What are the benefits of using the whole-genome tiling array set versus a promoter array for a ChIP-on-ChIP study?
The Affymetrix promoter arrays for human and mouse are tiled across over 25,000 promoters each. Each promoter region consists of approximately 7.5 kb upstream and 2.5 kb downstream of the transcription start site (TSS). Therefore, while protein-associated sites and methylated DNA regions within those regions will be identified, clearly the number of regions being examined is limited when using promoter arrays. Over the past 5 years, we (and others) have found that binding sites for transcription factors, histone marks and sites of DNA methylation are not restricted to promoters and in fact are generally found within genes, far upstream of genes and downstream of genes. For some transcription factors, e.g., steroid hormone receptors, only 2-10% of binding occurs in promoters.
