Selection against tandem splice sites affecting structured protein regions

Area of Science:

• Genomics
• Molecular Biology
• Evolutionary Biology

Background:

• Alternative splicing, a key mechanism generating protein diversity, involves selecting different splice sites.
• Tandem splice sites, particularly those creating in-frame insertions/deletions of 3-9 nucleotides, are a significant aspect of alternative splicing.

Purpose of the Study:

• To investigate whether in-frame tandem splice sites in human protein-coding sequences are under natural selection.
• To determine the selective pressures acting on subtle mRNA insertions/deletions caused by alternative splicing.

Main Methods:

• Analysis of human protein-coding sequences for evidence of selection against in-frame tandem splice events.
• Comparative genomics using three-species comparisons to estimate selection efficacy.
• Examination of protein domain structures to correlate selection strength with protein architecture.

Main Results:

• Human protein-coding sequences show significant selection against in-frame tandem splice events, indicating they are often deleterious.
• Selection strength varies across protein-coding sequences, with intrinsically ordered regions under stronger selection.
• Tandem acceptor sites are preferentially located on protein domain surfaces and outside structural elements like helices and sheets.
• Over half of mutations creating NAGNAG acceptors in coding regions are eliminated by selection.

Conclusions:

• A substantial number of introns (~2,400) are under selection to avoid possessing tandem splice sites.
• Natural selection plays a crucial role in maintaining coding sequence integrity by eliminating deleterious splice variants.