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.