A Deconvolution Protocol for ChIP-Seq Reveals Analogous Enhancer Structures on the Mouse and Human Ribosomal RNA Genes. Issue 1 (1st January 2018)

• Record Type: Journal Article
• Authors: Mars, Jean-Clement; Sabourin-Felix, Marianne; Tremblay, Michel G; Moss, Tom
• Is Part Of: G3. Volume 8:Issue 1(2018)
• Page Start: 303
• Page End: 314
• Publication Date: 2018-01-01
• Subjects: ChIP-Seq deconvolution -- RNA polymerase I (RPI, PolI, Polr1) -- ribosomal RNA (rRNA) genes -- upstream binding factor (UBF/UBTF) -- selectivity factor SL1; Genetics -- Research -- Periodicals; Genomics -- Periodicals; Genetics; Genomics; Genes; Genetics -- Research; Genomics; Electronic journals; Periodical; Periodicals; Fulltext; Internet Resources; Periodicals; 572.8
• DOI: 10.1534/g3.117.300225
• Languages: English
• ISSNs: 2160-1836

Abstract

Abstract: 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 the study of the ribosomal RNA genes, we found that a major limitation to resolution was imposed by the underlying variability in sequence coverage that very often dominates the protein–DNA interaction profiles. 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 determine the in vivo organization of the RNA polymerase I preinitiation complexes that form at the promoters and enhancers of the mouse ( Mus musculus ) and human ( Homo sapiens ) ribosomal RNA genes, and to reveal a phased binding of the HMG-box factor UBF across the rDNA. The data identify and map a "Spacer Promoter" and associated stalled polymerase in the intergenic spacer of the human ribosomal RNA genes, and reveal a very similar enhancer structure to that found in rodents and lower vertebrates.