Serial analysis of binding elements for human transcription factors

Serial analysis of binding elements (SABE) is a method that can be used to identify the genome-wide location of transcription factor binding sites in human or other mammalian cells. In this method, a specific antibody targeting a DNA-binding transcription factor of interest is used to pull down the transcription factor and its bound DNA elements through chromatin immunoprecipitation (ChIP). ChIP DNA fragments are further enriched by subtractive hybridization against non-enriched DNA using representational difference analysis (RDA) and analyzed through the generation of sequence tags similar to serial analysis of gene expression (SAGE). The SABE method circumvents the need for microarrays and is able to identify immunoprecipitated loci in an unbiased manner. The combination of ChIP, RDA and SAGE-type methods has advantages over other similar strategies in reducing the level of intrinsic noise sequences that are typically present in ChIP samples from human cells. This protocol takes about 2 weeks to complete.