This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Fairbrother, W. G.
Right arrow Articles by Chasin, L. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Fairbrother, W. G.
Right arrow Articles by Chasin, L. A.

 Previous Article  |  Next Article 

Molecular and Cellular Biology, September 2000, p. 6816-6825, Vol. 20, No. 18
0270-7306/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.

Human Genomic Sequences That Inhibit Splicing

William G. Fairbrother and Lawrence A. Chasin*

Department of Biological Sciences, Columbia University, New York, New York 10027

Received 25 February 2000/Returned for modification 17 April 2000/Accepted 23 June 2000

Mammalian genes are characterized by relatively small exons surrounded by variable lengths of intronic sequence. Sequences similar to the splice signals that define the 5' and 3' boundaries of these exons are also present in abundance throughout the surrounding introns. What causes the real sites to be distinguished from the multitude of pseudosites in pre-mRNA is unclear. Much progress has been made in defining additional sequence elements that enhance the use of particular sites. Less work has been done on sequences that repress the use of particular splice sites. To find additional examples of sequences that inhibit splicing, we searched human genomic DNA libraries for sequences that would inhibit the inclusion of a constitutively spliced exon. Genetic selection experiments suggested that such sequences were common, and we subsequently tested randomly chosen restriction fragments of about 100 bp. When inserted into the central exon of a three-exon minigene, about one in three inhibited inclusion, revealing a high frequency of inhibitory elements in human DNA. In contrast, only 1 in 27 Escherichia coli DNA fragments was inhibitory. Several previously identified silencing elements derived from alternatively spliced exons functioned weakly in this constitutively spliced exon. In contrast, a high-affinity site for U2AF65 strongly inhibited exon inclusion. Together, our results suggest that splicing occurs in a background of repression and, since many of our inhibitors contain splice like signals, we suggest that repression of some pseudosites may occur through an inhibitory arrangement of these sites.

* Corresponding author. Mailing address: Department of Biological Sciences, 912 Fairchild, MC 2433, Columbia University, New York, NY 10027. Phone: (212) 854-4645. Fax: (212) 531-0425. E-mail: lac2{at}columbia.edu.

Molecular and Cellular Biology, September 2000, p. 6816-6825, Vol. 20, No. 18
0270-7306/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.


This article has been cited by other articles:

  • Reid, D. C., Chang, B. L., Gunderson, S. I., Alpert, L., Thompson, W. A., Fairbrother, W. G. (2009). Next-generation SELEX identifies sequence and structural determinants of splicing factor binding in human pre-mRNA sequence. RNA 15: 2385-2397 [Abstract] [Full Text]  
  • Faa, V., Incani, F., Meloni, A., Corda, D., Masala, M., Baffico, A. M., Seia, M., Cao, A., Rosatelli, M. C. (2009). Characterization of a Disease-associated Mutation Affecting a Putative Splicing Regulatory Element in Intron 6b of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Gene. J. Biol. Chem. 284: 30024-30031 [Abstract] [Full Text]  
  • Ram, O., Schwartz, S., Ast, G. (2008). Multifactorial Interplay Controls the Splicing Profile of Alu-Derived Exons. Mol. Cell. Biol. 28: 3513-3525 [Abstract] [Full Text]  
  • Gal-Mark, N., Schwartz, S., Ast, G. (2008). Alternative splicing of Alu exons--two arms are better than one. Nucleic Acids Res 36: 2012-2023 [Abstract] [Full Text]  
  • Shi, J., Hu, Z., Pabon, K., Scotto, K. W. (2008). Caffeine Regulates Alternative Splicing in a Subset of Cancer-Associated Genes: a Role for SC35. Mol. Cell. Biol. 28: 883-895 [Abstract] [Full Text]  
  • Schoft, V. K., Schopoff, S., Jantsch, M. F. (2007). Regulation of glutamate receptor B pre-mRNA splicing by RNA editing. Nucleic Acids Res 35: 3723-3732 [Abstract] [Full Text]  
  • Zhang, X. H.-F., Chasin, L. A. (2006). Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons. Proc. Natl. Acad. Sci. USA 103: 13427-13432 [Abstract] [Full Text]  
  • Buratti, E., Baralle, M., Baralle, F. E. (2006). Defective splicing, disease and therapy: searching for master checkpoints in exon definition. Nucleic Acids Res 34: 3494-3510 [Abstract] [Full Text]  
  • Xing, Y., Wang, Q., Lee, C. (2006). Evolutionary Divergence of Exon Flanks: A Dissection of Mutability and Selection. Genetics 173: 1787-1791 [Abstract] [Full Text]  
  • Kralovicova, J., Vorechovsky, I. (2006). Position-Dependent Repression and Promotion of DQB1 Intron 3 Splicing by GGGG Motifs. J. Immunol. 176: 2381-2388 [Abstract] [Full Text]  
  • Parmley, J. L., Chamary, J. V., Hurst, L. D. (2006). Evidence for Purifying Selection Against Synonymous Mutations in Mammalian Exonic Splicing Enhancers. Mol Biol Evol 23: 301-309 [Abstract] [Full Text]  
  • Mercado, P. A., Ayala, Y. M., Romano, M., Buratti, E., Baralle, F. E. (2005). Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene. Nucleic Acids Res 33: 6000-6010 [Abstract] [Full Text]  
  • Baralle, D, Baralle, M (2005). Splicing in action: assessing disease causing sequence changes. J. Med. Genet. 42: 737-748 [Abstract] [Full Text]  
  • Lei, H., Vorechovsky, I. (2005). Identification of Splicing Silencers and Enhancers in Sense Alus: a Role for Pseudoacceptors in Splice Site Repression. Mol. Cell. Biol. 25: 6912-6920 [Abstract] [Full Text]  
  • Burnette, J. M., Miyamoto-Sato, E., Schaub, M. A., Conklin, J., Lopez, A. J. (2005). Subdivision of Large Introns in Drosophila by Recursive Splicing at Nonexonic Elements. Genetics 170: 661-674 [Abstract] [Full Text]  
  • Wagner, E. J., Baraniak, A. P., Sessions, O. M., Mauger, D., Moskowitz, E., Garcia-Blanco, M. A. (2005). Characterization of the Intronic Splicing Silencers Flanking FGFR2 Exon IIIb. J. Biol. Chem. 280: 14017-14027 [Abstract] [Full Text]  
  • James, P. D., O'Brien, L. A., Hegadorn, C. A., Notley, C. R. P., Sinclair, G. D., Hough, C., Poon, M.-C., Lillicrap, D. (2004). A novel type 2A von Willebrand factor mutation located at the last nucleotide of exon 26 (3538G>A) causes skipping of 2 nonadjacent exons. Blood 104: 2739-2745 [Abstract] [Full Text]  
  • Expert-Bezancon, A., Sureau, A., Durosay, P., Salesse, R., Groeneveld, H., Lecaer, J. P., Marie, J. (2004). hnRNP A1 and the SR Proteins ASF/SF2 and SC35 Have Antagonistic Functions in Splicing of {beta}-Tropomyosin Exon 6B. J. Biol. Chem. 279: 38249-38259 [Abstract] [Full Text]  
  • Zhang, X. H-F., Chasin, L. A. (2004). Computational definition of sequence motifs governing constitutive exon splicing. Genes Dev. 18: 1241-1250 [Abstract] [Full Text]  
  • Sironi, M., Menozzi, G., Riva, L., Cagliani, R., Comi, G. P., Bresolin, N., Giorda, R., Pozzoli, U. (2004). Silencer elements as possible inhibitors of pseudoexon splicing. Nucleic Acids Res 32: 1783-1791 [Abstract] [Full Text]  
  • Zhang, X. H-F., Heller, K. A., Hefter, I., Leslie, C. S., Chasin, L. A. (2003). Sequence Information for the Splicing of Human Pre-mRNA Identified by Support Vector Machine Classification. Genome Res 13: 2637-2650 [Abstract] [Full Text]  
  • Gualandi, F, Trabanelli, C, Rimessi, P, Calzolari, E, Toffolatti, L, Patarnello, T, Kunz, G, Muntoni, F, Ferlini, A (2003). Multiple exon skipping and RNA circularisation contribute to the severe phenotypic expression of exon 5 dystrophin deletion. J. Med. Genet. 40: e100-100 [Full Text]  
  • Zavolan, M., Kondo, S., Schonbach, C., Adachi, J., Hume, D. A., RIKEN GER Group, , GSL Members, , Hayashizaki, Y., Gaasterland, T. (2003). Impact of Alternative Initiation, Splicing, and Termination on the Diversity of the mRNA Transcripts Encoded by the Mouse Transcriptome. Genome Res 13: 1290-1300 [Abstract] [Full Text]  
  • Faustino, N. A., Cooper, T. A. (2003). Pre-mRNA splicing and human disease. Genes Dev. 17: 419-437 [Full Text]  
  • Maquat, L. E. (2002). NASty effects on fibrillin pre-mRNA splicing: another case of ESE does it, but proposals for translation-dependent splice site choice live on. Genes Dev. 16: 1743-1753 [Full Text]  
  • Le Guiner, C., Plet, A., Galiana, D., Gesnel, M.-C., Del Gatto-Konczak, F., Breathnach, R. (2001). Polypyrimidine Tract-binding Protein Represses Splicing of a Fibroblast Growth Factor Receptor-2 Gene Alternative Exon through Exon Sequences. J. Biol. Chem. 276: 43677-43687 [Abstract] [Full Text]  
  • Caputi, M., Zahler, A. M. (2001). Determination of the RNA Binding Specificity of the Heterogeneous Nuclear Ribonucleoprotein (hnRNP) H/H'/F/2H9 Family. J. Biol. Chem. 276: 43850-43859 [Abstract] [Full Text]  
  • Wagner, E. J., Garcia-Blanco, M. A. (2001). Polypyrimidine Tract Binding Protein Antagonizes Exon Definition. Mol. Cell. Biol. 21: 3281-3288 [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»