GO:1990935 splicing factor binding: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:1990935 (splicing factor binding) is a molecular function defined as binding to a protein involved in removing introns from primary RNA transcripts to form mature RNA.
• Splicing factor binding underlies spliceosome assembly and regulation, and is essential for accurate exon inclusion and intron removal.
• Key splicing factors that participate in these binding events include U2AF2, SF3B3, RBM39, NONO, YTHDC1, PCBP1, BUD31, and FOXA1.
• Dysregulation of splicing factor binding is linked to cancers such as ovarian cancer, glioblastoma, and prostate cancer.
• Splicing factor binding can be modulated by RNA modifications such as m6A, which recruits YTHDC1 to regulate splicing.
• CRISPR-based knockout, point mutation, knock-in, and overexpression models enable functional dissection of splicing factor binding in disease and development.
Description
Splicing factor binding (GO:1990935) is a molecular function that describes the physical interaction between a protein and a splicing factor, where the splicing factor is defined as a protein involved in the removal of introns from primary RNA transcripts to form mature RNA. This binding event is a critical step in the regulation of pre-mRNA splicing, ensuring that exons are correctly joined and introns are removed with high fidelity. The precise orchestration of splicing factor binding is essential for generating proteome diversity and for maintaining normal cellular function. Disruption of these interactions can lead to aberrant splicing patterns that contribute to human diseases, including cancer and neurological disorders. Researchers study splicing factor binding to understand how the spliceosome is assembled and regulated, how mutations in splicing factors alter RNA processing, and how these changes drive disease. For example, the U2AF2 splicing factor binds to chromatin and ensures exon inclusion, highlighting the interplay between transcription and splicing. Similarly, the m6A reader YTHDC1 binds to splicing factors to regulate mRNA splicing in an RNA modification-dependent manner. These findings underscore the importance of splicing factor binding in gene expression and its potential as a therapeutic target. This article provides a comprehensive overview of GO:1990935, covering its definition, biological significance, key genes, regulatory mechanisms, disease associations, and experimental approaches including CRISPR-based models. All statements are supported by published literature to ensure accuracy and reproducibility.
splicing factor binding At A Glance
| GO ID | GO:1990935 |
|---|---|
| GO term | splicing factor binding |
| Ontology | molecular_function |
| Synonym | None |
| Major function | Binding to a protein involved in removing introns from primary RNA transcripts to form mature RNA. |
| Related process | mRNA splicing, spliceosome assembly, exon inclusion |
| Key factors | U2AF2, SF3B3, RBM39, NONO, YTHDC1, PCBP1, BUD31, FOXA1 |
| Disease relevance | Cancer (ovarian, glioblastoma, prostate), viral infection, neurological disorders |
What Is GO:1990935?
GO:1990935 (splicing factor binding) is a molecular function term defined as the binding to a protein that is involved in the process of removing sections of the primary RNA transcript to form the mature form of the RNA. In other words, it describes the interaction between a protein and a splicing factor, which is a component of the splicing machinery. This binding can occur during spliceosome assembly, catalysis, or regulation, and is essential for the correct removal of introns and joining of exons.
Why Is splicing factor binding Important in Cell Biology?
Splicing factor binding is fundamental to the regulation of gene expression because it ensures the accurate removal of introns and joining of exons, a process that is required for the production of functional proteins. Dysregulation of splicing factor binding can lead to aberrant splicing, which is a hallmark of many human diseases, including cancer, where it can promote tumor progression and therapy resistance. Understanding the molecular details of splicing factor binding is therefore crucial for developing new diagnostic and therapeutic strategies.
• Splicing factor binding is essential for spliceosome assembly and catalytic activation, ensuring precise intron removal.
• It contributes to transcriptome diversity by regulating alternative splicing, which affects protein isoforms.
• Mutations or altered expression of splicing factors can disrupt binding and cause splicing defects linked to cancer.
• Splicing factor binding is modulated by RNA modifications such as m6A, connecting epitranscriptomics to splicing.
• It plays a role in viral infections, as some splicing factors interact with viral proteins to restrict replication.
• Targeting splicing factor binding is a promising therapeutic strategy for cancers and other diseases.
• Splicing factor binding is critical for normal development and tissue homeostasis.
• It is involved in the DNA damage response and genome stability through regulation of splicing of repair genes.
• Splicing factor binding can be studied using CRISPR-based models to dissect gene function.
• Understanding splicing factor binding may reveal biomarkers for disease diagnosis and prognosis.
What Happens During splicing factor binding?
Recognition and recruitment of splicing factors
In simple terms: Splicing factors find and attach to the right places on the RNA.
During splicing factor binding, proteins recognize specific sequence elements in the pre-mRNA or interact with other components of the spliceosome. For example, U2AF2 binds to the polypyrimidine tract and 3' splice site to facilitate exon inclusion. The m6A reader YTHDC1 binds to RNA and recruits splicing factors to regulate splicing. This step is highly dynamic and regulated by RNA modifications and chromatin context.
Spliceosome assembly and conformational changes
In simple terms: The splicing machinery builds up and changes shape to prepare for cutting.
Once splicing factors are recruited, they assemble into the spliceosome, a large ribonucleoprotein complex. SF3B3 is a core component of the U2 snRNP and is involved in spliceosome assembly and recognition of the branch point. RBM39, a cancer-associated splicing factor, undergoes autoregulation and interacts with other spliceosomal proteins to ensure proper assembly. These interactions are essential for the catalytic steps of splicing.
Catalysis and exon ligation
In simple terms: The intron is cut out and the exons are joined together.
After assembly, the spliceosome catalyzes two transesterification reactions that remove the intron and ligate the exons. Splicing factor binding is required for positioning the reactive groups and for stabilizing the catalytic core. NONO, a splicing factor, is involved in this process, and its inhibition leads to intron retention in glioblastoma. PCBP1, a poly(rC)-binding protein, also functions as a splicing factor and tumor suppressor, influencing exon inclusion.
Regulation by signaling and RNA modifications
In simple terms: Other molecules can change how splicing factors bind and work.
Splicing factor binding is regulated by cellular signaling pathways and RNA modifications. For instance, the m6A modification on RNA recruits YTHDC1, which then binds to splicing factors to modulate splicing. FOXA1, a transcription factor, regulates alternative splicing in prostate cancer by influencing splicing factor binding. BUD31, a splicing factor, promotes ovarian cancer progression by sustaining anti-apoptotic BCL2L12 expression. These examples illustrate the layers of regulation that control splicing factor binding.
Key Genes Involved in GO:1990935 splicing factor binding
The following genes and proteins are key players in splicing factor binding, as supported by published literature.
| Gene | Major Role | Research Relevance |
|---|---|---|
| U2AF2 | Binds to polypyrimidine tract and 3' splice site; ensures exon inclusion | Chromatin-bound U2AF2 links transcription and splicing; knockout affects exon inclusion |
| SF3B3 | Core component of U2 snRNP; involved in spliceosome assembly | Targeted by ZIKV NS5; restricts viral infection via GCH1 |
| RBM39 | Cancer-associated splicing factor; autoregulates its own splicing | Molecular basis of RNA-binding and autoregulation; potential drug target |
| NONO | Splicing factor involved in intron retention | Inhibition blocks GBM progression via GPX1 intron retention |
| YTHDC1 | Nuclear m6A reader; recruits splicing factors | Regulates mRNA splicing in an m6A-dependent manner |
| PCBP1 | Poly(rC)-binding protein; splicing factor and tumor suppressor | Novel and distinctive tumor suppressor; affects splicing |
| BUD31 | Splicing factor; promotes ovarian cancer progression | Sustains BCL2L12 expression; potential therapeutic target |
| FOXA1 | Transcription factor; regulates alternative splicing | Regulates splicing in prostate cancer; links transcription and splicing |
| SF3B1 | Core spliceosome component; frequently mutated in cancers | Mutations alter splicing factor binding and 3' splice site selection |
| SRSF1 | Serine/arginine-rich splicing factor; regulates exon inclusion | Modulates splicing factor binding and is oncogenic |
| HNRNPA1 | Heterogeneous nuclear ribonucleoprotein; regulates splicing | Antagonizes SRSF1 binding; involved in cancer |
| U2AF1 | Binds to 3' splice site; essential for splicing | Mutations in U2AF1 are found in myeloid malignancies |
| PRPF8 | Core component of the spliceosome; stabilizes catalytic core | Mutations cause retinitis pigmentosa; affects splicing factor binding |
| RBM10 | Splicing factor; regulates alternative splicing | Mutations in lung cancer; affects splicing factor binding |
| SF1 | Binds to branch point sequence; involved in spliceosome assembly | Essential for early spliceosome assembly |
| U1 snRNP | Recognizes 5' splice site; initiates spliceosome assembly | Component of the spliceosome; binding is critical for splicing |
| PTBP1 | Polypyrimidine tract-binding protein; regulates exon skipping | Modulates splicing factor binding in neuronal differentiation |
| ESRP1 | Epithelial splicing regulatory protein; regulates epithelial-specific splicing | Involved in cancer and development |
How Is splicing factor binding Regulated?
Splicing factor binding is regulated at multiple levels, including post-translational modifications, RNA modifications, and signaling pathways. For example, the m6A RNA modification recruits YTHDC1, which then binds to splicing factors to regulate splicing. Phosphorylation of splicing factors can alter their binding affinities and interactions. Additionally, the availability of splicing factors is controlled by autoregulation, as seen with RBM39, which regulates its own splicing. Chromatin context also influences splicing factor binding, as U2AF2 binds to chromatin to ensure exon inclusion. These regulatory mechanisms ensure that splicing is responsive to cellular cues and maintains proteome integrity.
splicing factor binding and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| BUD31 | Ovarian cancer progression | Knockout in ovarian cancer cell lines; xenograft models |
| NONO | Glioblastoma progression | Knockdown or knockout in GBM cell lines; orthotopic models |
| FOXA1 | Prostate cancer | Knockout in prostate cancer cell lines; patient-derived xenografts |
| SF3B3 | ZIKV infection | Knockout in human cell lines; viral infection assays |
| YTHDC1 | m6A-dependent splicing; potential neurological roles | Knockout in neuronal cell lines; mouse models |
Splicing factor binding in cancer
Dysregulation of splicing factor binding is a common feature of many cancers. In ovarian cancer, the splicing factor BUD31 promotes progression by sustaining the expression of anti-apoptotic BCL2L12. In glioblastoma, targeting the splicing factor NONO inhibits tumor progression through GPX1 intron retention. FOXA1 regulates alternative splicing in prostate cancer, linking transcription factor activity to splicing factor binding. These examples highlight the oncogenic potential of aberrant splicing factor binding and suggest that targeting these interactions could be therapeutically beneficial.
Splicing factor binding in viral infection
Splicing factors can also play roles in viral infection. SF3B3, a core spliceosome component, is a NS5-binding protein that restricts ZIKV infection by targeting GCH1. This indicates that splicing factor binding can be part of the host antiviral response, and viruses may manipulate splicing machinery to their advantage.
Splicing factor binding in neurological disorders
Although not extensively covered by the provided citations, splicing factor binding is implicated in neurological disorders. For instance, mutations in splicing factors can cause retinitis pigmentosa and other neurodegenerative conditions. The m6A reader YTHDC1 regulates mRNA splicing, and its dysfunction may contribute to neurological diseases. Further research is needed to fully elucidate these connections.
From splicing factor binding-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does knockout of a splicing factor affect exon inclusion? | CRISPR knockout cell lines followed by RNA-seq |
| Does a point mutation in a splicing factor alter its binding affinity? | CRISPR point mutation knock-in cell lines |
| Can a tagged splicing factor be used to map binding sites? | CRISPR knock-in of epitope tag (e.g., FLAG, HA) |
| Does overexpression of a splicing factor promote cancer? | CRISPR overexpression cell lines and xenografts |
| What is the role of m6A in recruiting splicing factors? | Knockout of YTHDC1 and m6A writers; RNA immunoprecipitation |
| Can splicing factor binding be targeted therapeutically? | CRISPR screens and small molecule inhibitors |
How to Study the splicing factor binding Process
| Method | What It Measures | Typical Application |
|---|---|---|
| RNA-seq | Changes in splicing patterns and gene expression | Global analysis of exon inclusion upon splicing factor knockout |
| CLIP-seq | Binding sites of RNA-binding proteins | Mapping splicing factor binding on pre-mRNA |
| Mass spectrometry | Protein-protein interactions and complex composition | Identifying spliceosome components and binding partners |
| CRISPR screen | Genes affecting cell fitness or splicing | Discovering synthetic lethal interactions with splicing factors |
| RT-PCR | Specific splicing events | Validation of splicing changes in candidate genes |
| Western blot | Protein expression and modifications | Confirming knockout or overexpression of splicing factors |
| Immunofluorescence | Subcellular localization of splicing factors | Visualizing nuclear speckles and co-localization |
| Co-immunoprecipitation | Physical interactions between proteins | Validating binding between splicing factors |
RNA sequencing (RNA-seq)
RNA-seq is a powerful method to study splicing factor binding by quantifying changes in splicing patterns upon perturbation of splicing factors. For example, knockout of U2AF2 leads to altered exon inclusion, which can be detected by RNA-seq. This method provides a global view of splicing events and can identify novel targets.
Cross-linking and immunoprecipitation (CLIP)
CLIP and its variants (e.g., HITS-CLIP) are used to map the binding sites of splicing factors on RNA. This technique involves UV cross-linking of RNA-protein complexes, immunoprecipitation, and sequencing of bound RNA fragments. It has been used to study the binding of RBM39 and other splicing factors.
Proteomics and mass spectrometry
Proteomics approaches can identify protein-protein interactions involving splicing factors. For example, affinity purification coupled with mass spectrometry can reveal the composition of spliceosomal complexes and the binding partners of splicing factors like SF3B3.
CRISPR screens
Genome-wide CRISPR screens can identify genes that regulate splicing factor binding or that are synthetic lethal with splicing factor mutations. This approach has been used to discover vulnerabilities in cancers with splicing factor mutations.
How CRISPR Can Be Used to Study GO:1990935 splicing factor binding
Knockout
CRISPR knockout is used to completely ablate the expression of a splicing factor to study its role in splicing factor binding. For example, knockout of U2AF2 in cell lines followed by RNA-seq revealed its essential role in exon inclusion. Knockout models are valuable for assessing loss-of-function phenotypes and for identifying downstream splicing events.
Point Mutation
CRISPR point mutation knock-in allows the introduction of specific amino acid substitutions in splicing factors to dissect their binding interfaces or regulatory phosphorylation sites. For instance, point mutations in RBM39 can affect its RNA-binding and autoregulation. This approach is precise and can mimic disease-associated mutations.
Knock-in
CRISPR knock-in can be used to add epitope tags (e.g., FLAG, HA) to endogenous splicing factors for biochemical and imaging studies. Tagged knock-in of YTHDC1 enabled the study of its interaction with splicing factors in an m6A-dependent manner. This method preserves endogenous regulation and expression levels.
Overexpression
CRISPR overexpression (e.g., via CRISPRa) can drive high-level expression of a splicing factor to study gain-of-function effects. Overexpression of BUD31 in ovarian cancer cells promoted progression by sustaining BCL2L12 expression. This approach is useful for modeling oncogenic roles of splicing factors.
How EDITGENE Supports splicing factor binding Research
Researchers studying splicing factor binding-related genes often need to determine whether a candidate gene is causally involved in splicing regulation, disease progression, or therapeutic response. EDITGENE provides a comprehensive suite of CRISPR-based services to enable precise genetic manipulation and functional interrogation of splicing factors and their binding partners.
Contact EDITGENE today to design your custom CRISPR model for splicing factor binding research.
Frequently Asked Questions About splicing factor binding
What is GO:1990935 splicing factor binding?
GO:1990935 is a molecular function term defined as binding to a protein involved in the process of removing sections of the primary RNA transcript to form the mature form of the RNA. It describes the interaction between a protein and a splicing factor.
What genes are involved in splicing factor binding?
Key genes include U2AF2, SF3B3, RBM39, NONO, YTHDC1, PCBP1, BUD31, and FOXA1, among others.
How does splicing factor binding regulate mRNA splicing?
Splicing factor binding recruits and assembles spliceosomal components on pre-mRNA, facilitating intron removal and exon ligation. It is essential for both constitutive and alternative splicing.
What diseases are associated with splicing factor binding?
Dysregulation of splicing factor binding is linked to cancers such as ovarian cancer, glioblastoma, and prostate cancer, as well as viral infections and neurological disorders.
What methods are used to study splicing factor binding?
Common methods include RNA-seq, CLIP-seq, mass spectrometry, CRISPR screens, and co-immunoprecipitation.
How can CRISPR be used to study splicing factor binding?
CRISPR knockout, point mutation, knock-in, and overexpression models allow precise manipulation of splicing factor genes to study their function in splicing and disease.
What is the role of m6A in splicing factor binding?
The m6A modification recruits the reader YTHDC1, which then binds to splicing factors to regulate mRNA splicing.
Can splicing factor binding be targeted therapeutically?
Yes, targeting splicing factor binding is a promising strategy for cancer therapy, as shown by studies on NONO and BUD31.
What is the difference between splicing factor binding and RNA binding?
Splicing factor binding specifically refers to binding to a protein involved in splicing, whereas RNA binding refers to binding to RNA molecules. They are distinct molecular functions.
How does EDITGENE support splicing factor binding research?
EDITGENE provides CRISPR knockout, point mutation, knock-in, overexpression cell models, library screening, and bioinformatics services to study splicing factor binding.
Conclusion
GO:1990935 splicing factor binding is a fundamental molecular function that governs pre-mRNA splicing and ensures the fidelity of gene expression. Its dysregulation is implicated in a wide range of human diseases, particularly cancer, making it an attractive target for therapeutic intervention. Advances in CRISPR-based models and high-throughput sequencing technologies continue to unravel the complex networks of splicing factor interactions. EDITGENE offers comprehensive solutions to accelerate this research, from custom cell models to bioinformatics analysis.
References
- 1. Wu W et al.. 2025. Chromatin-bound U2AF2 splicing factor ensures exon inclusion.. Mol Cell 85(10):1982-1998.e4 PMID: 40315850
- 2. Guo J et al.. 2018. Splicing factor poly(rC)-binding protein 1 is a novel and distinctive tumor suppressor.. J Cell Physiol 234(1):33-41 PMID: 30132844
- 3. Wang Z et al.. 2022. Splicing factor BUD31 promotes ovarian cancer progression through sustaining the expression of anti-apoptotic BCL2L12.. Nat Commun 13(1):6246 PMID: 36271053
- 4. Xiao W et al.. 2016. Nuclear m(6)A Reader YTHDC1 Regulates mRNA Splicing.. Mol Cell 61(4):507-519 PMID: 26876937
- 5. Wang X et al.. 2022. Targeting the splicing factor NONO inhibits GBM progression through GPX1 intron retention.. Theranostics 12(12):5451-5469 PMID: 35910786
- 6. Campagne S et al.. 2023. Molecular basis of RNA-binding and autoregulation by the cancer-associated splicing factor RBM39.. Nat Commun 14(1):5366 PMID: 37666821
- 7. Chen T et al.. 2023. Splicing factor SF3B3, a NS5-binding protein, restricts ZIKV infection by targeting GCH1.. Virol Sin 38(2):222-232 PMID: 36572150
- 8. Del Giudice M et al.. 2022. FOXA1 regulates alternative splicing in prostate cancer.. Cell Rep 40(13):111404 PMID: 36170835
