Refining clinically relevant parameters for mis-splicing risk in shortened introns with donor-to-branchpoint space constraint

Journal article

Intronic deletions that critically shorten donor-to-branchpoint (D-BP) distance of a precursor mRNA impose biophysical space constraint on assembly of the U1/U2 spliceosomal complex, leading to canonical splicing failure. Here we use a series of β-globin (HBB) gene constructs with intron 1 deletions to define D-BP lengths that present low/no risk of mis-splicing and lengths which are critically short and likely elicit clinically relevant mis-splicing. We extend our previous observation in EMD intron 5 of 46 nt as the minimal productive D-BP length, demonstrating spliceosome assembly constraint persists at D-BP lengths of 47-56 nt. We exploit the common HBB exon 1 β-thalassemia variant that strengthens a cryptic donor (NM_000518.5(HBB):c.79G > A) to provide a simple barometer for the earliest signs of space constraint, via cryptic donor activation. For clinical evaluation of intronic deletions, we assert D-BP lengths > 60 nt present low mis-splicing risk while space constraint increases exponentially with D-BP lengths < 55 nt, with critical risk and profound splicing abnormalities with D-BP lengths < 50 nt.

Authors: Zhang, KY; Joshi, H; Marchant, RG; Bryen, SJ; Dawes, R

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Springer Nature [academic journals on nature.com]
• Journal: European Journal of Human Genetics
• Volume: 32
• Issue: 8
• Pages: 972-979
• Publication date: 2024-05-27
• Acceptance date: 2024-05-09
• DOI: 10.1038/s41431-024-01632-9
• EISSN: 1476-5438
• ISSN: 1018-4813
• Language: English