Chen Jiguo
Department of Pediatrics, The University of Texas Health Science Center at San Antonio, Texas 78229, USA.
Nat Protoc. 2006;1(3):1481-93. doi: 10.1038/nprot.2006.237.
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.
结合元件的序列分析（SABE）是一种可用于在人类或其他哺乳动物细胞中鉴定全基因组范围内转录因子结合位点位置的方法。在该方法中，使用靶向感兴趣的DNA结合转录因子的特异性抗体，通过染色质免疫沉淀（ChIP）来拉下转录因子及其结合的DNA元件。ChIP DNA片段通过使用代表性差异分析（RDA）与未富集的DNA进行消减杂交进一步富集，并通过生成类似于基因表达序列分析（SAGE）的序列标签进行分析。SABE方法无需微阵列，并且能够以无偏差的方式鉴定免疫沉淀的位点。ChIP、RDA和SAGE类型方法的组合在降低人类细胞ChIP样品中通常存在的内在噪声序列水平方面比其他类似策略具有优势。该方案大约需要2周时间完成。
