Alternative splicing is regulated by RNA-binding proteins (RBPs) that interact with pre-mRNA to control splicing events. Each splicing event is influenced by multiple RBPs, and the combined action of these proteins determines the distribution of alternatively spliced products in a given cell type. RBPs also regulate each other's functions, including through mutual modulation of their binding activities on regulatory RNA elements. This review outlines the emerging rules governing the context-dependent and combinatorial nature of alternative splicing regulation.
The spliceosome, a dynamic RNA-protein complex, carries out splicing reactions in eukaryotes. It recognizes and incorporates different parts of pre-mRNA into mature mRNA under the influence of regulatory proteins. Alternative splicing allows pre-mRNA transcripts to be processed into mRNA isoforms with different stability or coding potential, enabling quantitative control of protein production and the synthesis of proteins with distinct functions.
The large number of splicing regulatory proteins that recognize distinct RNA sequences across the transcriptome suggests the existence of a 'splicing code' that could predict splicing responses in different cell types under various conditions. However, the complexity of this code remains poorly understood. Deciphering the splicing code requires a comprehensive list of splicing regulatory RNA-binding proteins (RBPs) and their cis-acting binding sites. Challenges include the same genomic sequences being recognized differently by RBPs in different cell types, depending on other RBPs expressed.
Regulatory elements are divided into two classes: splicing signals (5' splice site, branchpoint, 3' splice site) and splicing regulatory elements (SREs). The context and positional relationship of these signals are crucial for their function. For example, a weak 3' splice site is more efficiently recognized when there is a strong 5' splice site nearby. Exon definition and splice site pairing are key regulatory steps in alternative splicing.
SREs are classified into exonic splicing enhancers (ESEs), exonic splicing silencers (ESSs), intronic splicing enhancers (ISEs), and intronic splicing silencers (ISSs). These elements are identified through various methods, including reporter-based sequence library screens and in vitro selection of RNAs that bind to splicing regulatory proteins. These approaches have revealed sequence specificity that is not found using thermodynamic endpoint binding studies.
High-throughput approaches, such as CLIP (crosslinking and immunoprecipitation), have been used to identify binding sites of RBPs on RNA. These methods allow for the identification of specific binding sites and the deduction of consensus binding sequences. CLIP has revealed new sets of rules for context-sensitive and position-dependent splicing.
Trans-acting splicing regulators, such as SR proteins and hnRNPs, play critical roles in splicing regulation. SR proteins are positive splicing regulators that promote exon inclusion, while hnRNPs are negative regulators that inhibit splicing. These proteins interact with each other and withAlternative splicing is regulated by RNA-binding proteins (RBPs) that interact with pre-mRNA to control splicing events. Each splicing event is influenced by multiple RBPs, and the combined action of these proteins determines the distribution of alternatively spliced products in a given cell type. RBPs also regulate each other's functions, including through mutual modulation of their binding activities on regulatory RNA elements. This review outlines the emerging rules governing the context-dependent and combinatorial nature of alternative splicing regulation.
The spliceosome, a dynamic RNA-protein complex, carries out splicing reactions in eukaryotes. It recognizes and incorporates different parts of pre-mRNA into mature mRNA under the influence of regulatory proteins. Alternative splicing allows pre-mRNA transcripts to be processed into mRNA isoforms with different stability or coding potential, enabling quantitative control of protein production and the synthesis of proteins with distinct functions.
The large number of splicing regulatory proteins that recognize distinct RNA sequences across the transcriptome suggests the existence of a 'splicing code' that could predict splicing responses in different cell types under various conditions. However, the complexity of this code remains poorly understood. Deciphering the splicing code requires a comprehensive list of splicing regulatory RNA-binding proteins (RBPs) and their cis-acting binding sites. Challenges include the same genomic sequences being recognized differently by RBPs in different cell types, depending on other RBPs expressed.
Regulatory elements are divided into two classes: splicing signals (5' splice site, branchpoint, 3' splice site) and splicing regulatory elements (SREs). The context and positional relationship of these signals are crucial for their function. For example, a weak 3' splice site is more efficiently recognized when there is a strong 5' splice site nearby. Exon definition and splice site pairing are key regulatory steps in alternative splicing.
SREs are classified into exonic splicing enhancers (ESEs), exonic splicing silencers (ESSs), intronic splicing enhancers (ISEs), and intronic splicing silencers (ISSs). These elements are identified through various methods, including reporter-based sequence library screens and in vitro selection of RNAs that bind to splicing regulatory proteins. These approaches have revealed sequence specificity that is not found using thermodynamic endpoint binding studies.
High-throughput approaches, such as CLIP (crosslinking and immunoprecipitation), have been used to identify binding sites of RBPs on RNA. These methods allow for the identification of specific binding sites and the deduction of consensus binding sequences. CLIP has revealed new sets of rules for context-sensitive and position-dependent splicing.
Trans-acting splicing regulators, such as SR proteins and hnRNPs, play critical roles in splicing regulation. SR proteins are positive splicing regulators that promote exon inclusion, while hnRNPs are negative regulators that inhibit splicing. These proteins interact with each other and with