Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome.

The identification of regulatory elements from different cell types is necessary for understanding the mechanisms controlling cell type-specific and housekeeping gene expression. Mapping DNaseI hypersensitive (HS) sites is an accurate method for identifying the location of functional regulatory elements. We used a high throughput method called DNase-chip to identify 3,904 DNaseI HS sites from six cell types across 1% of the human genome.

Transcription factor binding and modified histones in human bidirectional promoters.

Bidirectional promoters have received considerable attention because of their ability to regulate two downstream genes (divergent genes). They are also highly abundant, directing the transcription of approximately 11% of genes in the human genome. We categorized the presence of DNA sequence motifs, binding of transcription factors, and modified histones as overrepresented, shared, or underrepresented in bidirectional promoters with respect to unidirectional promoters.

Systematic detection of statistically overrepresented DNA motif association rules.

DNA motifs, or cis-elements, are short nucleotide sequence patterns recognized by various transcription factors (TFs). In promoters, these TFs bind in a complex combinatorial manner in order to regulate the expression of a downstream gene. The combinatorial space is frequently large and difficult to manage since vertebrates have thousands of transcription factors and more than 20,000 genes.