To understand the molecular mechanisms that underlie global transcriptional 
regulation, it is essential to first identify all the transcriptional regulatory 
elements in the human genome. The advent of next-generation sequencing has 
provided a powerful platform for genome-wide analysis of different species and 
specific cell types; when combined with traditional techniques to identify 
regions of open chromatin [DNaseI hypersensitivity (DHS)] or specific binding 
locations of transcription factors [chromatin immunoprecipitation (ChIP)], and 
expression data from microarrays, we become uniquely poised to uncover the 
mysteries of the genome and its regulation. To this end, we have performed 
global meta-analysis of the relationship among data from DNaseI-seq, ChIP-seq 
and expression arrays, and found that specific correlations exist among 
regulatory elements and gene expression across different cell types. These 
correlations revealed four distinct modes of chromatin domain structure 
reflecting different functions: repressive, active, primed and bivalent. 
Furthermore, CCCTC-binding factor (CTCF) binding sites were identified based on 
these integrative data. Our findings uncovered a complex regulatory process 
involving by DNaseI HS sites and histone modifications, and suggest that these 
dynamic elements may be responsible for maintaining chromatin structure and 
integrity of the human genome. Our integrative approach provides an example by 
which data from diverse technology platforms may be integrated to provide more 
meaningful insights into global transcriptional regulation.