GENOME-WIDE DNASE I FOOTPRINTING OF YEAST CHROMATIN

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 DNA结合蛋白的互补性及其在整个基因组中的位点占有率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的程序。 一个详细的图片的因素结合在全基因组的基础上存在的酿酒酵母，获得了转录谱，染色质免疫沉淀的200多个转录因子，计算分析和其他测定的组合。 在另一种方法中，我们使用DNA酶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及性增加的位点。 由此产生的一组超过1000万个序列读段提供了染色质结构的全局视图以及通过结合蛋白的存在而免受消化的调控序列的基因逐个视图。 与染色质免疫沉淀的结果不同，这些基因-基因DNA酶I足迹可用于直接识别转录因子结合位点，从而推断其基序。 我们在基因组中发现了以前未知的结合位点，用于充分表征的因子，并观察到在我们的条件下似乎不受核酸酶消化保护的其他注释结合位点。

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.