GO:0008380 RNA splicing: Mechanism, Genes, Functions

RNA splicing (GO:0008380) is a fundamental biological process in which introns are removed from a primary RNA transcript and exons are ligated to generate the mature RNA. This definition, maintained by the Gene Ontology consortium, encompasses the chemical steps and the macromolecular machinery that ensure accurate exon joining, a prerequisite for correct protein expression in eukaryotes. Because most human genes contain multiple introns, splicing is not merely a housekeeping step but a major layer of gene regulation that influences transcript stability, coding capacity, and downstream translation. Researchers study RNA splicing to understand how genetic information is diversified and how its disruption contributes to disease [2,5]. The spliceosome, a large and dynamic complex of small nuclear RNAs and associated proteins, carries out the canonical splicing reaction through a series of ordered assembly and catalytic transitions. Beyond this core reaction, alternative splicing allows a single gene to produce multiple mRNA isoforms, thereby expanding the proteome and enabling tissue-specific and developmental-stage-specific gene expression programs. This regulatory flexibility is essential for normal development, including neurogenesis, and its perturbation is increasingly recognized as a hallmark of cancer and other disorders [2,5]. From a research perspective, GO:0008380 provides a structured framework for annotating genes, interpreting transcriptomic data, and designing functional experiments. Splicing factors are recurrently mutated in hematologic malignancies and solid tumors, and splicing alterations can create neoantigens or drive oncogenic isoform expression [2,4]. Consequently, splicing is being pursued as a therapeutic target, with splicing modifiers and RNA-targeting small molecules entering drug development pipelines [3,8]. Understanding the molecular players and regulatory logic of RNA splicing is therefore central to both basic biology and translational medicine.

RNA splicing (GO:0008380) is the process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA. In practical terms, it converts a precursor mRNA (pre-mRNA) containing exons and introns into a mature mRNA in which introns are excised and exons are covalently joined. This process is catalyzed by the spliceosome and is guided by cis-acting sequence elements and trans-acting splicing factors.

RNA splicing is essential because it determines the coding content of most eukaryotic genes and provides a major source of transcriptomic and proteomic diversity [1,6]. Dysregulation of splicing is causally linked to human disease, including hematologic malignancies, solid tumors, and neurologic disorders, making splicing factors and the spliceosome attractive targets for therapeutic intervention [2,3,4,5]. Moreover, splicing modulates cellular responses to stress and developmental cues, so understanding its regulation is critical for interpreting gene expression data and for designing RNA-based therapeutics [6,8].

The following genes encode core spliceosome components and regulatory splicing factors that are widely studied in the context of GO:0008380.

RNA splicing is regulated at multiple levels, including the expression and post-translational modification of splicing factors, the activity of splicing enhancers and silencers, and coupling to transcription. Signaling pathways can influence splicing factor phosphorylation and localization, thereby altering splice site selection. In cancer, mutations in splicing factors can change their RNA-binding preferences and alter splicing programs. The process is also subject to autoregulation, where splicing factors control their own mRNA levels through feedback loops.

Mutations in splicing factor genes such as SF3B1, SRSF2, and U2AF1 are frequent in myelodysplastic syndromes, acute myeloid leukemia, and some solid tumors, where they alter splicing patterns and contribute to oncogenesis [2,4]. Splicing changes can produce oncogenic isoforms, affect tumor suppressor function, and create neoantigens, making splicing a promising therapeutic target [2,7].

Myelodysplastic syndromes are characterized by recurrent mutations in splicing factors, and these mutations are associated with distinct clinical phenotypes and disease progression. Targeting splicing with small molecules or splicing modifiers is being explored as a therapeutic strategy in this disease.

Splicing regulators play critical roles in neurogenesis, and their dysfunction has been linked to neurodevelopmental disorders and neurodegeneration. Alternative splicing is essential for neuronal differentiation and synaptic function, and its disruption can contribute to neurologic disease.

RNA-seq is widely used to detect splicing events, including exon skipping, intron retention, and alternative splice site usage, by mapping reads to exon-exon junctions. Differential splicing analysis can identify changes associated with splicing factor mutations or knockdown.

Minigene reporters and in vitro splicing assays can measure the efficiency and accuracy of splicing in response to genetic perturbations. These assays help dissect the roles of specific splicing factors and regulatory elements.

Affinity purification coupled with mass spectrometry can identify spliceosome components and dynamic interactions during assembly. These approaches reveal the composition and remodeling of splicing complexes.

Genome-wide CRISPR screens can identify splicing factors required for cell growth or drug sensitivity, providing functional annotations for GO:0008380 genes. Such screens are valuable for target discovery in cancer and other diseases.

Researchers studying RNA splicing-related genes often need to determine whether a candidate gene is causally involved in splicing regulation or disease phenotypes. Establishing causality requires precise genetic models that can knockout, mutate, tag, or overexpress the gene of interest in relevant cell types. EDITGENE provides a suite of CRISPR-based services to generate such models, enabling functional dissection of splicing factors and their roles in disease.

RNA splicing (GO:0008380) is a central biological process that shapes the transcriptome and proteome, with the spliceosome executing intron removal and exon joining. Its dysregulation is implicated in cancer, myelodysplastic syndromes, and neurologic disorders, and it is increasingly pursued as a therapeutic target [2,3,4,5]. Advances in CRISPR-based models and RNA profiling continue to illuminate the mechanisms and disease relevance of splicing, offering new opportunities for intervention [4,6,8].