Systematic identification and analysis of exonic splicing silencers - PubMed (original) (raw)
. 2004 Dec 17;119(6):831-45.
doi: 10.1016/j.cell.2004.11.010.
Affiliations
- PMID: 15607979
- DOI: 10.1016/j.cell.2004.11.010
Free article
Systematic identification and analysis of exonic splicing silencers
Zefeng Wang et al. Cell. 2004.
Free article
Abstract
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.
Comment in
- Towards a splicing code.
Fu XD. Fu XD. Cell. 2004 Dec 17;119(6):736-8. doi: 10.1016/j.cell.2004.11.039. Cell. 2004. PMID: 15607969
Similar articles
- Towards a splicing code.
Fu XD. Fu XD. Cell. 2004 Dec 17;119(6):736-8. doi: 10.1016/j.cell.2004.11.039. Cell. 2004. PMID: 15607969 - Silencer elements as possible inhibitors of pseudoexon splicing.
Sironi M, Menozzi G, Riva L, Cagliani R, Comi GP, Bresolin N, Giorda R, Pozzoli U. Sironi M, et al. Nucleic Acids Res. 2004 Mar 19;32(5):1783-91. doi: 10.1093/nar/gkh341. Print 2004. Nucleic Acids Res. 2004. PMID: 15034146 Free PMC article. - An exon skipping-associated nonsense mutation in the dystrophin gene uncovers a complex interplay between multiple antagonistic splicing elements.
Disset A, Bourgeois CF, Benmalek N, Claustres M, Stevenin J, Tuffery-Giraud S. Disset A, et al. Hum Mol Genet. 2006 Mar 15;15(6):999-1013. doi: 10.1093/hmg/ddl015. Epub 2006 Feb 6. Hum Mol Genet. 2006. PMID: 16461336 - Searching for splicing motifs.
Chasin LA. Chasin LA. Adv Exp Med Biol. 2007;623:85-106. doi: 10.1007/978-0-387-77374-2_6. Adv Exp Med Biol. 2007. PMID: 18380342 Review. - Silencers regulate both constitutive and alternative splicing events in mammals.
Pozzoli U, Sironi M. Pozzoli U, et al. Cell Mol Life Sci. 2005 Jul;62(14):1579-604. doi: 10.1007/s00018-005-5030-6. Cell Mol Life Sci. 2005. PMID: 15905961 Free PMC article. Review.
Cited by
- From computational models of the splicing code to regulatory mechanisms and therapeutic implications.
Capitanchik C, Wilkins OG, Wagner N, Gagneur J, Ule J. Capitanchik C, et al. Nat Rev Genet. 2024 Oct 2. doi: 10.1038/s41576-024-00774-2. Online ahead of print. Nat Rev Genet. 2024. PMID: 39358547 Review. - Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences.
Xu C, Bao S, Wang Y, Li W, Chen H, Shen Y, Jiang T, Zhang C. Xu C, et al. Genome Res. 2024 Aug 20;34(7):1052-1065. doi: 10.1101/gr.279044.124. Genome Res. 2024. PMID: 39060028 Free PMC article. - An interpretable model of pre-mRNA splicing for animal and plant genes.
McCue K, Burge CB. McCue K, et al. Sci Adv. 2024 May 10;10(19):eadn1547. doi: 10.1126/sciadv.adn1547. Epub 2024 May 8. Sci Adv. 2024. PMID: 38718117 Free PMC article. - CRISPR-dCas13d-based deep screening of proximal and distal splicing-regulatory elements.
Recinos Y, Ustianenko D, Yeh YT, Wang X, Jacko M, Yesantharao LV, Wu Q, Zhang C. Recinos Y, et al. Nat Commun. 2024 May 7;15(1):3839. doi: 10.1038/s41467-024-47140-8. Nat Commun. 2024. PMID: 38714659 Free PMC article. - Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences.
Xu C, Bao S, Chen H, Jiang T, Zhang C. Xu C, et al. bioRxiv [Preprint]. 2024 Apr 8:2024.03.22.586363. doi: 10.1101/2024.03.22.586363. bioRxiv. 2024. PMID: 38586002 Free PMC article. Updated. Preprint.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Research Materials