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.
Keywords: transcription factor ; DNA binding ; binding affinity ; ChIP ; Mitomi ; Pbm ; Selex ; Surface-Plasmon Resonance ; Protein-Dna ; Gene-Regulation ; In-Vivo ; Regulatory Networks ; Chromatin-Immunoprecipitation ; Saccharomyces-Cerevisiae ; Gel-Electrophoresis ; Zinc Fingers ; Genome
Record created on 2011-01-17, modified on 2016-08-09