Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

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

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 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.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Homo sapiens

SUBMITTER: Thomas Moss

PROVIDER: E-MTAB-6032 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

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

Mars Jean-Clement JC Sabourin-Felix Marianne M Tremblay Michel G MG Moss Tom T

G3 (Bethesda, Md.) 20180104 1

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 profil ...[more]

PMID: 29158335

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Dataset Information

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

Publications

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

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