par Coulson, Richard Mr R R.;Brazma, Alvis;Manke, Thomas;Roider, Helge;Vingron, Martin;Palin, Kimmo;Ukkonen, Esko;Sand, Olivier ;van Helden, Jacques
Référence Modern Genome Annotation: The Biosapiens Network, Springer-Verlag Wien, page (105-119)
Publication Publié, 2008
Partie d'ouvrage collectif
Résumé : Transcription factors, by binding to particular DNA sequences termed transcription factor-binding sites, play an important role in regulating gene expression in both prokaryotic and eukaryotic organisms. These binding sites lie within promoters (which are located just upstream of a gene and promote transcription of that gene) and enhancers (short DNA elements enhancing transcription levels of genes in a gene cluster, and which need not be particularly close to the genes they act on, or even located on the same chromosome). Binding of transcription factors in these genomic regulatory regions can influence gene transcription rates either positively or negatively. The binding may also be dependant on the interaction with co-activators and co-repressors, in addition to context (e.g. particular histone modifications in the vicinity of the regulatory element). Identifying all transcription factors and their respective binding sites would be an important step towards a more thorough understanding of gene regulation. Regular expression type patterns, as well as nucleotide distribution matrices, have both been used for describing transcription factor-binding sites, e.g. (Bucher 1990; Ghosh 1990; Chen et al. 1995; Wingender et al. 1996). Here we will discuss some of the computational approaches that are used in binding site identification.