Identification and Characterization of Cell Type–Specific and Ubiquitous Chromatin Regulatory Structures in the Human Genome

Abstract

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. A significant number (22%) of DNaseI HS sites from each cell type are ubiquitously present among all cell types studied. Surprisingly, nearly all of these ubiquitous DNaseI HS sites correspond to either promoters or insulator elements: 86% of them are located near annotated transcription start sites and 10% are bound by CTCF, a protein with known enhancer-blocking insulator activity. We also identified a large number of DNaseI HS sites that are cell type specific (only present in one cell type); these regions are enriched for enhancer elements and correlate with cell type–specific gene expression as well as cell type–specific histone modifications. Finally, we found that approximately 8% of the genome overlaps a DNaseI HS site in at least one the six cell lines studied, indicating that a significant percentage of the genome is potentially functional.

A novel mode of enhancer evolution: The Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity

“…These latter elements are thought to play key roles in organizing higher order chromatin structure and can serve to protect a given gene locus from repressing influences of neighboring regions of heterochromatin. At the molecular level, insulator/boundary elements are characterized by the presence of ubiquitous DNase I-hypersensitive sites and binding by the multi-zinc finger protein CTCF (Xi et al 2007). In contrast, the Tal1 +18 region is characterized by a tissue-specific hypersensitive site and not bound by CTCF (see Supplemental Fig.…”

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

“…4A) Table S5). Seven of the sites were previously described (Xi et al 2007). Five were chosen specifically based on the absence of the 20-bp CTCF binding motif to test for insulator function even in the absence of this motif.…”

“…Several studies have shown that open chromatin is associated with all known classes of active DNA regulatory elements, including promoters, enhancers, silencers, insulators, and locus control regions (Gross and Garrard 1988;Cockerill 2011). We used DNase-seq and FAIRE-seq (Giresi et al 2007;Xi et al 2007;Boyle et al 2008a;Gaulton et al 2010;Stitzel et al 2010) to generate genome-wide open chromatin maps spanning seven diverse human cell types, thereby greatly expanding the number of human regulatory elements with experimental support.…”

Qualifying the relationship between sequence conservation and molecular function

“…Recently, however, high-throughput functional genomics techniques have allowed for an initial assessment of the converse relationship, namely, the quantification of selective constraint on large, unbiased collections of functional elements. These studies include cell-based assays on a genomic scale (Kim et al 2005;Borneman et al 2007;The ENCODE Project Consortium 2007;Heintzman et al 2007;Xi et al 2007) and in vivo assays for developmentally important functions in individual loci in animal model organisms Brown et al 2007). Interestingly, they have demonstrated that there are large numbers of functional sequences that are not detectably conserved across both distant (McGaughey et al 2008, this issue) and close Margulies et al 2007) evolutionary timescales.…”