In vitro DNA-binding profile of transcription factors: methods and new insights
- J Wang, Biomedicine, The State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China, Nanjing, China
- J Lu, Biomedcine, The State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China, Nanjing, China
- G Gu, Biomedcine, The State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China, Nanjing, China
- Y Liu, Biomedcine, The State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China, Nanjing, China
- ↵Correspondence: Jinke Wang, Email: wangjinke{at}seu.edu.cn
Abstract
DNA binding specificity of transcription factor (TF) has broad impact on cell physiology and development and in evolution. However, 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 serveral in vitro techniques permit high-throughput determination of relative binding affinity of a TF to all possible k-base-long DNA sequences, thus greatly promoted the characterization of DNA-binding specificity of many known TFs. All DNA sequences which can be bound by a TF with various binding affinities form its DNA-binding profile (DBP). The DBF is important to generate accurate DNA-binding model, identify all DNA-binding sites and target genes of TFs in the whole genome, and build transcription regulatory network. This paper reviewed these techniques, especially two master techniques, double-stranded DNA (dsDNA) microarray and Systematic Evolution of Ligands by Exponential Enrichment in combination with parallel DNA sequencing techniques (SELEX-seq).
- Received 6 January 2011
- Received in final form 28 February 2011
- Accepted 9 March 2011
- Made available online as an Accepted Preprint 9 March 2011
- Accepted Preprint first posted online on 9 March 2011
