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

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

PROVIDER: PRJEB22304 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2109140.fastq.gz	Fastqsanger.gz
	ERR2109141.fastq.gz	Fastqsanger.gz
	ERR2109138.fastq.gz	Fastqsanger.gz
	ERR2109139.fastq.gz	Fastqsanger.gz

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Deconvolution ChIP-seq profiling of UBF and RPA194 in K562 cells to identify analogous enhancer structures on mouse and human ribosomal RNA genes

Project description: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.

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A Deconvolution Protocol for ChIP-Seq Reveals Analogous Enhancer Structures on the Mouse and Human Ribosomal RNA Genes.

Project description: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.

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