GO:0048025 negative regulation of mRNA splicing, via spliceosome: Regulation, Genes, Functions and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0048025 describes any process that stops, prevents, or reduces the rate or extent of mRNA splicing via a spliceosomal mechanism.
• Negative regulation of splicing is essential for maintaining transcriptome fidelity and is often mediated by RNA-binding proteins, spliceosome inhibitors, and intragenic RNA elements [1, 2, 3].
• Dysregulation of splicing inhibition contributes to cancer, hematological disorders, and neurological diseases [5, 6, 7].
• Key regulators include RBM10, RBM5, SF3B1, PKR, and NOVA factors, which modulate splice site selection and spliceosome activity [1, 2, 3, 7].
• CRISPR-based models (knockout, point mutation, knock-in, overexpression) enable causal dissection of splicing regulation [4, 8].
• Understanding negative regulation of splicing informs therapeutic strategies such as splice-switching oligonucleotides and small-molecule spliceosome modulators [3, 4].
Description
The Gene Ontology term GO:0048025, negative regulation of mRNA splicing, via spliceosome, defines any process that stops, prevents, or reduces the rate or extent of mRNA splicing via a spliceosomal mechanism. This regulatory process is critical for controlling the diversity and abundance of mRNA isoforms, thereby influencing protein function and cellular physiology. Negative regulation of splicing ensures that splicing occurs accurately and at appropriate times, preventing aberrant exon inclusion or skipping that can lead to disease. Researchers study this term to understand how cells fine-tune gene expression, how pathogens and stress signals modulate splicing, and how splicing dysregulation contributes to cancer and other disorders [1, 5, 6]. The spliceosome is a dynamic ribonucleoprotein complex, and its negative regulation can occur through RNA-binding proteins, post-translational modifications, and small molecules that interfere with spliceosome assembly or catalysis [3, 7]. This article synthesizes current knowledge on the mechanisms, key genes, disease relevance, and experimental approaches for studying GO:0048025.
negative regulation of mRNA splicing, via spliceosome At A Glance
| GO ID | GO:0048025 |
|---|---|
| GO term | negative regulation of mRNA splicing, via spliceosome |
| Ontology | biological_process |
| Synonym | inhibition of nuclear mRNA splicing, via spliceosome; negative regulation of pre-mRNA splicing |
| Major function | Reduces the rate or extent of spliceosomal mRNA splicing |
| Related processes | mRNA processing, spliceosome assembly, alternative splicing |
| Key regulators | RBM10, RBM5, SF3B1, PKR, NOVA factors |
| Disease relevance | Cancer, hematological disorders, neurological diseases |
What Is GO:0048025?
GO:0048025 refers to any biological process that negatively regulates mRNA splicing via the spliceosome, meaning it reduces the frequency or efficiency of intron removal from pre-mRNA. This can occur through inhibition of spliceosome assembly, modulation of splice site recognition, or interference with catalytic steps [2, 3].
Why Is negative regulation of mRNA splicing, via spliceosome Important in Cell Biology?
Negative regulation of mRNA splicing is vital for maintaining cellular homeostasis and responding to stress. It allows cells to rapidly adjust splicing patterns without changing transcription, and its dysregulation is linked to a wide range of diseases including cancer, where aberrant splicing can activate oncogenes or inactivate tumor suppressors [5, 6]. Understanding this process provides insights into fundamental gene expression control and offers therapeutic targets for splicing-modulating drugs [3, 4].
• Controls alternative splicing to generate protein diversity.
• Prevents aberrant splicing that can cause disease.
• Mediates cellular stress responses via PKR activation.
• Influences cancer progression through mutant p53 and RAS signaling.
• Regulates hematopoiesis and ferroptosis in SF3B1-mutant cells.
• Involved in neurological disorders via NOVA factors.
• Target for splice-switching oligonucleotides and small molecules.
• Essential for viral mRNA regulation and antiviral defense.
• Modulates RNA stability through nonsense-mediated decay coupling.
• Provides a mechanism for feedback autoregulation of splicing factors.
What Happens During negative regulation of mRNA splicing, via spliceosome?
Inhibition of Spliceosome Assembly
In simple terms: The cell blocks the building of the splicing machinery.
Negative regulation can occur by preventing the assembly of the spliceosome on pre-mRNA. For example, SF3B1 inhibitors such as pladienolide and E7107 bind to the SF3B1 subunit and disrupt spliceosome assembly, leading to massive aberrant exon skipping. This inhibition reduces the rate of splicing and can trigger cell death in cancer cells.
Modulation by RNA-Binding Proteins
In simple terms: Proteins that bind RNA can stop splicing.
RNA-binding proteins such as RBM10 and RBM5 negatively regulate splicing by competing with spliceosome components or promoting exon skipping. RBM10 autoregulates its own expression and cross-regulates RBM5 via alternative splicing coupled to nonsense-mediated decay. NOVA factors also modulate alternative splicing in neurons, influencing cell physiology and pathology.
Intragenic RNA Elements and PKR Activation
In simple terms: RNA sequences within a gene can activate a stress kinase that blocks splicing.
Intragenic RNA elements can activate the stress kinase PKR, which then inhibits splicing of cellular and viral mRNAs. This represents an antiviral mechanism where PKR activation leads to negative regulation of splicing.
Small Molecule and Oligonucleotide Interference
In simple terms: Drugs or designer molecules can block splicing.
Small molecules targeting the spliceosome, such as those inhibiting SF3B1, result in aberrant exon skipping and negative regulation of splicing. Additionally, AI/ML-derived splice-switching oligonucleotides can be designed to modulate splicing, including negative regulation.
Coupling with Nonsense-Mediated Decay
In simple terms: When splicing is blocked, the resulting mRNA may be destroyed.
Negative regulation of splicing can lead to the production of mRNA isoforms that are targeted for degradation by nonsense-mediated decay. This coupling provides a feedback mechanism to control gene expression, as seen with RBM10 and RBM5.
Key Genes Involved in GO:0048025 negative regulation of mRNA splicing, via spliceosome
The following genes and proteins are key players in the negative regulation of mRNA splicing via the spliceosome, based on published literature.
| Gene | Major Role | Research Relevance |
|---|---|---|
| RBM10 | RNA-binding protein that inhibits splicing and autoregulates via NMD | Tumor suppressor, regulates RBM5 |
| RBM5 | Splicing regulator, cross-regulated by RBM10 | Apoptosis and cancer |
| SF3B1 | Spliceosome component, target of inhibitors | Cancer mutations, splicing inhibition [3, 5] |
| PKR (EIF2AK2) | Stress kinase activated by RNA elements, inhibits splicing | Antiviral defense |
| NOVA1 | Neuron-specific splicing factor | Neurological disorders |
| NOVA2 | Neuron-specific splicing factor | Neurological disorders |
| p53 (TP53) | Mutant p53 alters splicing | Pancreatic cancer |
| RAS | Oncogene activated by altered splicing | Pancreatic cancer |
| ALOX5 | Upregulated upon BRD9 depletion, linked to ferroptosis | SF3B1-mutant hematopoiesis |
| BRD9 | Chromatin regulator, depletion affects splicing | SF3B1-mutant hematopoiesis |
| Pinin (PNN) | Modulates alternative splicing in vivo | Splicing regulation |
| SF3B1 mutants | Altered splicing and ferroptosis | Hematological malignancies |
| U2AF | Spliceosome component | Splicing regulation |
| SR proteins | Splicing enhancers | General splicing |
| hnRNPs | Splicing repressors | General splicing |
| Splice-switching oligos | Designed to modulate splicing | Therapeutic development |
How Is negative regulation of mRNA splicing, via spliceosome Regulated?
Negative regulation of mRNA splicing is itself regulated by various signaling pathways. For instance, the stress kinase PKR is activated by intragenic RNA elements and subsequently inhibits splicing, linking cellular stress to splicing control. Additionally, the expression of splicing regulators like RBM10 is autoregulated through a negative feedback loop involving alternative splicing and nonsense-mediated decay. Small molecules and oligonucleotides can also exogenously regulate splicing by targeting spliceosome components or splice sites [3, 4].
negative regulation of mRNA splicing, via spliceosome and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| TP53 | Pancreatic cancer, altered splicing activates RAS | Knock-in mutant p53 in pancreatic cell lines |
| SF3B1 | Hematological malignancies, ferroptosis | SF3B1-mutant knockout or knock-in models |
| RBM10 | Cancer, autoregulation via NMD | RBM10 knockout and overexpression |
| NOVA1/2 | Neurological disorders | NOVA knockout mice or neurons |
| PKR | Antiviral defense | PKR knockout cells |
Cancer
Dysregulation of splicing inhibition is common in cancer. Mutant p53 alters RNA splicing to activate oncogenic RAS signaling in pancreatic cancer. SF3B1 mutations, which affect spliceosome function, are found in hematological malignancies and lead to aberrant splicing and ferroptosis upon BRD9 depletion. Inhibiting splicing with small molecules can induce exon skipping and cell death in cancer cells.
Neurological Disorders
NOVA factors regulate alternative splicing in neurons, and their dysfunction is linked to neurological diseases. NOVA proteins control gene expression at the post-transcriptional level, influencing cell physiology and pathology.
Hematological Disorders
SF3B1 mutations are prevalent in myelodysplastic syndromes and other hematological disorders. BRD9 depletion in SF3B1-mutant cells leads to ALOX5 upregulation via chromatin dysregulation, inducing ferroptosis, highlighting a potential therapeutic vulnerability.
Viral Infections
PKR activation by intragenic RNA elements negatively regulates splicing of viral mRNAs, serving as an antiviral mechanism. This highlights the role of splicing inhibition in host defense.
From negative regulation of mRNA splicing, via spliceosome-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does gene X negatively regulate splicing? | Knockout cell line followed by RNA-seq |
| Does a point mutation in SF3B1 alter splicing inhibition? | Point mutation knock-in via CRISPR |
| Can a splicing factor be tagged for localization? | Tagged knock-in (e.g., GFP) |
| Does overexpression of RBM10 reduce splicing? | Overexpression cell line |
| What is the effect of PKR activation on splicing? | PKR knockout and RNA element knock-in |
| Can splice-switching oligonucleotides modulate splicing? | Patient-derived cells and AI-designed oligos |
How to Study the negative regulation of mRNA splicing, via spliceosome Process
| Method | What It Measures | Typical Application |
|---|---|---|
| RNA-seq | Splicing isoforms and expression levels | Detect exon skipping upon RBM10 knockout |
| RT-PCR | Specific splicing events | Validate splice-switching oligos |
| CRISPR screen | Genes affecting splicing inhibition | Identify modifiers of SF3B1 inhibitor sensitivity |
| Proteomics | Protein interactions | Identify spliceosome components |
| Immunofluorescence | Localization of splicing factors | Study pinin modulation |
| Nonsense-mediated decay assay | mRNA stability | Analyze RBM10 autoregulation |
| Small molecule treatment | Splicing inhibition | Test SF3B1 inhibitors |
| AI/ML design | Oligonucleotide sequences | Generate splice-switching oligos |
RNA Sequencing (RNA-seq)
RNA-seq is used to quantify splicing changes upon negative regulation. It can detect exon skipping, intron retention, and alternative splice site usage. Studies of SF3B1 inhibition and RBM10 knockout have utilized RNA-seq to reveal widespread splicing alterations [2, 3].
CRISPR Screens
Genome-wide CRISPR screens can identify genes that regulate splicing. For example, screens have uncovered factors that modulate sensitivity to splicing inhibitors.
Splice-Switching Oligonucleotides
AI/ML-derived splice-switching oligonucleotides are designed to modulate splicing, including negative regulation. These can be validated by RT-PCR and RNA-seq.
Proteomics and Immunoprecipitation
Proteomic approaches can identify proteins associated with the spliceosome under negative regulation conditions. Immunoprecipitation of tagged splicing factors followed by mass spectrometry reveals interaction partners.
How CRISPR Can Be Used to Study GO:0048025 negative regulation of mRNA splicing, via spliceosome
Knockout
CRISPR knockout of splicing regulators such as RBM10 or SF3B1 can reveal their role in negative regulation of splicing. For example, RBM10 knockout leads to altered splicing of its targets.
Point Mutation
Point mutations in SF3B1, commonly found in cancer, can be introduced via CRISPR to study their impact on splicing inhibition and drug sensitivity.
Knock-in
Knock-in of tagged splicing factors (e.g., GFP-RBM10) allows visualization and immunoprecipitation to study negative regulation of splicing.
Overexpression
Overexpression of splicing inhibitors like RBM10 can enhance negative regulation of splicing, providing a gain-of-function model.
How EDITGENE Supports negative regulation of mRNA splicing, via spliceosome Research
Researchers studying negative regulation of mRNA splicing, via spliceosome-related genes often need to determine whether a candidate gene is causally involved in splicing control or is merely correlated. EDITGENE provides CRISPR-based services to create precise cell models for such functional studies.
Contact EDITGENE today to design your custom CRISPR model for negative regulation of mRNA splicing, via spliceosome research.
Frequently Asked Questions About negative regulation of mRNA splicing, via spliceosome
What is negative regulation of mRNA splicing, via spliceosome?
It is any process that reduces the rate or extent of mRNA splicing via the spliceosome, as defined by GO:0048025.
What genes are involved in negative regulation of mRNA splicing?
Key genes include RBM10, RBM5, SF3B1, PKR, and NOVA factors [1, 2, 3, 7].
How does SF3B1 inhibition affect splicing?
SF3B1 inhibitors disrupt spliceosome assembly, leading to massive aberrant exon skipping.
What diseases are linked to dysregulated splicing inhibition?
Cancer, hematological disorders, and neurological diseases are linked to splicing dysregulation [5, 6, 7].
How can CRISPR be used to study negative regulation of splicing?
CRISPR knockout, point mutation knock-in, and overexpression models can reveal causal roles of splicing regulators [2, 5].
What methods detect negative regulation of splicing?
RNA-seq, RT-PCR, and splice-switching oligonucleotides are commonly used [2, 4].
What is the role of PKR in splicing?
PKR is activated by intragenic RNA elements and inhibits splicing as an antiviral mechanism.
How does RBM10 regulate splicing?
RBM10 negatively regulates splicing and autoregulates its own expression via nonsense-mediated decay.
What are NOVA factors?
NOVA factors are neuron-specific splicing regulators that modulate alternative splicing.
Can small molecules inhibit splicing?
Yes, small molecules targeting SF3B1 can inhibit splicing and induce exon skipping.
Conclusion
Negative regulation of mRNA splicing via the spliceosome (GO:0048025) is a fundamental process that controls gene expression and is implicated in numerous diseases. Understanding its mechanisms and key regulators provides opportunities for therapeutic intervention. EDITGENE offers comprehensive CRISPR services to facilitate research in this field.
References
- 1. Kaempfer R. 2023. Positive Regulation of Splicing of Cellular and Viral mRNA by Intragenic RNA Elements That Activate the Stress Kinase PKR, an Antiviral Mechanism.. Genes (Basel) 14(5) PMID: 37239334
- 2. Sun Y et al.. 2017. Autoregulation of RBM10 and cross-regulation of RBM10/RBM5 via alternative splicing-coupled nonsense-mediated decay.. Nucleic Acids Res 45(14):8524-8540 PMID: 28586478
- 3. Wu G et al.. 2018. Inhibition of SF3B1 by molecules targeting the spliceosome results in massive aberrant exon skipping.. RNA 24(8):1056-1066 PMID: 29844105
- 4. Fronk AD et al.. 2024. Development and validation of AI/ML derived splice-switching oligonucleotides.. Mol Syst Biol 20(6):676-701 PMID: 38664594
- 5. Saika W et al.. 2026. BRD9 depletion-mediated ALOX5 upregulation via chromatin dysregulation induces ferroptosis in SF3B1-mutant hematopoiesis.. Int J Hematol 123(3):342-355 PMID: 41219678
- 6. Escobar-Hoyos LF et al.. 2020. Altered RNA Splicing by Mutant p53 Activates Oncogenic RAS Signaling in Pancreatic Cancer.. Cancer Cell 38(2):198-211.e8 PMID: 32559497
- 7. Meldolesi J. 2020. Alternative Splicing by NOVA Factors: From Gene Expression to Cell Physiology and Pathology.. Int J Mol Sci 21(11) PMID: 32486302
- 8. Wang P et al.. 2002. Modulation of alternative pre-mRNA splicing in vivo by pinin.. Biochem Biophys Res Commun 294(2):448-55 PMID: 12051732
