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A Kaleidoscope of Keratin Gene Expression and the Mosaic of Its Regulatory Mechanisms. Int J Mol Sci 2023; 24:ijms24065603. [PMID: 36982676 PMCID: PMC10052683 DOI: 10.3390/ijms24065603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Keratins are a family of intermediate filament-forming proteins highly specific to epithelial cells. A combination of expressed keratin genes is a defining property of the epithelium belonging to a certain type, organ/tissue, cell differentiation potential, and at normal or pathological conditions. In a variety of processes such as differentiation and maturation, as well as during acute or chronic injury and malignant transformation, keratin expression undergoes switching: an initial keratin profile changes accordingly to changed cell functions and location within a tissue as well as other parameters of cellular phenotype and physiology. Tight control of keratin expression implies the presence of complex regulatory landscapes within the keratin gene loci. Here, we highlight patterns of keratin expression in different biological conditions and summarize disparate data on mechanisms controlling keratin expression at the level of genomic regulatory elements, transcription factors (TFs), and chromatin spatial structure.
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2
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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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3
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Impact of KLF4 on Cell Proliferation and Epithelial Differentiation in the Context of Cystic Fibrosis. Int J Mol Sci 2020; 21:ijms21186717. [PMID: 32937756 PMCID: PMC7555189 DOI: 10.3390/ijms21186717] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 12/13/2022] Open
Abstract
Cystic fibrosis (CF) cells display a more cancer-like phenotype vs. non-CF cells. KLF4 overexpression has been described in CF and this transcriptional factor acts as a negative regulator of wt-CFTR. KLF4 is described as exerting its effects in a cell-context-dependent fashion, but it is generally considered a major regulator of proliferation, differentiation, and wound healing, all the processes that are also altered in CF. Therefore, it is relevant to characterize the differential role of KLF4 in these processes in CF vs. non-CF cells. To this end, we used wt- and F508del-CFTR CFBE cells and their respective KLF4 knockout (KO) counterparts to evaluate processes like cell proliferation, polarization, and wound healing, as well as to compare the expression of several epithelial differentiation markers. Our data indicate no major impact of KLF4 KO in proliferation and a differential impact of KLF4 KO in transepithelial electrical resistance (TEER) acquisition and wound healing in wt- vs. F508del-CFTR cells. In parallel, we also observed a differential impact on the levels of some differentiation markers and epithelial-mesencymal transition (EMT)-associated transcription factors. In conclusion, KLF4 impacts TEER acquisition, wound healing, and the expression of differentiation markers in a way that is partially dependent on the CFTR-status of the cell.
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Sousa L, Pankonien I, Clarke LA, Silva I, Kunzelmann K, Amaral MD. KLF4 Acts as a wt-CFTR Suppressor through an AKT-Mediated Pathway. Cells 2020; 9:cells9071607. [PMID: 32630830 PMCID: PMC7408019 DOI: 10.3390/cells9071607] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 06/24/2020] [Accepted: 06/30/2020] [Indexed: 02/06/2023] Open
Abstract
Cystic Fibrosis (CF) is caused by >2000 mutations in the CF transmembrane conductance regulator (CFTR) gene, but one mutation-F508del-occurs in ~80% of patients worldwide. Besides its main function as an anion channel, the CFTR protein has been implicated in epithelial differentiation, tissue regeneration, and, when dysfunctional, cancer. However, the mechanisms that regulate such relationships are not fully elucidated. Krüppel-like factors (KLFs) are a family of transcription factors (TFs) playing central roles in development, stem cell differentiation, and proliferation. Herein, we hypothesized that these TFs might have an impact on CFTR expression and function, being its missing link to differentiation. Our results indicate that KLF4 (but not KLF2 nor KLF5) is upregulated in CF vs. non-CF cells and that it negatively regulates wt-CFTR expression and function. Of note, F508del-CFTR expressing cells are insensitive to KLF4 modulation. Next, we investigated which KLF4-related pathways have an effect on CFTR. Our data also show that KLF4 modulates wt-CFTR (but not F508del-CFTR) via both the serine/threonine kinase AKT1 (AKT) and glycogen synthase kinase 3 beta (GSK3β) signaling. While AKT acts positively, GSK3β is a negative regulator of CFTR. This crosstalk between wt-CFTR and KLF4 via AKT/ GSK3β signaling, which is disrupted in CF, constitutes a novel mechanism linking CFTR to the epithelial differentiation.
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Affiliation(s)
- Luis Sousa
- BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal; (L.S.); (I.P.); (L.A.C.); (I.S.)
| | - Ines Pankonien
- BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal; (L.S.); (I.P.); (L.A.C.); (I.S.)
| | - Luka A Clarke
- BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal; (L.S.); (I.P.); (L.A.C.); (I.S.)
| | - Iris Silva
- BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal; (L.S.); (I.P.); (L.A.C.); (I.S.)
| | - Karl Kunzelmann
- Department of Physiology, University of Regensburg, 93053 Regensburg, Germany;
| | - Margarida D Amaral
- BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal; (L.S.); (I.P.); (L.A.C.); (I.S.)
- Correspondence: ; Tel.: +351-21-750-08-61; Fax: +351-21-750-00-88
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5
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Yin S, Ray G, Kerschner JL, Hao S, Perez A, Drumm ML, Browne JA, Leir SH, Longworth M, Harris A. Functional genomics analysis of human colon organoids identifies key transcription factors. Physiol Genomics 2020; 52:234-244. [PMID: 32390556 DOI: 10.1152/physiolgenomics.00113.2019] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Organoids are a valuable three-dimensional (3D) model to study the differentiated functions of the human intestinal epithelium. They are a particularly powerful tool to measure epithelial transport processes in health and disease. Though biological assays such as organoid swelling and intraluminal pH measurements are well established, their underlying functional genomics are not well characterized. Here we combine genome-wide analysis of open chromatin by ATAC-Seq with transcriptome mapping by RNA-Seq to define the genomic signature of human intestinal organoids (HIOs). These data provide an important tool for investigating key physiological and biochemical processes in the intestinal epithelium. We next compared the transcriptome and open chromatin profiles of HIOs with equivalent data sets from the Caco2 colorectal carcinoma line, which is an important two-dimensional (2D) model of the intestinal epithelium. Our results define common features of the intestinal epithelium in HIO and Caco2 and further illustrate the cancer-associated program of the cell line. Generation of Caco2 cysts enabled interrogation of the molecular divergence of the 2D and 3D cultures. Overrepresented motif analysis of open chromatin peaks identified caudal type homeobox 2 (CDX2) as a key activating transcription factor in HIO, but not in monolayer cultures of Caco2. However, the CDX2 motif becomes overrepresented in open chromatin from Caco2 cysts, reinforcing the importance of this factor in intestinal epithelial differentiation and function. Intersection of the HIO and Caco2 transcriptomes further showed functional overlap in pathways of ion transport and tight junction integrity, among others. These data contribute to understanding human intestinal organoid biology.
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Affiliation(s)
- Shiyi Yin
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland Ohio
| | - Greeshma Ray
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland Ohio
| | - Jenny L Kerschner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland Ohio
| | - Shuyu Hao
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland Ohio
| | - Aura Perez
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland Ohio
| | - Mitchell L Drumm
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland Ohio
| | - James A Browne
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland Ohio
| | - Shih-Hsing Leir
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland Ohio
| | - Michelle Longworth
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland Ohio
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland Ohio
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6
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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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7
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Swahn H, Sabith Ebron J, Lamar K, Yin S, Kerschner JL, NandyMazumdar M, Coppola C, Mendenhall EM, Leir S, Harris A. Coordinate regulation of ELF5 and EHF at the chr11p13 CF modifier region. J Cell Mol Med 2019; 23:7726-7740. [PMID: 31557407 PMCID: PMC6815777 DOI: 10.1111/jcmm.14646] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/02/2019] [Accepted: 08/10/2019] [Indexed: 12/21/2022] Open
Abstract
E74-like factor 5 (ELF5) and ETS-homologous factor (EHF) are epithelial selective ETS family transcription factors (TFs) encoded by genes at chr11p13, a region associated with cystic fibrosis (CF) lung disease severity. EHF controls many key processes in lung epithelial function so its regulatory mechanisms are important. Using CRISPR/Cas9 technology, we removed three key cis-regulatory elements (CREs) from the chr11p13 region and also activated multiple open chromatin sites with CRISPRa in airway epithelial cells. Deletion of the CREs caused subtle changes in chromatin architecture and site-specific increases in EHF and ELF5. CRISPRa had most effect on ELF5 transcription. ELF5 levels are low in airway cells but higher in LNCaP (prostate) and T47D (breast) cancer cells. ATAC-seq in these lines revealed novel peaks of open chromatin at the 5' end of chr11p13 associated with an expressed ELF5 gene. Furthermore, 4C-seq assays identified direct interactions between the active ELF5 promoter and sites within the EHF locus, suggesting coordinate regulation between these TFs. ChIP-seq for ELF5 in T47D cells revealed ELF5 occupancy within EHF introns 1 and 6, and siRNA-mediated depletion of ELF5 enhanced EHF expression. These results define a new role for ELF5 in lung epithelial biology.
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Affiliation(s)
- Hannah Swahn
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Jey Sabith Ebron
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Kay‐Marie Lamar
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Shiyi Yin
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Jenny L. Kerschner
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Monali NandyMazumdar
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Candice Coppola
- Department of Biological SciencesUniversity of Alabama in HuntsvilleHuntsvilleALUSA
| | - Eric M. Mendenhall
- Department of Biological SciencesUniversity of Alabama in HuntsvilleHuntsvilleALUSA
| | - Shih‐Hsing Leir
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Ann Harris
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
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8
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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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9
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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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10
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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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11
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Stolzenburg LR, Yang R, Kerschner JL, Fossum S, Xu M, Hoffmann A, Lamar KM, Ghosh S, Wachtel S, Leir SH, Harris A. Regulatory dynamics of 11p13 suggest a role for EHF in modifying CF lung disease severity. Nucleic Acids Res 2017; 45:8773-8784. [PMID: 28549169 PMCID: PMC5587731 DOI: 10.1093/nar/gkx482] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 05/01/2017] [Accepted: 05/17/2017] [Indexed: 02/02/2023] Open
Abstract
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause cystic fibrosis (CF), but are not good predictors of lung phenotype. Genome-wide association studies (GWAS) previously identified additional genomic sites associated with CF lung disease severity. One of these, at chromosome 11p13, is an intergenic region between Ets homologous factor (EHF) and Apaf-1 interacting protein (APIP). Our goal was to determine the functional significance of this region, which being intergenic is probably regulatory. To identify cis-acting elements, we used DNase-seq and H3K4me1 and H3K27Ac ChIP-seq to map open and active chromatin respectively, in lung epithelial cells. Two elements showed strong enhancer activity for the promoters of EHF and the 5' adjacent gene E47 like ETS transcription factor 5 (ELF5) in reporter gene assays. No enhancers of the APIP promoter were found. Circular chromosome conformation capture (4C-seq) identified direct physical interactions of elements within 11p13. This confirmed the enhancer-promoter associations, identified additional interacting elements and defined topologically associating domain (TAD) boundaries, enriched for CCCTC-binding factor (CTCF). No strong interactions were observed with the APIP promoter, which lies outside the main TAD encompassing the GWAS signal. These results focus attention on the role of EHF in modifying CF lung disease severity.
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Affiliation(s)
- Lindsay R. Stolzenburg
- 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
| | - 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
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44016, USA
| | - Sara Fossum
- 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
| | - Matthew Xu
- 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
| | - Andrew Hoffmann
- 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
| | - Kay-Marie Lamar
- 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
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44016, USA
| | - Sujana Ghosh
- 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
| | - Sarah Wachtel
- 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
| | - 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
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44016, 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
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44016, USA
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12
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Novel variation at chr11p13 associated with cystic fibrosis lung disease severity. Hum Genome Var 2016; 3:16020. [PMID: 27408752 PMCID: PMC4935763 DOI: 10.1038/hgv.2016.20] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/06/2016] [Accepted: 05/09/2016] [Indexed: 12/28/2022] Open
Abstract
Published genome-wide association studies (GWASs) identified an intergenic region with regulatory features on chr11p13 associated with cystic fibrosis (CF) lung disease severity. Targeted resequencing in n=377, followed by imputation to n=6,365 CF subjects, was used to identify unrecognized genetic variants (including indels and microsatellite repeats) associated with phenotype. Highly significant associations were in strong linkage disequilibrium and were seen only in Phe508del homozygous CF subjects, indicating a CFTR genotype-specific mechanism.
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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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Browne JA, Yang R, Eggener SE, Leir SH, Harris A. HNF1 regulates critical processes in the human epididymis epithelium. Mol Cell Endocrinol 2016; 425:94-102. [PMID: 26808453 PMCID: PMC4799753 DOI: 10.1016/j.mce.2016.01.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 12/26/2015] [Accepted: 01/20/2016] [Indexed: 01/22/2023]
Abstract
The luminal environment of the epididymis participates in sperm maturation and impacts male fertility. It is dependent on the coordinated expression of many genes encoding proteins with a role in epithelial transport. We identified cis-regulatory elements for critical genes in epididymis function, by mapping open chromatin genome-wide in human epididymis epithelial (HEE) cells. Bioinformatic predictions of transcription factors binding to the regulatory elements suggested an important role for hepatocyte nuclear factor 1 (HNF1) in the transcriptional program of these cells. Chromatin immunoprecipitation and deep sequencing (ChIP-seq) revealed HNF1 target genes in HEE cells. In parallel, the contribution of HNF1 to the transcriptome of HEE cells was determined by RNA-seq, following siRNA-mediated depletion of both HNF1α and HNF1β transcription factors. Repression of these factors caused differential expression of 1892 transcripts (902 were downregulated and 990 upregulated) in comparison to non-targeting siRNAs. Differentially expressed genes with HNF1 ChIP-seq peaks within 20 kb were subject to gene ontology process enrichment analysis. Among the most significant processes associated with down-regulated genes were epithelial transport of water, phosphate and bicarbonate, all critical processes in epididymis epithelial function. Measurements of intracellular pH (pHi) confirmed a role for HNF1 in regulating the epididymis luminal environment.
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Affiliation(s)
- James A Browne
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL, USA
| | - Rui Yang
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL, USA
| | - Scott E Eggener
- 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
| | - Ann Harris
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL, USA.
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15
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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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16
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Fossum SL, Mutolo MJ, Yang R, Dang H, O'Neal WK, Knowles MR, Leir SH, Harris A. Ets homologous factor regulates pathways controlling response to injury in airway epithelial cells. Nucleic Acids Res 2014; 42:13588-98. [PMID: 25414352 PMCID: PMC4267623 DOI: 10.1093/nar/gku1146] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Ets homologous factor (EHF) is an Ets family transcription factor expressed in many epithelial cell types including those lining the respiratory system. Disruption of the airway epithelium is central to many lung diseases, and a network of transcription factors coordinates its normal function. EHF can act as a transcriptional activator or a repressor, though its targets in lung epithelial cells are largely uncharacterized. Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq), showed that the majority of EHF binding sites in lung epithelial cells are intergenic or intronic and coincide with putative enhancers, marked by specific histone modifications. EHF occupies many genomic sites that are close to genes involved in intercellular and cell–matrix adhesion. RNA-seq after EHF depletion or overexpression showed significant alterations in the expression of genes involved in response to wounding. EHF knockdown also targeted genes in pathways of epithelial development and differentiation and locomotory behavior. These changes in gene expression coincided with alterations in cellular phenotype including slowed wound closure and increased transepithelial resistance. Our data suggest that EHF regulates gene pathways critical for epithelial response to injury, including those involved in maintenance of barrier function, inflammation and efficient wound repair.
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Affiliation(s)
- Sara L Fossum
- 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
| | - Michael J Mutolo
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA
| | - 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
| | - Hong Dang
- Marsico Lung Institute, University of North Carolina Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Wanda K O'Neal
- Marsico Lung Institute, University of North Carolina Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael R Knowles
- Marsico Lung Institute, University of North Carolina Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, 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 Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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Zhang W, Zhang T, Wu Y, Jiang J. Open Chromatin in Plant Genomes. Cytogenet Genome Res 2014; 143:18-27. [DOI: 10.1159/000362827] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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18
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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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Immune mediators regulate CFTR expression through a bifunctional airway-selective enhancer. Mol Cell Biol 2013; 33:2843-53. [PMID: 23689137 DOI: 10.1128/mcb.00003-13] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
An airway-selective DNase-hypersensitive site (DHS) at kb -35 (DHS-35kb) 5' to the cystic fibrosis transmembrane conductance regulator (CFTR) gene is evident in many lung cell lines and primary human tracheal epithelial cells but is absent from intestinal epithelia. The DHS-35kb contains an element with enhancer activity in 16HBE14o- airway epithelial cells and is enriched for monomethylated H3K4 histones (H3K4me1). We now define a 350-bp region within DHS-35kb which has full enhancer activity and binds interferon regulatory factor 1 (IRF1) and nuclear factor Y (NF-Y) in vitro and in vivo. Small interfering RNA (siRNA)-mediated depletion of IRF1 or overexpression of IRF2, an antagonist of IRF1, reduces CFTR expression in 16HBE14o- cells. NF-Y is critical for maintenance of H3K4me1 enrichment at DHS-35kb since depletion of NF-YA, a subunit of NF-Y, reduces H3K4me1 enrichment at this site. Moreover, depletion of SETD7, an H3K4 monomethyltransferase, reduces both H3K4me1 and NF-Y occupancy, suggesting a requirement of H3K4me1 for NF-Y binding. NF-Y depletion also represses Sin3A and reduces its occupancy across the CFTR locus, which is accompanied by an increase in p300 enrichment at multiple sites. Our results reveal that the DHS-35kb airway-selective enhancer element plays a pivotal role in regulation of CFTR expression by two independent regulatory mechanisms.
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ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet 2012; 13:840-52. [PMID: 23090257 DOI: 10.1038/nrg3306] [Citation(s) in RCA: 485] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chromatin immunoprecipitation experiments followed by sequencing (ChIP-seq) detect protein-DNA binding events and chemical modifications of histone proteins. Challenges in the standard ChIP-seq protocol have motivated recent enhancements in this approach, such as reducing the number of cells that are required and increasing the resolution. Complementary experimental approaches - for example, DNaseI hypersensitive site mapping and analysis of chromatin interactions that are mediated by particular proteins - provide additional information about DNA-binding proteins and their function. These data are now being used to identify variability in the functions of DNA-binding proteins across genomes and individuals. In this Review, I describe the latest advances in methods to detect and functionally characterize DNA-bound proteins.
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