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Experimental strategies for studying transcription factor-DNA binding specificities


Geertz, Marcel; Maerkl, Sebastian J (2010). Experimental strategies for studying transcription factor-DNA binding specificities. Briefings in Functional Genomics:1-12.

Abstract

The specific binding of transcription factors (TF) determines in a large part the connectivity of gene regulatory networks as well as the quantitative level of gene expression. A multiplicity of both experimental and computational methods is currently used to discover and characterize the underlying TF-DNA interactions. Experimental methods can be further subdivided into in vitro- and in vivo-based approaches, each accenting different aspects of TF binding events. In this review we summarize the flexibility and performance of a selection of both types of experimental methods. In conclusion, we argue that a serial combination of methods with different throughput and information content constitutes an optimal experimental strategy.

Abstract

The specific binding of transcription factors (TF) determines in a large part the connectivity of gene regulatory networks as well as the quantitative level of gene expression. A multiplicity of both experimental and computational methods is currently used to discover and characterize the underlying TF-DNA interactions. Experimental methods can be further subdivided into in vitro- and in vivo-based approaches, each accenting different aspects of TF binding events. In this review we summarize the flexibility and performance of a selection of both types of experimental methods. In conclusion, we argue that a serial combination of methods with different throughput and information content constitutes an optimal experimental strategy.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:Special Collections > SystemsX.ch
Special Collections > SystemsX.ch > Research, Technology and Development Projects > DynamiX
Special Collections > SystemsX.ch > Research, Technology and Development Projects
Dewey Decimal Classification:570 Life sciences; biology
Language:English
Date:September 2010
Deposited On:22 Jun 2013 14:48
Last Modified:05 Apr 2016 16:49
Publisher:Oxford University Press
ISSN:2041-2649
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1093/bfgp/elq023

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