The Role of Transcription Factor Binding Sites in Promoters and Their In Silico Detection

As detailed in this chapter TFBSs are among the most important elements of transcription control in promoters, enhancers, locus control regions, and Scaffold/Matrix Attachment regions, to name only the best known. So far, the best way to identify TFBSs in genomic sequences is by sequence similarity searches with whatever method is suitable for the task. As detailed, nucleotide weight matrices are the most popular and developed tools for this purpose. However, all of these methods locate TFBSs one by one and independent of each other, yielding what is called physical binding sites. The only answer such results can provide is the physical binding probabilities of a whole group of different TFs. Neither specific binding of a particular TF can be deduced from such data nor can any functional properties of the stretch of DNA where the TFBS was found be determined. TFBSs do not act as isolated individual binding sites but always as part of a larger context.

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