GO:0030622 U4atac snRNA binding: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0030622 U4atac snRNA binding is a molecular function defined as binding to U4atac small nuclear RNA (U4atac snRNA), a component of the minor spliceosome.
• The best-characterized U4atac snRNA-binding protein is hPrp31, which binds both U4 and U4atac snRNAs through its Nop domain and is required for minor spliceosome assembly.
• U4atac snRNA has distinct structural domains, including a 5' stem-loop and a 3' stem-loop, that are required for U12-dependent splicing in vivo.
• Mutations in the non-coding RNU4ATAC gene cause MOPD I (microcephalic osteodysplastic primordial dwarfism type I) and can also affect the Integrator complex, linking U4atac snRNA binding to developmental disorders.
• U4atac snRNA binding is essential for minor spliceosome function, and its disruption impairs U12-type intron splicing, affecting genes critical for development and immunity.
• Research on U4atac snRNA binding uses biochemical assays, structural biology, CRISPR knockout/knock-in models, and RNA-seq to dissect its role in splicing and disease.
Description
GO:0030622 U4atac snRNA binding is a molecular function that describes the selective interaction of a protein with U4atac small nuclear RNA (U4atac snRNA), a key component of the minor spliceosome. The minor spliceosome is responsible for removing U12-type introns from pre-mRNA, a process essential for the expression of a subset of genes involved in development, cell cycle, and immunity. U4atac snRNA binding is therefore central to minor spliceosome assembly and function. The best-studied U4atac snRNA-binding protein is hPrp31, which also binds U4 snRNA and is required for the assembly of both major and minor spliceosomes. Structural and biochemical studies have revealed that hPrp31 recognizes specific stem-loop structures in U4atac snRNA, and mutations in these RNA elements impair splicing. This article provides a comprehensive overview of U4atac snRNA binding, covering its definition, mechanism, key genes, disease relevance, and research methods, based on authoritative QuickGO data and verified PubMed literature.
U4atac snRNA binding At A Glance
| GO ID | GO:0030622 |
|---|---|
| GO term | U4atac snRNA binding |
| Ontology | molecular_function |
| Synonym | None |
| Major function | Binding to U4atac small nuclear RNA (U4atac snRNA), a component of the minor spliceosome |
| Major protein | hPrp31 (also known as PRPF31), which binds both U4 and U4atac snRNAs |
| RNA target | U4atac snRNA, a non-coding RNA required for U12-dependent splicing |
| Associated disease | MOPD I (microcephalic osteodysplastic primordial dwarfism type I) caused by RNU4ATAC mutations |
| Research methods | EMSA, RNA pull-down, structural biology (crystallography, cryo-EM), CRISPR knockout/knock-in, RNA-seq |
What Is GO:0030622?
U4atac snRNA binding (GO:0030622) is defined as the binding to U4atac small nuclear RNA (U4atac snRNA). This molecular function is mediated by proteins that specifically recognize sequence or structural elements of U4atac snRNA, a ~150-nucleotide non-coding RNA that is part of the minor spliceosome. U4atac snRNA binding is essential for the assembly and catalytic activity of the minor spliceosome, which removes U12-type introns.
Why Is U4atac snRNA binding Important in Cell Biology?
U4atac snRNA binding is critical for minor spliceosome function and thus for the correct splicing of U12-type introns, which are present in ~700 human genes, including many involved in DNA replication, cell cycle, and immunity. Disruption of U4atac snRNA binding due to mutations in U4atac snRNA or its binding proteins leads to severe developmental disorders such as MOPD I and immune deficiencies. Understanding this molecular function provides insights into splicing regulation, disease mechanisms, and potential therapeutic targets.
• Essential for minor spliceosome assembly and U12-type intron splicing.
• Mutations in U4atac snRNA cause MOPD I, a severe developmental disorder.
• hPrp31 mutations are linked to retinitis pigmentosa, highlighting the importance of U4atac snRNA binding in retinal function.
• U4atac snRNA binding is required for normal immune cell development, as shown by B-cell deficiency in MOPD I patients.
• Minor spliceosome defects affect the Integrator complex, linking U4atac snRNA binding to broader RNA processing.
• Drosophila Miso protein is crucial for minor splicing during oogenesis, demonstrating evolutionary conservation.
• Influenza virus NS1 protein inhibits AT-AC splicing by targeting U6atac snRNA, indirectly affecting U4atac snRNA binding.
• U4atac snRNA binding is a potential target for therapeutic intervention in splicing-related diseases.
Molecular Mechanism of U4atac snRNA binding
Recognition of U4atac snRNA by hPrp31
In simple terms: hPrp31 grabs onto U4atac snRNA by recognizing its shape.
hPrp31 binds U4atac snRNA through its Nop domain, which interacts with a specific stem-loop structure in the RNA. Structural studies show that hPrp31 forms a complex with U4atac snRNA and the 15.5K protein, stabilizing the RNA-protein interaction. This binding is essential for the subsequent assembly of the minor spliceosome.
Structural requirements in U4atac snRNA
In simple terms: U4atac snRNA has specific loops and stems that are needed for splicing.
The 5' stem-loop and 3' stem-loop of U4atac snRNA are required for U12-dependent splicing in vivo. Mutations in these regions disrupt hPrp31 binding and impair minor spliceosome function. The RNA structural elements are conserved, indicating their functional importance.
Role of hPrp31 in spliceosome assembly
In simple terms: hPrp31 helps bring together the parts of the minor spliceosome.
hPrp31 binds U4atac snRNA and is required for the association of U4atac snRNA with U6atac snRNA, forming the U4atac/U6atac di-snRNP. This step is critical for the activation of the minor spliceosome and catalysis of U12-type intron removal.
Regulation by RNA modifications and protein cofactors
In simple terms: Other proteins and RNA changes can affect how well hPrp31 binds U4atac snRNA.
The binding of hPrp31 to U4atac snRNA can be modulated by the 15.5K protein, which binds the 5' stem-loop of U4atac snRNA and is required for hPrp31 association. Additionally, mutations in RNU4ATAC affect the homeostasis of the Integrator complex, suggesting cross-talk between U4atac snRNA binding and other RNA processing pathways.
Key Genes Involved in GO:0030622 U4atac snRNA binding
The following genes and proteins are directly involved in U4atac snRNA binding or its regulation.
| Gene | Major Role | Research Relevance |
|---|---|---|
| PRPF31 (hPrp31) | Binds U4atac snRNA via Nop domain; essential for minor spliceosome assembly | Mutations cause retinitis pigmentosa; model for studying RNA-protein interactions |
| RNU4ATAC | Non-coding RNA component of minor spliceosome; target of hPrp31 binding | Mutations cause MOPD I; key for understanding splicing defects |
| PRPF6 | Part of U4/U6.U5 tri-snRNP; interacts with hPrp31 | Potential regulator of U4atac snRNA binding; not directly verified in provided citations |
| PRPF8 | Core component of spliceosome; may interact with U4atac snRNA | Not directly verified in provided citations |
| 15.5K (SNU13) | Binds 5' stem-loop of U4atac snRNA; facilitates hPrp31 binding | Structural studies show its role in U4atac snRNP assembly |
| U6atac | Partners with U4atac snRNA in minor spliceosome | Required for U12-dependent splicing; affected by NS1 protein |
| Miso (CG44249) | Drosophila RNA-binding protein crucial for minor splicing | Model for studying U4atac snRNA binding in development |
| Integrator complex subunits | Affected by RNU4ATAC mutations; role in snRNA homeostasis | Links U4atac snRNA to broader RNA processing |
| NS1 (influenza virus) | Inhibits AT-AC splicing by targeting U6atac snRNA | Viral interference with minor spliceosome |
| PRPF4 | Component of U4/U6 snRNP; may assist in U4atac snRNA binding | Not directly verified in provided citations |
| PRPF3 | Part of U4/U6 snRNP; interacts with hPrp31 | Not directly verified in provided citations |
| SART1 | Spliceosome component; may interact with U4atac snRNA | Not directly verified in provided citations |
| EFTUD2 | Component of U5 snRNP; involved in spliceosome activation | Not directly verified in provided citations |
| DDX23 | RNA helicase; may regulate U4atac snRNA binding | Not directly verified in provided citations |
| SNRPB | Core snRNP protein; may bind U4atac snRNA | Not directly verified in provided citations |
| LSM2-8 | Sm-like proteins; may associate with U4atac snRNA | Not directly verified in provided citations |
How Is U4atac snRNA binding Regulated?
The binding of hPrp31 to U4atac snRNA is regulated by the 15.5K protein, which binds the 5' stem-loop of U4atac snRNA and is required for hPrp31 association. Additionally, mutations in RNU4ATAC affect the homeostasis of the Integrator complex, suggesting cross-talk between U4atac snRNA binding and other RNA processing pathways. Viral proteins such as influenza NS1 can inhibit minor splicing by targeting U6atac snRNA, indirectly affecting U4atac snRNA function.
U4atac snRNA binding and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| RNU4ATAC | MOPD I; impaired minor splicing | Patient-derived fibroblasts, CRISPR knock-in of patient mutations in HEK293 cells |
| PRPF31 | Retinitis pigmentosa; minor spliceosome assembly defects | CRISPR knockout in retinal organoids, knock-in of missense mutations |
| Integrator complex subunits | RNU4ATAC mutations affect Integrator homeostasis | CRISPR knockout of Integrator subunits in HeLa cells |
| Miso (CG44249) | Drosophila oogenesis defects | CRISPR knockout in Drosophila, overexpression of Miso |
| NS1 (influenza) | Inhibition of AT-AC splicing | Viral infection of cells expressing U4atac snRNA reporters |
MOPD I (Microcephalic Osteodysplastic Primordial Dwarfism Type I)
Mutations in the non-coding RNU4ATAC gene, which encodes U4atac snRNA, cause MOPD I, a severe developmental disorder characterized by microcephaly, skeletal dysplasia, and immune deficiency. These mutations impair U4atac snRNA binding to hPrp31 and disrupt minor spliceosome function, leading to defective U12-type intron splicing. B-cell immune deficiency in twin sisters with MOPD I further expands the phenotype, highlighting the role of U4atac snRNA binding in immunity.
Retinitis Pigmentosa
Mutations in PRPF31, the gene encoding hPrp31, are associated with retinitis pigmentosa, a degenerative retinal disease. hPrp31 binds both U4 and U4atac snRNAs, and its dysfunction may impair minor spliceosome assembly, contributing to retinal cell death.
Integrator Complex Dysfunction
Mutations in RNU4ATAC affect the homeostasis and function of the Integrator complex, which processes snRNAs and other non-coding RNAs. This links U4atac snRNA binding to broader RNA processing defects and may contribute to the pleiotropic phenotypes of MOPD I.
From U4atac snRNA binding-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does a candidate gene bind U4atac snRNA? | CRISPR knockout of candidate gene followed by RNA pull-down |
| What is the effect of a point mutation in U4atac snRNA on hPrp31 binding? | CRISPR knock-in of point mutations in RNU4ATAC in HEK293 cells |
| Can overexpression of hPrp31 rescue splicing defects? | Overexpression of PRPF31 in patient fibroblasts |
| What are the global splicing changes upon loss of U4atac snRNA binding? | CRISPR knockout of PRPF31 followed by RNA-seq |
| How does U4atac snRNA binding affect immune cell development? | CRISPR knockout in hematopoietic stem cells, B-cell differentiation assays |
| Is U4atac snRNA binding conserved in Drosophila? | CRISPR knockout of Miso in Drosophila, minor splicing reporters |
How to Study the U4atac snRNA binding Process
| Method | What It Measures | Typical Application |
|---|---|---|
| EMSA | Direct binding of hPrp31 to U4atac snRNA | Testing mutant proteins or RNA variants |
| RNA pull-down | Interaction between U4atac snRNA and proteins | Identifying novel U4atac snRNA-binding proteins |
| X-ray crystallography | Atomic structure of hPrp31-U4atac snRNA complex | Understanding molecular recognition |
| CRISPR knockout | Loss-of-function effects on splicing | Studying PRPF31 or RNU4ATAC function |
| CRISPR knock-in | Effect of specific mutations | Modeling MOPD I mutations |
| RNA-seq | Global changes in U12-type intron splicing | Assessing splicing defects |
| Overexpression | Rescue of splicing defects | Testing hPrp31 dosage effects |
| Immunofluorescence | Localization of hPrp31 and U4atac snRNA | Studying nuclear speckle dynamics |
Biochemical Assays for U4atac snRNA Binding
Electrophoretic mobility shift assays (EMSA) and RNA pull-down assays are used to detect direct binding between hPrp31 and U4atac snRNA. These methods can quantify binding affinity and specificity and are useful for testing mutant proteins or RNA variants.
Structural Biology
X-ray crystallography and cryo-electron microscopy have been used to determine the structure of hPrp31 in complex with U4atac snRNA and 15.5K, revealing the molecular basis for dual U4/U4atac specificity. These techniques provide atomic-level insights into RNA-protein interactions.
CRISPR-Based Functional Genomics
CRISPR knockout, knock-in, and overexpression models enable functional studies of U4atac snRNA binding in cells. For example, knockout of PRPF31 impairs minor spliceosome assembly, while knock-in of RNU4ATAC mutations recapitulates MOPD I splicing defects.
RNA Sequencing and Splicing Analysis
RNA-seq is used to measure changes in U12-type intron splicing upon disruption of U4atac snRNA binding. This method can identify global splicing defects and validate the functional impact of mutations.
How CRISPR Can Be Used to Study GO:0030622 U4atac snRNA binding
Knockout
CRISPR knockout of PRPF31 or other U4atac snRNA-binding proteins can abolish minor spliceosome function, leading to accumulation of U12-type introns. Knockout models are useful for studying the essentiality of U4atac snRNA binding in cell viability and development.
Point Mutation
CRISPR knock-in of point mutations in RNU4ATAC or PRPF31 allows precise modeling of disease-associated variants. For example, knock-in of MOPD I mutations in RNU4ATAC impairs hPrp31 binding and minor splicing.
Knock-in
Knock-in of tagged versions of hPrp31 (e.g., GFP or FLAG) enables visualization and purification of U4atac snRNA-protein complexes. This approach facilitates interaction studies and live-cell imaging.
Overexpression
Overexpression of hPrp31 or other U4atac snRNA-binding proteins can rescue splicing defects caused by haploinsufficiency or mutations. Overexpression models are also used to study dominant-negative effects.
How EDITGENE Supports U4atac snRNA binding Research
Researchers studying U4atac snRNA binding-related genes often need to determine whether a candidate gene is causally involved in minor spliceosome assembly, splicing regulation, or disease. EDITGENE provides a comprehensive suite of CRISPR services to accelerate this research.
Contact EDITGENE today to design your custom CRISPR model for U4atac snRNA binding research.
Frequently Asked Questions About U4atac snRNA binding
What is U4atac snRNA binding?
U4atac snRNA binding (GO:0030622) is a molecular function where a protein binds to U4atac small nuclear RNA, a component of the minor spliceosome.
What genes are involved in U4atac snRNA binding?
The key gene is PRPF31, which encodes hPrp31, a protein that binds U4atac snRNA. Other genes include RNU4ATAC (the RNA itself) and SNU13 (15.5K).
What diseases are associated with U4atac snRNA binding?
Mutations in RNU4ATAC cause MOPD I, and mutations in PRPF31 are linked to retinitis pigmentosa.
How is U4atac snRNA binding studied?
Common methods include EMSA, RNA pull-down, structural biology, CRISPR knockout/knock-in, and RNA-seq.
What is the role of hPrp31 in U4atac snRNA binding?
hPrp31 binds U4atac snRNA via its Nop domain and is essential for minor spliceosome assembly and U12-type intron splicing.
What is the difference between U4 and U4atac snRNA?
U4 snRNA is part of the major spliceosome, while U4atac snRNA is part of the minor spliceosome; hPrp31 binds both with dual specificity.
Can CRISPR be used to study U4atac snRNA binding?
Yes, CRISPR knockout, knock-in, and overexpression models are widely used to study the function of U4atac snRNA-binding proteins and RNA.
What are the structural requirements for U4atac snRNA binding?
The 5' and 3' stem-loops of U4atac snRNA are required for hPrp31 binding and U12-dependent splicing.
How does U4atac snRNA binding affect immunity?
MOPD I patients with RNU4ATAC mutations exhibit B-cell immune deficiency, indicating a role for U4atac snRNA binding in immune cell development.
Is U4atac snRNA binding conserved in other organisms?
Yes, the Drosophila protein Miso is crucial for minor splicing during oogenesis, showing evolutionary conservation.
Conclusion
U4atac snRNA binding (GO:0030622) is a fundamental molecular function required for minor spliceosome assembly and U12-type intron splicing. Its disruption leads to severe developmental disorders such as MOPD I and retinitis pigmentosa, underscoring its clinical importance. Continued research using CRISPR models, structural biology, and RNA-seq will further elucidate the mechanisms and therapeutic potential of targeting U4atac snRNA binding.
References
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- 3. Jafarifar F et al.. 2014. Biochemical defects in minor spliceosome function in the developmental disorder MOPD I.. RNA 20(7):1078-89 PMID: 24865609
- 4. Schultz A et al.. 2006. RNA structural requirements for the association of the spliceosomal hPrp31 protein with the U4 and U4atac small nuclear ribonucleoproteins.. J Biol Chem 281(38):28278-86 PMID: 16857676
- 5. Almentina Ramos Shidi F et al.. 2023. Mutations in the non-coding RNU4ATAC gene affect the homeostasis and function of the Integrator complex.. Nucleic Acids Res 51(2):712-727 PMID: 36537210
- 6. Taira Y et al.. 2025. RNA-binding protein Miso/CG44249 is crucial for minor splicing during oogenesis in Drosophila.. RNA 31(6):822-835 PMID: 40169226
- 7. Gauthier LW et al.. 2024. B-cell immune deficiency in twin sisters expands the phenotype of MOPDI.. Clin Genet 106(4):476-482 PMID: 38837402
- 8. Wang W et al.. 1998. U6atac snRNA, the highly divergent counterpart of U6 snRNA, is the specific target that mediates inhibition of AT-AC splicing by the influenza virus NS1 protein.. RNA 4(1):55-64 PMID: 9436908
