1
|
Méchin MC, Simon M. Deimination in epidermal barrier and hair formation. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220245. [PMID: 37778378 PMCID: PMC10542453 DOI: 10.1098/rstb.2022.0245] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/13/2023] [Indexed: 10/03/2023] Open
Abstract
Peptidylarginine deiminases (PADs) transform a protein arginine residue into the non-standard amino acid citrulline. This calcium-dependent post-translational modification of proteins is called citrullination or deimination. As described in this special issue, PADs play a role in various physiological processes, and PAD deregulations are involved in many human diseases. Three PADs are expressed in the epidermis, where their roles begin to be deciphered. PAD1 and PAD3 are involved in keratinocyte differentiation, particularly in the epidermal barrier function, keratins, filaggrin and filaggrin-related proteins being the most abundant deiminated epidermal proteins. Reduced amounts of deiminated proteins and PAD1 expression may be involved in the pathogenesis of psoriasis and atopic dermatitis, two very frequent and chronic skin inflammatory diseases. The trichohyalin/PAD3/transglutaminase three pathway is important for hair shaft formation. Mutations of the PADI3 gene, leading to a decreased activity or abnormal localization of the corresponding isotype, are the cause of a rare hair disorder called uncombable hair syndrome, and are associated with the central centrifugal cicatricial alopecia, a frequent alopecia mainly affecting women of African ancestry. This article is part of the Theo Murphy meeting issue 'The virtues and vices of protein citrullination'.
Collapse
Affiliation(s)
- Marie-Claire Méchin
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), University of Toulouse, CNRS, INSERM, University Paul Sabatier, 31024 Toulouse, France
| | - Michel Simon
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), University of Toulouse, CNRS, INSERM, University Paul Sabatier, 31024 Toulouse, France
| |
Collapse
|
2
|
Zhang H, Qin Z, Yue X, Liu Y, Sun X, Feng J, Xu Z, Zhao J, Li K, Qiu J, Yang W, He F, Ding C. Proteome-wide profiling of transcriptional machinery on accessible chromatin with biotinylated transposons. SCIENCE ADVANCES 2021; 7:eabh1022. [PMID: 34678055 PMCID: PMC10763760 DOI: 10.1126/sciadv.abh1022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
To directly and quantitatively identify the transcriptional protein complexes assembled on accessible chromatin, we develop an assay for transposase-accessible chromatin using mass spectrum (ATAC-MS) based on direct transposition of biotinylated adaptors into open chromatin. Coupling with activated gene sequence information by ATAC-seq, ATAC-MS can profile the accessible chromatin-protein machinery. ATAC-MS, combined with fractionation strategies (fATAC-MS), can provide a high-resolution chromatin-transcriptional machinery atlas. ATAC-MS with a novel Tn5-dCas9 fusion protein [dCas9-targeted ATAC-MS (ctATAC-MS)] further facilitates systematic pinpointing of the transcriptional machinery at specific open chromatin regions. We used ATAC-MS and ATAC-seq to investigate transcriptional regulation during C2C12 cell differentiation and demonstrated the role of RFX1 in regulating the proliferation and differentiation of C2C12 cells. Our strategy provides a universal toolbox including ATAC-MS, fATAC-MS, and ctATAC-MS, which enables us to portray the transcriptional regulation machinery atlas in genome scale and investigate the protein-DNA complex at a specific genomic locus.
Collapse
Affiliation(s)
- Haizhu Zhang
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Zhaoyu Qin
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Xuetong Yue
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Yang Liu
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Xiaogang Sun
- State Key Laboratory Cell Differentiation and Regulation, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis, (111 Project), College of Life Science, Henan Normal University, Xinxiang, Henan 453007, China
| | - Jinwen Feng
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Ziyan Xu
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Jiangyan Zhao
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Kai Li
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Jiange Qiu
- Cell Signaling and Proteomics Research Center, Academy of Medical Science, Zhengzhou University, Zhengzhou 450000, China
| | - Wenjun Yang
- Department of Pediatric Orthopedics, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Fuchu He
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing 102206, China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
- State Key Laboratory Cell Differentiation and Regulation, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis, (111 Project), College of Life Science, Henan Normal University, Xinxiang, Henan 453007, China
- Cell Signaling and Proteomics Research Center, Academy of Medical Science, Zhengzhou University, Zhengzhou 450000, China
| |
Collapse
|
3
|
Briot J, Simon M, Méchin MC. Deimination, Intermediate Filaments and Associated Proteins. Int J Mol Sci 2020; 21:E8746. [PMID: 33228136 PMCID: PMC7699402 DOI: 10.3390/ijms21228746] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 02/07/2023] Open
Abstract
Deimination (or citrullination) is a post-translational modification catalyzed by a calcium-dependent enzyme family of five peptidylarginine deiminases (PADs). Deimination is involved in physiological processes (cell differentiation, embryogenesis, innate and adaptive immunity, etc.) and in autoimmune diseases (rheumatoid arthritis, multiple sclerosis and lupus), cancers and neurodegenerative diseases. Intermediate filaments (IF) and associated proteins (IFAP) are major substrates of PADs. Here, we focus on the effects of deimination on the polymerization and solubility properties of IF proteins and on the proteolysis and cross-linking of IFAP, to finally expose some features of interest and some limitations of citrullinomes.
Collapse
Affiliation(s)
| | | | - Marie-Claire Méchin
- UDEAR, Institut National de la Santé Et de la Recherche Médicale, Université Toulouse III Paul Sabatier, Université Fédérale de Toulouse Midi-Pyrénées, U1056, 31059 Toulouse, France; (J.B.); (M.S.)
| |
Collapse
|
4
|
Schmidt F, Kern F, Schulz MH. Integrative prediction of gene expression with chromatin accessibility and conformation data. Epigenetics Chromatin 2020; 13:4. [PMID: 32029002 PMCID: PMC7003490 DOI: 10.1186/s13072-020-0327-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 01/06/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Enhancers play a fundamental role in orchestrating cell state and development. Although several methods have been developed to identify enhancers, linking them to their target genes is still an open problem. Several theories have been proposed on the functional mechanisms of enhancers, which triggered the development of various methods to infer promoter-enhancer interactions (PEIs). The advancement of high-throughput techniques describing the three-dimensional organization of the chromatin, paved the way to pinpoint long-range PEIs. Here we investigated whether including PEIs in computational models for the prediction of gene expression improves performance and interpretability. RESULTS We have extended our [Formula: see text] framework to include DNA contacts deduced from chromatin conformation capture experiments and compared various methods to determine PEIs using predictive modelling of gene expression from chromatin accessibility data and predicted transcription factor (TF) motif data. We designed a novel machine learning approach that allows the prioritization of TFs binding to distal loop and promoter regions with respect to their importance for gene expression regulation. Our analysis revealed a set of core TFs that are part of enhancer-promoter loops involving YY1 in different cell lines. CONCLUSION We present a novel approach that can be used to prioritize TFs involved in distal and promoter-proximal regulatory events by integrating chromatin accessibility, conformation, and gene expression data. We show that the integration of chromatin conformation data can improve gene expression prediction and aids model interpretability.
Collapse
Affiliation(s)
- Florian Schmidt
- High-throughput Genomics & Systems Biology, Cluster of Excellence on Multimodal Computing and Interaction, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Computational Biology & Applied Algorithmics, Max-Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Center for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Singapore, 138672 Singapore
| | - Fabian Kern
- High-throughput Genomics & Systems Biology, Cluster of Excellence on Multimodal Computing and Interaction, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Center for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Chair for Clinical Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Marcel H. Schulz
- High-throughput Genomics & Systems Biology, Cluster of Excellence on Multimodal Computing and Interaction, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Computational Biology & Applied Algorithmics, Max-Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Center for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Institute of Cardiovascular Regeneration, Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner Site Rhein-Main, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| |
Collapse
|
5
|
Cau L, Méchin MC, Simon M. Peptidylarginine deiminases and deiminated proteins at the epidermal barrier. Exp Dermatol 2018; 27:852-858. [PMID: 29756256 DOI: 10.1111/exd.13684] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2018] [Indexed: 12/13/2022]
Abstract
Deimination or citrullination is a post-translational modification catalysed by a family of calcium-dependent enzymes called peptidylarginine deiminases (PADs). It corresponds to the transformation of arginine residues within a peptide sequence into citrulline residues. Deimination induces a decreased net charge of targeted proteins; therefore, it alters their folding and changes intra- and intermolecular ionic interactions. Deimination is involved in several physiological processes (inflammation, gene regulation, etc.) and human diseases (rheumatoid arthritis, neurodegenerative diseases, cancer, etc.). Here, we describe the PADs expressed in the epidermis and their known substrates, focusing on their role in the epidermal barrier function.
Collapse
Affiliation(s)
- Laura Cau
- UDEAR, Institut National de la Santé Et de la Recherche Médicale, Université Paul Sabatier, Université de Toulouse Midi-Pyrénées, Toulouse, France
| | - Marie-Claire Méchin
- UDEAR, Institut National de la Santé Et de la Recherche Médicale, Université Paul Sabatier, Université de Toulouse Midi-Pyrénées, Toulouse, France
| | - Michel Simon
- UDEAR, Institut National de la Santé Et de la Recherche Médicale, Université Paul Sabatier, Université de Toulouse Midi-Pyrénées, Toulouse, France
| |
Collapse
|
6
|
Botchkarev VA. The Molecular Revolution in Cutaneous Biology: Chromosomal Territories, Higher-Order Chromatin Remodeling, and the Control of Gene Expression in Keratinocytes. J Invest Dermatol 2017; 137:e93-e99. [PMID: 28411854 DOI: 10.1016/j.jid.2016.04.040] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 03/05/2016] [Accepted: 04/15/2016] [Indexed: 12/16/2022]
Abstract
Three-dimensional organization of transcription in the nucleus and mechanisms controlling the global chromatin folding, including spatial interactions between the genes, noncoding genome elements, and epigenetic and transcription machinery, are essential for establishing lineage-specific gene expression programs during cell differentiation. Spatial chromatin interactions in the nucleus involving gene promoters and distal regulatory elements are currently considered major forces that drive cell differentiation and genome evolution in general, and such interactions are substantially reorganized during many pathological conditions. During terminal differentiation of the epidermal keratinocytes, the nucleus undergoes programmed transformation from highly active status, associated with execution of the genetic program of epidermal barrier formation, to a fully inactive condition and finally becomes a part of the keratinized cells of the cornified epidermal layer. This transition is accompanied by marked remodeling of the three-dimensional nuclear organization and microanatomy, including changes in the spatial arrangement of lineage-specific genes, nuclear bodies, and heterochromatin. This mini-review highlights the important landmarks in the accumulation of our current knowledge on three-dimensional organization of the nucleus, spatial arrangement of the genes, and their distal regulatory elements, and it provides an update on the mechanisms that control higher-order chromatin remodeling in the context of epidermal keratinocyte differentiation in the skin.
Collapse
Affiliation(s)
- Vladimir A Botchkarev
- Centre for Skin Sciences, Faculty of Life Sciences, University of Bradford, Bradford, UK; Department of Dermatology, Boston University School of Medicine, Boston, Massachusetts, USA.
| |
Collapse
|
7
|
Amin B, Voelter W. Human Deiminases: Isoforms, Substrate Specificities, Kinetics, and Detection. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2017; 106:203-240. [PMID: 28762090 DOI: 10.1007/978-3-319-59542-9_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Peptidylarginine deiminase (PAD) enzymes are of enormous interest in biomedicine. They catalyze the conversion of a positively-charged guanidinium at an arginine side chain into a neutral ureido group. As a result of this conversion, proteins acquire the non-ribosomally encoded amino acid "citrulline". This imposes critical influences on the structure and function of the target molecules. In multiple sclerosis, myelin hyper-citrullination promotes demyelination by reducing its compaction and triggers auto-antibody production. Immune responses to citrulline-containing proteins play a central role in the pathogenesis of autoimmune diseases. Moreover, auto-antibodies, specific to citrullinated proteins, such as collagen type I and II and filaggrin, are early detectable in rheumatoid arthritis, serving as diagnostic markers of the disease. Despite their significance, little is understood about the role in demyelinating disorders, diversified cancers, and auto-immune diseases. To impart their biological and pathological effects, it is crucial to better understand the reaction mechanism, kinetic properties, substrate selection, and specificities of peptidylarginine deiminase isoforms.Many aspects of PAD biochemistry and physiology have been ignored in past, but, herein is presented a comprehensive survey to improve our current understandings of the underlying mechanism and regulation of PAD enzymes.
Collapse
Affiliation(s)
- Bushra Amin
- Department of Chemistry, University of Pittsburgh, Pittsburgh, 15260, PA, USA.
| | - Wolfgang Voelter
- Interfacultary Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076, Tübingen, BW, Germany
| |
Collapse
|
8
|
Vogelsang M, Paccez JD, Schäfer G, Dzobo K, Zerbini LF, Parker MI. Aberrant methylation of the MSH3 promoter and distal enhancer in esophageal cancer patients exposed to first-hand tobacco smoke. J Cancer Res Clin Oncol 2014; 140:1825-33. [PMID: 24934723 DOI: 10.1007/s00432-014-1736-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 06/04/2014] [Indexed: 12/15/2022]
Abstract
PURPOSE Polymorphisms in MSH3 gene confer risk of esophageal cancer when in combination with tobacco smoke exposure. The purpose of this study was to investigate the methylation status of MSH3 gene in esophageal cancer patients in order to further elucidate possible role of MSH3 in esophageal tumorigenesis. METHODS We applied nested methylation-specific polymerase chain reaction to investigate the methylation status of the MSH3 promoter in tumors and matching adjacent normal-looking tissues of 84 esophageal cancer patients from a high-risk South African population. The Cancer Genome Atlas data were used to examine DNA methylation profiles at 17 CpG sites located in the MSH3 locus. RESULTS Overall, promoter methylation was detected in 91.9 % of tumors, which was significantly higher compared to 76.0 % in adjacent normal-looking esophageal tissues (P = 0.008). When samples were grouped according to different demographics (including age, gender and ethnicity) and smoking status of patients, methylation frequencies were found to be significantly higher in tumor tissues of Black subjects (P = 0.024), patients of 55-65 years of age (P = 0.032), males (P = 0.037) and tobacco smokers (P = 0.015). Furthermore, methylation of the MSH3 promoter was significantly more frequent in tumor samples from smokers compared to tumor samples from non-smokers [odds ratio (OR) = 31.9, P = 0.031]. The TCGA data confirmed significantly higher DNA methylation level at the MSH3 promoter region in tumors (P = 0.0024). In addition, we found evidence of an aberrantly methylated putative MSH3-associated distal enhancer element. CONCLUSION Our results suggest that methylation of MSH3 together with exposure to tobacco smoke is involved in esophageal carcinogenesis. Due to the active role of the MSH3 protein in modulating chemosensitivity of cells, methylation of MSH3 should further be examined in association with the outcome of esophageal cancer treatment using anticancer drugs.
Collapse
Affiliation(s)
- Matjaz Vogelsang
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, UCT Medical Campus, Anzio Road, Observatory, Cape Town, 7925, South Africa
| | | | | | | | | | | |
Collapse
|
9
|
U KP, Subramanian V, Nicholas AP, Thompson PR, Ferretti P. Modulation of calcium-induced cell death in human neural stem cells by the novel peptidylarginine deiminase-AIF pathway. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1162-71. [PMID: 24607566 PMCID: PMC3996523 DOI: 10.1016/j.bbamcr.2014.02.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/19/2014] [Accepted: 02/24/2014] [Indexed: 11/29/2022]
Abstract
PADs (peptidylarginine deiminases) are calcium-dependent enzymes that change protein-bound arginine to citrulline (citrullination/deimination) affecting protein conformation and function. PAD up-regulation following chick spinal cord injury has been linked to extensive tissue damage and loss of regenerative capability. Having found that human neural stem cells (hNSCs) expressed PAD2 and PAD3, we studied PAD function in these cells and investigated PAD3 as a potential target for neuroprotection by mimicking calcium-induced secondary injury responses. We show that PAD3, rather than PAD2 is a modulator of cell growth/death and that PAD activity is not associated with caspase-3-dependent cell death, but is required for AIF (apoptosis inducing factor)-mediated apoptosis. PAD inhibition prevents association of PAD3 with AIF and AIF cleavage required for its translocation to the nucleus. Finally, PAD inhibition also hinders calcium-induced cytoskeleton disassembly and association of PAD3 with vimentin, that we show to be associated also with AIF; together this suggests that PAD-dependent cytoskeleton disassembly may play a role in AIF translocation to the nucleus. This is the first study highlighting a role of PAD activity in balancing hNSC survival/death, identifying PAD3 as an important upstream regulator of calcium-induced apoptosis, which could be targeted to reduce neural loss, and shedding light on the mechanisms involved.
Collapse
Affiliation(s)
- Kin Pong U
- Developmental Biology Unit, UCL Institute of Child Health, London WC1N 1EH, UK
| | | | - Antony P Nicholas
- Department of Neurology, University of Alabama at Birmingham and Birmingham VA Medical Center, Birmingham, AL 35294, USA
| | - Paul R Thompson
- Department of Chemistry, TSRI, Scripps Florida, FL 33458, USA
| | - Patrizia Ferretti
- Developmental Biology Unit, UCL Institute of Child Health, London WC1N 1EH, UK.
| |
Collapse
|
10
|
Meyer MB, Goetsch PD, Pike JW. VDR/RXR and TCF4/β-catenin cistromes in colonic cells of colorectal tumor origin: impact on c-FOS and c-MYC gene expression. Mol Endocrinol 2012; 26:37-51. [PMID: 22108803 PMCID: PMC3248320 DOI: 10.1210/me.2011-1109] [Citation(s) in RCA: 161] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Many of the transcriptional and growth regulating activities of 1α,25-dihydroxyvitamin D(3) [1,25-(OH)(2)D(3)] in the intestine and colon are recapitulated in the human colorectal cancer cell LS180. We therefore used this line together with chromatin immunoprecipitation-seq and gene expression analyses to identify the vitamin D receptor (VDR)/retinoid X receptor (RXR) and transcription factor 7-like 2 (TCF7L2/TCF4)/β-catenin cistromes and the genes that they regulate. VDR and RXR colocalized to predominantly promoter distal, vitamin D response element-containing sites in a largely ligand-dependent manner. These regulatory sites control the expression of both known as well as novel 1,25-(OH)(2)D(3) target genes. TCF4 and β-catenin cistromes partially overlapped, contained TCF/lymphoid enhancer-binding factor consensus elements, and were only modestly influenced by 1,25-(OH)(2)D(3). However, the two heterodimer complexes colocalized at sites near a limited set of genes that included c-FOS and c-MYC; the expression of both genes was modulated by 1,25-(OH)(2)D(3). At the c-FOS gene, both VDR/RXR and TCF4/β-catenin bound to a single distal enhancer located 24 kb upstream of the transcriptional start site. At the c-MYC locus, however, binding was noted at a cluster of sites between -139 and -165 kb and at a site located -335 kb upstream. Examined as isolated enhancer fragments, these regions exhibited basal and 1,25-(OH)(2)D(3)-inducible activities that were interlinked to both VDR and β-catenin activation. These data reveal additional complexity in the regulation of target genes by 1,25-(OH)(2)D(3) and support a direct action of both VDR and the TCF4/β-catenin regulatory complex at c-FOS and c-MYC.
Collapse
Affiliation(s)
- Mark B Meyer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | | | | |
Collapse
|
11
|
Amin S, Kumar A, Nilchi L, Wright K, Kozlowski M. Breast cancer cells proliferation is regulated by tyrosine phosphatase SHP1 through c-jun N-terminal kinase and cooperative induction of RFX-1 and AP-4 transcription factors. Mol Cancer Res 2011; 9:1112-25. [PMID: 21719561 DOI: 10.1158/1541-7786.mcr-11-0097] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this study, we show that proliferation of breast cancer cells is suppressed by IGF-1-activated JNK MAPK pathway. The molecular mechanism by which c-jun-NH,-kinase (JNK) activation induces antiproliferative signals in IGF-1-stimulated breast cancer cells remains unknown. Tyrosine phosphatase SHP1 is known to negatively regulate signal transduction pathways activated by cell surface receptors including IGF-1. Moreover, SHP1 transcript and protein levels are increased in epithelial tumors. Therefore, we hypothesized that IGF-activated JNK induces expression of SHP1 in breast cancer cells. To further clarify the role of SHP1 in tumor growth, we correlated the proliferation rates of breast adenocarcinoma cells with SHP1 expression and JNK activation. We show that proliferation of serum- or IGF-1-stimulated breast adenocarcinoma cells is negatively regulated by SHP1 and show for the first time that IGF-1-activated JNK induces SHP1 expression in MCF-7 cells used as experimental model. In an attempt to understand the mechanism by which serum- or IGF-1-activated JNK induces SHP1 expression resulting in suppression of cell proliferation, we reveal for the first time that in serum- or IGF-1-stimulated breast cancer MCF-7 cells, JNK induces SHP1 expression through the binding of AP-4 and RFX-1 transcription factors to the epithelial tissue-specific SHP1 promoter. Overall, we show for the first time that IGF-1-stimulated proliferation of breast adenocarcinoma cells is negatively regulated by SHP1 through activation of JNK.
Collapse
Affiliation(s)
- Shahreen Amin
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | | | | | | | | |
Collapse
|
12
|
Méchin MC, Nachat R, Coudane F, Adoue V, Arnaud J, Serre G, Simon M. [Deimination or citrullination, a post-translational modification with many physiological and pathophysiological facets]. Med Sci (Paris) 2011; 27:49-54. [PMID: 21299962 DOI: 10.1051/medsci/201127149] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Deimination or citrullination, is a post-translational modification with many facets. It is involved in several basic cellular processes, including gene regulation, embryonic development and terminal differentiation, and also in various pathophysiological mechanisms linked to severe human diseases such as multiple sclerosis and rheumatoid arthritis. Deimination, the calcium-dependent enzymatic conversion of peptidyl-arginine to peptidyl-citrulline, induces a decrease in the charge of the modified proteins with major consequences on their conformation, stability and/or interactions, and therefore on their functions. Five isotypes of peptidylarginine deiminases (1-4 and 6), exist in humans with a variable tissue expression. These highly conserved enzymes are closely regulated at transcriptional and post-transcriptional levels, probably including auto-deimination.
Collapse
Affiliation(s)
- Marie-Claire Méchin
- UMR 5165 CNRS/ Université Paul Sabatier, Hôpital Purpan, place du Docteur Baylac, TSA 40031, 31059 Toulouse Cedex 9, France. marie-claire.mechin@ udear.cnrs.fr
| | | | | | | | | | | | | |
Collapse
|
13
|
Shanley L, Davidson S, Lear M, Thotakura AK, McEwan IJ, Ross RA, MacKenzie A. Long-range regulatory synergy is required to allow control of the TAC1 locus by MEK/ERK signalling in sensory neurones. Neurosignals 2010; 18:173-85. [PMID: 21160161 PMCID: PMC3718575 DOI: 10.1159/000322010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Accepted: 10/13/2010] [Indexed: 01/05/2023] Open
Abstract
Changes in the expression of the neuropeptide substance P (SP) in different populations of sensory neurones are associated with the progression of chronic inflammatory disease. Thus, understanding the genomic and cellular mechanisms driving the expression of the TAC1 gene, which encodes SP, in sensory neurones is essential to understanding its role in inflammatory disease. We used a novel combination of computational genomics, primary-cell culture and mouse transgenics to determine the genomic and cellular mechanisms that control the expression of TAC1 in sensory neurones. Intriguingly, we demonstrated that the promoter of the TAC1 gene must act in synergy with a remote enhancer, identified using comparative genomics, to respond to MAPK signalling that modulates the expression of TAC1 in sensory neurones. We also reveal that noxious stimulation of sensory neurones triggers this synergy in larger diameter sensory neurones – an expression of SP associated with hyperalgesia. This noxious stimulation of TAC1 enhancer-promotor synergy could be strongly blocked by antagonism of the MEK pathway. This study provides a unique insight into the role of long-range enhancer-promoter synergy and selectivity in the tissue-specific response of promoters to specific signal transduction pathways and suggests a possible new avenue for the development of novel anti-inflammatory therapies.
Collapse
Affiliation(s)
- Lynne Shanley
- School of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | | | | | | | | | | | | |
Collapse
|
14
|
Levran O, Awolesi O, Linzy S, Adelson M, Kreek MJ. Haplotype block structure of the genomic region of the mu opioid receptor gene. J Hum Genet 2010; 56:147-55. [PMID: 21160491 PMCID: PMC3075619 DOI: 10.1038/jhg.2010.150] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The opioid system is involved in the action of opiate drugs, opioid addiction, pain experience and analgesia. Individual differences in opioid effect may be attributed in part to genetic variations. Long-range cis regulatory elements and intronic variants are potential sources of functional diversity. Recently, we have detected association of two intronic OPRM1 variants with heroin addiction in European Americans. In the current study, we analyzed the genetic variations in the OPRM1 100 kb 5′ flanking region and intron 1 in the HapMap Caucasian population. Four major linkage disequilibrium (LD) blocks were identified, consisting of 28, 22, 15 and 42 SNPs, respectively. The locations of these blocks are (−100 – −90), (−90 – −67), (−20 - −1) and (+1 – +44) kb, respectively. The two intronic variants, indicated in our recent study, are part of a distinct haplogroup that include SNPs from intron 1, and the proximal 5′ region. The 118G (rs1799971) allele is part of a different haplogroup that includes several variants in the distal 5′ region that may have a regulatory potential. These findings were corroborated by genotyping eight SNPs in a sample of European Americans and suggest an extended OPRM1 locus with potential new regulatory regions.
Collapse
Affiliation(s)
- Orna Levran
- Laboratory of the Biology of Addictive Diseases, The Rockefeller University, New York, NY 10065, USA.
| | | | | | | | | |
Collapse
|
15
|
Ying S, Kojima T, Kawada A, Nachat R, Serre G, Simon M, Takahara H. An intronic enhancer driven by NF-κB contributes to transcriptional regulation of peptidylarginine deiminase type I gene in human keratinocytes. J Invest Dermatol 2010; 130:2543-52. [PMID: 20596086 DOI: 10.1038/jid.2010.179] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Peptidylarginine deiminases (PADs) catalyze the conversion of protein-bound arginine to citrulline residues. In human epidermis, where filaggrin is the main deiminated protein, three PADs are detected with specific patterns of expression depending on the keratinocyte (KC) differentiation state. Previous characterizations of the PAD-encoding gene promoters have shown that proximal regulation alone is not sufficient to explain this specificity of expression. In this work, we describe an evolutionarily highly conserved nucleotide segment located in the first intron of the PAD1 gene (PADI1). Luciferase reporter assays showed that it enhances the activity of the PADI1 promoter, in a calcium- and orientation-independent manner. Mutation of a putative NF-κB cis-element markedly reduced its enhancer activity, which also confirmed its potential regulatory function. Chromatin immunoprecipitation assays evidenced the binding of both p65 and p50 NF-κB subunits to the cis-element, and RNA interference inhibition assays confirmed that NF-κB contributes to the PADI1 transcriptional control. Furthermore, the intronic enhancer and promoter of PADI1 potentially interact through chromatin looping, as indicated by chromosome conformation capture assays. Our findings provide evidence that an NF-κB-mediated signaling pathway is involved in PADI1 regulation in human epidermal KCs.
Collapse
Affiliation(s)
- Shibo Ying
- Department of Applied Life Sciences, United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | | | | | | | | | | | | |
Collapse
|
16
|
Méchin MC, Coudane F, Adoue V, Arnaud J, Duplan H, Charveron M, Schmitt AM, Takahara H, Serre G, Simon M. Deimination is regulated at multiple levels including auto-deimination of peptidylarginine deiminases. Cell Mol Life Sci 2010; 67:1491-503. [PMID: 20111885 PMCID: PMC11115946 DOI: 10.1007/s00018-010-0262-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 12/01/2009] [Accepted: 01/07/2010] [Indexed: 10/19/2022]
Abstract
Peptidylarginine deiminases (PADs) catalyze deimination, converting arginyl to citrullyl residues. Only three PAD isotypes are detected in the epidermis where they play a crucial role, targeting filaggrin, a key actor for the tissue hydration and barrier functions. Their expression and activation depends on the keratinocyte differentiation state. To investigate this regulation, we used primary keratinocytes induced to differentiate either by increasing cell-density or by treatment with vitamin D. High cell-density increased PAD1 and 3, but not PAD2, at the mRNA and protein levels, and up-regulated protein deimination. By contrast, vitamin D increased PAD1-3 mRNA amounts, with distinct kinetics, but neither the proteins nor the deimination rate. Furthermore, auto-deimination was shown to decrease PAD activity, increasing the distances between the four major amino acids of the active site. In summary, deimination can be regulated at multiple levels: transcription of the PADI genes, translation of the corresponding mRNAs, and auto-deimination of PADs.
Collapse
Affiliation(s)
- Marie-Claire Méchin
- CNRS-University of Toulouse III, UMR5165, Institut Fédératif de Recherche 150 (INSERM-CNRS-Université paul Sabatier-Centre Hospitalier Universitaire de Toulouse), CHU Purpan, Place du Dr Baylac TSA40031, 31059 Toulouse Cedex 9, France
| | - Fanny Coudane
- CNRS-University of Toulouse III, UMR5165, Institut Fédératif de Recherche 150 (INSERM-CNRS-Université paul Sabatier-Centre Hospitalier Universitaire de Toulouse), CHU Purpan, Place du Dr Baylac TSA40031, 31059 Toulouse Cedex 9, France
| | - Véronique Adoue
- CNRS-University of Toulouse III, UMR5165, Institut Fédératif de Recherche 150 (INSERM-CNRS-Université paul Sabatier-Centre Hospitalier Universitaire de Toulouse), CHU Purpan, Place du Dr Baylac TSA40031, 31059 Toulouse Cedex 9, France
| | - Jacques Arnaud
- CNRS-University of Toulouse III, UMR5165, Institut Fédératif de Recherche 150 (INSERM-CNRS-Université paul Sabatier-Centre Hospitalier Universitaire de Toulouse), CHU Purpan, Place du Dr Baylac TSA40031, 31059 Toulouse Cedex 9, France
| | - Hélène Duplan
- Centre Européen de Recherche sur la Peau et les Epithéliums de Revêtement (CERPER), Pierre Fabre Dermo-Cosmétique, Toulouse, France
| | - Marie Charveron
- Centre Européen de Recherche sur la Peau et les Epithéliums de Revêtement (CERPER), Pierre Fabre Dermo-Cosmétique, Toulouse, France
| | - Anne-Marie Schmitt
- Centre Européen de Recherche sur la Peau et les Epithéliums de Revêtement (CERPER), Pierre Fabre Dermo-Cosmétique, Toulouse, France
| | - Hidenari Takahara
- Department of Applied Biological Resource Sciences, School of Agriculture, University of Ibaraki, Ibaraki, Japan
| | - Guy Serre
- CNRS-University of Toulouse III, UMR5165, Institut Fédératif de Recherche 150 (INSERM-CNRS-Université paul Sabatier-Centre Hospitalier Universitaire de Toulouse), CHU Purpan, Place du Dr Baylac TSA40031, 31059 Toulouse Cedex 9, France
| | - Michel Simon
- CNRS-University of Toulouse III, UMR5165, Institut Fédératif de Recherche 150 (INSERM-CNRS-Université paul Sabatier-Centre Hospitalier Universitaire de Toulouse), CHU Purpan, Place du Dr Baylac TSA40031, 31059 Toulouse Cedex 9, France
| |
Collapse
|
17
|
Deshane J, Kim J, Bolisetty S, Hock TD, Hill-Kapturczak N, Agarwal A. Sp1 regulates chromatin looping between an intronic enhancer and distal promoter of the human heme oxygenase-1 gene in renal cells. J Biol Chem 2010; 285:16476-86. [PMID: 20351094 DOI: 10.1074/jbc.m109.058586] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
HO-1 (heme oxygenase-1) is an inducible microsomal enzyme that catalyzes the degradation of pro-oxidant heme. The goal of this study was to characterize a minimal enhancer region within the human HO-1 gene and delineate its role in modulating HO-1 expression by participation with its promoter elements in renal epithelial cells. Deletion analysis and site-directed mutagenesis identified a 220-bp minimal enhancer in intron 1 of the HO-1 gene, which regulates hemin-mediated HO-1 gene expression. Small interfering RNA, decoy oligonucleotides, site-directed mutagenesis, and chromatin immunoprecipitation assays confirmed the functional interaction of Sp1 with a consensus binding sequence within the 220-bp region. Mutations of regulatory elements within the -4.5 kb promoter region (a cyclic AMP response and a downstream NF-E2/AP-1 element, both located at -4.0 kb, and/or an E-box sequence located at -44 bp) resulted in the loss of enhancer activity. A chromosome conformation capture assay performed in human renal epithelial (HK-2) cells demonstrated hemin-inducible chromatin looping between the intronic enhancer and the -4.0 kb promoter region in a time-dependent manner. Restriction digestion with ApaLI (which cleaves the 220-bp enhancer) led to a loss of stimulus-dependent chromatin looping. Sp1 small interfering RNA and mithramycin A, a Sp1 binding site inhibitor, resulted in loss of the loop formation between the intronic enhancer and the distal HO-1 promoter by the chromosome conformation capture assay. These results provide novel insight into the complex molecular interactions that underlie human HO-1 regulation in renal epithelial cells.
Collapse
Affiliation(s)
- Jessy Deshane
- Department of Medicine, Nephrology Research and Training Center, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | | | | | | | | | | |
Collapse
|