1
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Chen Q, Li J. Molecular mechanism analysis of nontuberculous mycobacteria infection in patients with cystic fibrosis. Future Microbiol 2024; 19:877-888. [PMID: 38700285 PMCID: PMC11290754 DOI: 10.2217/fmb-2023-0237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 03/27/2024] [Indexed: 05/05/2024] Open
Abstract
Aim: This study aims to explore the molecular mechanisms of cystic fibrosis (CF) complicated with nontuberculous mycobacteria (NTM) infection. Materials & methods: Expression profiles of CF with NTM-infected patients were downloaded from GEO database. Intersection analysis yielded 78 genes associated with CF with NTM infection. The protein-protein interaction (PPI) network and the functions of hub genes were investigated. Results: Five hub genes (PIK3R1, IL1A, CXCR4, ACTN1, PFN1) were identified, which were primarily enriched in actin-related biological processes and pathways. Transcription factors RELA, JUN, NFKB1 and FOS that regulated hub genes modulated IL1A expression, while 21 other transcription factors regulated CXCR4 expression. Conclusion: In summary, this study may provide new insights into the mechanisms of CF with NTM infection.
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Affiliation(s)
- Qihuang Chen
- Department of Tuberculosis, 900TH Hospital of Joint Logistics Support Force, Fuzhou, 350025, China
| | - Jin Li
- Department of Tuberculosis, 900TH Hospital of Joint Logistics Support Force, Fuzhou, 350025, China
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2
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Coatti GC, Vaghela N, Gillurkar P, Leir SH, Harris A. A promoter-dependent upstream activator augments CFTR expression in diverse epithelial cell types. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195031. [PMID: 38679287 DOI: 10.1016/j.bbagrm.2024.195031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/01/2024]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) gene encodes an anion-selective channel found in epithelial cell membranes. Mutations in CFTR cause cystic fibrosis (CF), an inherited disorder that impairs epithelial function in multiple organs. Most men with CF are infertile due to loss of intact genital ducts. Here we investigated a novel epididymis-selective cis-regulatory element (CRE), located within a peak of open chromatin at -9.5 kb 5' to the CFTR gene promoter. Activation of the -9.5 kb CRE alone by CRISPRa had no impact on CFTR gene expression. However, CRISPRa co-activation of the -9.5 kb CRE and the CFTR gene promoter in epididymis cells significantly augmented CFTR mRNA and protein expression when compared to promoter activation alone. This increase was accompanied by enhanced chromatin accessibility at both sites. Furthermore, the combined CRISPRa strategy activated CFTR expression in other epithelial cells that lack open chromatin at the -9.5 kb site and in which the locus is normally inactive. However, the -9.5 kb CRE does not function as a classical enhancer of the CFTR promoter in transient reporter gene assays. These data provide a novel mechanism for activating/augmenting CFTR expression, which may have therapeutic utility for mutations that perturb CFTR transcription.
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Affiliation(s)
- Giuliana C Coatti
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Nirbhayaditya Vaghela
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Pulak Gillurkar
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Shih-Hsing Leir
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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3
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Kerschner JL, Meckler F, Coatti GC, Vaghela N, Paranjapye A, Harris A. The impact of genomic distance on enhancer-promoter interactions at the CFTR locus. J Cell Mol Med 2024; 28:e18142. [PMID: 38372567 PMCID: PMC10875976 DOI: 10.1111/jcmm.18142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 01/08/2024] [Accepted: 01/16/2024] [Indexed: 02/20/2024] Open
Abstract
We identified and characterized multiple cell-type selective enhancers of the CFTR gene promoter in previous work and demonstrated active looping of these elements to the promoter. Here we address the impact of genomic spacing on these enhancer:promoter interactions and on CFTR gene expression. Using CRISPR/Cas9, we generated clonal cell lines with deletions between the -35 kb airway enhancer and the CFTR promoter in the 16HBE14o- airway cell line, or between the intron 1 (185 + 10 kb) intestinal enhancer and the promoter in the Caco2 intestinal cell line. The effect of these deletions on CFTR transcript abundance, as well as the 3D looping structure of the locus was investigated in triplicate clones of each modification. Our results indicate that both small and larger deletions upstream of the promoter can perturb CFTR expression and -35 kb enhancer:promoter interactions in the airway cells, though the larger deletions are more impactful. In contrast, the small intronic deletions have no effect on CFTR expression and intron 1 enhancer:promoter interactions in the intestinal cells, whereas larger deletions do. Clonal variation following a specific CFTR modification is a confounding factor particularly in 16HBE14o- cells.
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Affiliation(s)
- Jenny L. Kerschner
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
| | - Frederick Meckler
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
| | - Giuliana C. Coatti
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
| | - Nirbhayaditya Vaghela
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
| | - Alekh Paranjapye
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
- Present address:
Department of GeneticsUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Ann Harris
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
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4
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Blotas C, Férec C, Moisan S. Tissue-Specific Regulation of CFTR Gene Expression. Int J Mol Sci 2023; 24:10678. [PMID: 37445855 DOI: 10.3390/ijms241310678] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/21/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
More than 2000 variations are described within the CFTR (Cystic Fibrosis Transmembrane Regulator) gene and related to large clinical issues from cystic fibrosis to mono-organ diseases. Although these CFTR-associated diseases have been well documented, a large phenotype spectrum is observed and correlations between phenotypes and genotypes are still not well established. To address this issue, we present several regulatory elements that can modulate CFTR gene expression in a tissue-specific manner. Among them, cis-regulatory elements act through chromatin loopings and take part in three-dimensional structured organization. With tissue-specific transcription factors, they form chromatin modules and can regulate gene expression. Alterations of specific regulations can impact and modulate disease expressions. Understanding all those mechanisms highlights the need to expand research outside the gene to enhance our knowledge.
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Affiliation(s)
- Clara Blotas
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Claude Férec
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Stéphanie Moisan
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, CHU Brest, F-29200 Brest, France
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5
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Kerschner JL, Paranjapye A, Vaghela N, Wilson MD, Harris A. An ectopic enhancer restores CFTR expression through de novo chromatin looping. Gene Ther 2023; 30:478-486. [PMID: 36510002 PMCID: PMC11227122 DOI: 10.1038/s41434-022-00378-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 10/30/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022]
Abstract
Transcription of the cystic fibrosis transmembrane conductance regulator (CFTR) gene is regulated by both ubiquitous and cell-type selective cis-regulatory elements (CREs). These CREs include extragenic and intronic enhancers that bind lineage-specific transcription factors, and architectural protein-marked structural elements. Deletion of the airway-selective -35 kb enhancer in 16HBE14o- lung epithelial cells was shown earlier to disrupt normal enhancer-promoter looping at the CFTR locus and nearly abolish its expression. Using a 16HBE14o- clone that lacks the endogenous -35 kb CRE, we explore the impact of relocating the functional core of this element to an ectopic site in intron 1. The -35 kb sequence establishes a de novo enhancer signature in chromatin at the insertion site, and augments CFTR expression, albeit not fully restoring WT levels. The relocated -35 kb enhancer also initiates de novo chromatin contacts with the CFTR promoter and other known CFTR CREs. These results are broadly relevant to therapeutic gene editing.
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Affiliation(s)
- Jenny L Kerschner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44116, USA
| | - Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44116, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Nirbhayaditya Vaghela
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44116, USA
| | - Michael D Wilson
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44116, USA
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44116, USA.
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6
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Kerschner JL, Paranjapye A, Harris A. Cellular heterogeneity in the 16HBE14o - airway epithelial line impacts biological readouts. Physiol Rep 2023; 11:e15700. [PMID: 37269165 PMCID: PMC10238858 DOI: 10.14814/phy2.15700] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/15/2023] [Accepted: 04/16/2023] [Indexed: 06/04/2023] Open
Abstract
The airway epithelial cell line, 16HBE14o- , is an important cell model for studying airway disease. 16HBE14o- cells were originally generated from primary human bronchial epithelial cells by SV40-mediated immortalization, a process that is associated with genomic instability through long-term culture. Here, we explore the heterogeneity of these cells, with respect to expression of the cystic fibrosis transmembrane conductance regulator (CFTR) transcript and protein. We isolate clones of 16HBE14o- with stably higher and lower levels of CFTR in comparison to bulk 16HBE14o- , designated CFTRhigh and CFTRlow . Detailed characterization of the CFTR locus in these clones by ATAC-seq and 4C-seq showed open chromatin profiles and higher order chromatin structure that correlate with CFTR expression levels. Transcriptomic profiling of CFTRhigh and CFTRlow cells showed that the CFTRhigh cells had an elevated inflammatory/innate immune response phenotype. These results encourage caution in interpreting functional data from clonal lines of 16HBE14o- cells, generated after genomic or other manipulations.
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Affiliation(s)
- Jenny L. Kerschner
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
| | - Alekh Paranjapye
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
- Present address:
Department of GeneticsUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Ann Harris
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
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7
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Yin S, Mazumdar MN, Paranjapye A, Harris A. Cross-talk between enhancers, structural elements and activating transcription factors maintains the 3D architecture and expression of the CFTR gene. Genomics 2022; 114:110350. [PMID: 35346781 PMCID: PMC9509493 DOI: 10.1016/j.ygeno.2022.110350] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/13/2022] [Accepted: 03/23/2022] [Indexed: 01/14/2023]
Abstract
Robust protocols to examine 3D chromatin structure have greatly advanced knowledge of gene regulatory mechanisms. Here we focus on the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which provides a paradigm for validating models of gene regulation built upon genome-wide analysis. We examine the mechanisms by which multiple cis-regulatory elements (CREs) at the CFTR gene coordinate its expression in intestinal epithelial cells. Using CRISPR/Cas9 to remove CREs, individually and in tandem, followed by assays of gene expression and higher-order chromatin structure (4C-seq), we reveal the cross-talk and dependency of two cell-specific intronic enhancers. The results suggest a mechanism whereby the locus responds when CREs are lost, which may involve activating transcription factors such as FOXA2. Also, by removing the 5' topologically-associating domain (TAD) boundary, we illustrate its impact on CFTR gene expression and architecture. These data suggest a multi-layered regulatory hierarchy that is highly sensitive to perturbations.
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8
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Paranjapye A, NandyMazumdar M, Harris A. Krüppel-Like Factor 5 Regulates CFTR Expression Through Repression by Maintaining Chromatin Architecture Coupled with Direct Enhancer Activation. J Mol Biol 2022; 434:167561. [PMID: 35341742 DOI: 10.1016/j.jmb.2022.167561] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 02/06/2023]
Abstract
Single cell RNA-sequencing has accurately identified cell types within the human airway that express the Cystic Fibrosis Transmembrane Conductance regulator (CFTR) gene. Low abundance CFTR transcripts are seen in many secretory cells, while high levels are restricted to rare pulmonary ionocytes. Here we focus on the mechanisms coordinating basal CFTR expression in the secretory compartment. Cell-selective regulation of CFTR is achieved within its invariant topologically associating domain by the recruitment of cis-regulatory elements (CREs). CRE activity is coordinated by cell-type-selective transcription factors. One such factor, Krüppel-Like Factor 5 (KLF5), profoundly represses CFTR transcript and protein in primary human airway epithelial cells and airway cell lines. Here we reveal the mechanism of action of KLF5 upon the CFTR gene. We find that depletion or ablation of KLF5 from airway epithelial cells changes higher order chromatin structure at the CFTR locus. Critical looping interactions that are required for normal gene expression are altered, the H3K27ac active chromatin mark is redistributed, and CTCF occupancy is modified. However, mutation of a single KLF5 binding site within a pivotal airway cell CRE abolishes CFTR expression. Hence, KLF5 has both direct activating and indirect repressive effects, which together coordinate CFTR expression in the airway.
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Affiliation(s)
- Alekh Paranjapye
- Department of Genetics and Genome Sciences, and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Monali NandyMazumdar
- Department of Genetics and Genome Sciences, and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Ann Harris
- Department of Genetics and Genome Sciences, and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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9
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Kabadi AM, Machlin L, Dalal N, Lee RE, McDowell I, Shah NN, Drowley L, Randell SH, Reddy TE. Epigenome editing of the CFTR-locus for treatment of cystic fibrosis. J Cyst Fibros 2022; 21:164-171. [PMID: 34049825 PMCID: PMC8613331 DOI: 10.1016/j.jcf.2021.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/31/2021] [Accepted: 04/19/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND Mechanisms governing the diversity of CFTR gene expression throughout the body are complex. Multiple intronic and distal regulatory elements are responsible for regulating differential CFTR expression across tissues. METHODS Drawing on published data, 18 high-priority genomic regions were identified and interrogated for CFTR-enhancer function using CRISPR/dCas9-based epigenome editing tools. Each region was evaluated by dCas9p300 and dCas9KRAB for its ability to enhance or repress CFTR expression, respectively. RESULTS Multiple genomic regions were tested for enhancer activity using CRISPR/dCas9 epigenome editing. dCas9p300 mediates a significant increase in CFTR mRNA levels when targeted to the promoter and a region 44 kb upstream of the transcriptional start site in a CFTR-low expressing cell line. Multiple gRNAs targeting the promoter induced a robust increase in CFTR protein levels. In contrast, dCas9KRAB-mediated repression is much more robust with 10 of the 18 evaluated genomic regions inducing CFTR protein knockdown. To evaluate the therapeutic efficacy of modulating CFTR gene regulation, dCas9p300 was used to induce elevated levels of CFTR from the endogenous locus in ΔF508/ΔF508 human bronchial epithelial cells. Ussing chamber studies demonstrated a synergistic increase in ion transport in response to CRISPR-induced expression of ΔF508 CFTR mRNA along with VX809 treatment. CONCLUSIONS CRISPR/dCas9-based epigenome-editing provides a previously unexplored tool for interrogating CFTR enhancer function. Here, we demonstrate that therapeutic interventions that increase the expression of CFTR may improve the efficacy of CFTR modulators. A better understanding CFTR regulatory mechanisms could uncover novel therapeutic interventions for the development of cystic fibrosis therapies.
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Affiliation(s)
- Ami M Kabadi
- Element Genomics, a UCB Pharma company, Durham, NC, USA.
| | - Leah Machlin
- Element Genomics, a UCB Pharma company, Durham, NC, USA
| | - Nikita Dalal
- Element Genomics, a UCB Pharma company, Durham, NC, USA
| | - Rhianna E Lee
- Marsico Lung Institute, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ian McDowell
- Element Genomics, a UCB Pharma company, Durham, NC, USA
| | - Nirav N Shah
- Element Genomics, a UCB Pharma company, Durham, NC, USA
| | | | - Scott H Randell
- Marsico Lung Institute, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Timothy E Reddy
- Element Genomics, a UCB Pharma company, Durham, NC, USA; Department of Biostatistics and Bioinformatics, Duke University Medical School, Durham, NC, USA.
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10
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Farinha CM, Gentzsch M. Revisiting CFTR Interactions: Old Partners and New Players. Int J Mol Sci 2021; 22:13196. [PMID: 34947992 PMCID: PMC8703571 DOI: 10.3390/ijms222413196] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 01/07/2023] Open
Abstract
Remarkable progress in CFTR research has led to the therapeutic development of modulators that rescue the basic defect in cystic fibrosis. There is continuous interest in studying CFTR molecular disease mechanisms as not all cystic fibrosis patients have a therapeutic option available. Addressing the basis of the problem by comprehensively understanding the critical molecular associations of CFTR interactions remains key. With the availability of CFTR modulators, there is interest in comprehending which interactions are critical to rescue CFTR and which are altered by modulators or CFTR mutations. Here, the current knowledge on interactions that govern CFTR folding, processing, and stability is summarized. Furthermore, we describe protein complexes and signal pathways that modulate the CFTR function. Primary epithelial cells display a spatial control of the CFTR interactions and have become a common system for preclinical and personalized medicine studies. Strikingly, the novel roles of CFTR in development and differentiation have been recently uncovered and it has been revealed that specific CFTR gene interactions also play an important role in transcriptional regulation. For a comprehensive understanding of the molecular environment of CFTR, it is important to consider CFTR mutation-dependent interactions as well as factors affecting the CFTR interactome on the cell type, tissue-specific, and transcriptional levels.
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Affiliation(s)
- Carlos M. Farinha
- BioISI—Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
| | - Martina Gentzsch
- Marsico Lung Institute and Cystic Fibrosis Research Center, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Pediatrics, Division of Pediatric Pulmonology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Cell Biology and Physiology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
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11
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BACH1, the master regulator of oxidative stress, has a dual effect on CFTR expression. Biochem J 2021; 478:3741-3756. [PMID: 34605540 PMCID: PMC8589331 DOI: 10.1042/bcj20210252] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 02/07/2023]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) gene lies within a topologically associated domain (TAD) in which multiple cis-regulatory elements (CREs) and transcription factors (TFs) regulate its cell-specific expression. The CREs are recruited to the gene promoter by a looping mechanism that depends upon both architectural proteins and specific TFs. An siRNA screen to identify TFs coordinating CFTR expression in airway epithelial cells suggested an activating role for BTB domain and CNC homolog 1 (BACH1). BACH1 is a ubiquitous master regulator of the cellular response to oxidative stress. Here, we show that BACH1 may have a dual effect on CFTR expression by direct occupancy of CREs at physiological oxygen (∼8%), while indirectly modulating expression under conditions of oxidative stress. Hence BACH1, can activate or repress the same gene, to fine tune expression in response to environmental cues such as cell stress. Furthermore, our 4C-seq data suggest that BACH1 can also directly regulate CFTR gene expression by modulating locus architecture through occupancy at known enhancers and structural elements, and depletion of BACH1 alters the higher order chromatin structure.
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12
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Kerschner JL, Paranjapye A, NandyMazumdar M, Yin S, Leir SH, Harris A. OTX2 regulates CFTR expression during endoderm differentiation and occupies 3' cis-regulatory elements. Dev Dyn 2021; 250:684-700. [PMID: 33386644 PMCID: PMC11227118 DOI: 10.1002/dvdy.293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/29/2020] [Accepted: 12/29/2020] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Cell-specific and developmental mechanisms contribute to expression of the cystic fibrosis transmembrane conductance regulator (CFTR) gene; however, its developmental regulation is poorly understood. Here we use human induced pluripotent stem cells differentiated into pseudostratified airway epithelial cells to study these mechanisms. RESULTS Changes in gene expression and open chromatin profiles were investigated by RNA-seq and ATAC-seq, and revealed that alterations in CFTR expression are associated with differences in stage-specific open chromatin. Additionally, two novel open chromatin regions, at +19.6 kb and +22.6 kb 3' to the CFTR translational stop signal, were observed in definitive endoderm (DE) cells, prior to an increase in CFTR expression in anterior foregut endoderm (AFE) cells. Chromatin studies in DE and AFE cells revealed enrichment of active enhancer marks and occupancy of OTX2 at these sites in DE cells. Loss of OTX2 in DE cells alters histone modifications across the CFTR locus and results in a 2.5-fold to 5-fold increase in CFTR expression. However, deletion of the +22.6 kb site alone does not affect CFTR expression in DE or AFE cells. CONCLUSIONS These results suggest that a network of interacting cis-regulatory elements recruit OTX2 to the locus to impact CFTR expression during early endoderm differentiation.
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Affiliation(s)
- Jenny L Kerschner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Monali NandyMazumdar
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Shiyi Yin
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Shih-Hsing Leir
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
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13
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NandyMazumdar M, Yin S, Paranjapye A, Kerschner JL, Swahn H, Ge A, Leir SH, Harris A. Looping of upstream cis-regulatory elements is required for CFTR expression in human airway epithelial cells. Nucleic Acids Res 2020; 48:3513-3524. [PMID: 32095812 PMCID: PMC7144911 DOI: 10.1093/nar/gkaa089] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 01/14/2020] [Accepted: 02/03/2020] [Indexed: 12/14/2022] Open
Abstract
The CFTR gene lies within an invariant topologically associated domain (TAD) demarcated by CTCF and cohesin, but shows cell-type specific control mechanisms utilizing different cis-regulatory elements (CRE) within the TAD. Within the respiratory epithelium, more than one cell type expresses CFTR and the molecular mechanisms controlling its transcription are likely divergent between them. Here, we determine how two extragenic CREs that are prominent in epithelial cells in the lung, regulate expression of the gene. We showed earlier that these CREs, located at -44 and -35 kb upstream of the promoter, have strong cell-type-selective enhancer function. They are also responsive to inflammatory mediators and to oxidative stress, consistent with a key role in CF lung disease. Here, we use CRISPR/Cas9 technology to remove these CREs from the endogenous locus in human bronchial epithelial cells. Loss of either site extinguished CFTR expression and abolished long-range interactions between these sites and the gene promoter, suggesting non-redundant enhancers. The deletions also greatly reduced promoter interactions with the 5' TAD boundary. We show substantial recruitment of RNAPII to the -35 kb element and identify CEBPβ as a key activator of airway expression of CFTR, likely through occupancy at this CRE and the gene promoter.
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Affiliation(s)
- Monali NandyMazumdar
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44116, USA
| | - Shiyi Yin
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44116, USA
| | - Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44116, USA
| | - Jenny L Kerschner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44116, USA
| | - Hannah Swahn
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44116, USA
| | - Alex Ge
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44116, USA
| | - Shih-Hsing Leir
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44116, USA
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44116, USA
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14
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Paranjapye A, Ruffin M, Harris A, Corvol H. Genetic variation in CFTR and modifier loci may modulate cystic fibrosis disease severity. J Cyst Fibros 2020; 19 Suppl 1:S10-S14. [PMID: 31734115 PMCID: PMC7036019 DOI: 10.1016/j.jcf.2019.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/04/2019] [Accepted: 11/07/2019] [Indexed: 12/11/2022]
Abstract
In patients with cystic fibrosis (CF), genetic variants within and outside the CFTR locus contribute to the variability of the disease severity. CFTR transcription is tightly regulated by cis-regulatory elements (CREs) that control the three-dimensional structure of the locus, chromatin accessibility and transcription factor recruitment. Variants within these CREs may contribute to the pathophysiology and to the phenotypic heterogeneity by altering CFTR transcript abundance. In addition to the CREs, variants outside the CFTR locus, namely "modifiers genes", may also be associated with the clinical variability. This review addresses variants at the CFTR locus itself and CFTR CREs, together with the outcomes of the latest modifier gene studies with respect to the different CF phenotypes.
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Affiliation(s)
- Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University Medical School, 10900 Euclid Avenue, Cleveland, OH, USA
| | - Manon Ruffin
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University Medical School, 10900 Euclid Avenue, Cleveland, OH, USA.
| | - Harriet Corvol
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Paris, France; AP-HP, Hôpital Trousseau, Service de Pneumologie Pédiatrique, Paris, France.
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15
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Gawenis LR, Hodges CA, McHugh DR, Valerio DM, Miron A, Cotton CU, Liu J, Walker NM, Strubberg AM, Gillen AE, Mutolo MJ, Kotzamanis G, Bosch J, Harris A, Drumm ML, Clarke LL. A BAC Transgene Expressing Human CFTR under Control of Its Regulatory Elements Rescues Cftr Knockout Mice. Sci Rep 2019; 9:11828. [PMID: 31413336 PMCID: PMC6694137 DOI: 10.1038/s41598-019-48105-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/30/2019] [Indexed: 01/25/2023] Open
Abstract
Small-molecule modulators of cystic fibrosis transmembrane conductance regulator (CFTR) biology show promise in the treatment of cystic fibrosis (CF). A Cftr knockout (Cftr KO) mouse expressing mutants of human CFTR would advance in vivo testing of new modulators. A bacterial artificial chromosome (BAC) carrying the complete hCFTR gene including regulatory elements within 40.1 kb of DNA 5' and 25 kb of DNA 3' to the gene was used to generate founder mice expressing hCFTR. Whole genome sequencing indicated a single integration site on mouse chromosome 8 (8qB2) with ~6 gene copies. hCFTR+ offspring were bred to murine Cftr KO mice, producing hCFTR+/mCftr- (H+/m-) mice, which had normal survival, growth and goblet cell function as compared to wild-type (WT) mice. Expression studies showed hCFTR protein and transcripts in tissues typically expressing mCftr. Functionally, nasal potential difference and large intestinal short-circuit (Isc) responses to cAMP stimulation were similar in magnitude to WT mice, whereas small intestinal cAMP ΔIsc responses were reduced. A BAC transgenic mouse with functional hCFTR under control of its regulatory elements has been developed to enable the generation of mouse models of hCFTR mutations by gene editing for in vivo testing of new CF therapies.
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Affiliation(s)
- Lara R Gawenis
- Dalton Cardiovascular Research Center, University of Missouri, 134 Research Park Dr, Columbia, Missouri, 65211-3300, USA
- Department of Biomedical Sciences, University of Missouri, E102 Veterinary Medicine Bldg., Columbia, Missouri, 65211, USA
| | - Craig A Hodges
- Departments of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Departments of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Daniel R McHugh
- Departments of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Dana M Valerio
- Departments of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Alexander Miron
- Departments of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Calvin U Cotton
- Departments of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Departments of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Jinghua Liu
- Dalton Cardiovascular Research Center, University of Missouri, 134 Research Park Dr, Columbia, Missouri, 65211-3300, USA
| | - Nancy M Walker
- Dalton Cardiovascular Research Center, University of Missouri, 134 Research Park Dr, Columbia, Missouri, 65211-3300, USA
| | - Ashlee M Strubberg
- Dalton Cardiovascular Research Center, University of Missouri, 134 Research Park Dr, Columbia, Missouri, 65211-3300, USA
- Department of Biomedical Sciences, University of Missouri, E102 Veterinary Medicine Bldg., Columbia, Missouri, 65211, USA
| | - Austin E Gillen
- Human Molecular Genetics Program, Lurie Children's Research Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60614, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
| | - Michael J Mutolo
- Human Molecular Genetics Program, Lurie Children's Research Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60614, USA
| | - George Kotzamanis
- Department of Histology and Embryology, School of Medicine, University of Athens, Athens, Greece
| | - Jürgen Bosch
- Departments of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- InterRayBio, LLC, Baltimore, MD, USA
| | - Ann Harris
- Departments of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Mitchell L Drumm
- Departments of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Departments of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Lane L Clarke
- Dalton Cardiovascular Research Center, University of Missouri, 134 Research Park Dr, Columbia, Missouri, 65211-3300, USA.
- Department of Biomedical Sciences, University of Missouri, E102 Veterinary Medicine Bldg., Columbia, Missouri, 65211, USA.
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16
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Swahn H, Harris A. Cell-Selective Regulation of CFTR Gene Expression: Relevance to Gene Editing Therapeutics. Genes (Basel) 2019; 10:E235. [PMID: 30893953 PMCID: PMC6471542 DOI: 10.3390/genes10030235] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 02/26/2019] [Accepted: 02/27/2019] [Indexed: 12/19/2022] Open
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) gene is an attractive target for gene editing approaches, which may yield novel therapeutic approaches for genetic diseases such as cystic fibrosis (CF). However, for gene editing to be effective, aspects of the three-dimensional (3D) structure and cis-regulatory elements governing the dynamic expression of CFTR need to be considered. In this review, we focus on the higher order chromatin organization required for normal CFTR locus function, together with the complex mechanisms controlling expression of the gene in different cell types impaired by CF pathology. Across all cells, the CFTR locus is organized into an invariant topologically associated domain (TAD) established by the architectural proteins CCCTC-binding factor (CTCF) and cohesin complex. Additional insulator elements within the TAD also recruit these factors. Although the CFTR promoter is required for basal levels of expression, cis-regulatory elements (CREs) in intergenic and intronic regions are crucial for cell-specific and temporal coordination of CFTR transcription. These CREs are recruited to the promoter through chromatin looping mechanisms and enhance cell-type-specific expression. These features of the CFTR locus should be considered when designing gene-editing approaches, since failure to recognize their importance may disrupt gene expression and reduce the efficacy of therapies.
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Affiliation(s)
- Hannah Swahn
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44067, USA.
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44067, USA.
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17
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Kerschner JL, Ghosh S, Paranjapye A, Cosme WR, Audrézet MP, Nakakuki M, Ishiguro H, Férec C, Rommens J, Harris A. Screening for Regulatory Variants in 460 kb Encompassing the CFTR Locus in Cystic Fibrosis Patients. J Mol Diagn 2018; 21:70-80. [PMID: 30296588 DOI: 10.1016/j.jmoldx.2018.08.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/18/2018] [Accepted: 08/10/2018] [Indexed: 12/30/2022] Open
Abstract
It is estimated that up to 5% of cystic fibrosis transmembrane conductance regulator (CFTR) pathogenic alleles are unidentified. Some of these errors may lie in noncoding regions of the locus and affect gene expression. To identify regulatory element variants in the CFTR locus, SureSelect targeted enrichment of 460 kb encompassing the gene was optimized to deep sequence genomic DNA from 80 CF patients with an unequivocal clinical diagnosis but only one or no CFTR-coding region pathogenic variants. Bioinformatics tools were used to identify sequence variants and predict their impact, which were then assayed in transient reporter gene luciferase assays. The effect of five variants in the CFTR promoter and four in an intestinal enhancer of the gene were assayed in relevant cell lines. The initial analysis of sequence data revealed previously known CF-causing variants, validating the robustness of the SureSelect design, and showed that 85 of 160 CF alleles were undefined. Of a total 1737 variants revealed across the extended 460-kb CFTR locus, 51 map to known CFTR cis-regulatory elements, and many of these are predicted to alter transcription factor occupancy. Four promoter variants and all those in the intestinal enhancer significantly repress reporter gene activity. These data suggest that CFTR regulatory elements may harbor novel CF disease-causing variants that warrant further investigation, both for genetic screening protocols and functional assays.
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Affiliation(s)
- Jenny L Kerschner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Sujana Ghosh
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, Illinois; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Wilmel R Cosme
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | | | - Miyuki Nakakuki
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroshi Ishiguro
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | - Johanna Rommens
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio; Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, Illinois; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.
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18
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Strug LJ, Stephenson AL, Panjwani N, Harris A. Recent advances in developing therapeutics for cystic fibrosis. Hum Mol Genet 2018; 27:R173-R186. [PMID: 30060192 PMCID: PMC6061831 DOI: 10.1093/hmg/ddy188] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 05/07/2018] [Accepted: 05/10/2018] [Indexed: 12/23/2022] Open
Abstract
Despite hope that a cure was imminent when the causative gene was cloned nearly 30 years ago, cystic fibrosis (CF [MIM: 219700]) remains a life-shortening disease affecting more than 70 000 individuals worldwide. However, within the last 6 years the Food and Drug Administration's approval of Ivacaftor, the first drug that corrects the defective cystic fibrosis transmembrane conductance regulator protein [CFTR (MIM: 602421)] in patients with the G551D mutation, marks a watershed in the development of novel therapeutics for this devastating disease. Here we review recent progress in diverse research areas, which all focus on curing CF at the genetic, biochemical or physiological level. In the near future it seems probable that development of mutation-specific therapies will be the focus, since it is unlikely that any one approach will be efficient in correcting the more than 2000 disease-associated variants. We discuss the new drugs and combinations of drugs that either enhance delivery of misfolded CFTR protein to the cell membrane, where it functions as an ion channel, or that activate channel opening. Next we consider approaches to correct the causative genetic lesion at the DNA or RNA level, through repressing stop mutations and nonsense-mediated decay, modulating splice mutations, fixing errors by gene editing or using novel routes to gene replacement. Finally, we explore how modifier genes, loci elsewhere in the genome that modify CF disease severity, may be used to restore a normal phenotype. Progress in all of these areas has been dramatic, generating enthusiasm that CF may soon become a broadly treatable disease.
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Affiliation(s)
- Lisa J Strug
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anne L Stephenson
- Department of Respirology, Adult Cystic Fibrosis Program, St. Michael’s Hospital, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Naim Panjwani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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19
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A transcription factor network represses CFTR gene expression in airway epithelial cells. Biochem J 2018; 475:1323-1334. [PMID: 29572268 DOI: 10.1042/bcj20180044] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/19/2018] [Accepted: 03/22/2018] [Indexed: 02/06/2023]
Abstract
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause the inherited disorder cystic fibrosis (CF). Lung disease is the major cause of CF morbidity, though CFTR expression levels are substantially lower in the airway epithelium than in pancreatic duct and intestinal epithelia, which also show compromised function in CF. Recently developed small molecule therapeutics for CF are highly successful for one specific CFTR mutation and have a positive impact on others. However, the low abundance of CFTR transcripts in the airway limits the opportunity for drugs to correct the defective substrate. Elucidation of the transcriptional mechanisms for the CFTR locus has largely focused on intragenic and intergenic tissue-specific enhancers and their activating trans-factors. Here, we investigate whether the low CFTR levels in the airway epithelium result from the recruitment of repressive proteins directly to the locus. Using an siRNA screen to deplete ∼1500 transcription factors (TFs) and associated regulatory proteins in Calu-3 lung epithelial cells, we identified nearly 40 factors that upon depletion elevated CFTR mRNA levels more than 2-fold. A subset of these TFs was validated in primary human bronchial epithelial cells. Among the strongest repressors of airway expression of CFTR were Krüppel-like factor 5 and Ets homologous factor, both of which have pivotal roles in the airway epithelium. Depletion of these factors, which are both recruited to an airway-selective cis-regulatory element at -35 kb from the CFTR promoter, improved CFTR production and function, thus defining novel therapeutic targets for enhancement of CFTR.
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20
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Gillen AE, Yang R, Cotton CU, Perez A, Randell SH, Leir SH, Harris A. Molecular characterization of gene regulatory networks in primary human tracheal and bronchial epithelial cells. J Cyst Fibros 2018; 17:444-453. [PMID: 29459038 DOI: 10.1016/j.jcf.2018.01.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/26/2018] [Accepted: 01/27/2018] [Indexed: 10/18/2022]
Abstract
BACKGROUND Robust methods to culture primary airway epithelial cells were developed several decades ago and these cells provide the model of choice to investigate many diseases of the human lung. However, the molecular signature of cells from different regions of the airway epithelium has not been well characterized. METHODS We utilize DNase-seq and RNA-seq to examine the molecular signatures of primary cells derived from human tracheal and bronchial tissues, as well as healthy and diseased (cystic fibrosis (CF)) donor lung tissue. RESULTS Our data reveal an airway cell signature that is divergent from other epithelial cell types and from common airway epithelial cell lines. The differences between tracheal and bronchial cells are clearly evident as are common regulatory features. Only minor variation is seen between bronchial cells from healthy or CF donors. CONCLUSIONS These data are a valuable resource for functional genomics analysis of airway epithelial tissues in human disease.
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Affiliation(s)
- Austin E Gillen
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL, 60614, United States; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, United States
| | - Rui Yang
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL, 60614, United States; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, United States
| | - Calvin U Cotton
- Departments of Pediatrics, Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, United States
| | - Aura Perez
- Departments of Pediatrics, Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, United States
| | - Scott H Randell
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, United States
| | - Shih-Hsing Leir
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL, 60614, United States; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, United States; Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, United States
| | - Ann Harris
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL, 60614, United States; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, United States; Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, United States.
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21
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Yang R, Kerschner JL, Gosalia N, Neems D, Gorsic LK, Safi A, Crawford GE, Kosak ST, Leir SH, Harris A. Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus. Nucleic Acids Res 2016; 44:3082-94. [PMID: 26673704 PMCID: PMC4838340 DOI: 10.1093/nar/gkv1358] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 11/21/2015] [Accepted: 11/24/2015] [Indexed: 12/18/2022] Open
Abstract
Higher order chromatin structure establishes domains that organize the genome and coordinate gene expression. However, the molecular mechanisms controlling transcription of individual loci within a topological domain (TAD) are not fully understood. The cystic fibrosis transmembrane conductance regulator (CFTR) gene provides a paradigm for investigating these mechanisms.CFTR occupies a TAD bordered by CTCF/cohesin binding sites within which are cell-type-selective cis-regulatory elements for the locus. We showed previously that intronic and extragenic enhancers, when occupied by specific transcription factors, are recruited to the CFTR promoter by a looping mechanism to drive gene expression. Here we use a combination of CRISPR/Cas9 editing of cis-regulatory elements and siRNA-mediated depletion of architectural proteins to determine the relative contribution of structural elements and enhancers to the higher order structure and expression of the CFTR locus. We found the boundaries of the CFTRTAD are conserved among diverse cell types and are dependent on CTCF and cohesin complex. Removal of an upstream CTCF-binding insulator alters the interaction profile, but has little effect on CFTR expression. Within the TAD, intronic enhancers recruit cell-type selective transcription factors and deletion of a pivotal enhancer element dramatically decreases CFTR expression, but has minor effect on its 3D structure.
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Affiliation(s)
- Rui Yang
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jenny L Kerschner
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nehal Gosalia
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Daniel Neems
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Lidija K Gorsic
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Alexias Safi
- Division of Medical Genetics, Department of Pediatrics and Center for Genomic and Computational Biology, Duke University Medical School, Durham, NC 27708, USA
| | - Gregory E Crawford
- Division of Medical Genetics, Department of Pediatrics and Center for Genomic and Computational Biology, Duke University Medical School, Durham, NC 27708, USA
| | - Steven T Kosak
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Shih-Hsing Leir
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ann Harris
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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22
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Smith EM, Lajoie BR, Jain G, Dekker J. Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus. Am J Hum Genet 2016; 98:185-201. [PMID: 26748519 PMCID: PMC4716690 DOI: 10.1016/j.ajhg.2015.12.002] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 12/03/2015] [Indexed: 11/29/2022] Open
Abstract
Three-dimensional genome structure plays an important role in gene regulation. Globally, chromosomes are organized into active and inactive compartments while, at the gene level, looping interactions connect promoters to regulatory elements. Topologically associating domains (TADs), typically several hundred kilobases in size, form an intermediate level of organization. Major questions include how TADs are formed and how they are related to looping interactions between genes and regulatory elements. Here we performed a focused 5C analysis of a 2.8 Mb chromosome 7 region surrounding CFTR in a panel of cell types. We find that the same TAD boundaries are present in all cell types, indicating that TADs represent a universal chromosome architecture. Furthermore, we find that these TAD boundaries are present irrespective of the expression and looping of genes located between them. In contrast, looping interactions between promoters and regulatory elements are cell-type specific and occur mostly within TADs. This is exemplified by the CFTR promoter that in different cell types interacts with distinct sets of distal cell-type-specific regulatory elements that are all located within the same TAD. Finally, we find that long-range associations between loci located in different TADs are also detected, but these display much lower interaction frequencies than looping interactions within TADs. Interestingly, interactions between TADs are also highly cell-type-specific and often involve loci clustered around TAD boundaries. These data point to key roles of invariant TAD boundaries in constraining as well as mediating cell-type-specific long-range interactions and gene regulation.
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Affiliation(s)
- Emily M Smith
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605-0103, USA
| | - Bryan R Lajoie
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605-0103, USA
| | - Gaurav Jain
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605-0103, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605-0103, USA; Howard Hughes Medical Institute.
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23
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Chromatin Dynamics in the Regulation of CFTR Expression. Genes (Basel) 2015; 6:543-58. [PMID: 26184320 PMCID: PMC4584316 DOI: 10.3390/genes6030543] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/03/2015] [Accepted: 07/07/2015] [Indexed: 12/31/2022] Open
Abstract
The contribution of chromatin dynamics to the regulation of human disease-associated loci such as the cystic fibrosis transmembrane conductance regulator (CFTR) gene has been the focus of intensive experimentation for many years. Recent technological advances in the analysis of transcriptional mechanisms across the entire human genome have greatly facilitated these studies. In this review we describe the complex machinery of tissue-specific regulation of CFTR expression, and put earlier observations in context by incorporating them into datasets generated by the most recent genomics methods. Though the gene promoter is required for CFTR expression, cell-type specific regulatory elements are located elsewhere in the gene and in flanking intergenic regions. Probably within its own topological domain established by the architectural proteins CTCF and cohesin, the CFTR locus utilizes chromatin dynamics to remodel nucleosomes, recruit cell-selective transcription factors, and activate intronic enhancers. These cis-acting elements are then brought to the gene promoter by chromatin looping mechanisms, which establish long-range interactions across the locus. Despite its complexity, the CFTR locus provides a paradigm for elucidating the critical role of chromatin dynamics in the transcription of individual human genes.
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24
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Zhang Z, Leir SH, Harris A. Oxidative stress regulates CFTR gene expression in human airway epithelial cells through a distal antioxidant response element. Am J Respir Cell Mol Biol 2015; 52:387-96. [PMID: 25259561 DOI: 10.1165/rcmb.2014-0263oc] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Cystic fibrosis transmembrane conductance regulator gene (CFTR) expression in human airway epithelial cells involves the recruitment of distal cis-regulatory elements, which are associated with airway-selective DNase hypersensitive sites at -44 kb and -35 kb from the gene. The -35-kb site encompasses an enhancer that is regulated by the immune mediators interferon regulatory factor 1 and 2 and by nuclear factor Y. Here we investigate the -44-kb element, which also has enhancer activity in vitro in airway epithelial cells but is inactive in intestinal epithelial cells. This site contains an antioxidant response element (ARE) that plays a critical role in its function in airway cell lines and primary human bronchial epithelial cells. The natural antioxidant sulforaphane (SFN) induces nuclear translocation of nuclear factor, erythroid 2-like 2 (Nrf2), a transcription factor that regulates genes with AREs in their promoters, many of which are involved in response to injury. Under normal conditions, the -44-kb ARE is occupied by the repressor BTB and CNC homology 1, basic leucine zipper transcription factor (Bach1), and v-Maf avian musculoaponeurotic fibrosarcoma oncogene homolog K (MafK) heterodimers. After 2 hours of SFN treatment, Nrf2 displaces these repressive factors and activates CFTR expression. Site-directed mutagenesis shows that both the ARE and an adjacent NF-κB binding site are required for activation of the -44-kb element in airway epithelial cells. Moreover, this element is functionally linked to the -35-kb enhancer in modulating CFTR expression in response to environmental stresses in the airway.
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Affiliation(s)
- Zhaolin Zhang
- Human Molecular Genetics Program, Lurie Children's Research Center, and Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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25
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Viart V, Bergougnoux A, Bonini J, Varilh J, Chiron R, Tabary O, Molinari N, Claustres M, Taulan-Cadars M. Transcription factors and miRNAs that regulate fetal to adult CFTR expression change are new targets for cystic fibrosis. Eur Respir J 2014; 45:116-28. [PMID: 25186262 DOI: 10.1183/09031936.00113214] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The CFTR gene displays a tightly regulated tissue-specific and temporal expression. Mutations in this gene cause cystic fibrosis (CF). In this study we wanted to identify trans-regulatory elements responsible for CFTR differential expression in fetal and adult lung, and to determine the importance of inhibitory motifs in the CFTR-3'UTR with the aim of developing new tools for the correction of disease-causing mutations within CFTR. We show that lung development-specific transcription factors (FOXA, C/EBP) and microRNAs (miR-101, miR-145, miR-384) regulate the switch from strong fetal to very low CFTR expression after birth. By using miRNome profiling and gene reporter assays, we found that miR-101 and miR-145 are specifically upregulated in adult lung and that miR-101 directly acts on its cognate site in the CFTR-3'UTR in combination with an overlapping AU-rich element. We then designed miRNA-binding blocker oligonucleotides (MBBOs) to prevent binding of several miRNAs to the CFTR-3'UTR and tested them in primary human nasal epithelial cells from healthy individuals and CF patients carrying the p.Phe508del CFTR mutation. These MBBOs rescued CFTR channel activity by increasing CFTR mRNA and protein levels. Our data offer new understanding of the control of the CFTR gene regulation and new putative correctors for cystic fibrosis.
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Affiliation(s)
- Victoria Viart
- INSERM U827, Laboratoire de Génétique de Maladies Rares, Montpellier, France Université Montpellier I, UFR de Médecine, Montpellier, France Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - Anne Bergougnoux
- INSERM U827, Laboratoire de Génétique de Maladies Rares, Montpellier, France Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - Jennifer Bonini
- INSERM U827, Laboratoire de Génétique de Maladies Rares, Montpellier, France Université Montpellier I, UFR de Médecine, Montpellier, France
| | - Jessica Varilh
- INSERM U827, Laboratoire de Génétique de Maladies Rares, Montpellier, France Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - Raphaël Chiron
- Centre de Ressources et de Compétences de la Mucoviscidose (CRCM), CHU Montpellier, Montpellier, France
| | - Olivier Tabary
- CDR St Antoine, INSERM UMR-S 938, Paris, France UPMC Université Paris 06, Paris, France
| | - Nicolas Molinari
- Département d'Information Médicale, CHU Montpellier, Montpellier, France UMR 729 MISTEA, Université Montpellier I, Montpellier, France
| | - Mireille Claustres
- INSERM U827, Laboratoire de Génétique de Maladies Rares, Montpellier, France Université Montpellier I, UFR de Médecine, Montpellier, France Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - Magali Taulan-Cadars
- INSERM U827, Laboratoire de Génétique de Maladies Rares, Montpellier, France Université Montpellier I, UFR de Médecine, Montpellier, France
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Gosalia N, Neems D, Kerschner JL, Kosak ST, Harris A. Architectural proteins CTCF and cohesin have distinct roles in modulating the higher order structure and expression of the CFTR locus. Nucleic Acids Res 2014; 42:9612-22. [PMID: 25081205 PMCID: PMC4150766 DOI: 10.1093/nar/gku648] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 07/02/2014] [Accepted: 07/03/2014] [Indexed: 01/02/2023] Open
Abstract
Higher order chromatin structures across the genome are maintained in part by the architectural proteins CCCTC binding factor (CTCF) and the cohesin complex, which co-localize at many sites across the genome. Here, we examine the role of these proteins in mediating chromatin structure at the cystic fibrosis transmembrane conductance regulator (CFTR) gene. CFTR encompasses nearly 200 kb flanked by CTCF-binding enhancer-blocking insulator elements and is regulated by cell-type-specific intronic enhancers, which loop to the promoter in the active locus. SiRNA-mediated depletion of CTCF or the cohesin component, RAD21, showed that these two factors have distinct roles in regulating the higher order organization of CFTR. CTCF mediates the interactions between CTCF/cohesin binding sites, some of which have enhancer-blocking insulator activity. Cohesin shares this tethering role, but in addition stabilizes interactions between the promoter and cis-acting intronic elements including enhancers, which are also dependent on the forkhead box A1/A2 (FOXA1/A2) transcription factors (TFs). Disruption of the three-dimensional structure of the CFTR gene by depletion of CTCF or RAD21 increases gene expression, which is accompanied by alterations in histone modifications and TF occupancy across the locus, and causes internalization of the gene from the nuclear periphery.
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Affiliation(s)
- Nehal Gosalia
- Human Molecular Genetics Program, Lurie Children's Research Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Daniel Neems
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60614, USA
| | - Jenny L Kerschner
- Human Molecular Genetics Program, Lurie Children's Research Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Steven T Kosak
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60614, USA
| | - Ann Harris
- Human Molecular Genetics Program, Lurie Children's Research Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
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27
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Bergougnoux A, Rivals I, Liquori A, Raynal C, Varilh J, Magalhães M, Perez MJ, Bigi N, Des Georges M, Chiron R, Squalli-Houssaini AS, Claustres M, De Sario A. A balance between activating and repressive histone modifications regulates cystic fibrosis transmembrane conductance regulator (CFTR) expression in vivo. Epigenetics 2014; 9:1007-17. [PMID: 24782114 DOI: 10.4161/epi.28967] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The genetic mechanisms that regulate CFTR, the gene responsible for cystic fibrosis, have been widely investigated in cultured cells. However, mechanisms responsible for tissue-specific and time-specific expression are not completely elucidated in vivo. Through the survey of public databases, we found that the promoter of CFTR was associated with bivalent chromatin in human embryonic stem (ES) cells. In this work, we analyzed fetal (at different stages of pregnancy) and adult tissues and showed that, in digestive and lung tissues, which expressed CFTR, H3K4me3 was maintained in the promoter. Histone acetylation was high in the promoter and in two intronic enhancers, especially in fetal tissues. In contrast, in blood cells, which did not express CFTR, the bivalent chromatin was resolved (the promoter was labeled by the silencing mark H3K27me3). Cis-regulatory sequences were associated with lowly acetylated histones. We also provide evidence that the tissue-specific expression of CFTR is not regulated by dynamic changes of DNA methylation in the promoter. Overall, this work shows that a balance between activating and repressive histone modifications in the promoter and intronic enhancers results in the fine regulation of CFTR expression during development, thereby ensuring tissue specificity.
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Affiliation(s)
- Anne Bergougnoux
- INSERM U827; Montpellier, France; Université Montpellier 1; Montpellier, France; CHU Montpellier; Montpellier, France
| | - Isabelle Rivals
- Equipe de Statistique Appliquée; ESPCI ParisTech; Paris, France
| | - Alessandro Liquori
- INSERM U827; Montpellier, France; Université Montpellier 1; Montpellier, France
| | - Caroline Raynal
- INSERM U827; Montpellier, France; Université Montpellier 1; Montpellier, France; CHU Montpellier; Montpellier, France
| | - Jessica Varilh
- INSERM U827; Montpellier, France; Université Montpellier 1; Montpellier, France; CHU Montpellier; Montpellier, France
| | - Milena Magalhães
- INSERM U827; Montpellier, France; Université Montpellier 1; Montpellier, France
| | | | | | - Marie Des Georges
- INSERM U827; Montpellier, France; Université Montpellier 1; Montpellier, France; CHU Montpellier; Montpellier, France
| | | | | | - Mireille Claustres
- INSERM U827; Montpellier, France; Université Montpellier 1; Montpellier, France; CHU Montpellier; Montpellier, France
| | - Albertina De Sario
- INSERM U827; Montpellier, France; Université Montpellier 1; Montpellier, France
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Kerschner JL, Gosalia N, Leir SH, Harris A. Chromatin remodeling mediated by the FOXA1/A2 transcription factors activates CFTR expression in intestinal epithelial cells. Epigenetics 2014; 9:557-65. [PMID: 24440874 DOI: 10.4161/epi.27696] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The forkhead box A transcription factors, FOXA1 and FOXA2, function as pioneer factors to open condensed chromatin and facilitate binding of other proteins. We showed previously that these factors are key components of a transcriptional network that drives enhancer function at the cystic fibrosis transmembrane conductance regulator (CFTR) locus in intestinal epithelial cells. The CFTR promoter apparently lacks tissue-specific regulatory elements and expression of the gene is controlled by multiple cis-acting elements, which coordinate gene expression in different cell types. Here we show that concurrent depletion of FOXA1 and FOXA2 represses CFTR expression and alters the three-dimensional architecture of the active locus by diminishing interactions between the promoter and intronic cis-acting elements. Reduction of FOXA1/A2 also modifies the enrichment profile of the active enhancer marks H3K27ac and H3K4me2 across the CFTR locus and alters chromatin accessibility at individual cis-elements. Moreover, loss of FOXA1/A2 suppresses the recruitment of other members of the transcriptional network including HNF1 and CDX2, to multiple cis-elements. These data reveal a complex molecular mechanism underlying the role of FOXA1/A2 in achieving high levels of CFTR expression in intestinal epithelial cells.
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Affiliation(s)
- Jenny L Kerschner
- Human Molecular Genetics Program; Lurie Children's Research Center; Chicago, IL USA; Department of Pediatrics; Northwestern University Feinberg School of Medicine; Chicago, IL USA
| | - Nehal Gosalia
- Human Molecular Genetics Program; Lurie Children's Research Center; Chicago, IL USA; Department of Pediatrics; Northwestern University Feinberg School of Medicine; Chicago, IL USA
| | - Shih-Hsing Leir
- Human Molecular Genetics Program; Lurie Children's Research Center; Chicago, IL USA; Department of Pediatrics; Northwestern University Feinberg School of Medicine; Chicago, IL USA
| | - Ann Harris
- Human Molecular Genetics Program; Lurie Children's Research Center; Chicago, IL USA; Department of Pediatrics; Northwestern University Feinberg School of Medicine; Chicago, IL USA
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29
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Bischof JM, Gillen AE, Song L, Gosalia N, London D, Furey TS, Crawford GE, Harris A. A genome-wide analysis of open chromatin in human epididymis epithelial cells reveals candidate regulatory elements for genes coordinating epididymal function. Biol Reprod 2013; 89:104. [PMID: 24006278 DOI: 10.1095/biolreprod.113.110403] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The epithelium lining the epididymis has a pivotal role in ensuring a luminal environment that can support normal sperm maturation. Many of the individual genes that encode proteins involved in establishing the epididymal luminal fluid are well characterized. They include ion channels, ion exchangers, transporters, and solute carriers. However, the molecular mechanisms that coordinate expression of these genes and modulate their activities in response to biological stimuli are less well understood. To identify cis-regulatory elements for genes expressed in human epididymis epithelial cells, we generated genome-wide maps of open chromatin by DNase-seq. This analysis identified 33,542 epididymis-selective DNase I hypersensitive sites (DHS), which were not evident in five cell types of different lineages. Identification of genes with epididymis-selective DHS at their promoters revealed gene pathways that are active in immature epididymis epithelial cells. These include processes correlating with epithelial function and also others with specific roles in the epididymis, including retinol metabolism and ascorbate and aldarate metabolism. Peaks of epididymis-selective chromatin were seen in the androgen receptor gene and the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which has a critical role in regulating ion transport across the epididymis epithelium. In silico prediction of transcription factor binding sites that were overrepresented in epididymis-selective DHS identified epithelial transcription factors, including ELF5 and ELF3, the androgen receptor, Pax2, and Sox9, as components of epididymis transcriptional networks. Active genes, which are targets of each transcription factor, reveal important biological processes in the epididymis epithelium.
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Affiliation(s)
- Jared M Bischof
- Human Molecular Genetics Program, Lurie Children's Research Center, and Department of Pediatrics, Northwestern University Feinberg School of Medicine Chicago, Illinois
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