ArticleThorax2012
A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function.
Article in Thorax, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 23 citations in OpenAlex.
- A Kaleidoscope of Keratin Gene Expression and the Mosaic of Its Regulatory Mechanisms.International journal of molecular sciences · 2023Review
- Krüppel-Like Factor 5 Regulates CFTR Expression Through Repression by Maintaining Chromatin Architecture Coupled with Direct Enhancer Activation.Journal of molecular biology · 2022Article
- Impact of KLF4 on Cell Proliferation and Epithelial Differentiation in the Context of Cystic Fibrosis.International journal of molecular sciences · 2020Article
- Article
- Functional genomics analysis of human colon organoids identifies key transcription factors.Physiological genomics · 2020Article
- Looping of upstream cis-regulatory elements is required for CFTR expression in human airway epithelial cells.Nucleic acids research · 2020Article
- Coordinate regulation of ELF5 and EHF at the chr11p13 CF modifier region.Journal of cellular and molecular medicine · 2019Article
- Recent advances in developing therapeutics for cystic fibrosis.Human molecular genetics · 2018Review
- Molecular characterization of gene regulatory networks in primary human tracheal and bronchial epithelial cells.Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society · 2018Article
- A transcription factor network repressesThe Biochemical journal · 2018Article
- Regulatory dynamics of 11p13 suggest a role for EHF in modifying CF lung disease severity.Nucleic acids research · 2017Article
- Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus.Nucleic acids research · 2016Article
- HNF1 regulates critical processes in the human epididymis epithelium.Molecular and cellular endocrinology · 2016Article
- Novel variation at chr11p13 associated with cystic fibrosis lung disease severity.Human genome variation · 2016Article
- Oxidative stress regulates CFTR gene expression in human airway epithelial cells through a distal antioxidant response element.American journal of respiratory cell and molecular biology · 2015Article
- Ets homologous factor regulates pathways controlling response to injury in airway epithelial cells.Nucleic acids research · 2014Article
- A genome-wide analysis of open chromatin in human epididymis epithelial cells reveals candidate regulatory elements for genes coordinating epididymal function.Biology of reproduction · 2013Article
- Immune mediators regulate CFTR expression through a bifunctional airway-selective enhancer.Molecular and cellular biology · 2013Article
- ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions.Nature reviews. Genetics · 2012Review
Corrections and comments
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Authors and funding
10 authors at 5 institutions in 1 country.
Funding
Abstract
backgroundDistal 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.
methodsHere 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.
resultsGenes 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.
conclusionSince 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.