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The intronic splicing code: multiple factors involved in ATM pseudoexon definition

Ashish Dhir, Emanuele Buratti, Maria A van Santen, Reinhard Lührmann, Francisco E Baralle

Author Affiliations

  1. Ashish Dhir1,
  2. Emanuele Buratti1,
  3. Maria A van Santen2,
  4. Reinhard Lührmann2 and
  5. Francisco E Baralle*,1
  1. 1 Molecular Pathology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
  2. 2 Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
  1. *Corresponding author. Molecular Pathology Group, International Centre for Genetic Engineering and Biotechnology, Padriciano 99, Trieste 34149, Italy. Tel.: +39 040 3757 337; Fax: +39 040 375 7361; E-mail: baralle{at}icgeb.org
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Abstract

Abundance of pseudo splice sites in introns can potentially give rise to innumerable pseudoexons, outnumbering the real ones. Nonetheless, these are efficiently ignored by the splicing machinery, a process yet to be understood completely. Although numerous 5′ splice site‐like sequences functioning as splicing silencers have been found to be enriched in predicted human pseudoexons, the lack of active pseudoexons pose a fundamental challenge to how these U1snRNP‐binding sites function in splicing inhibition. Here, we address this issue by focusing on a previously described pathological ATM pseudoexon whose inhibition is mediated by U1snRNP binding at intronic splicing processing element (ISPE), composed of a consensus donor splice site. Spliceosomal complex assembly demonstrates inefficient A complex formation when ISPE is intact, implying U1snRNP‐mediated unproductive U2snRNP recruitment. Furthermore, interaction of SF2/ASF with its motif seems to be dependent on RNA structure and U1snRNP interaction. Our results suggest a complex combinatorial interplay of RNA structure and trans‐acting factors in determining the splicing outcome and contribute to understanding the intronic splicing code for the ATM pseudoexon.

  • Received July 28, 2009.
  • Accepted December 8, 2009.
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