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lüll In vitro DNA-binding profile of transcription factors: methods and new insights Wang J; Lu J; Gu G; Liu YJ Endocrinol 2011[Jul]; 210 (1): 15-27The DNA-binding specificity of transcription factors (TFs) has broad impacts on cell physiology, cell development and in evolution. However, the DNA-binding specificity of most known TFs still remains unknown. The specificity of a TF protein is determined by its relative affinity to all possible binding sites. In recent years, the development of several in vitro techniques permits high-throughput determination of relative binding affinity of a TF to all possible k bp-long DNA sequences, thus greatly promoting the characterization of DNA-binding specificity of many known TFs. All DNA sequences that can be bound by a TF with various binding affinities form their DNA-binding profile (DBP). The DBP is important to generate an accurate DNA-binding model, identify all DNA-binding sites and target genes of TFs in the whole genome, and build transcription regulatory network. This study reviewed these techniques, especially two master techniques: double-stranded DNA microarray and systematic evolution of ligands by exponential enrichment in combination with parallel DNA sequencing techniques (SELEX-seq).|*Oligonucleotide Array Sequence Analysis[MESH]|*SELEX Aptamer Technique[MESH]|Animals[MESH]|Binding Sites[MESH]|DNA-Binding Proteins/*metabolism[MESH]|DNA/chemistry/*metabolism[MESH]|Endocrinology/methods/trends[MESH]|Gene Expression Profiling[MESH]|Gene Regulatory Networks[MESH]|High-Throughput Nucleotide Sequencing/methods[MESH]|Humans[MESH]|Transcription Factors/*metabolism[MESH] |