A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function

Abstract

Background Distal cell-type-specific regulatory elements may be located at very large distances from the genes that they control and are often hidden within intergenic regions or in introns of other genes. The development of methods that enable mapping of regions of open chromatin genome wide has greatly advanced the identification and characterisation of these elements. Methods Here we use DNase I hypersensitivity mapping followed by deep sequencing (DNase-seq) to generate a map of open chromatin in primary human tracheal epithelial (HTE) cells and use bioinformatic approaches to characterise the distribution of these sites within the genome and with respect to gene promoters, intronic and intergenic regions. Results Genes with HTE-selective open chromatin at their promoters were associated with multiple pathways of epithelial function and differentiation. The data predict novel cell-type-specific regulatory elements for genes involved in HTE cell function, such as structural proteins and ion channels, and the transcription factors that may interact with them to control gene expression. Moreover, the map of open chromatin can identify the location of potentially critical regulatory elements in genome-wide association studies (GWAS) in which the strongest association is with single nucleotide polymorphisms in non-coding regions of the genome. We demonstrate its relevance to a recent GWAS that identifies modifiers of cystic fibrosis lung disease severity. Conclusion Since HTE cells have many functional similarities with bronchial epithelial cells and other differentiated cells in the respiratory epithelium, these data are of direct relevance to elucidating the molecular basis of normal lung function and lung disease.

A Genome-Wide Analysis of Open Chromatin in Human Epididymis Epithelial Cells Reveals Candidate Regulatory Elements for Genes Coordinating Epididymal Function1

“…In the context of the ENCODE project [2], multiple techniques are now available to analyze regulatory elements genome-wide in primary cells. Though early data sets were generated on immortalized or tumor cell lines, an increasing number of primary cells relevant to human disease are now becoming available, including pancreatic islets [33] and tracheal epithelial cells [30].…”

“…Comparison of DHS across this locus shows epididymis epithelial cell-selective open chromatin (Fig. 5 marked by arrows) in several introns and a site in the 3 0 UTR that is not present in the five ENCODE lines but is also seen in human tracheal epithelial cells [30]. These regions of open chromatin likely bind critical cell-type-selective transcription factors, which warrant further investigation.…”

“…Since all epithelia share some common functions, such as acting as a barrier to the external environment, in addition to organ-specific functions, it was of interest to compare the epididymal (HEE) data with those we generated previously for the airway epithelium (human tracheal epithelial [HTE] cells [30]). The list of 1,564 NCBI RefSeq genes with a greater representation of promoter and coding region DHS in HEE cells than the five background cell types combined (Supplemental Table S1) was compared with the equivalent list of 974 genes from HTE cells ( [30]; Supplemental Table S1).…”

“…The list of 1,564 NCBI RefSeq genes with a greater representation of promoter and coding region DHS in HEE cells than the five background cell types combined (Supplemental Table S1) was compared with the equivalent list of 974 genes from HTE cells ( [30]; Supplemental Table S1). Three hundred and twenty-seven genes were found in both lists (Supplemental Table S5), suggesting that the method was quite powerful in identifying cell-type-selective processes in addition to those that are common to all epithelial cells.…”

Open Chromatin in Plant Genomes

“…Most importantly, DHSs were found to be associated with phenotypic variations in humans, including human diseases [Schaub et al, 2012], such as lung disease [Bischof et al, 2012] and Type 2 diabetes [Stitzel et al, 2010].…”