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

Hualin Xi,Yutao Fu,Teresa R Vales,Zhiping Weng,Gregory E Crawford,Bing Ren,Hennady P Shulha,Jane M Lin,David M Bodine,Ronald D G Mckay,Josh G Chenoweth,Paul J Tesar,Terrence S Furey,Michael Snyder

doi:10.1371/journal.pgen.0030136

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.

Highlights

Biological processes such as proliferation, apoptosis, differentiation, development, and aging require carefully orchestrated spatial and temporal gene expression [1,2]
We find that approximately 22% of all DNaseI hypersensitive site (HS) sites from each cell type are ubiquitously present in all six cell types, while the remainder are a mixture of cell type specific or common
We find that only 22% of gene regulatory elements are shared among all cell types studied

Summary

Introduction

Biological processes such as proliferation, apoptosis, differentiation, development, and aging require carefully orchestrated spatial and temporal gene expression [1,2]. To understand the molecular mechanisms that underlie global transcriptional regulation, it is essential to identify all the DNA regulatory elements in the human genome. DNaseI hypersensitive site (HS) mapping, chromatin immunoprecipitation followed by hybridization to tiled arrays (ChIP-chip), and expression arrays identify gene regulatory elements in different ways. DNaseI HS sites identify regions of open chromatin, which encompass all different types of regulatory elements, including promoters, enhancers, silencers, insulators, and locus control regions (LCR) [3]. DNaseI HS mapping does not directly reveal the transcription factor(s) that bind within each DNaseI HS site. To completely understand how chromatin structure regulates gene expression, a multi-pronged integrated experimental approach using all three methods is needed

Methods

Results

Discussion

Conclusion