Current methods for protein- DNA interaction identification at a genomic scale are limited because of their inability for mapping binding sites with high resolution, they are not very cost- effective and they are mostly non- high- throughput. Besides these technologies are usually based on ChIP assays, and therefore they share the same problems (low accuracy, limited coberture, poor resolution). Here the authors report a large- scale ChIP assay ("ChIPSeq"), that consists of a first step of standard ChIP, followed by size selection of the generated immuno- enriched DNA fragments (a step that increases resolution), and then a ultrahigh- throughput sequencing -the Solexa/Illumina method- is performed. The sequencing reads are computationally filtered and mapped, and because of the very large number of reads produced by the Solexa/Illumina system, a greater sensitivity and statistical certainty is achieved (which is especially helpful when the desired goal is to identify a motif). Unlike other related techniques, this involves no plasmid library construction, single copy sites are available, and is feasible for any sequenced genome, rather than only for those whose arrays have been developed. The authors evaluated the utility and power of their method by building an interactome map for the NRSF/REST transcription factor. They also suggested that other ultrahigh- throughput sequencing platforms could be used instead of the Solexa/Illumina system.
Johnson DS. et al. 2007. Science 316:1497-1501
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