comprehensive identification and annotation of cell type-specific and ubiquitous ctcf-binding sites in the human genome全面识别和注释的细胞特定类型和无处不在的ctcf-binding网站在人类基因组中.pdfVIP

Comprehensive Identification and Annotation of Cell Type-Specific and Ubiquitous CTCF-Binding Sites in the Human Genome . . Hebing Chen , Yao Tian , Wenjie Shu*, Xiaochen Bo*, Shengqi Wang* Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, China Abstract Chromatin insulators are DNA elements that regulate the level of gene expression either by preventing gene silencing through the maintenance of heterochromatin boundaries or by preventing gene activation by blocking interactions between enhancers and promoters. CCCTC-binding factor (CTCF), a ubiquitously expressed 11-zinc-finger DNA-binding protein, is the only protein implicated in the establishment of insulators in vertebrates. While CTCF has been implicated in diverse regulatory functions, CTCF has only been studied in a limited number of cell types across human genome. Thus, it is not clear whether the identified cell type-specific differences in CTCF-binding sites are functionally significant. Here, we identify and characterize cell type-specific and ubiquitous CTCF-binding sites in the human genome across 38 cell types designated by the Encyclopedia of DNA Elements (ENCODE) consortium. These cell type-specific and ubiquitous CTCF- binding sites show uniquely versatile transcriptional functions and characteristic chromatin features. In addition, we confirm the insulator barrier function of CTCF-binding and explore the novel function of CTCF in DNA replication. These results represent a critical step toward the comprehensive and systematic understanding of CTCF-dependent insulators and their versatile roles in the human genome. Citation: Chen H, Tian Y, Shu W, Bo X, Wang S (2012) Comprehensive Identification and Annotation of Cell Type-