Transposon clusters as substrates for aberrant splice-site activation.

Area of Science:

• Genomics and Molecular Biology
• RNA Structure and Function
• Evolutionary Biology

Background:

• Transposable elements (TEs) significantly influence genome evolution and disease by altering exon-intron structures.
• The cooperative mechanisms of recent TE insertions into older TEs for generating novel coding sequences remain largely unknown.
• Understanding TE-induced exon formation is crucial for deciphering gene regulation and disease pathogenesis.

Purpose of the Study:

• To identify novel TE clusters that facilitate exon selection using an updated repository of mutation-induced exon-intron boundaries (DBASS).
• To investigate the RNA secondary structure maintenance of TE-derived exons compared to their progenitors.
• To elucidate the impact of specific mutations on TE exon structure and spliceosome interaction.

Main Methods:

• Utilized the DBASS database to identify TE-mediated exon creation.
• Performed structural studies on a composite exon derived from LTR78 and AluJ elements.
• Employed SHAPE, DMS, and enzymatic probing to analyze RNA secondary structure and mutation effects.

Main Results:

• Identified novel TE clusters enabling exon selection and activation of existing Alu exons.
• Demonstrated that a C>T mutation disrupted a conserved AluJ stem, liberating a 5' splice site.
• Revealed cross-talk between traditional and auxiliary splicing motifs mediated by RNA structure changes.

Conclusions:

• TE exon models derived from LTR78 and AluJ provide insights into pre-mRNA building block formation and splice-site selection.
• Mutation-induced structural alterations in TE exons highlight mechanisms of aberrant splice-site activation.
• Findings contribute to understanding exon/intron size constraints and fine-tuning splicing motifs in disease contexts.