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Leśniak W. Dynamics and Epigenetics of the Epidermal Differentiation Complex. EPIGENOMES 2024; 8:9. [PMID: 38534793 DOI: 10.3390/epigenomes8010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/05/2024] [Accepted: 02/08/2024] [Indexed: 03/28/2024] Open
Abstract
Epidermis is the outer skin layer built of specialized cells called keratinocytes. Keratinocytes undergo a unique differentiation process, also known as cornification, during which their gene expression pattern, morphology and other properties change remarkably to the effect that the terminally differentiated, cornified cells can form a physical barrier, which separates the underlying tissues from the environment. Many genes encoding proteins that are important for epidermal barrier formation are located in a gene cluster called epidermal differentiation complex (EDC). Recent data provided valuable information on the dynamics of the EDC locus and the network of interactions between EDC gene promoters, enhancers and other regions, during keratinocytes differentiation. These data, together with results concerning changes in epigenetic modifications, provide a valuable insight into the mode of regulation of EDC gene expression.
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Affiliation(s)
- Wiesława Leśniak
- Laboratory of Calcium Binding Proteins, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., 02-093 Warsaw, Poland
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2
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Holthaus KB, Eckhart L. Development-Associated Genes of the Epidermal Differentiation Complex (EDC). J Dev Biol 2024; 12:4. [PMID: 38248869 PMCID: PMC10801484 DOI: 10.3390/jdb12010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/28/2023] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
The epidermal differentiation complex (EDC) is a cluster of genes that encode protein components of the outermost layers of the epidermis in mammals, reptiles and birds. The development of the stratified epidermis from a single-layered ectoderm involves an embryo-specific superficial cell layer, the periderm. An additional layer, the subperiderm, develops in crocodilians and over scutate scales of birds. Here, we review the expression of EDC genes during embryonic development. Several EDC genes are expressed predominantly or exclusively in embryo-specific cell layers, whereas others are confined to the epidermal layers that are maintained in postnatal skin. The S100 fused-type proteins scaffoldin and trichohyalin are expressed in the avian and mammalian periderm, respectively. Scaffoldin forms the so-called periderm granules, which are histological markers of the periderm in birds. Epidermal differentiation cysteine-rich protein (EDCRP) and epidermal differentiation protein containing DPCC motifs (EDDM) are expressed in the avian subperiderm where they are supposed to undergo cross-linking via disulfide bonds. Furthermore, a histidine-rich epidermal differentiation protein and feather-type corneous beta-proteins, also known as beta-keratins, are expressed in the subperiderm. The accumulating evidence for roles of EDC genes in the development of the epidermis has implications on the evolutionary diversification of the skin in amniotes.
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Affiliation(s)
| | - Leopold Eckhart
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
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3
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Sui JY, Eichenfield DZ, Sun BK. The role of enhancers in psoriasis and atopic dermatitis. Br J Dermatol 2023; 190:10-19. [PMID: 37658835 DOI: 10.1093/bjd/ljad321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/25/2023] [Accepted: 08/27/2023] [Indexed: 09/05/2023]
Abstract
Regulatory elements, particularly enhancers, play a crucial role in disease susceptibility and progression. Enhancers are DNA sequences that activate gene expression and can be affected by epigenetic modifications, interactions with transcription factors (TFs) or changes to the enhancer DNA sequence itself. Altered enhancer activity impacts gene expression and contributes to disease. In this review, we define enhancers and the experimental techniques used to identify and characterize them. We also discuss recent studies that examine how enhancers contribute to atopic dermatitis (AD) and psoriasis. Articles in the PubMed database were identified (from 1 January 2010 to 28 February 2023) that were relevant to enhancer variants, enhancer-associated TFs and enhancer histone modifications in psoriasis or AD. Most enhancers associated with these conditions regulate genes affecting epidermal homeostasis or immune function. These discoveries present potential therapeutic targets to complement existing treatment options for AD and psoriasis.
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Affiliation(s)
- Jennifer Y Sui
- Department of Dermatology, University of California San Diego School of Medicine, CA, USA
- Division of Pediatric and Adolescent Dermatology, Rady Children's Hospital of San Diego, CA, USA
| | - Dawn Z Eichenfield
- Department of Dermatology, University of California San Diego School of Medicine, CA, USA
- Division of Pediatric and Adolescent Dermatology, Rady Children's Hospital of San Diego, CA, USA
| | - Bryan K Sun
- Department of Dermatology, University of California San Diego School of Medicine, CA, USA
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4
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Jayathirtha M, Jayaweera T, Whitham D, Petre BA, Neagu AN, Darie CC. Two-Dimensional Polyacrylamide Gel Electrophoresis Coupled with Nanoliquid Chromatography-Tandem Mass Spectrometry-Based Identification of Differentially Expressed Proteins and Tumorigenic Pathways in the MCF7 Breast Cancer Cell Line Transfected for Jumping Translocation Breakpoint Protein Overexpression. Int J Mol Sci 2023; 24:14714. [PMID: 37834160 PMCID: PMC10572688 DOI: 10.3390/ijms241914714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
The identification of new genes/proteins involved in breast cancer (BC) occurrence is widely used to discover novel biomarkers and understand the molecular mechanisms of BC initiation and progression. The jumping translocation breakpoint (JTB) gene may act both as a tumor suppressor or oncogene in various types of tumors, including BC. Thus, the JTB protein could have the potential to be used as a biomarker in BC, but its neoplastic mechanisms still remain unknown or controversial. We previously analyzed the interacting partners of JTBhigh protein extracted from transfected MCF7 BC cell line using SDS-PAGE complemented with in-solution digestion, respectively. The previous results suggested the JTB contributed to the development of a more aggressive phenotype and behavior for the MCF7 BC cell line through synergistic upregulation of epithelial-mesenchymal transition (EMT), mitotic spindle, and fatty acid metabolism-related pathways. In this work, we aim to complement the previously reported JTB proteomics-based experiments by investigating differentially expressed proteins (DEPs) and tumorigenic pathways associated with JTB overexpression using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). Statistically different gel spots were picked for protein digestion, followed by nanoliquid chromatography-tandem mass spectrometry (nLC-MS/MS) analysis. We identified six DEPs related to the JTBhigh condition vs. control that emphasize a pro-tumorigenic (PT) role. Twenty-one proteins, which are known to be usually overexpressed in cancer cells, emphasize an anti-tumorigenic (AT) role when low expression occurs. According to our previous results, proteins that have a PT role are mainly involved in the activation of the EMT process. Interestingly, JTB overexpression has been correlated here with a plethora of significant upregulated and downregulated proteins that sustain JTB tumor suppressive functions. Our present and previous results sustain the necessity of the complementary use of different proteomics-based methods (SDS-PAGE, 2D-PAGE, and in-solution digestion) followed by tandem mass spectrometry to avoid their limitations, with each method leading to the delineation of specific clusters of DEPs that may be merged for a better understanding of molecular pathways and neoplastic mechanisms related to the JTB's role in BC initiation and progression.
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Affiliation(s)
- Madhuri Jayathirtha
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (B.A.P.)
| | - Taniya Jayaweera
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (B.A.P.)
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (B.A.P.)
| | - Brîndușa Alina Petre
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (B.A.P.)
- Laboratory of Biochemistry, Department of Chemistry, “Alexandru Ioan Cuza” University of Iasi, Carol I Bvd., No. 11, 700506 Iasi, Romania
- Center for Fundamental Research and Experimental Development in Translation Medicine—TRANSCEND, Regional Institute of Oncology, 700483 Iasi, Romania
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, “Alexandru Ioan Cuza” University of Iasi, Carol I Bvd., No. 20A, 700505 Iasi, Romania;
| | - Costel C. Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (B.A.P.)
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5
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Nayak S, Jiang K, Hope E, Cross M, Overmiller A, Naz F, Worrell S, Bajpai D, Hasneen K, Brooks SR, Dell'Orso S, Morasso MI. Chromatin Landscape Governing Murine Epidermal Differentiation. J Invest Dermatol 2023; 143:1220-1232.e9. [PMID: 36708949 PMCID: PMC10293054 DOI: 10.1016/j.jid.2022.12.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/16/2022] [Accepted: 12/12/2022] [Indexed: 01/27/2023]
Abstract
Chromatin landscape and regulatory networks are determinants in lineage specification and differentiation. To define the temporospatial differentiation axis in murine epidermal cells in vivo, we generated datasets profiling expression dynamics (RNA sequencing), chromatin accessibility (assay for transposase-accessible chromatin using sequencing), architecture (Hi-C), and histone modifications (chromatin immunoprecipitation followed by sequencing) in the epidermis. We show that many differentially regulated genes are suppressed during the differentiation process, with superenhancers controlling differentiation-specific epigenomic changes. Our data shows the relevance of the Dlx/Klf/Grhl combinatorial regulatory network in maintaining correct temporospatial gene expression during epidermal differentiation. We determined differential open compartments, topologically associating domain score, and looping in the basal cell and suprabasal cell epidermal fractions, with the evolutionarily conserved epidermal differentiation complex region showing distinct suprabasal cell-specific topologically associating domain and loop formation that coincided with superenhancer sites. Overall, our study provides a global genome-wide resource of chromatin dynamics that define unrecognized regulatory networks and the epigenetic control of Dlx3-bound superenhancer elements during epidermal differentiation.
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Affiliation(s)
- Subhashree Nayak
- Laboratory of Skin Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kan Jiang
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Emma Hope
- Laboratory of Skin Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael Cross
- Laboratory of Skin Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrew Overmiller
- Laboratory of Skin Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Faiza Naz
- Genomic Technology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephen Worrell
- Laboratory of Skin Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Deepti Bajpai
- Laboratory of Skin Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kowser Hasneen
- Laboratory of Skin Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephen R Brooks
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Stefania Dell'Orso
- Genomic Technology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Maria I Morasso
- Laboratory of Skin Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA.
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Botchkarev VA, Fessing MY, Sharov AA. Deciphering a Message from the Nucleus: How Transcription Factors and Spatial Chromatin Interactions Orchestrate Epidermal Differentiation. J Invest Dermatol 2023; 143:1117-1120. [PMID: 37045617 PMCID: PMC10715816 DOI: 10.1016/j.jid.2023.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 04/14/2023]
Affiliation(s)
- Vladimir A Botchkarev
- Department of Dermatology, Boston University School of Medicine, Boston, Massachusetts, USA.
| | - Michael Y Fessing
- Centre for Skin Sciences, School of Chemistry and Biosciences, University of Bradford, West Yorkshire, United Kingdom
| | - Andrey A Sharov
- Department of Dermatology, Boston University School of Medicine, Boston, Massachusetts, USA
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7
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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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8
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Chen GD, Fatima I, Xu Q, Rozhkova E, Fessing MY, Mardaryev AN, Sharov AA, Xu GL, Botchkarev VA. DNA dioxygenases Tet2/3 regulate gene promoter accessibility and chromatin topology in lineage-specific loci to control epithelial differentiation. SCIENCE ADVANCES 2023; 9:eabo7605. [PMID: 36630508 PMCID: PMC9833667 DOI: 10.1126/sciadv.abo7605] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 12/05/2022] [Indexed: 05/03/2023]
Abstract
Execution of lineage-specific differentiation programs requires tight coordination between many regulators including Ten-eleven translocation (TET) family enzymes, catalyzing 5-methylcytosine oxidation in DNA. Here, by using Keratin 14-Cre-driven ablation of Tet genes in skin epithelial cells, we demonstrate that ablation of Tet2/Tet3 results in marked alterations of hair shape and length followed by hair loss. We show that, through DNA demethylation, Tet2/Tet3 control chromatin accessibility and Dlx3 binding and promoter activity of the Krt25 and Krt28 genes regulating hair shape, as well as regulate interactions between the Krt28 gene promoter and distal enhancer. Moreover, Tet2/Tet3 also control three-dimensional chromatin topology in Keratin type I/II gene loci via DNA methylation-independent mechanisms. These data demonstrate the essential roles for Tet2/3 in establishment of lineage-specific gene expression program and control of Dlx3/Krt25/Krt28 axis in hair follicle epithelial cells and implicate modulation of DNA methylation as a novel approach for hair growth control.
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Affiliation(s)
- Guo-Dong Chen
- Department of Dermatology, Boston University, Boston, MA, USA
| | - Iqra Fatima
- Department of Dermatology, Boston University, Boston, MA, USA
| | - Qin Xu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Elena Rozhkova
- Department of Dermatology, Boston University, Boston, MA, USA
| | - Michael Y. Fessing
- Centre for Skin Sciences, School of Chemistry and Biosciences, University of Bradford, Bradford, UK
| | - Andrei N. Mardaryev
- Centre for Skin Sciences, School of Chemistry and Biosciences, University of Bradford, Bradford, UK
| | | | - Guo-Liang Xu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Medical College of Fudan University, Shanghai, China
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9
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From Nucleus to Organs: Insights of Aryl Hydrocarbon Receptor Molecular Mechanisms. Int J Mol Sci 2022; 23:ijms232314919. [PMID: 36499247 PMCID: PMC9738205 DOI: 10.3390/ijms232314919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) is a markedly established regulator of a plethora of cellular and molecular processes. Its initial role in the detoxification of xenobiotic compounds has been partially overshadowed by its involvement in homeostatic and organ physiology processes. In fact, the discovery of its ability to bind specific target regulatory sequences has allowed for the understanding of how AHR modulates such processes. Thereby, AHR presents functions in transcriptional regulation, chromatin architecture modifications and participation in different key signaling pathways. Interestingly, such fields of influence end up affecting organ and tissue homeostasis, including regenerative response both to endogenous and exogenous stimuli. Therefore, from classical spheres such as canonical transcriptional regulation in embryonic development, cell migration, differentiation or tumor progression to modern approaches in epigenetics, senescence, immune system or microbiome, this review covers all aspects derived from the balance between regulation/deregulation of AHR and its physio-pathological consequences.
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Tayem R, Niemann C, Pesch M, Morgner J, Niessen CM, Wickström SA, Aumailley M. Laminin 332 Is Indispensable for Homeostatic Epidermal Differentiation Programs. J Invest Dermatol 2021; 141:2602-2610.e3. [PMID: 33965403 DOI: 10.1016/j.jid.2021.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/24/2021] [Accepted: 04/13/2021] [Indexed: 12/16/2022]
Abstract
The skin epidermis is attached to the underlying dermis by a laminin 332 (Lm332)-rich basement membrane. Consequently, loss of Lm332 leads to the severe blistering disorder epidermolysis bullosa junctionalis in humans and animals. Owing to the indispensable role of Lm332 in keratinocyte adhesion in vivo, the severity of the disease has limited research into other functions of the protein. We have conditionally disrupted Lm332 expression in basal keratinocytes of adult mice. Although blisters develop along the interfollicular epidermis, hair follicle basal cells provide sufficient anchorage of the epidermis to the dermis, making inducible deletion of the Lama3 gene compatible with life. Loss of Lm332 promoted the thickening of the epidermis and exaggerated desquamation. Global RNA expression analysis revealed major changes in the expression of keratins, cornified envelope proteins, and cellular stress markers. These modifications of the keratinocyte genetic program are accompanied by changes in cell shape and disorganization of the actin cytoskeleton. These data indicate that loss of Lm332-mediated progenitor cell adhesion alters cell fate and disturbs epidermal homeostasis.
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Affiliation(s)
- Raneem Tayem
- Center for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Catherin Niemann
- Center for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Monika Pesch
- Center for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Jessica Morgner
- Paul Gerson Unna Group 'Skin Homeostasis and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany; Division of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Carien M Niessen
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Medical Faculty, Department of Cell Biology of the Skin, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Sara A Wickström
- Paul Gerson Unna Group 'Skin Homeostasis and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland; Wihuri Research Institute, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Monique Aumailley
- Center for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, Germany.
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Lin GW, Lai YC, Liang YC, Widelitz RB, Wu P, Chuong CM. Regional Specific Differentiation of Integumentary Organs: Regulation of Gene Clusters within the Avian Epidermal Differentiation Complex and Impacts of SATB2 Overexpression. Genes (Basel) 2021; 12:genes12081291. [PMID: 34440465 PMCID: PMC8394334 DOI: 10.3390/genes12081291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 12/24/2022] Open
Abstract
The epidermal differentiation complex (EDC) encodes a group of unique proteins expressed in late epidermal differentiation. The EDC gave integuments new physicochemical properties and is critical in evolution. Recently, we showed β-keratins, members of the EDC, undergo gene cluster switching with overexpression of SATB2 (Special AT-rich binding protein-2), considered a chromatin regulator. We wondered whether this unique regulatory mechanism is specific to β-keratins or may be derived from and common to EDC members. Here we explore (1) the systematic expression patterns of non-β-keratin EDC genes and their preferential expression in different skin appendages during development, (2) whether the expression of non-β-keratin EDC sub-clusters are also regulated in clusters by SATB2. We analyzed bulk RNA-seq and ChIP-seq data and also evaluated the disrupted expression patterns caused by overexpressing SATB2. The results show that the expression of whole EDDA and EDQM sub-clusters are possibly mediated by enhancers in E14-feathers. Overexpressing SATB2 down-regulates the enriched EDCRP sub-cluster in feathers and the EDCH sub-cluster in beaks. These results reveal the potential of complex epigenetic regulation activities within the avian EDC, implying transcriptional regulation of EDC members acting at the gene and/or gene cluster level in a temporal and skin regional-specific fashion, which may contribute to the evolution of diverse avian integuments.
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Affiliation(s)
- Gee-Way Lin
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (G.-W.L.); (Y.-C.L.); (Y.-C.L.); (R.B.W.); (P.W.)
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan
| | - Yung-Chih Lai
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (G.-W.L.); (Y.-C.L.); (Y.-C.L.); (R.B.W.); (P.W.)
- Integrative Stem Cell Center, China Medical University Hospital, Taichung 40447, Taiwan
- Institute of New Drug Development, China Medical University, Taichung 40402, Taiwan
| | - Ya-Chen Liang
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (G.-W.L.); (Y.-C.L.); (Y.-C.L.); (R.B.W.); (P.W.)
- Integrative Stem Cell Center, China Medical University Hospital, Taichung 40447, Taiwan
| | - Randall B. Widelitz
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (G.-W.L.); (Y.-C.L.); (Y.-C.L.); (R.B.W.); (P.W.)
| | - Ping Wu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (G.-W.L.); (Y.-C.L.); (Y.-C.L.); (R.B.W.); (P.W.)
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (G.-W.L.); (Y.-C.L.); (Y.-C.L.); (R.B.W.); (P.W.)
- Correspondence:
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12
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Affiliation(s)
- Bogi Andersen
- Departments of Medicine and Biological Chemistry, University of California, Irvine
| | - Sarah Millar
- Black Family Stem Cell Institute, Departments of Cell, Developmental and Regenerative Biology and Dermatology, Icahn School of Medicine at Mount Sinai
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13
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Rahim AB, Lim HK, Tan CYR, Jia L, Leo VI, Uemura T, Hardman-Smart J, Common JEA, Lim TC, Bellanger S, Paus R, Igarashi K, Yang H, Vardy LA. The Polyamine Regulator AMD1 Upregulates Spermine Levels to Drive Epidermal Differentiation. J Invest Dermatol 2021; 141:2178-2188.e6. [PMID: 33984347 DOI: 10.1016/j.jid.2021.01.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 01/15/2021] [Accepted: 01/27/2021] [Indexed: 12/29/2022]
Abstract
Maintaining tissue homeostasis depends on a balance between cell proliferation, differentiation, and apoptosis. Within the epidermis, the levels of the polyamines putrescine, spermidine, and spermine are altered in many different skin conditions, yet their role in epidermal tissue homeostasis is poorly understood. We identify the polyamine regulator, Adenosylmethionine decarboxylase 1 (AMD1), as a crucial regulator of keratinocyte (KC) differentiation. AMD1 protein is upregulated on differentiation and is highly expressed in the suprabasal layers of the human epidermis. During KC differentiation, elevated AMD1 promotes decreased putrescine and increased spermine levels. Knockdown or inhibition of AMD1 results in reduced spermine levels and inhibition of KC differentiation. Supplementing AMD1-knockdown KCs with exogenous spermidine or spermine rescued aberrant differentiation. We show that the polyamine shift is critical for the regulation of key transcription factors and signaling proteins that drive KC differentiation, including KLF4 and ZNF750. These findings show that human KCs use controlled changes in polyamine levels to modulate gene expression to drive cellular behavior changes. Modulation of polyamine levels during epidermal differentiation could impact skin barrier formation or can be used in the treatment of hyperproliferative skin disorders.
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Affiliation(s)
- Anisa B Rahim
- Skin Research Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Hui Kheng Lim
- Skin Research Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Christina Yan Ru Tan
- Skin Research Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Li Jia
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Vonny Ivon Leo
- Skin Research Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Takeshi Uemura
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Jonathan Hardman-Smart
- Centre for Dermatology Research, School of Biology, University of Manchester, Manchester, United Kingdom; NIHR Manchester Biomedical Research Centre, Manchester, United Kingdom; St John's Institute of Dermatology, King's College London, London, United Kingdom
| | - John E A Common
- Skin Research Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Thiam Chye Lim
- Division of Plastic, Reconstructive & Aesthetic Surgery, Department of Surgery, National University Hospital, National University of Singapore, Singapore, Singapore
| | - Sophie Bellanger
- Skin Research Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Ralf Paus
- Centre for Dermatology Research, School of Biology, University of Manchester, Manchester, United Kingdom; NIHR Manchester Biomedical Research Centre, Manchester, United Kingdom; Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Kazuei Igarashi
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Leah A Vardy
- Skin Research Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore.
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14
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Mathyer ME, Brettmann EA, Schmidt AD, Goodwin ZA, Oh IY, Quiggle AM, Tycksen E, Ramakrishnan N, Matkovich SJ, Guttman-Yassky E, Edwards JR, de Guzman Strong C. Selective sweep for an enhancer involucrin allele identifies skin barrier adaptation out of Africa. Nat Commun 2021; 12:2557. [PMID: 33963188 PMCID: PMC8105351 DOI: 10.1038/s41467-021-22821-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/30/2021] [Indexed: 02/03/2023] Open
Abstract
The genetic modules that contribute to human evolution are poorly understood. Here we investigate positive selection in the Epidermal Differentiation Complex locus for skin barrier adaptation in diverse HapMap human populations (CEU, JPT/CHB, and YRI). Using Composite of Multiple Signals and iSAFE, we identify selective sweeps for LCE1A-SMCP and involucrin (IVL) haplotypes associated with human migration out-of-Africa, reaching near fixation in European populations. CEU-IVL is associated with increased IVL expression and a known epidermis-specific enhancer. CRISPR/Cas9 deletion of the orthologous mouse enhancer in vivo reveals a functional requirement for the enhancer to regulate Ivl expression in cis. Reporter assays confirm increased regulatory and additive enhancer effects of CEU-specific polymorphisms identified at predicted IRF1 and NFIC binding sites in the IVL enhancer (rs4845327) and its promoter (rs1854779). Together, our results identify a selective sweep for a cis regulatory module for CEU-IVL, highlighting human skin barrier evolution for increased IVL expression out-of-Africa.
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Affiliation(s)
- Mary Elizabeth Mathyer
- grid.4367.60000 0001 2355 7002Division of Dermatology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Erin A. Brettmann
- grid.4367.60000 0001 2355 7002Division of Dermatology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Alina D. Schmidt
- grid.4367.60000 0001 2355 7002Division of Dermatology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Zane A. Goodwin
- grid.4367.60000 0001 2355 7002Division of Dermatology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Inez Y. Oh
- grid.4367.60000 0001 2355 7002Division of Dermatology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Ashley M. Quiggle
- grid.4367.60000 0001 2355 7002Division of Dermatology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Eric Tycksen
- grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Natasha Ramakrishnan
- grid.4367.60000 0001 2355 7002Division of Dermatology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Scot J. Matkovich
- grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Emma Guttman-Yassky
- grid.59734.3c0000 0001 0670 2351Department of Dermatology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029 USA
| | - John R. Edwards
- grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Cristina de Guzman Strong
- grid.4367.60000 0001 2355 7002Division of Dermatology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
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15
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Folding Keratin Gene Clusters during Skin Regional Specification. Dev Cell 2021; 53:561-576.e9. [PMID: 32516596 DOI: 10.1016/j.devcel.2020.05.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 02/19/2020] [Accepted: 05/11/2020] [Indexed: 02/08/2023]
Abstract
Regional specification is critical for skin development, regeneration, and evolution. The contribution of epigenetics in this process remains unknown. Here, using avian epidermis, we find two major strategies regulate β-keratin gene clusters. (1) Over the body, macro-regional specificities (scales, feathers, claws, etc.) established by typical enhancers control five subclusters located within the epidermal differentiation complex on chromosome 25; (2) within a feather, micro-regional specificities are orchestrated by temporospatial chromatin looping of the feather β-keratin gene cluster on chromosome 27. Analyses suggest a three-factor model for regional specification: competence factors (e.g., AP1) make chromatin accessible, regional specifiers (e.g., Zic1) target specific genome regions, and chromatin regulators (e.g., CTCF and SATBs) establish looping configurations. Gene perturbations disrupt morphogenesis and histo-differentiation. This chicken skin paradigm advances our understanding of how regulation of big gene clusters can set up a two-dimensional body surface map.
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16
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Abstract
Mechanisms controlling skin heterogeneity are poorly understood. In this issue of Developmental Cell, Liang et al. show that in chicken, the difference in β-keratin genes expressed in feathered and scaly skin is regulated via typical enhancers, while differential expression within individual feathers correlates with chromatin looping within the gene cluster.
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Affiliation(s)
- Mingang Xu
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sarah E Millar
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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17
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Caputo V, Strafella C, Termine A, Dattola A, Mazzilli S, Lanna C, Cosio T, Campione E, Novelli G, Giardina E, Cascella R. Overview of the molecular determinants contributing to the expression of Psoriasis and Psoriatic Arthritis phenotypes. J Cell Mol Med 2020; 24:13554-13563. [PMID: 33128843 PMCID: PMC7754002 DOI: 10.1111/jcmm.15742] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/07/2020] [Accepted: 07/30/2020] [Indexed: 12/17/2022] Open
Abstract
Psoriasis and psoriatic arthritis are multifactorial chronic disorders whose etiopathogenesis essentially derives from the alteration of several signalling pathways and the co-occurrence of genetic, epigenetic and non-genetic susceptibility factors that altogether affect the functional and structural property of the skin. Although shared and differential susceptibility genes and molecular pathways are known to contribute to the onset of pathological phenotypes, further research is needed to dissect the molecular causes of psoriatic disease and its progression towards Psoriatic Arthritis. This review will therefore be addressed to explore differences and similarities in the etiopathogenesis and progression of both disorders, with a particular focus on genes involved in the maintenance of the skin structure and integrity (keratins and collagens), modulation of patterns of recognition (through Toll-like receptors and dectin-1) and immuno-inflammatory response (by NLRP3-dependent inflammasome) to microbial pathogens. In addition, special emphasis will be given to the contribution of epigenetic elements (methylation pattern, non-coding RNAs, chromatin modifiers and 3D genome organization) to the etiopathogenesis and progression of psoriasis and psoriatic arthritis. The evidence discussed in this review highlights how the knowledge of patients' clinical and (epi)genomic make-up could be helpful for improving the available therapeutic strategies for psoriasis and psoriatic arthritis treatment.
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Affiliation(s)
- Valerio Caputo
- Medical Genetics LaboratoryDepartment of Biomedicine and PreventionTor Vergata UniversityRomeItaly
- Genomic Medicine Laboratory UILDMIRCCS Santa Lucia FoundationRomeItaly
| | - Claudia Strafella
- Medical Genetics LaboratoryDepartment of Biomedicine and PreventionTor Vergata UniversityRomeItaly
- Genomic Medicine Laboratory UILDMIRCCS Santa Lucia FoundationRomeItaly
| | - Andrea Termine
- Genomic Medicine Laboratory UILDMIRCCS Santa Lucia FoundationRomeItaly
| | - Annunziata Dattola
- Dermatologic ClinicDepartment of Systems MedicineTor Vergata UniversityRomeItaly
| | - Sara Mazzilli
- Dermatologic ClinicDepartment of Systems MedicineTor Vergata UniversityRomeItaly
| | - Caterina Lanna
- Dermatologic ClinicDepartment of Systems MedicineTor Vergata UniversityRomeItaly
| | - Terenzio Cosio
- Dermatologic ClinicDepartment of Systems MedicineTor Vergata UniversityRomeItaly
| | - Elena Campione
- Dermatologic ClinicDepartment of Systems MedicineTor Vergata UniversityRomeItaly
| | - Giuseppe Novelli
- Medical Genetics LaboratoryDepartment of Biomedicine and PreventionTor Vergata UniversityRomeItaly
- Neuromed Institute IRCCSPozzilliItaly
| | - Emiliano Giardina
- Genomic Medicine Laboratory UILDMIRCCS Santa Lucia FoundationRomeItaly
- Department of Biomedicine and PreventionUILDM Lazio Onlus FoundationTor Vergata UniversityRomeItaly
| | - Raffaella Cascella
- Medical Genetics LaboratoryDepartment of Biomedicine and PreventionTor Vergata UniversityRomeItaly
- Department of Biomedical SciencesCatholic University Our Lady of Good CounselTiranaAlbania
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18
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3D-FISH Analysis of the Spatial Genome Organization in Skin Cells in Situ. Methods Mol Biol 2020. [PMID: 32314220 DOI: 10.1007/978-1-0716-0648-3_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Spatial genome organization in the cell nucleus plays a crucial role in the control of genome functions. Our knowledge about spatial genome organization is relying on the advances in gene imaging technologies and the biochemical approaches based on the spatial dependent ligation of the genomic regions. Fluorescent in situ hybridization using specific fluorescent DNA and RNA probes in cells and tissues with the spatially preserved nuclear and genome architecture (3D-FISH) provides a powerful tool for the further advancement of our knowledge about genome structure and functions. Here we describe the 3D-FISH protocols allowing for such an analysis in mammalian tissue in situ including in the skin. These protocols include DNA probe amplification and labeling; tissue fixation; preservation and preparation for hybridization; hybridization of the DNA probes with genomic DNA in the tissue; and post-hybridization tissue sample processing.
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19
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González-Rico FJ, Vicente-García C, Fernández A, Muñoz-Santos D, Montoliu L, Morales-Hernández A, Merino JM, Román AC, Fernández-Salguero PM. Alu retrotransposons modulate Nanog expression through dynamic changes in regional chromatin conformation via aryl hydrocarbon receptor. Epigenetics Chromatin 2020; 13:15. [PMID: 32169107 PMCID: PMC7071633 DOI: 10.1186/s13072-020-00336-w] [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: 08/03/2019] [Accepted: 03/02/2020] [Indexed: 12/19/2022] Open
Abstract
Transcriptional repression of Nanog is an important hallmark of stem cell differentiation. Chromatin modifications have been linked to the epigenetic profile of the Nanog gene, but whether chromatin organization actually plays a causal role in Nanog regulation is still unclear. Here, we report that the formation of a chromatin loop in the Nanog locus is concomitant to its transcriptional downregulation during human NTERA-2 cell differentiation. We found that two Alu elements flanking the Nanog gene were bound by the aryl hydrocarbon receptor (AhR) and the insulator protein CTCF during cell differentiation. Such binding altered the profile of repressive histone modifications near Nanog likely leading to gene insulation through the formation of a chromatin loop between the two Alu elements. Using a dCAS9-guided proteomic screening, we found that interaction of the histone methyltransferase PRMT1 and the chromatin assembly factor CHAF1B with the Alu elements flanking Nanog was required for chromatin loop formation and Nanog repression. Therefore, our results uncover a chromatin-driven, retrotransposon-regulated mechanism for the control of Nanog expression during cell differentiation.
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Affiliation(s)
- Francisco J González-Rico
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Extremadura, Av. de Elvas s/n, 06071, Badajoz, Spain
| | - Cristina Vicente-García
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, C/Darwin 3, 28049, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Almudena Fernández
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, C/Darwin 3, 28049, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Diego Muñoz-Santos
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, C/Darwin 3, 28049, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Lluís Montoliu
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, C/Darwin 3, 28049, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Antonio Morales-Hernández
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Extremadura, Av. de Elvas s/n, 06071, Badajoz, Spain
| | - Jaime M Merino
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Extremadura, Av. de Elvas s/n, 06071, Badajoz, Spain
| | - Angel-Carlos Román
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Extremadura, Av. de Elvas s/n, 06071, Badajoz, Spain.
| | - Pedro M Fernández-Salguero
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Extremadura, Av. de Elvas s/n, 06071, Badajoz, Spain.
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20
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Phosphatase Regulator NIPP1 Restrains Chemokine-Driven Skin Inflammation. J Invest Dermatol 2020; 140:1576-1588. [PMID: 31972250 DOI: 10.1016/j.jid.2020.01.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/20/2019] [Accepted: 01/05/2020] [Indexed: 02/06/2023]
Abstract
Nuclear inhibitor of protein phosphatase 1 (NIPP1) is a ubiquitously expressed nuclear protein that regulates functions of protein serine/threonine phosphatase-1 in cell proliferation and lineage specification. The role of NIPP1 in tissue homeostasis is not fully understood. This study shows that the selective deletion of NIPP1 in mouse epidermis resulted in epidermal hyperproliferation, a reduced adherence of basal keratinocytes, and a gradual decrease in the stemness of hair follicle stem cells, culminating in hair loss. This complex phenotype was associated with chronic sterile skin inflammation and could be partially rescued by dexamethasone treatment. NIPP1-deficient keratinocytes massively expressed proinflammatory chemokines and immunomodulatory proteins in a cell-autonomous manner. Chemokines subsequently induced the recruitment and activation of immune cells, in particular conventional dendritic cells and Langerhans cells, accounting for the chronic inflammation phenotype. The data identifies NIPP1 as a key regulator of epidermal homeostasis and as a potential target for the treatment of inflammatory skin diseases.
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21
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Campbell MJ. Tales from topographic oceans: topologically associated domains and cancer. Endocr Relat Cancer 2019; 26:R611-R626. [PMID: 31505466 PMCID: PMC7664306 DOI: 10.1530/erc-19-0348] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/09/2019] [Indexed: 01/03/2023]
Abstract
The 3D organization of the genome within the cell nucleus has come into sharp focus over the last decade. This has largely arisen because of the application of genomic approaches that have revealed numerous levels of genomic and chromatin interactions, including topologically associated domains (TADs). The current review examines how these domains were identified, are organized, how their boundaries arise and are regulated, and how genes within TADs are coordinately regulated. There are many examples of the disruption to TAD structure in cancer and the altered regulation, structure and function of TADs are discussed in the context of hormone responsive cancers, including breast, prostate and ovarian cancer. Finally, some aspects of the statistical insight and computational skills required to interrogate TAD organization are considered and future directions discussed.
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Affiliation(s)
- Moray J Campbell
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
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22
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Lachner J, Ehrlich F, Mlitz V, Hermann M, Alibardi L, Tschachler E, Eckhart L. Immunolocalization and phylogenetic profiling of the feather protein with the highest cysteine content. PROTOPLASMA 2019; 256:1257-1265. [PMID: 31037447 PMCID: PMC6713690 DOI: 10.1007/s00709-019-01381-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
Feathers are the most complex skin appendages of vertebrates. Mature feathers consist of interconnected dead keratinocytes that are filled with heavily cross-linked proteins. Although the molecular architecture determines essential functions of feathers, only few feather proteins have been characterized with regard to their amino acid sequences and evolution. Here, we identify Epidermal Differentiation protein containing DPCC Motifs (EDDM) as a cysteine-rich protein that has co-evolved with other feather proteins. The EDDM gene is located within the avian epidermal differentiation complex (EDC), a cluster of genes that has originated and diversified in amniotes. EDDM shares the exon-intron organization with EDC genes of other amniotes, including humans, and a gene encoding an EDDM-like protein is present in crocodilians, suggesting that avian EDDM arose by sequence modification of an epidermal differentiation gene present in a common ancestor of archosaurs. The EDDM protein contains multiple sequence repeats and a higher number of cysteine residues than any other protein encoded in the EDC. Immunohistochemical analysis of chicken skin and skin appendages showed expression of EDDM in barb and barbules of feathers as well as in the subperiderm on embryonic scutate scales. These results suggest that the diversification and differential expression of EDDM, besides other EDC genes, was instrumental in facilitating the evolution of the most complex molecular architecture of feathers.
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Affiliation(s)
- Julia Lachner
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Florian Ehrlich
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Veronika Mlitz
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Marcela Hermann
- Department of Medical Biochemistry, Medical University of Vienna, Vienna, Austria
| | | | - Erwin Tschachler
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Leopold Eckhart
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria.
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23
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Miroshnikova YA, Cohen I, Ezhkova E, Wickström SA. Epigenetic gene regulation, chromatin structure, and force-induced chromatin remodelling in epidermal development and homeostasis. Curr Opin Genet Dev 2019; 55:46-51. [PMID: 31112907 DOI: 10.1016/j.gde.2019.04.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/05/2019] [Accepted: 04/15/2019] [Indexed: 01/14/2023]
Abstract
The skin epidermis is a constantly renewing stratified epithelium that provides essential protective barrier functions throughout life. Epidermal stratification is governed by a step-wise differentiation program that requires precise spatiotemporal control of gene expression. How epidermal self-renewal and differentiation are regulated remains a fundamental open question. Cell-intrinsic and cell-extrinsic mechanisms that modify chromatin structure and interactions have been identified as key regulators of epidermal differentiation and stratification. Here, we will review the recent advances in our understanding of how chromatin modifiers, tissue-specific transcription factors, and force-induced nuclear remodeling processes function to shape chromatin and to control epidermal tissue development and homeostasis.
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Affiliation(s)
- Yekaterina A Miroshnikova
- Helsinki Institute of Life Science, University of Helsinki, Biomedicum Helsinki, Haartmaninkatu 8, 00290, Finland; Wihuri Research Institute, University of Helsinki, Finland; Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Finland; Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Idan Cohen
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Elena Ezhkova
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA.
| | - Sara A Wickström
- Helsinki Institute of Life Science, University of Helsinki, Biomedicum Helsinki, Haartmaninkatu 8, 00290, Finland; Wihuri Research Institute, University of Helsinki, Finland; Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Finland; Max Planck Institute for Biology of Ageing, Cologne, Germany.
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24
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Kang S, Chovatiya G, Tumbar T. Epigenetic control in skin development, homeostasis and injury repair. Exp Dermatol 2019; 28:453-463. [PMID: 30624812 PMCID: PMC6488370 DOI: 10.1111/exd.13872] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 12/11/2018] [Accepted: 01/05/2019] [Indexed: 12/14/2022]
Abstract
Cell-type- and cell-state-specific patterns of covalent modifications on DNA and histone tails form global epigenetic profiles that enable spatiotemporal regulation of gene expression. These epigenetic profiles arise from coordinated activities of transcription factors and epigenetic modifiers, which result in cell-type-specific outputs in response to dynamic environmental conditions and signalling pathways. Recent mouse genetic and functional studies have highlighted the physiological significance of global DNA and histone epigenetic modifications in skin. Importantly, specific epigenetic profiles are emerging for adult skin stem cells that are associated with their cell fate plasticity and proper activity in tissue regeneration. We can now begin to draw a more comprehensive picture of how epigenetic modifiers orchestrate their cell-intrinsic role with microenvironmental cues for proper skin development, homeostasis and wound repair. The field is ripe to begin to implement these findings from the laboratory into skin therapies.
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Affiliation(s)
- Sangjo Kang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York
| | - Gopal Chovatiya
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York
| | - Tudorita Tumbar
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York
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25
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Huang P, Ge P, Tian QF, Huang GB. Prediction of key transcription factors during skin regeneration by combining gene expression data and regulatory network information analysis. INT J BIOMATH 2019. [DOI: 10.1142/s1793524519500244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Purpose: Burn is one of the most common injuries in clinical practice. The use of transcription factors (TFs) has been reported to reverse the epigenetic rewiring process and has great promise for skin regeneration. To better identify key TFs for skin reprogramming, we proposed a predictive system that conjoint analyzed gene expression data and regulatory network information. Methods: Firstly, the gene expression data in skin tissues were downloaded and the LIMMA package was used to identify differential-expressed genes (DEGs). Then three ways, including identification of TFs from the DEGs, enrichment analysis of TFs by a Fisher’s test, the direct and network-based influence degree analysis of TFs, were used to identify the key TFs related to skin regeneration. Finally, to obtain most comprehensive combination of TFs, the coverage extent of all the TFs were analyzed by Venn diagrams. Results: The top 30 TFs combinations with higher coverage were acquired. Especially, TFAP2A, ZEB1, and NFKB1 exerted greater regulatory influence on other DEGs in the local network and presented relatively higher degrees in the protein–protein interaction (PPI) networks. Conclusion: These TFs identification could give a deeper understanding of the molecular mechanism of cell trans-differentiation, and provide a reference for the skin regeneration and burn treatment.
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Affiliation(s)
- Ping Huang
- Medical Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, Jinan 250013, Shandong, P. R. China
| | - Peng Ge
- Department of Burn and Plastic Surgery, The People’s Hospital of Zhangqiu Area, Jinan 250200, Shandong, P. R. China
| | - Qing-Fen Tian
- Department of Burn and Plastic Surgery, Jinan Central Hospital Affiliated to Shandong University, Jinan 250013, Shandong, P. R. China
| | - Guo-Bao Huang
- Department of Burn and Plastic Surgery, Jinan Central Hospital Affiliated to Shandong University, Jinan 250013, Shandong, P. R. China
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Ali EI, Loidl J, Howard-Till RA. A streamlined cohesin apparatus is sufficient for mitosis and meiosis in the protist Tetrahymena. Chromosoma 2018; 127:421-435. [PMID: 29948142 PMCID: PMC6208729 DOI: 10.1007/s00412-018-0673-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/18/2018] [Accepted: 05/28/2018] [Indexed: 02/03/2023]
Abstract
In order to understand its diverse functions, we have studied cohesin in the evolutionarily distant ciliate model organism Tetrahymena thermophila. In this binucleate cell, the heritable germline genome is maintained separately from the transcriptionally active somatic genome. In a previous study, we showed that a minimal cohesin complex in Tetrahymena consisted of homologs of Smc1, Smc3, and Rec8, which are present only in the germline nucleus, where they are needed for normal chromosome segregation as well as meiotic DNA repair. In this study, we confirm that a putative homolog of Scc3 is a member of this complex. In the absence of Scc3, Smc1 and Rec8 fail to localize to germline nuclei, Rec8 is hypo-phosphorylated, and cells show phenotypes similar to depletion of Smc1 and Rec8. We also identify a homolog of Scc2, which in other organisms is part of a heterodimeric complex (Scc2/Scc4) that helps load cohesin onto chromatin. In Tetrahymena, Scc2 interacts with Rec8 and Scc3, and its absence causes defects in mitotic and meiotic divisions. Scc2 is not required for chromosomal association of cohesin, but Rec8 is hypo-phosphorylated in its absence. Moreover, we did not identify a homolog of the cohesin loader Scc4, and no evidence was found of auxiliary factors, such as Eco1, Pds5, or WAPL. We propose that in Tetrahymena, a single, minimal cohesin complex performs all necessary functions for germline mitosis and meiosis, but is dispensable for transcription regulation and chromatin organization of the somatic genome.
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Affiliation(s)
- Emine I Ali
- Department of Chromosome Biology, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Josef Loidl
- Department of Chromosome Biology, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Rachel A Howard-Till
- Department of Chromosome Biology, Vienna Biocenter, University of Vienna, Vienna, Austria.
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Holthaus KB, Strasser B, Lachner J, Sukseree S, Sipos W, Weissenbacher A, Tschachler E, Alibardi L, Eckhart L. Comparative Analysis of Epidermal Differentiation Genes of Crocodilians Suggests New Models for the Evolutionary Origin of Avian Feather Proteins. Genome Biol Evol 2018; 10:694-704. [PMID: 29447391 PMCID: PMC5827346 DOI: 10.1093/gbe/evy035] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2018] [Indexed: 12/22/2022] Open
Abstract
The epidermis of amniotes forms a protective barrier against the environment and the differentiation program of keratinocytes, the main cell type in the epidermis, has undergone specific alterations in the course of adaptation of amniotes to a broad variety of environments and lifestyles. The epidermal differentiation complex (EDC) is a cluster of genes expressed at late stages of keratinocyte differentiation in both sauropsids and mammals. In the present study, we identified and analyzed the crocodilian equivalent of the EDC. The gene complement of the EDC of both the American alligator and the saltwater crocodile were determined by comparative genomics, de novo gene prediction and identification of EDC transcripts in published transcriptome data. We found that crocodilians have an organization of the EDC similar to that of their closest living relatives, the birds, with which they form the clade Archosauria. Notable differences include the specific expansion of a subfamily of EDC genes in crocodilians and the loss of distinct ancestral EDC genes in birds. Identification and comparative analysis of crocodilian orthologs of avian feather proteins suggest that the latter evolved by cooption and sequence modification of ancestral EDC genes, and that the amplification of an internal highly cysteine-enriched amino acid sequence motif gave rise to the feather component epidermal differentiation cysteine-rich protein in the avian lineage. Thus, sequence diversification of EDC genes contributed to the evolutionary divergence of the crocodilian and avian integuments.
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Affiliation(s)
- Karin Brigit Holthaus
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Austria
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali (BiGeA), University of Bologna, Italy
| | - Bettina Strasser
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Austria
| | - Julia Lachner
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Austria
| | - Supawadee Sukseree
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Austria
| | - Wolfgang Sipos
- Clinical Department for Farm Animals and Herd Management, University of Veterinary Medicine Vienna, Austria
| | | | - Erwin Tschachler
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Austria
| | - Lorenzo Alibardi
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali (BiGeA), University of Bologna, Italy
| | - Leopold Eckhart
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Austria
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Banerji R, Skibbens RV, Iovine MK. Cohesin mediates Esco2-dependent transcriptional regulation in a zebrafish regenerating fin model of Roberts Syndrome. Biol Open 2017; 6:1802-1813. [PMID: 29084713 PMCID: PMC5769645 DOI: 10.1242/bio.026013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Robert syndrome (RBS) and Cornelia de Lange syndrome (CdLS) are human developmental disorders characterized by craniofacial deformities, limb malformation and mental retardation. These birth defects are collectively termed cohesinopathies as both arise from mutations in cohesion genes. CdLS arises due to autosomal dominant mutations or haploinsufficiencies in cohesin subunits (SMC1A, SMC3 and RAD21) or cohesin auxiliary factors (NIPBL and HDAC8) that result in transcriptional dysregulation of developmental programs. RBS arises due to autosomal recessive mutations in cohesin auxiliary factor ESCO2, the gene that encodes an N-acetyltransferase which targets the SMC3 subunit of the cohesin complex. The mechanism that underlies RBS, however, remains unknown. A popular model states that RBS arises due to mitotic failure and loss of progenitor stem cells through apoptosis. Previous findings in the zebrafish regenerating fin, however, suggest that Esco2-knockdown results in transcription dysregulation, independent of apoptosis, similar to that observed in CdLS patients. Previously, we used the clinically relevant CX43 to demonstrate a transcriptional role for Esco2. CX43 is a gap junction gene conserved among all vertebrates that is required for direct cell-cell communication between adjacent cells such that cx43 mutations result in oculodentodigital dysplasia. Here, we show that morpholino-mediated knockdown of smc3 reduces cx43 expression and perturbs zebrafish bone and tissue regeneration similar to those previously reported for esco2 knockdown. Also similar to Esco2-dependent phenotypes, Smc3-dependent bone and tissue regeneration defects are rescued by transgenic Cx43 overexpression, suggesting that Smc3 and Esco2 cooperatively act to regulate cx43 transcription. In support of this model, chromatin immunoprecipitation assays reveal that Smc3 binds to a discrete region of the cx43 promoter, suggesting that Esco2 exerts transcriptional regulation of cx43 through modification of Smc3 bound to the cx43 promoter. These findings have the potential to unify RBS and CdLS as transcription-based mechanisms.
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Affiliation(s)
- Rajeswari Banerji
- Department of Biological Science, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Robert V Skibbens
- Department of Biological Science, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - M Kathryn Iovine
- Department of Biological Science, Lehigh University, Bethlehem, Pennsylvania 18015, USA
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