Abstract
Transcription is the general process of copying part of the genomic DNA into RNA. This RNA either has functions of its own or is used to produce proteins. This is a multi-step process requiring the coordinated interaction of a plethora of proteins with the genomic DNA at various loci. The major regions of DNA involved in transcription are the regulatory regions like locus control regions, enhancers, and promoters.
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.
Suggested Readings
The Promoter
Sauer, F. and Tjian, R. (1997) Mechanisms of transcriptional activation: Differences and similarities between yeast, Drosophila, and man, Curr. Op. Gen. Dev. 7, 176–181.
Stamatoyannopoulos, J. A., Clegg, C. H., and Li, Q. (1997) Sheltering of gammaglobin expression from position effects requires both an upstream locus control region and a regulatory element 3′ to the (A)gamma-globin gene, Mol. Cell. Biol. 17, 240–247.
The Characteristics of TF Binding Sites
Frech, K., Herrmann, G., and Werner, T. (1993) Computer-Assisted prediction, classification, and delimitation of protein binding sites in nucleic acids, Nucleic Acids Res. 21, 1655–1664.
Quandt, K., Frech, K., Karas, H., Wingender, E., and Werner, T. (1995) Matlnd and MatInspector: New fast and versatile tools for detection of consensus matches in nucleotide sequence data, Nucleic Acids Res. 23, 4878–4884.
Risse, G., Jooss, K., Neuberg, M., Brüller, H.-J., Müller, R. (1989) Asymmetrical recognition of the palindromic AP1 binding site (TRE) by Fos protein complexes, EMBO J. 8, 3825–3832.
The Nucleotide Weight Matrix
Bucher, P. (1990) Weight matrix description of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences, J. Mol. Biol. 212, 563–578.
Chen, Q. K., Hertz, G. Z., and Stormo, G. D. (1995) Matrix Search 1.0: A computer program that scans DNA sequences for transcriptional elements using a database of weight matrices, Comp. Appl. Biosci. 11, 563–566.
Frech, K., Quandt, K., and Werner, T. (1997) Finding protein-binding sites in DNA sequences: The next generation, Trends Biochem. Sci. 22, 103–104.
Frech, K., Quandt, K., and Werner, T. (1997) Software for the analysis of DNA sequence elements of transcription, Comp. Appl. Biosci. 13, 89–97.
Ghosh, D. (1993) Status of the transcription factors database (TFD), Nucleic Acids Res. 21, 3117–3118.
Heinemeyer, T., Wingender, E., Reuter, I., Hermjakob, H., Kel, A.E., Kel, O. V., et al. (1998) Databases on transcriptional regulation: TRANSFAC, TRRD and COM-PEL, Nucleic Acids Res. 26, 362–367.
Naitou, M., Hagiwara, H., Hanaoka, F., Eki, T., and Murakami, Y. (1997) Expression profiles of transcripts from 126 open reading frames in the entire chromosome VI of Saccharomyces cerevisiae by systematic northern analyses, Yeast 13, 1275–1290.
Nagase, T., Ishikawa, K., Miyajima, N., Tanaka, A., Kotani, H., Nomura, N., and Ohara, O. (1998) Prediction of the coding sequences of unidentified human genes. IX. The complete sequences of 100 new cDNA clones from brain, which can code for large proteins in vitro, DNA Res. 5, 31–39.
Quandt, K., Frech, K., Karas, H., Wingender, E., and Werner, T. (1995) Matlnd and Matlnspector: New fast and versatile tools for detection of consensus matches in nucleotide sequence data, Nucleic Acids Res. 23, 4878–4884.
Stormo, G. D. and Hartzell, III, G. W. (1989) Identifying protein-binding sites from unaligned DNA fragments, Proc. Natl. Acad. Sci. USA 86, 1183–1187.
How to Define Unknown Transcription Factor Binding Sites
Brazma, A., Jonassen, I., Vilo, J., and Ukkonen, E. (1998) Predicting gene regulatory elements in silico on a genomic scale. Genome Res. 8, 1202–1215.
Cardon, L. R. and Stormo, G. D. (1992). Expectation maximization algorithm for identifying protein-binding sites with variable lengths from unaligned DNA fragments, J. Mol. Biol. 223, 159–170.
Neuwald, A. F., Liu, J. S., and Lawrence, C. E. (1995). Gibbs motif sampling: Detection of bacterial outer membrane protein repeats, Prot. Sci. 4, 1618–1632.
Scherf, M., Klingenhoff, A., and Werner, T. (2000) Highly specific localization of promoter regions in large genomic sequences by PromoterInspector: A Novel Context Analysis Approach, J. Mol. Biol. 297, 599–606.
Wolfertstetter, F., Frech, K., Herrmann, G., and Werner, T. (1996) Identification of functional elements in unaligned nucleic acid sequences by a novel tuple search algorithm, Comp. Appl. Biosci. 12, 71–80.
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2003 Springer Science+Business Media New York
About this chapter
Cite this chapter
Werner, T. (2003). The Role of Transcription Factor Binding Sites in Promoters and Their In Silico Detection. In: Krawetz, S.A., Womble, D.D. (eds) Introduction to Bioinformatics. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-59259-335-4_30
Download citation
DOI: https://doi.org/10.1007/978-1-59259-335-4_30
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-58829-241-4
Online ISBN: 978-1-59259-335-4
eBook Packages: Springer Book Archive