Systematic identification and analysis of exonic splicing silencers

Cell. 2004 Dec 17;119(6):831-45. doi: 10.1016/j.cell.2004.11.010.


Exonic splicing silencers (ESSs) are cis-regulatory elements that inhibit the use of adjacent splice sites, often contributing to alternative splicing (AS). To systematically identify ESSs, an in vivo splicing reporter system was developed to screen a library of random decanucleotides. The screen yielded 141 ESS decamers, 133 of which were unique. The silencer activity of over a dozen of these sequences was also confirmed in a heterologous exon/intron context and in a second cell type. Of the unique ESS decamers, most could be clustered into groups to yield seven putative ESS motifs, some resembling known motifs bound by hnRNPs H and A1. Potential roles of ESSs in constitutive splicing were explored using an algorithm, ExonScan, which simulates splicing based on known or putative splicing-related motifs. ExonScan and related bioinformatic analyses suggest that these ESS motifs play important roles in suppression of pseudoexons, in splice site definition, and in AS.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms*
  • Animals
  • Base Sequence
  • Cells, Cultured
  • Cluster Analysis
  • Computer Simulation*
  • Exons / genetics
  • Gene Library
  • Heterogeneous Nuclear Ribonucleoprotein A1
  • Heterogeneous-Nuclear Ribonucleoprotein Group A-B / genetics
  • Heterogeneous-Nuclear Ribonucleoprotein Group F-H / genetics
  • Humans
  • Molecular Sequence Data
  • RNA Splicing / genetics*
  • RNA Splicing / physiology
  • Regulatory Sequences, Ribonucleic Acid / genetics*
  • Silencer Elements, Transcriptional / genetics*


  • Heterogeneous Nuclear Ribonucleoprotein A1
  • Heterogeneous-Nuclear Ribonucleoprotein Group A-B
  • Heterogeneous-Nuclear Ribonucleoprotein Group F-H
  • Regulatory Sequences, Ribonucleic Acid