A new type of mutation causes a splicing defect in ATM

Nat Genet. 2002 Apr;30(4):426-9. doi: 10.1038/ng858. Epub 2002 Mar 11.


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 elements. The gene ATM is mutated in individuals with ataxia-telangiectasia; we have identified 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Alternative Splicing*
  • Ataxia Telangiectasia Mutated Proteins
  • Base Sequence
  • Binding Sites
  • Cell Cycle Proteins
  • Cell Line
  • Cell Nucleus / metabolism
  • DNA-Binding Proteins
  • Exons
  • Gene Deletion
  • Heterozygote
  • Humans
  • Introns
  • Male
  • Molecular Sequence Data
  • Mutation
  • Nucleic Acid Hybridization
  • Plasmids / metabolism
  • Point Mutation
  • Protein Serine-Threonine Kinases / genetics*
  • Ribonucleoprotein, U1 Small Nuclear / metabolism
  • Tumor Suppressor Proteins


  • Cell Cycle Proteins
  • DNA-Binding Proteins
  • Ribonucleoprotein, U1 Small Nuclear
  • Tumor Suppressor Proteins
  • ATM protein, human
  • Ataxia Telangiectasia Mutated Proteins
  • Protein Serine-Threonine Kinases