Protein Interactions in Splicing

Protein Interactions in Splicing

• Proteins interact with U1 snRNP and U2 snRNP, binding to specific sequences near splice sites.
• Mutational analysis reveals that sequences around splice junctions and the branch point are crucial for splicing, distinct from the actual splice sites.
• RNA-binding proteins recognize short sequence motifs and either promote or inhibit splicing.

Exonic Splicing Enhancers (ESEs)

• Located within exons.
• Promote splicing at nearby splice junctions.
• Bound by SR proteins (RNA-binding proteins).

SR Proteins

• Contain RNA-binding motifs and protein-protein interaction domains.
• Directly interact with U1 snRNP and indirectly with U2 snRNP through factors near the 3' splice site.
• Bind to ESEs, marking exons and guiding the splicing machinery.

U2 snRNP and the 3' Splice Site

• U2 snRNP binds to the branch point, recruiting accessory factors.
• U2AF65 binds to the polypyrimidine stretch near the 3' splice site.
• U2AF35 binds to the RNA at the 3' splice site.
• These interactions guide the splicing machinery.
• SR proteins also participate in marking the exon to ensure proper splicing.

Alternative Splicing

• Definition: Multiple splicing patterns produce different mRNAs (and proteins) from a single pre-mRNA.
• Increases coding capacity of the genome.
• Allows a single gene to produce multiple protein isoforms.

Regulation of Alternative Splicing

• Can be cell type-specific, with different cell types splicing the same pre-mRNA in distinct ways.
• Example 1: Fibronectin gene - different cell types (fibroblasts/hepatocytes) include or exclude specific exons, producing tailored mRNAs. Fibroblasts have two exons encoding "sticky" proteins. Hepatocytes exclude these.
• Example 2: Calcium-activated potassium channel in the ear – allows for 576 splicing variations, each responding to specific calcium concentrations related to different sound frequencies. This adaptation is essential for hearing a wide range of frequencies.

Key Aspects of Alternative Splicing

• SR proteins mark exons and guide splicing machinery.
• This process increases protein diversity and tailors gene expression to specific cell types or functions.
• In some cases, a single gene can give rise to hundreds of isoforms, as shown by different isoforms of the calcium-activated potassium channel in the cochlea.

This quiz explores the interactions between proteins and snRNPs during the splicing process, including the roles of U1 and U2 snRNP. It covers key concepts such as Exonic Splicing Enhancers (ESEs), the function of SR proteins, and the significance of splice junctions and branch points. Test your knowledge about the intricate mechanisms of RNA splicing and protein binding.