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Pushkarev O, van Mierlo G, Kribelbauer JF, Saelens W, Gardeux V, Deplancke B. Non-coding variants impact cis-regulatory coordination in a cell type-specific manner. Genome Biol 2024; 25:190. [PMID: 39026229 PMCID: PMC11256678 DOI: 10.1186/s13059-024-03333-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 07/09/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND Interactions among cis-regulatory elements (CREs) play a crucial role in gene regulation. Various approaches have been developed to map these interactions genome-wide, including those relying on interindividual epigenomic variation to identify groups of covariable regulatory elements, referred to as chromatin modules (CMs). While CM mapping allows to investigate the relationship between chromatin modularity and gene expression, the computational principles used for CM identification vary in their application and outcomes. RESULTS We comprehensively evaluate and streamline existing CM mapping tools and present guidelines for optimal utilization of epigenome data from a diverse population of individuals to assess regulatory coordination across the human genome. We showcase the effectiveness of our recommended practices by analyzing distinct cell types and demonstrate cell type specificity of CRE interactions in CMs and their relevance for gene expression. Integration of genotype information revealed that many non-coding disease-associated variants affect the activity of CMs in a cell type-specific manner by affecting the binding of cell type-specific transcription factors. We provide example cases that illustrate in detail how CMs can be used to deconstruct GWAS loci, assess variable expression of cell surface receptors in immune cells, and reveal how genetic variation can impact the expression of prognostic markers in chronic lymphocytic leukemia. CONCLUSIONS Our study presents an optimal strategy for CM mapping and reveals how CMs capture the coordination of CREs and its impact on gene expression. Non-coding genetic variants can disrupt this coordination, and we highlight how this may lead to disease predisposition in a cell type-specific manner.
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Affiliation(s)
- Olga Pushkarev
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Guido van Mierlo
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
| | - Judith Franziska Kribelbauer
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Wouter Saelens
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Vincent Gardeux
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
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2
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Pulugulla SH, Workman R, Rutter NW, Yang Z, Adamik J, Lupish B, Macar DA, El Abdouni S, Esposito EX, Galson DL, Camacho CJ, Madura JD, Auron PE. A combined computational and experimental approach reveals the structure of a C/EBPβ-Spi1 interaction required for IL1B gene transcription. J Biol Chem 2018; 293:19942-19956. [PMID: 30355733 DOI: 10.1074/jbc.ra118.005627] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/09/2018] [Indexed: 01/19/2023] Open
Abstract
We previously reported that transcription of the human IL1B gene, encoding the proinflammatory cytokine interleukin 1β, depends on long-distance chromatin looping that is stabilized by a mutual interaction between the DNA-binding domains (DBDs) of two transcription factors: Spi1 proto-oncogene at the promoter and CCAAT enhancer-binding protein (C/EBPβ) at a far-upstream enhancer. We have also reported that the C-terminal tail sequence beyond the C/EBPβ leucine zipper is critical for its association with Spi1 via an exposed residue (Arg-232) located within a pocket at one end of the Spi1 DNA-recognition helix. Here, combining in vitro interaction studies with computational docking and molecular dynamics of existing X-ray structures for the Spi1 and C/EBPβ DBDs, along with the C/EBPβ C-terminal tail sequence, we found that the tail sequence is intimately associated with Arg-232 of Spi1. The Arg-232 pocket was computationally screened for small-molecule binding aimed at IL1B transcription inhibition, yielding l-arginine, a known anti-inflammatory amino acid, revealing a potential for disrupting the C/EBPβ-Spi1 interaction. As evaluated by ChIP, cultured lipopolysaccharide (LPS)-activated THP-1 cells incubated with l-arginine had significantly decreased IL1B transcription and reduced C/EBPβ's association with Spi1 on the IL1B promoter. No significant change was observed in direct binding of either Spi1 or C/EBPβ to cognate DNA and in transcription of the C/EBPβ-dependent IL6 gene in the same cells. These results support the notion that disordered sequences extending from a leucine zipper can mediate protein-protein interactions and can serve as druggable targets for regulating gene promoter activity.
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Affiliation(s)
- Sree H Pulugulla
- From the Departments of Biological Sciences and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282
| | - Riley Workman
- Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282
| | - Nathan W Rutter
- Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282
| | - Zhiyong Yang
- the Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115
| | - Juraj Adamik
- the Department of Medicine, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Brian Lupish
- From the Departments of Biological Sciences and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282
| | - David A Macar
- From the Departments of Biological Sciences and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282
| | - Samir El Abdouni
- the Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | | | - Deborah L Galson
- the Department of Medicine, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15213,; the Department of Microbiology & Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania 15219
| | - Carlos J Camacho
- the Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Jeffry D Madura
- From the Departments of Biological Sciences and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282; Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282
| | - Philip E Auron
- From the Departments of Biological Sciences and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282; the Department of Microbiology & Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania 15219.
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Galatro TF, Holtman IR, Lerario AM, Vainchtein ID, Brouwer N, Sola PR, Veras MM, Pereira TF, Leite REP, Möller T, Wes PD, Sogayar MC, Laman JD, den Dunnen W, Pasqualucci CA, Oba-Shinjo SM, Boddeke EWGM, Marie SKN, Eggen BJL. Transcriptomic analysis of purified human cortical microglia reveals age-associated changes. Nat Neurosci 2017; 20:1162-1171. [PMID: 28671693 DOI: 10.1038/nn.4597] [Citation(s) in RCA: 459] [Impact Index Per Article: 65.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/16/2017] [Indexed: 12/14/2022]
Abstract
Microglia are essential for CNS homeostasis and innate neuroimmune function, and play important roles in neurodegeneration and brain aging. Here we present gene expression profiles of purified microglia isolated at autopsy from the parietal cortex of 39 human subjects with intact cognition. Overall, genes expressed by human microglia were similar to those in mouse, including established microglial genes CX3CR1, P2RY12 and ITGAM (CD11B). However, a number of immune genes, not identified as part of the mouse microglial signature, were abundantly expressed in human microglia, including TLR, Fcγ and SIGLEC receptors, as well as TAL1 and IFI16, regulators of proliferation and cell cycle. Age-associated changes in human microglia were enriched for genes involved in cell adhesion, axonal guidance, cell surface receptor expression and actin (dis)assembly. Limited overlap was observed in microglial genes regulated during aging between mice and humans, indicating that human and mouse microglia age differently.
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Affiliation(s)
- Thais F Galatro
- Department of Neuroscience, Section Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Neurology, Laboratory of Molecular and Cellular Biology, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Inge R Holtman
- Department of Neuroscience, Section Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Antonio M Lerario
- Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, Michigan, USA
| | - Ilia D Vainchtein
- Department of Neuroscience, Section Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Nieske Brouwer
- Department of Neuroscience, Section Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Paula R Sola
- Department of Neurology, Laboratory of Molecular and Cellular Biology, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Mariana M Veras
- Brazilian Aging Brain Study Group, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Tulio F Pereira
- Center for Studies of Cellular and Molecular Therapy (NAP-NETCEM-NUCEL), University of São Paulo, São Paulo, Brazil.,Chemistry Institute, Department of Biochemistry, University of São Paulo, São Paulo, Brazil
| | - Renata E P Leite
- Brazilian Aging Brain Study Group, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Thomas Möller
- Neuroinflammation Disease Biology Unit, Lundbeck Research USA, Paramus, New Jersey, USA
| | - Paul D Wes
- Neuroinflammation Disease Biology Unit, Lundbeck Research USA, Paramus, New Jersey, USA
| | - Mari C Sogayar
- Center for Studies of Cellular and Molecular Therapy (NAP-NETCEM-NUCEL), University of São Paulo, São Paulo, Brazil
| | - Jon D Laman
- Department of Neuroscience, Section Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Wilfred den Dunnen
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Carlos A Pasqualucci
- Brazilian Aging Brain Study Group, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Sueli M Oba-Shinjo
- Department of Neurology, Laboratory of Molecular and Cellular Biology, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Erik W G M Boddeke
- Department of Neuroscience, Section Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Suely K N Marie
- Department of Neurology, Laboratory of Molecular and Cellular Biology, School of Medicine, University of São Paulo, São Paulo, Brazil.,Center for Studies of Cellular and Molecular Therapy (NAP-NETCEM-NUCEL), University of São Paulo, São Paulo, Brazil
| | - Bart J L Eggen
- Department of Neuroscience, Section Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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5
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Shimokawa T, Nunomura S, Fujisawa D, Ra C. Identification of the C/EBPα C-terminal tail residues involved in the protein interaction with GABP and their potency in myeloid differentiation of K562 cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:1207-17. [PMID: 24076158 DOI: 10.1016/j.bbagrm.2013.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 09/18/2013] [Accepted: 09/19/2013] [Indexed: 11/17/2022]
Abstract
The CCAAT/enhancer-binding protein α (C/EBPα) is the member of a family of related basic leucine zipper (bZIP) transcription factors and is critical for granulopoiesis. We previously demonstrated that C/EBPα interacts with the ETS domain of widely expressed GABPα, which leads to cooperative transcriptional activation of the myeloid-specific promoter for human FCAR encoding the Fc receptor for IgA (FcαR, CD89) in part by facilitating recruitment of C/EBPα to the promoter. The C/EBPα molecule contains transactivation domains (TADs) at its N-terminus and a DNA-binding and dimerization bZIP structure at its C-terminus. We demonstrate here that GABPα interacts with the last 18 residues of the C/EBPα C-terminus beyond the bZIP DNA-binding and dimerizing region. Deletion of this C-terminus resulted in loss of GABPα interaction but not affecting its DNA binding ability, indicating that it is not required for homodimer formation. Moreover, the C-terminus confers the ability to functionally synergize with GABP on a heterologous TAD when fused to the C-terminus of the VP16 TAD. We identified a three-amino acid stretch (amino acids 341-343) that is important for both functional and protein interactions with GABP. Ectopic expression in K562 cells of C/EBPα mutant incapable of interacting with GABPα does not induce expression of granulocytic differentiation markers including CD15, CD11b, GCSF-R and C/EBPε, and does not inhibit proliferation, whereas wild type does. These results demonstrate the functional importance of the C/EBPα C-terminus beyond the bZIP DNA-binding and dimerization region, which may mediate cooperative activation by C/EBPα and GABP of myeloid-specific genes involved in C/EBPα-dependent granulopoiesis.
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Affiliation(s)
- Toshibumi Shimokawa
- Division of Molecular Cell Immunology and Allergology, Department of Biomedical Sciences, Nihon University School of Medicine, Itabashi-ku, Tokyo 173-8610, Japan.
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Ristola M, Arpiainen S, Shimokawa T, Ra C, Tienari J, Saleem MA, Holthöfer H, Lehtonen S. Regulation of nephrin gene by the Ets transcription factor, GA-binding protein. Nephrol Dial Transplant 2012. [PMID: 23197680 DOI: 10.1093/ndt/gfs482] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Transcription factor GA-binding protein (GABP) is suggested to be involved in the formation of the neuromuscular junctions by regulating the transcription of synapse genes. Interestingly, neurons and podocytes share molecular and functional similarities that led us to investigate the expression and function of GABP in podocytes and its role in transcriptional regulation of nephrin, the key molecule of the podocyte slit diaphragm that is essential for normal glomerular ultrafiltration. METHODS The expression and localization of GABP in the rat and human kidney as well as in human embryonic kidney A293 cells and undifferentiated and differentiated human podocytes were analysed by immunoblotting and immunostaining. The role of GABP in activating the nephrin promoter was investigated by reporter gene assay and site-directed mutagenesis of the GABP-binding elements, and the interaction of GABP with the nephrin promoter was analysed by chromatin immunoprecipitation. The function of GABP in podocytes was studied by knocking down GABPα in differentiated human podocytes using lentiviral shRNA targeting GABPα. RESULTS GABP is expressed in the nuclei in rat and human glomeruli. In addition, in A293 cells and undifferentiated and differentiated human podocytes, GABP highly enriches in the nucleus. GABP activates and binds nephrin proximal promoter and Ets sites are essential for this activity. Knock-down of GABPα stimulates apoptosis in cultured podocytes. CONCLUSIONS The results show that GABP is expressed in podocytes and is involved in the regulation of nephrin gene expression. Furthermore, GABP may be important in the maintenance of podocyte function by regulating apoptosis.
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Affiliation(s)
- Mervi Ristola
- Department of Pathology, Haartman Institute, University of Helsinki, Helsinki, Finland
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7
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The human immunoglobulin A Fc receptor FcαRI: a multifaceted regulator of mucosal immunity. Mucosal Immunol 2011; 4:612-24. [PMID: 21937986 DOI: 10.1038/mi.2011.36] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Immunoglobulin A (IgA) is commonly recognized as the most prevalent antibody (Ab) at mucosal sites with an important role in defense by shielding mucosal surfaces from invasion by pathogens. However, its potential to both actively dampen excessive immune responses or to initiate potent proinflammatory cellular processes is less well known. Interestingly, either functional outcome is mediated through interaction with the myeloid IgA Fc receptor FcαRI (CD89). Monomeric interaction of IgA with FcαRI triggers inhibitory signals that block activation via other receptors, whereas multimeric FcαRI crosslinking induces phagocytosis, reactive oxygen species production, antigen presentation, Ab-dependent cellular cytotoxicity, and cytokine release. Thus, FcαRI acts as a regulator between anti- and proinflammatory responses of IgA. As such, the biology of FcαRI, and its multifaceted role in immunity will be the focus of this review.
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8
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Vuong MT, Hahn-Zoric M, Lundberg S, Gunnarsson I, van Kooten C, Wramner L, Seddighzadeh M, Fernström A, Hanson LÅ, Do LT, Jacobson SH, Padyukov L. Association of soluble CD89 levels with disease progression but not susceptibility in IgA nephropathy. Kidney Int 2010; 78:1281-7. [PMID: 20811333 DOI: 10.1038/ki.2010.314] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The Fc-α receptor (FcαR/CD89) is involved in IgA complex formation and may affect the development of IgA nephropathy (IgAN). In this study, we tested the genetic variations of the CD89 gene in relation to disease susceptibility in IgAN and the expression of soluble CD89 (sCD89) in sera of patients with IgAN and in controls. There was a significant difference between the levels of sCD89-IgA complexes, measured by sandwich enzyme-linked immunosorbent assay (ELISA), in 177 patients with IgAN with and without disease progression at the time of first diagnosis. No such difference was found in 42 patients with other renal diseases. The patients with IgAN without disease progression had stable but high levels of sCD89 over 5-15 years of follow-up in contrast to stable but low levels of sCD89 in the disease progression group. Moreover, levels of sCD89 complexes were correlated with one of the five CD89 genetic variants in 212 patients with IgAN and 477 healthy Caucasians; the single-nucleotide polymorphism (SNP) rs11084377 was significantly associated with a lower expression of sCD89. However, no association between CD89 gene polymorphisms and susceptibility to IgAN was detected. Thus, we found an association between the levels of sCD89-IgA complexes in serum and the severity of IgAN, and a possible genetic component in regulating the production or expression of sCD89.
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Affiliation(s)
- Mai T Vuong
- Rheumatology Unit, Department of Medicine, Karolinska Institutet, Karolinska University Hospital at Solna, Stockholm, Sweden
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Amino acid residues in the β3 strand and subsequent loop of the conserved ETS domain that mediate basic leucine zipper (bZIP) recruitment and potentially distinguish functional attributes of Ets proteins. Biochem J 2010; 430:129-39. [DOI: 10.1042/bj20091742] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Ets family members share a conserved DNA-binding ETS domain, and serve a variety of roles in development, differentiation and oncogenesis. Besides DNA binding, the ETS domain also participates in protein–protein interactions with other structurally unrelated transcription factors. Although this mechanism appears to confer tissue- or development stage-specific functions on individual Ets proteins, the biological significance of many of these interactions remains to be evaluated, because their molecular basis has been elusive. We previously demonstrated a direct interaction between the ETS domain of the widely expressed GABPα (GA-binding protein α) and the granulocyte inducer C/EBPα (CCAAT/enhancer-binding protein α), and suggested its involvement in co-operative transcriptional activation of myeloid-specific genes, such as human FCAR encoding FcαR [Fc receptor for IgA (CD89)]. By deletion analysis, we identified helix α3 and the β3/β4 region as the C/EBPα-interacting region. Domain-swapping of individual sub-domains with those of other Ets proteins allowed us to highlight β-strand 3 and the subsequent loop, which when exchanged by those of Elf-1 (E74-like factor 1) reduced the ability to recruit C/EBPα. Further analysis identified a four-amino acid swap mutation of this region (I387L/C388A/K393Q/F395L) that reduces both physical interaction and co-operative transcriptional activation with C/EBPα without affecting its transactivation capacity by itself. Moreover, re-ChIP (re-chromatin immunoprecipitation) analysis demonstrated that GABPα recruits C/EBPα to the FCAR promoter, depending on these residues. The identified amino acid residues could confer the specificity of the action on the Ets proteins in diverse biological processes through mediating the recruitment of its partner factor.
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Le Bras A, Soncin F. [Genes that make the endothelial identity]. JOURNAL DE LA SOCIETE DE BIOLOGIE 2009; 203:125-41. [PMID: 19527626 DOI: 10.1051/jbio/2009016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The endothelium is a tissue with a distinct identity due to the specific expression of molecular markers by endothelial cells. Further, the endothelium displays a structural heterogeneity illustrated by the expression of specific markers in arteries and in veins. Here, we present a review of the transcriptional and epigenetic mechanisms regulating the expression of the main markers of endothelial cells in man and mouse, demonstrating that there is no common and unique mechanism of specific expression of genes in these cells.
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Affiliation(s)
- Alexandra Le Bras
- Institut de Biologie de Lille, CNRS UMR8161, Equipe Labellisée Ligue Nationale contre le Cancer 2008, Université de Lille I, Université de Lille II, Institut Pasteur de Lille, 1, rue Calmette, 59021 Lille Cedex, France
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11
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Lai CB, Zhang Y, Rogers SL, Mager DL. Creation of the two isoforms of rodent NKG2D was driven by a B1 retrotransposon insertion. Nucleic Acids Res 2009; 37:3032-43. [PMID: 19304755 PMCID: PMC2685100 DOI: 10.1093/nar/gkp174] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The mouse gene for the natural killer (NK) cell-activating receptor Nkg2d produces two protein isoforms, NKG2D-S and NKG2D-L, which differ by 13 amino acids at the N-terminus and have different signalling capabilities. These two isoforms are produced through differential splicing, but their regulation has not been investigated. In this study, we show that rat Nkg2d has the same splicing pattern as that of the mouse, and we mapped transcriptional start sites in both species. We found that the splice forms arise from alternative promoters and that the NKG2D-L promoter is derived from a rodent B1 retrotransposon that inserted before mouse–rat divergence. This B1 insertion is associated with loss of a nearby splice acceptor site that subsequently allowed creation of the short NKG2D isoform found in mouse but not human. Transient reporter assays indicate that the B1 element is a strong promoter with no inherent lymphoid tissue-specificity. We have also identified different binding sites for the ETS family member GABP within both the mouse and rat B1 elements that are necessary for high-promoter activity and for full Nkg2d-L expression. These findings demonstrate that a retroelement insertion has led to gene-regulatory change and functional diversification of rodent NKG2D.
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Affiliation(s)
- C Benjamin Lai
- Department of Medical Genetics, Terry Fox Laboratory, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, Canada
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12
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Takahashi K, Hayashi N, Shimokawa T, Umehara N, Kaminogawa S, Ra C. Cooperative regulation of Fc receptor gamma-chain gene expression by multiple transcription factors, including Sp1, GABP, and Elf-1. J Biol Chem 2008; 283:15134-41. [PMID: 18378679 PMCID: PMC3258888 DOI: 10.1074/jbc.m800498200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Revised: 03/05/2008] [Indexed: 11/06/2022] Open
Abstract
The Fc receptor gamma-chain (FcRgamma), which was first identified as a constituent of the high affinity IgE receptor, associates with various cell surface receptors to mediate intracellular signals. We identified three transcriptional enhancer elements in the 5' region of the human FcRgamma gene; one of the cis-elements was recognized by the transcription factor Sp-1 and another was recognized by GABP or Elf-1. The sequence of the other element was similar to a binding motif of the C/EBP family. Overexpression experiments showed that these transcription factors cooperatively activated the FcRgamma promoter. Furthermore, inactivation of the GABP-binding site by nucleotide substitutions as well as repression of GABPalpha expression by RNA interference reduced Sp1-mediated transactivation of the FcRgamma promoter, demonstrating that Sp1 and GABP synergistically activated the FcRgamma promoter. This synergistic activation was suggested to require physical interaction between the two transcription factors, because the Ets domain of GABPalpha was demonstrated to directly bind Sp1. On the other hand, GABP and Elf-1, whose recognition sequences overlapped, were shown to bind the FcRgamma gene with similar affinity in the context of chromatin, although Elf-1 exerted weaker enhancer activity for FcRgamma gene expression than did GABP. Both were thought to compete for binding to the element, because additional expression of Elf-1 in combination with Sp1 and GABP reduced FcRgamma promoter activity. Such functional and physical interactions among transcription factors involved in the cooperative regulation of FcRgamma gene expression as revealed in this study will become promising targets for medical applications against various immune diseases involving FcRgamma.
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Affiliation(s)
- Kyoko Takahashi
- Department of Molecular Cell Immunology and Allergology, Nihon University Graduate School of Medical Sciences, 30-1 Oyaguchi Kamima-chi, Itabashi-ku, Tokyo, Japan.
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Kang HS, Nelson ML, Mackereth CD, Schärpf M, Graves BJ, McIntosh LP. Identification and structural characterization of a CBP/p300-binding domain from the ETS family transcription factor GABP alpha. J Mol Biol 2008; 377:636-46. [PMID: 18295234 DOI: 10.1016/j.jmb.2008.01.054] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2007] [Revised: 01/16/2008] [Accepted: 01/17/2008] [Indexed: 12/20/2022]
Abstract
Using NMR spectroscopy, we identified and characterized a previously unrecognized structured domain near the N-terminus (residues 35-121) of the ETS family transcription factor GABP alpha. The monomeric domain folds as a five-stranded beta-sheet crossed by a distorted helix. Although globally resembling ubiquitin, the GABP alpha fragment differs in its secondary structure topology and thus appears to represent a new protein fold that we term the OST (On-SighT) domain. The surface of the GABP alpha OST domain contains two predominant clusters of negatively-charged residues suggestive of electrostatically driven interactions with positively-charged partner proteins. Following a best-candidate approach to identify such a partner, we demonstrated through NMR-monitored titrations and glutathione S-transferase pulldown assays that the OST domain binds to the CH1 and CH3 domains of the co-activator histone acetyltransferase CBP/p300. This provides a direct structural link between GABP and a central component of the transcriptional machinery.
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Affiliation(s)
- Hyun-Seo Kang
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
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Chen J, Blackwell TW, Fermin D, Menon R, Chen Y, Gao J, Lee AW, States DJ. Evolutionary-conserved gene expression response profiles across mammalian tissues. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2007; 11:96-115. [PMID: 17411398 DOI: 10.1089/omi.2006.0007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Gene expression responses are complex and frequently involve the actions of many genes to effect coordinated patterns. We hypothesized these coordinated responses are evolutionarily conserved and used a comparison of human and mouse gene expression profiles to identify the most prominent conserved features across a set of normal mammalian tissues. Based on data from multiple studies across multiple tissues in human and mouse, 13 gene expression modes across multiple tissues were identified in each of these species using principal component analysis. Strikingly, 1-to-1 pairing of human and mouse modes was observed in 12 out of 13 modes obtained from the two species independently. These paired modes define evolutionarily conserved gene expression response modes (CGEMs). Notably, in this study we were able to extract biological responses that are not overwhelmed by laboratory-to-laboratory or species-to-species variation. Of the variation in our gene expression dataset, 84% can be explained using these CGEMs. Functional annotation was performed using Gene Ontology, pathway, and transcription factor binding site over representation. Our conclusion is that we found an unbiased way of obtaining conserved gene response modes that accounts for a considerable portion of gene expression variation in a given dataset, as well as validates the conservation of major gene expression response modes across the mammals.
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Affiliation(s)
- Ji Chen
- Bioinformatics Program, University of Michigan, Ann Arbor, Michigan 48109, USA
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15
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Watanabe A, Shimokawa T, Moriyama M, Komine F, Amaki S, Arakawa Y, Ra C. Genetic variants of the IgA Fc receptor (FcαR, CD89) promoter in chronic hepatitis C patients. Immunogenetics 2006; 58:937-46. [PMID: 17033823 DOI: 10.1007/s00251-006-0159-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2006] [Accepted: 08/31/2006] [Indexed: 01/26/2023]
Abstract
Fc receptor for IgA (FcalphaR, CD89) is capable of triggering IgA-mediated immune responses to pathogens and has been proposed to function in circulating IgA clearance. Because inheritable variations modifying individual immune responses or immunoglobulin catabolism may affect the chronicity of viral infection, we investigated whether promoter polymorphisms of the FcalphaR gene (FCAR) affect chronic hepatitis C virus (HCV) infection and its disease progression. The two -311T/C and -142T/C single-nucleotide polymorphisms (SNPs) were studied by direct DNA sequencing in 177 Japanese patients with chronic hepatitis C (CHC). Both -311CC and -142CC genotypes were more frequent in CHC patients (15.9 and 18.6%) compared with 210 healthy controls (5.7 and 10.0%) [p = 0.001, odds ratio (OR) = 3.10, 95% confidence interval CI) = 1.53-6.30 and p = 0.014, OR = 2.06, 95% CI = 1.14-3.72, respectively], and were associated with infection with HCV genotype 2a/2b (p = 0.019 and p = 0.005, respectively). Conversely, -311CC and -142CC were decreased in 59 patients at advanced stages of disease as assessed on the basis of hepatic fibrosis markers such as decreased platelet count (PLT) (< 150,000/microl) (5.1 and 8.5%) compared with 91 patients with normal PLT (> or = 150,000/microl) (24.2 and 26.4%) (p = 0.006 and p = 0.005, respectively). Moreover, among the patients with normal PLT (but not with decreased PLT), -311CC or -142CC was significantly associated with decreased serum IgA levels (p = 0.023 or p = 0.007, respectively). These results suggest that the FCAR promoter SNPs may be related to chronic HCV infection and disease progression in Japanese CHC, which might be explained by altered FcalphaR expression affecting IgA-mediated immune responses and/or IgA catabolism.
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Affiliation(s)
- Azuma Watanabe
- Division of Molecular Cell Immunology and Allergology, Advanced Medical Research Center, Nihon University Graduate School of Medical Sciences, Tokyo, 173-8610, Japan
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Yaneva M, Kippenberger S, Wang N, Su Q, McGarvey M, Nazarian A, Lacomis L, Erdjument-Bromage H, Tempst P. PU.1 and a TTTAAA Element in the MyeloidDefensin-1Promoter Create an Operational TATA Box That Can Impose Cell Specificity onto TFIID Function. THE JOURNAL OF IMMUNOLOGY 2006; 176:6906-17. [PMID: 16709851 DOI: 10.4049/jimmunol.176.11.6906] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Defensins are major components of a peptide-based, antimicrobial system in human neutrophils. While packed with peptide, circulating cells contain no defensin-1 (def1) transcripts, except in some leukemia patients and in derivative promyelocytic leukemia cell lines. Expression is modulated by serum factors, mediators of inflammation, and kinase activators and inhibitors, but the underlying mechanisms are not fully understood. A minimal def1 promoter drives transcription in HL-60 cells under control of PU.1 and a def1-binding protein ("D1BP"), acting through, respectively, proximal (-22/-19) and distal (-62/-59) GGAA elements. In this study, we identify D1BP, biochemically and functionally, as GA-binding protein (GABP)alpha/GABPbeta. Whereas GABP operates as an essential upstream activator, PU.1 assists the flanking "TTTAAA" element (-32/-27), a "weak" but essential TATA box, to bring TBP/TFIID to the transcription start site. PU.1 thus imparts a degree of cell specificity to the minimal promoter and provides a potential link between a number of signaling pathways and TFIID. However, a "strong" TATA box ("TATAAA") eliminates the need for the PU.1 binding site and for PU.1, but not for GABP. As GABP is widely expressed, a strong TATA box thus alleviates promyelocytic cell specificity of the def1 promoter. These findings suggest how the myeloid def1 promoter may have evolutionarily acquired its current properties.
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Affiliation(s)
- Mariana Yaneva
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, and Weill Graduate School of Medical Sciences, Cornell University, New York, NY 10021, USA
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