA-mediated depletion of CD44 v5 decreases tumor cell invasion. Reduction of SRm160 by siRNA transfection downregulates the endogenous levels of CD44 isoforms, including v5, and correlates with a decrease in tumor cell invasiveness.

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Neurodegenerative diseases: a hotbed for splicing defects and the potential therapies

Translational Neurodegeneration ◽

10.1186/s40035-021-00240-7 ◽

2021 ◽

Vol 10 (1) ◽

Author(s):

Dunhui Li ◽

Craig Stewart McIntosh ◽

Frank Louis Mastaglia ◽

Steve Donald Wilton ◽

May Thandar Aung-Htut

Keyword(s):

Alternative Splicing ◽

Neurodegenerative Diseases ◽

Messenger Rna ◽

Muscular Atrophy ◽

Single Gene ◽

Synaptic Function ◽

Coding Regions ◽

Splicing Defects ◽

The Impact ◽

Splicing Patterns

AbstractPrecursor messenger RNA (pre-mRNA) splicing is a fundamental step in eukaryotic gene expression that systematically removes non-coding regions (introns) and ligates coding regions (exons) into a continuous message (mature mRNA). This process is highly regulated and can be highly flexible through a process known as alternative splicing, which allows for several transcripts to arise from a single gene, thereby greatly increasing genetic plasticity and the diversity of proteome. Alternative splicing is particularly prevalent in neuronal cells, where the splicing patterns are continuously changing to maintain cellular homeostasis and promote neurogenesis, migration and synaptic function. The continuous changes in splicing patterns and a high demand on many cis- and trans-splicing factors contribute to the susceptibility of neuronal tissues to splicing defects. The resultant neurodegenerative diseases are a large group of disorders defined by a gradual loss of neurons and a progressive impairment in neuronal function. Several of the most common neurodegenerative diseases involve some form of splicing defect(s), such as Alzheimer’s disease, Parkinson’s disease and spinal muscular atrophy. Our growing understanding of RNA splicing has led to the explosion of research in the field of splice-switching antisense oligonucleotide therapeutics. Here we review our current understanding of the effects alternative splicing has on neuronal differentiation, neuronal migration, synaptic maturation and regulation, as well as the impact on neurodegenerative diseases. We will also review the current landscape of splice-switching antisense oligonucleotides as a therapeutic strategy for a number of common neurodegenerative disorders.

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