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A new type of mutation causes a splicing defect in ATM

Abstract

Disease-causing splicing mutations described in the literature primarily produce changes in splice sites and, to a lesser extent, variations in exon-regulatory sequences such as the enhancer elements1,2,3,4,5,6. The gene ATM is mutated in individuals with ataxia-telangiectasia; we have indentified the aberrant inclusion of a cryptic exon of 65 bp in one affected individual with a deletion of four nucleotides (GTAA) in intron 20. The deletion is located 12 bp downstream and 53 bp upstream from the 5′ and 3′ ends of the cryptic exon, respectively. Through analysis of the splicing defect using a hybrid minigene system, we identified a new intron-splicing processing element (ISPE) complementary to U1 snRNA, the RNA component of the U1 small nuclear ribonucleoprotein (snRNP). This element mediates accurate intron processing and interacts specifically with U1 snRNP particles. The 4-nt deletion completely abolished this interaction, causing activation of the cryptic exon. On the basis of this analysis, we describe a new type of U1 snRNP binding site in an intron that is essential for accurate intron removal. Deletion of this sequence is directly involved in the splicing processing defect.

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Figure 1: The splicing processing defect in ATM intron 20 does not affect canonical splicing regulatory elements.
Figure 2: Base-pairing between ISPE and U1 RNA regulates intron splicing processing.
Figure 3: The 4-bp deletion disrupts the interaction between the U1 snRNP and the ATM ISPE.
Figure 4: Restoring complementarity between U1 snRNA and ISPE induces normal intron processing in vivo.
Figure 5: ISPE converts exonic sequences to intronic sequences.

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Acknowledgements

We thank N.J. Proudfoot and A. Furger for the WT U1 snRNA plasmid and I.W. Mattaj and A. Segref for the anti-U1A antibody. This work was supported by a Telethon Onlus Foundation Grant.

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Correspondence to Francisco E. Baralle.

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The authors declare no competing financial interests.

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Pagani, F., Buratti, E., Stuani, C. et al. A new type of mutation causes a splicing defect in ATM. Nat Genet 30, 426–429 (2002). https://doi.org/10.1038/ng858

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