Experimental strategies for studying transcription factor-DNA binding specificities.
Specific binding of transcription factors (TFs) 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 data type constitutes an optimal experimental strategy.
Geertz
Marcel
M
University of Geneva, Switzerland.
Maerkl
Sebastian J
SJ
D000818:Animals; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D053263:Gene Regulatory Networks; D006801:Humans; D008722:Methods; D011485:Protein Binding / Q000235:genetics; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
D014157:Transcription Factors; D004247:DNA