Systematic identification and analysis of exonic splicing silencers.
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.
Wang
Zefeng
Z
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Rolish
Michael E
ME
Yeo
Gene
G
Tung
Vivian
V
Mawson
Matthew
M
Burge
Christopher B
CB
D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D002478:Cells, Cultured; D016000:Cluster Analysis; D003198:Computer Simulation; D005091:Exons / Q000235:genetics; D015723:Gene Library; D000076245:Heterogeneous Nuclear Ribonucleoprotein A1; D034481:Heterogeneous-Nuclear Ribonucleoprotein Group A-B / Q000235:genetics; D034541:Heterogeneous-Nuclear Ribonucleoprotein Group F-H / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D012326:RNA Splicing / Q000235:genetics* / Q000502:physiology; D038621:Regulatory Sequences, Ribonucleic Acid / Q000235:genetics*; D037941:Silencer Elements, Transcriptional / Q000235:genetics*
D000076245:Heterogeneous Nuclear Ribonucleoprotein A1; D034481:Heterogeneous-Nuclear Ribonucleoprotein Group A-B; D034541:Heterogeneous-Nuclear Ribonucleoprotein Group F-H; D038621:Regulatory Sequences, Ribonucleic Acid