A deconvolution protocol for chip-seq reveals analogous enhancer structures on the mouse and human ribosomal RNA genes

The combination of Chromatin Immunoprecipitation and Massively Parallel Sequencing, or ChIP-Seq, has greatly advanced our genome-wide understanding of chromatin and enhancer structures. However, its resolution at any given genetic locus is limited by several factors. In applying ChIP-Seq to study the ribosomal RNA genes we found that a major limitation to resolution was imposed by the often dominant variability in sequence coverage provided by the massively parallel sequencing technology. Here we describe a simple numerical deconvolution approach that in large part corrects for this variability and significantly improves both the resolution and quantitation of protein-DNA interaction maps deduced from ChIP-Seq data. This approach has allowed us to study the in vivo organization of the RNA Polymerase I pre-initiation complexes that form at the promoters of the mouse and human ribosomal RNA genes. The data identify and map a “Spacer Promoter” and associated stalled polymerase in the intergenic spacer of the human ribosomal genes and show that a very similar Enhancer structure and organization to that found in rodents and even in lower vertebrates also exists in human.