GENOME-WIDE DNASE I FOOTPRINTING OF YEAST CHROMATIN

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 DNA结合蛋白的互补及其在整个基因组中的位置决定了生物体的基因表达、DNA复制和其他基于染色体的过程。酿酒酵母通过转录图谱、200多个转录因子的染色质免疫沉淀、计算分析和其他分析，获得了全基因组基础上的因子结合的详细图景。在另一种方法中，我们使用DNase I消化染色质，然后进行高通量DNA测序，以确定整个酵母基因组中核酸酶可获得性增加的位置。由此产生的1000多万条序列读数既提供了染色质结构的全局视图，也提供了因结合蛋白的存在而免受消化的调控序列的逐个基因的视图。与染色质免疫沉淀结果不同的是，这些逐个基因的DNase I足迹可以用来直接识别转录因子结合位点，从而推断它们的基序。我们在基因组中发现了以前未知的结合位点，可以很好地描述因子，并观察到在我们的条件下，其他带注释的结合位点似乎不受核酸酶消化的保护。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The complement of DNA-binding proteins and their occupancy of sites throughout the genome determine an organism's programs of gene expression, DNA replication and other chromosome-based processes. A detailed picture of factor binding on a genome-wide basis exists for Saccharomyces cerevisiae, obtained by a combination of transcriptional profiles, chromatin immunoprecipitation of more than 200 transcription factors, computational analyses and other assays. In an alternative approach, we have used digestion of chromatin by DNase I followed by high throughput DNA sequencing to identify sites of increased nuclease accessibility throughout the yeast genome. The resulting set of more than 10 million sequence reads provides both a global view of chromatin architecture as well as a gene-by-gene view of regulatory sequences protected from digestion by the presence of bound proteins. Unlike the case with results from chromatin immunoprecipitation, these gene-by-gene DNase I footprints can be used to directly identify transcription factor binding sites, and thereby infer their motifs. We found previously unknown binding sites in the genome for well-characterized factors, and observed other annotated binding sites that appear not to be protected from nuclease digestion under our conditions.