Induction of cryptic pre-mRNA splice-switching by antisense oligonucleotides

Area of Science:

• Molecular Biology
• RNA Biology
• Drug Discovery

Background:

• Antisense oligomers (AOs) are utilized to modify RNA splicing for research and therapeutic applications.
• While typically designed for whole exon skipping, AOs can also trigger partial exon skipping by activating cryptic splice sites.

Purpose of the Study:

• To investigate the mechanisms behind AO-induced cryptic splice site activation.
• To analyze the impact of AO binding on RNA secondary structure and splice factor accessibility.

Main Methods:

• Examination of seven AO-induced cryptic splice sites across six genes.
• Modeling of AO binding effects on RNA secondary structure.
• Analysis of how AO binding influences splice factor accessibility.

Main Results:

• A common effect of AO binding was the disruption of the exon definition signal.
• This disruption occurred within the exon's excluded segment, leading to partial exon skipping.
• Seven AO-induced cryptic splice sites were analyzed, with five newly identified.

Conclusions:

• AO-induced cryptic splice site activation is a mechanism that can lead to partial exon skipping.
• Disruption of exon definition signals by AO binding is a key factor in this process.
• Understanding these mechanisms is crucial for refining AO-based therapeutic strategies.