Journal of Molecular Evolution

, Volume 65, Issue 3, pp 349–357 | Cite as

Gene Expression, Intron Density, and Splice Site Strength in Drosophila and Caenorhabditis

  • Marie E. FaheyEmail author
  • Desmond G. Higgins


In this paper we investigate the relationships among intron density (number of introns per kilobase of coding sequence), gene expression level, and strength of splicing signals in two species: Drosophila melanogaster and Caenorhabditis elegans. We report a negative correlation between intron density and gene expression levels, opposite to the effect previously observed in human. An increase in splice site strength has been observed in long introns in D. melanogaster. We show this is also true of C. elegans. We also examine the relationship between intron density and splice site strength. There is an increase in splice site strength as the intron structure becomes less dense. This could suggest that introns are not recognized in isolation but could function in a cooperative manner to ensure proper splicing. This effect remains if we control for the effects of alternative splicing on splice site strength.


Intron content Intron density Gene expression Alternative splicing mRNA splice sites 



We wish to thank Laurent Duret for helpful discussions. This work was funded by Science Foundation Ireland and the Irish Health Research Board.


  1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402PubMedCrossRefGoogle Scholar
  2. Bennetzen JL, Hall BD (1982) Codon selection in yeast. J Biol Chem 257:3026–3031PubMedGoogle Scholar
  3. Bortoluzzi S, Danieli GA (1999) Towards an in silico analysis of transcription patterns. Trends Genet 15:118–119PubMedCrossRefGoogle Scholar
  4. Castillo-Davis CI, Mekhedov SL, Hartl DL, Koonin EV, Kondrashov FA (2002) Selection for short introns in highly expressed genes. Nat Genet 31:415–418PubMedGoogle Scholar
  5. Comeron JM (2004) Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and intron presence. Genetics 167:1293–1304PubMedCrossRefGoogle Scholar
  6. Duret L, Mouchiroud D (1999) Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proc Natl Acad Sci USA 96:4482–4487PubMedCrossRefGoogle Scholar
  7. Fields C (1990) Information content of Caenorhabditis elegans splice site sequences varies with intron length. Nucleic Acids Res 18:1509–1512PubMedCrossRefGoogle Scholar
  8. Fox-Walsh KL, Dou Y, Lam BJ, Hung SP, Baldi PF, Hertel KJ (2005) The architecture of pre-mRNAs affects mechanisms of splice-site pairing. Proc Natl Acad Sci USA 102:16176–16181PubMedCrossRefGoogle Scholar
  9. Gouy M, Gautier C (1982) Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res 10:7055–7074PubMedCrossRefGoogle Scholar
  10. Grantham R, Gautier C, Gouy M, Jacobzone M, Mercier R (1981) Codon catalog usage is a genome strategy modulated for gene expressivity. Nucleic Acids Res 9:r43–r74PubMedCrossRefGoogle Scholar
  11. Ikemura T (1981a) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J Mol Biol 146:1–21Google Scholar
  12. Ikemura T (1981b) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J Mol Biol 151:389–409Google Scholar
  13. Mount SM, Burks C, Hertz G, Stormo GD, White O, Fields C (1992) Splicing signals in Drosophila: intron size, information content, and consensus sequences. Nucleic Acids Res 20:4255–4262PubMedCrossRefGoogle Scholar
  14. Munoz ET, Bogarad LD, Deem MW (2004) Microarray and EST database estimates of mRNA expression levels differ: the protein length versus expression curve for C. elegans. BMC Genomics 5:30CrossRefGoogle Scholar
  15. Rice P, Longden I, Bleasby A (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16:276–277PubMedCrossRefGoogle Scholar
  16. Rogan PK, Faux BM, Schneider TD (1998) Information analysis of human splice site mutations. Hum Mutat 12:153–171PubMedCrossRefGoogle Scholar
  17. Sharp PM, Li WH (1987) The Codon Adaptation Index—a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15:1281–1295PubMedCrossRefGoogle Scholar
  18. Urrutia AO, Hurst LD (2003) The signature of selection mediated by expression on human genes. Genome Res 13:2260–2264PubMedCrossRefGoogle Scholar
  19. Weir M, Rice M (2004) Ordered partitioning reveals extended splice-site consensus information. Genome Res 14:67–78PubMedCrossRefGoogle Scholar
  20. Weir M, Eaton M, Rice M (2006) Challenging the spliceosome machine. Genome Biol 7:R3PubMedCrossRefGoogle Scholar
  21. Zheng CL, Fu XD, Gribskov M (2005) Characteristics and regulatory elements defining constitutive splicing and different modes of alternative splicing in human and mouse. RNA 11:1777–1787PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  1. 1.UCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinBelfieldIreland

Personalised recommendations