期刊
G3-GENES GENOMES GENETICS
卷 8, 期 1, 页码 303-314出版社
GENETICS SOCIETY AMERICA
DOI: 10.1534/g3.117.300225
关键词
ChIP-Seq deconvolution; RNA polymerase I (RPI, PolI, Polr1) ribosomal RNA (rRNA) genes; upstream binding factor (UBF/UBTF); selectivity factor SL1
资金
- Canadian Institutes of Health Research [MOP12205/PJT153266]
- National Science and Engineering Council of Canada
- Fonds de Recherche du Quebec-Sante
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.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据