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A Handbook of Transcription FactorsMethods for Analysis of Transcription Factor DNA-Binding Specificity In Vitro

A Handbook of Transcription Factors: Methods for Analysis of Transcription Factor DNA-Binding... [Transcription of genes during development and in response to environmental stimuli is determined by genomic DNA sequence. The DNA sequences regulating transcription are read by sequence-specific transcription factors (TFs) that recognize relatively short sequences, generally between four and twenty base pairs in length. Transcriptional regulation generally requires binding of multiple TFs in close proximity to each other. Mechanistic understanding of transcription in an organism thus requires detailed knowledge of binding affinities of all its TFs to all possible DNA sequences, and the co–operative interactions between the TFs. However, very little is known about such co-operative binding interactions, and even the simple TF-DNA binding information exists only for a very small proportion of all TFs – for example, mammals have approximately 1,300–2,000 TFs [1, 2], yet the largest public databases for TF binding specificity, Jaspar and Uniprobe [3, 4] currently list only approximately 500 moderate to high resolution profiles for human or mouse. This lack of knowledge is in part due to the fact that analysis of TF DNA binding has been laborious and expensive. In this chapter, we review methods that can be used to determine binding specificity of TFs to DNA, mainly focusing on recently developed assays that allow high-resolution analysis of TF binding specificity in relatively high throughput.] http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png

A Handbook of Transcription FactorsMethods for Analysis of Transcription Factor DNA-Binding Specificity In Vitro

Part of the Subcellular Biochemistry Book Series (volume 52)
Editors: Hughes, Timothy R.
Jolma, Arttu; Taipale, Jussi
A Handbook of Transcription Factors — Apr 14, 2011
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References (68)

Publisher
Springer Netherlands
Copyright
© Springer Science+Business Media B.V. 2011
ISBN
978-90-481-9068-3
Pages
155 –173
DOI
10.1007/978-90-481-9069-0_7
Publisher site
See Chapter on Publisher Site

Abstract

[Transcription of genes during development and in response to environmental stimuli is determined by genomic DNA sequence. The DNA sequences regulating transcription are read by sequence-specific transcription factors (TFs) that recognize relatively short sequences, generally between four and twenty base pairs in length. Transcriptional regulation generally requires binding of multiple TFs in close proximity to each other. Mechanistic understanding of transcription in an organism thus requires detailed knowledge of binding affinities of all its TFs to all possible DNA sequences, and the co–operative interactions between the TFs. However, very little is known about such co-operative binding interactions, and even the simple TF-DNA binding information exists only for a very small proportion of all TFs – for example, mammals have approximately 1,300–2,000 TFs [1, 2], yet the largest public databases for TF binding specificity, Jaspar and Uniprobe [3, 4] currently list only approximately 500 moderate to high resolution profiles for human or mouse. This lack of knowledge is in part due to the fact that analysis of TF DNA binding has been laborious and expensive. In this chapter, we review methods that can be used to determine binding specificity of TFs to DNA, mainly focusing on recently developed assays that allow high-resolution analysis of TF binding specificity in relatively high throughput.]

Published: Apr 14, 2011

Keywords: Protein–DNA interactions; Co-operative binding; Affinity; SELEX; Protein binding microarrays

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