Serial Analysis of Binding Elements for Transcription Factors

Abstract

The ability to determine genome-wide location of transcription factor binding sites (TFBS) is crucial for elucidating gene regulatory networks in human cells during normal development and disease such as tumorigenesis. To achieve this goal, we developed a method called serial analysis of binding elements for transcription factors (SABE) for globally identifying TFBS in human or other mammalian genomes. 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 and analyzed through 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, subtractive hybridization, and SAGE-type methods is advantageous over other similar strategies to reduce the level of intrinsic noise sequences that is typically present in ChIP samples from human or other mammalian cells.