Abstract
A comparative analysis of olignucleotide frequencies in two sets of introns of genes highly-transcribed and lowly-transcribed respectively has suggested that the existence of potential positive regulatory motifs of transcription in yeast introns. To further reveal the distribution feature of these motifs, we detected significant clusters of these motifs (mainly pentanucleotides) in introns by r-scan analysis. The results showed that there are more clusters of regulatory motifs in the introns of ribosomal protein genes (highly-transcribed genes) than in lowly-transcribed introns. Experimental studies show that the transcription factors function cooperatively in transcriptional activation and the corresponding binding sites for factors generally cluster in DNA. Accordingly, we speculated that the cluster distribution of regulatory motifs of transcription in yeast introns could becorrelated with the cooperative action of transcription factors and the transcriptional rates of genes could be improved by the cooperativity.
This work wa s supported by grants from The National Natural Science foundation of China (no.30360027).
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Bhattacharyya, N., Banerjee, D.: Transcriptional Regulatory Sequences within the First Intron of the Chicken Apolipoprotein AI (apo AI) Gene. Gene. 234(2), 371–380 (1999)
Brinster, R.L., Allen, J.M., Behringer, R.R., Gelinas, R.E., Palmiter, R.D.: Introns Increase Transcriptional Efficiency in Transgenic Mice. Proc. Natl. Acad. Sci. USA 85(3), 836–840 (1988)
Chen, J., Hayes, P., Roy, K., Sirotnak, F.M.: Two Promoters Regulate Transcription of the Mouse Folypolyglutamate Synthetase Gene: Three Tightly Clustered Sp1 Sites within the First Intron Markedly Enhance Activity of Promoter B. Gene. 242(1-2), 257–264 (2000)
Surinya, K.H., Cox, T.C., May, B.K.: Identification and Characterization of a Conserved Erythroid-specific Enhancer Located in Intron 8 of the Human 5-Aminolevulinate Synthase 2 Gene. J. Biol. Chem. 273(27), 16798–16809 (1998)
Zhang, J., Shi, X.F.: Statistical Analysis of Sequence Features of Introns with Positive Transcriptional Regulation in Yeast Gene. Prog. Biochem. Biophys. 30(2), 231–238 (2003)
Zhang, J., Hu, J., Shi, X.F., Cao, H., et al.: Detection of Potential Positive Regulatory Motifs of Transcription in Yeast Introns by Comparative Analysis of Oligonucleotide Frequencies. Comput. Biol. Chem. 27(4-5), 497–506 (2003)
Wagner, A.: A Computational Genomics Approach to the Identification of Gene Networks. Nucleic Acids Research 25(18), 3594–3604 (1997)
Wagner, A.: Genes Regulated Cooperatively by One or More Transcription Factors and Their Identification in Whole Eukaryotic Genomes. Bioinformatics 15(10), 776–784 (1999)
Dembo, A., Karlin, S.: Poisson Approximations for R-scan Process. Annals of Applied Probability 2(2), 329–357 (1992)
Karlin, S., Brendel, V.: Chance and Statistical Significance in Protein and DNA Sequence Analysis. Science 257(3), 39–49 (1992)
Karlin, S., Macken, C.: Some Statitcal Problems in the Assessment of Inhomogeneities of DNA Sequence Data. Journal of American Statistical Association 86(413), 27–35 (1991)
Xue, W., Wang, J., Huang, Q.L., Zheng, W.J., Hua, Z.C.: Synergistic Activation of Eukaryotic Gene Transcription by Multiple Uptream Sites. Prog. biochem. biophys. 29(4), 510–513 (2002)
Della, S.F., Ciafre, S.A., Marck, C., Santoro, B., Presutti, C., Sentenac, A., Bozzoni, I.: The ABF1 Factor Is the Transcriptional Activator of the L2 Ribosomal Protein Genes in Saccharomyces Cerevisiae. Mol. Cell. Biol. (5), 2437–2441 (1990)
Lieb, J.D., Liu, X., Botstein, D., Brown, P.O.: Promoter-specific Binding of RAP1 Revealed by Genome-wide Maps of Protein-DNA Association. Nat. Genet. 28(4), 327–334 (2001)
Dorsman, J.C., Doorenbosch, M.M., Maurer, C.T., Winde, J.H., Mager, W.H., Planta, R.J., Grivell, L.A.: An ARS/silencer Binding Factor Also Activates Two Ribosomal Protein Genes in Yeast. Nucleic Acids Res. 17(13), 4917–4923 (1989)
Wingender, E., Chen, X., Fricke, E., Geffers, R., Hehl, R., Liebich, I., Krull, M., Matys, V., Michael, H., Ohnhauser, R., Pruss, M., Schacherer, F., Thiele, S., Urbach, S.: The Transfac System on Gene Expression Regulation. Nucl. Acids. Res. 29(1), 281–283 (2001)
Matys, V.E., Fricke, R., Geffers, E., Gossling, E., Haubrock, M., Hehl, R., Hornischer, K., Karas, D., Kel, A.E., Kel-Margoulis, O.V., et al.: TRANSFAC®: Transcriptional Regulation, from Patterns to Profiles. Nucl. Acids Res. 31(1), 374–378 (2003)
Bickel, P.J., Doksum, K.A.: Mathematical Statistics: Basic Ideas and Selected Topics, pp. 378–388. Prentice Hall, Englewood Cliffs (1977)
Carey, M., Smale, S.T.: Transcriptional Regulation in Eukaryotes Concepts Strategies and Techniques, pp. 8–42. CSHL Press, New York (2002)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Hu, J., Zhang, J. (2005). The Cluster Distribution of Regulatory Motifs of Transcription in Yeast Introns. In: Huang, DS., Zhang, XP., Huang, GB. (eds) Advances in Intelligent Computing. ICIC 2005. Lecture Notes in Computer Science, vol 3645. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11538356_6
Download citation
DOI: https://doi.org/10.1007/11538356_6
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-28227-3
Online ISBN: 978-3-540-31907-8
eBook Packages: Computer ScienceComputer Science (R0)