Structure of two rat genes coding for closely related rolipram-sensitive cAMP phosphodiesterases. Multiple mRNA variants originate from alternative splicing and multiple start sites.

Alternative splicing is a combinatorial mechanism by which exons are joined to produce multiple mRNA variants, thus expanding the coding potential and plasticity of eukaryotic genomes. Defects in alternative splicing regulation are associated with several human diseases, including cancer. Ewing sarcoma is an aggressive tumor of bone and soft tissue, mainly affecting adolescents and young adults. DHX9 is a key player in Ewing sarcoma malignancy, and its expression correlates with worse prognosis in patients. In this study, by screening a library of siRNAs, we have identified splicing factors that regulate the alternative inclusion of a poison exon in DHX9 mRNA, leading to its downregulation. In particular, we found that hnRNPM and SRSF3 bind in vivo to this poison exon and suppress its inclusion. Notably, DHX9 expression correlates with that of SRSF3 and hnRNPM in Ewing sarcoma patients. Furthermore, downregulation of SRSF3 or hnRNPM inhibited DHX9 expression and Ewing sarcoma cell proliferation, while sensitizing cells to chemotherapeutic treatment. Hence, our study suggests that inhibition of hnRNPM and SRSF3 expression or activity could be exploited as a therapeutic tool to enhance the efficacy of chemotherapy in Ewing sarcoma.

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Alternative REST Splicing Underappreciated

10.1101/119552 ◽

2017 ◽

Author(s):

Guo-Lin Chen ◽

Gregory M. Miller

Keyword(s):

Alternative Splicing ◽

Stop Codon ◽

Premature Stop Codon ◽

Protein Isoforms ◽

Multiple Protein ◽

Mrna Variants ◽

Cellular Context ◽

Active Transcription ◽

Context Dependent ◽

Ageing Brain

As a major orchestrator of the cellular epigenome, the repressor element-1 silencing transcription factor (REST) can either repress or activate thousands of genes depending on cellular context, suggesting a highly context-dependent REST function tuned by environmental cues. While REST shows cell-type non-selective active transcription1, an N-terminal REST4 isoform caused by alternative splicing – inclusion of an extra exon (N3c) which introduces a premature stop codon – has been implicated in neurogenesis and tumorigenesis2-5. Recently, in line with established epigenetic regulation of pre-mRNA splicing6,7, we demonstrated that REST undergoes extensive, context-dependent alternative splicing which results in the formation of a large number of mRNA variants predictive of multiple protein isoforms8. Supported by that immunoblotting/-staining with different anti-REST antibodies yield inconsistent results, alternative splicing allows production of various structurally and functionally different REST protein isoforms in response to shifting physiological requirements, providing a reasonable explanation for the diverse, highly context-dependent REST function. However, REST isoforms might be differentially assayed or manipulated, leading to data misinterpretation and controversial findings. For example, in contrast to the proposed neurotoxicity of elevated nuclear REST in ischemia9 and Huntington’s disease10,11, Lu et al. recently reported decreased nuclear REST in Alzheimer’s disease and neuroprotection of REST in ageing brain12. Unfortunately, alternative REST splicing was largely neglected by Lu et al., making it necessary for a reevaluation of their findings.

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MicroRNA miR-1002 enhances NMNAT-mediated stress response by modulating alternative splicing

10.1101/641944 ◽

2019 ◽

Author(s):

Joun Park ◽

Yi Zhu ◽

Xianzun Tao ◽

Jennifer M. Brazill ◽

Chong Li ◽

...

Keyword(s):

Alternative Splicing ◽

Stress Response ◽

Stress Resistance ◽

Stem Loop ◽

Stress Protection ◽

Stem Loop Structure ◽

Nicotinamide Mononucleotide ◽

Mrna Variants ◽

Alternatively Spliced ◽

Essential Enzyme

SUMMARYUnderstanding endogenous regulation of stress resistance and homeostasis maintenance is critical to developing neuroprotective therapies. Nicotinamide mononucleotide adenylyltransferase (NMNAT) is a conserved essential enzyme that confers extraordinary protection and stress resistance in many neurodegenerative disease models. Drosophila Nmnat is alternatively spliced to two mRNA variants, RA and RB. RB translates to protein isoform PD with robust protective activity and is upregulated upon stress to confer enhanced neuroprotection. The mechanisms regulating alternative splicing and stress response of NMNAT remain unclear. We have discovered a Drosophila microRNA, dme-miR-1002, which promotes the splicing of NMNAT pre-mRNA to RB by disrupting a pre-mRNA stem-loop structure. While NMNAT pre-mRNA is preferentially spliced to RA in basal conditions, miR-1002 enhances NMNAT PD-mediated stress protection by binding via RISC component Argonaute1 to the pre-mRNA, facilitating the splicing switch to RB. These results outline a new process for microRNAs in regulating alternative splicing and modulating stress resistance.

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Comprehensive quantitative analysis of alternative splicing variants reveals the HNF1B mRNA splicing pattern in various tumour and non-tumour tissues

Scientific Reports ◽

10.1038/s41598-021-03989-z ◽

2022 ◽

Vol 12 (1) ◽

Author(s):

Jan Hojny ◽

Romana Michalkova ◽

Eva Krkavcova ◽

Quang Hiep Bui ◽

Michaela Bartu ◽

...

Keyword(s):

Alternative Splicing ◽

Mrna Expression ◽

Large Intestine ◽

Digital Pcr ◽

Splicing Pattern ◽

Mrna Variants ◽

Splicing Variants ◽

Quantitative Changes ◽

Nuclear Factor 1 ◽

Regulatory Functions

AbstractHepatocyte nuclear factor-1-beta (HNF1B) is a transcription factor and putative biomarker of solid tumours. Recently, we have revealed a variety of HNF1B mRNA alternative splicing variants (ASVs) with unknown, but potentially regulatory, functions. The aim of our work was to quantify the most common variants and compare their expression in tumour and non-tumour tissues of the large intestine, prostate, and kidney. The HNF1B mRNA variants 3p, Δ7, Δ7–8, and Δ8 were expressed across all the analysed tissues in 28.2–33.5%, 1.5–2%, 0.8–1.7%, and 2.3–6.9% of overall HNF1B mRNA expression, respectively, and occurred individually or in combination. The quantitative changes of ASVs between tumour and non-tumour tissue were observed for the large intestine (3p, Δ7–8), prostate (3p), and kidney samples (Δ7). Decreased expression of the overall HNF1B mRNA in the large intestine and prostate cancer samples compared with the corresponding non-tumour samples was observed (p = 0.019 and p = 0.047, respectively). The decreased mRNA expression correlated with decreased protein expression in large intestine carcinomas (p < 0.001). The qualitative and quantitative pattern of the ASVs studied by droplet digital PCR was confirmed by next-generation sequencing, which suggests the significance of the NGS approach for further massive evaluation of the splicing patterns in a variety of genes.

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Synthesis of Turkey Pit-1 mRNA Variants by Alternative Splicing and Transcription Initiation

DNA and Cell Biology ◽

10.1089/dna.1998.17.93 ◽

1998 ◽

Vol 17 (1) ◽

pp. 93-103 ◽

Cited By ~ 16

Author(s):

KIYOTO KURIMA ◽

KRISTY L. WEATHERLY ◽

LUDMILA SHAROVA ◽

ERIC A. WONG

Keyword(s):

Alternative Splicing ◽

Transcription Initiation ◽

Mrna Variants

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RBM10 variants and RBM5 involve in alternative splicing of RBM10v1 pre-mRNA: RBM10v1 includes its own exon 4, but RBM10v2 and RBM5 skip it

10.1101/516930 ◽

2019 ◽

Author(s):

Koji Nishio

Keyword(s):

Alternative Splicing ◽

Rna Binding ◽

A549 Cells ◽

Molecular Structures ◽

Binding Motif ◽

H9c2 Cells ◽

Mrna Variants ◽

Exon 4 ◽

Lung Adenocarcinoma A549 ◽

High Degree

AbstractRNA binding motif (RBM) proteins, RBM10v1, RBM10v2 and RBM5 have quite similar molecular structures with a high degree of the conserved domains. Alternative splicing of RBM10 pre-mRNA produces the two mRNA variants, RBM10v1 (exon 4-included) and RBM10v2 (exon 4-skipped). RBM10v1 has a 77 amino acids-domain coded by its exon 4, but RBM10v2 lacks it. I explored the alternative splicing of the RBM10 pre-mRNA by the above three RBMs in COS-7, lung adenocarcinoma A549 and differentiated mouse cardiomyocytes H9c2 cells. Firstly, COS-7 and A549 cells express both RBM10v1 and RBM10v2 mRNA variants in contrast to H9c2 cells which express RBM10v2 variant alone. Transfection experiments of RBM10v1, RBM10v2 or RBM5 were performed to examine the alternative splicing of RBM10v1 pre-mRNA in COS-7, A549 and H9c2 cells. The result showed that RBM10v1 includes, by itself, its own exon 4 of the pre-mRNA in contrast to RBM10v2 and RBM5 which exclude the exon 4. The inclusion of the exon 4 seems to be repressed in differentiated H9c2 cells.

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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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Two Human ACAT2 mRNA Variants Produced by Alternative Splicing and Coding for Novel Isoenzymes

Acta Biochimica et Biophysica Sinica ◽

10.1111/j.1745-7270.2005.00118.x ◽

2005 ◽

Vol 37 (12) ◽

pp. 797-806 ◽

Cited By ~ 2

Author(s):

Xiao-Min Yao ◽

Can-Hua Wang ◽

Bao-Liang Song ◽

Xin-Ying Yang ◽

Zhen-Zhen Wang ◽

...

Keyword(s):

Amino Acids ◽

Alternative Splicing ◽

Fetal Liver ◽

Cholesterol Acyltransferase ◽

Cholesterol Absorption ◽

The Novel ◽

Pathological Conditions ◽

Mrna Variants ◽

Alternatively Spliced ◽

Acyl Coenzyme A

Abstract Acyl coenzyme A: cholesterol acyltransferase 2 (ACAT2) plays an important role in cholesterol absorption. Human ACAT2 is highly expressed in small intestine and fetal liver, but its expression is greatly diminished in adult liver. The full-length human ACAT2 mRNA encodes a protein, designated ACAT2a, with 522 amino acids. We have previously reported the organization of the human ACAT2 gene and the differentiation-dependent promoter activity in intestinal Caco-2 cells. In the current work, two human ACAT2 mRNA variants produced by alternative splicing are cloned and predicted to encode two novel ACAT2 isoforms, named ACAT2b and ACAT2c, with 502 and 379 amino acids, respectively. These mRNA variants differ from ACAT2a mRNA by lack of the exon 4 (ACAT2b mRNA) and exons 4-5 plus 8-9-10 (ACAT2c mRNA). Significantly, comparable amounts of the alternatively spliced ACAT2 mRNA variants were detected by RT-PCR, and Western blot analysis confirmed the presence of their corresponding proteins in human liver and intestine cells. Furthermore, phosphorylation and enzymatic activity analyses demonstrated that the novel isoenzymes ACAT2b and ACAT2c lacked the phosphorylatable site SLLD, and their enzymatic activities reduced to 25%-35% of that of ACAT2a. These evidences indicate that alternative splicing produces two human ACAT2 mRNA variants that encode the novel ACAT2 isoenzymes. Our findings might help to understand the regulation of the ACAT2 gene expression under certain physiological and pathological conditions.

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