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Kim SH, In Choi H, Choi MR, An GY, Binas B, Jung KH, Chai YG. Epigenetic regulation of IFITM1 expression in lipopolysaccharide-stimulated human mesenchymal stromal cells. Stem Cell Res Ther 2020; 11:16. [PMID: 31910882 PMCID: PMC6945778 DOI: 10.1186/s13287-019-1531-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 11/21/2019] [Accepted: 12/13/2019] [Indexed: 12/17/2022] Open
Abstract
Background Toll-like receptor 4 (TLR4) ligands such as lipopolysaccharide (LPS) activate immunomodulatory functions and the migration of human mesenchymal stromal cells (hMSCs). Here, we study the migration-related gene expression of LPS-stimulated hMSCs and the role and regulation of one of the upregulated genes, encoding the interferon-induced transmembrane protein 1 (IFITM1). Methods Gene expression profiles were determined by whole-transcriptome analysis (RNA-seq) and quantitative real-time PCR (qRT-PCR). Bioinformatics approaches were used to perform network and pathway analyses. The cell migration-related genes were identified with an in vitro wound healing assay. RNA interference (RNAi) was used to suppress the IFITM1 gene expression. The IFITM1 gene enhancer was analyzed by chromatin immunoprecipitation (ChIP) sequencing, ChIP-to-PCR, luciferase reporter assays, and qRT-PCR for enhancer RNAs (eRNAs). Results RNA-seq confirmed IFITM1 as an LPS-stimulated gene, and RNAi demonstrated its importance for the LPS-stimulated migration. LPS treatment increased the eRNA expression in enhancer region R2 (2 kb upstream) of the IFITM1 gene and enriched R2 for H3K27ac. Bioinformatics implicated the transcription factors NF-κB and IRF1, ChIP assays revealed their binding to R2, and chemical inhibition of NF-κB and RNAi directed against IRF1 prevented R2 eRNA and IFITM1 gene expression. Conclusions Increased expression of the IFITM1 gene is required for LPS-stimulated hMSC migration. We described several underlying changes in the IFITM1 gene enhancer, most notably the NF-κB-mediated activation of enhancer region R2.
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Affiliation(s)
- Sun Hwa Kim
- Department of Molecular & Life Science, Hanyang University, Ansan, 15588, Republic of Korea
| | - Hae In Choi
- Department of Bionanotechnology, Hanyang University, Seoul, 04673, Republic of Korea
| | - Mi Ran Choi
- Department of Psychiatry, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Ga Yeong An
- Department of Bionanotechnology, Hanyang University, Seoul, 04673, Republic of Korea
| | - Bert Binas
- Department of Molecular & Life Science, Hanyang University, Ansan, 15588, Republic of Korea.
| | - Kyoung Hwa Jung
- Convergence Technology Campus of Korea Polytechnic II, Incheon, 21417, Republic of Korea.
| | - Young Gyu Chai
- Department of Molecular & Life Science, Hanyang University, Ansan, 15588, Republic of Korea. .,Department of Bionanotechnology, Hanyang University, Seoul, 04673, Republic of Korea.
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Li P, Shi ML, Shen WL, Zhang Z, Xie DJ, Zhang XY, He C, Zhang Y, Zhao ZH. Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:885-893. [PMID: 28511927 PMCID: PMC7102783 DOI: 10.1016/j.bbagrm.2017.05.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/21/2017] [Accepted: 05/08/2017] [Indexed: 11/26/2022]
Abstract
Interferon-induced transmembrane protein (IFITM) 1, 2 and 3 genes encode a family of interferon (IFN)-induced transmembrane proteins that block entry of a broad spectrum of pathogens. However, the transcriptional regulation of these genes, especially whether there exist any enhancers and their roles during the IFN induction process remain elusive. Here, through public data mining, episomal luciferase reporter assay and in vivo CRISPR-Cas9 genome editing, we identified an IFN-responsive enhancer located 35kb upstream of IFITM3 gene promoter upregulating the IFN-induced expression of IFITM1, 2 and 3 genes. Chromatin immunoprecipitation (ChIP), electrophoretic mobility shift assay (EMSA) and luciferase reporter assay demonstrated that signal transducers and activators of transcription (STAT) 1 bound to the enhancer with the treatment of IFN and was indispensable for the enhancer activity. Furthermore, using chromosome conformation capture technique, we revealed that the IFITM1, 2 and 3 genes physically clustered together and constitutively looped to the distal enhancer through long-range interactions in both HEK293 and A549 cells, providing structural basis for coordinated regulation of IFITM1, 2 and 3 by the enhancer. Finally, we showed that in vivo truncation of the enhancer impaired IFN-induced resistance to influenza A virus (IAV) infection. These findings expand our understanding of the mechanisms underlying the transcriptional regulation of IFITM1, 2 and 3 expression and its ability to mediate IFN signaling.
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Affiliation(s)
- Ping Li
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Ming-Lei Shi
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Wen-Long Shen
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Zhang Zhang
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Fengtai District, Beijing 100071, China
| | - De-Jian Xie
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Xiang-Yuan Zhang
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Chao He
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Yan Zhang
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Fengtai District, Beijing 100071, China.
| | - Zhi-Hu Zhao
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Fengtai District, Beijing 100071, China.
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Abstract
The 9p21.3 locus was the first to yield to genome-wide association studies (GWAS) seeking common genetic variants predisposing to increased risk of coronary artery atherosclerotic disease (CAD). The 59 single nucleotide polymorphisms that show highest association with CAD are clustered in a region 100,000 to 150,000 base pairs 5' to the cyclin-dependent kinase inhibitors CDKN2B (coding for p15(ink4b)) and CDKN2A (coding for p16(ink4a) and p14(ARF)). This region also covers the 3' end of a long noncoding RNA transcribed antisense to CDKN2B (CDKN2BAS, aka ANRIL for antisense noncoding RNA at the ink4 locus) whose expression has been linked to chromatin remodeling at the locus. Despite intensive investigation over the past 7 years, the functional significance of the 9p21.3 locus remains elusive. Other variants at this locus have been associated with glaucoma, glioma, and type 2 diabetes mellitus, diseases that implicate tissue-resident macrophages. Here, we review the evidence that genetic variants at 9p21.3 disrupt tissue-specific enhancers and propose new insights to guide future studies.
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Shen C, Wu XR, Jiao WW, Sun L, Feng WX, Xiao J, Miao Q, Liu F, Yin QQ, Zhang CG, Guo YJ, Shen AD. A functional promoter polymorphism of IFITM3 is associated with susceptibility to pediatric tuberculosis in Han Chinese population. PLoS One 2013; 8:e67816. [PMID: 23874452 PMCID: PMC3706438 DOI: 10.1371/journal.pone.0067816] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 05/22/2013] [Indexed: 12/02/2022] Open
Abstract
A susceptibility locus for tuberculosis, a re-emerging infectious disease throughout the world, was previously discovered to exist on chromosome 11p15. IFITM3 gene encoding for interferon inducible transmembrane protein 3, is located at 11p15. It acts as an effector molecule for interferon-gamma, which is essential for anti-tuberculosis immune response. In order to investigate the association between susceptibility to TB and genetic polymorphisms of the IFITM3 core promoter, a case-control study including 368 TB patients and 794 healthy controls was performed in Han Chinese children in northern China. The rs3888188 polymorphism showed significant association with susceptibility to TB. The rs3888188 G allele, acting recessively, was more frequent in TB patients (95% confidence interval: 1.08–1.56, Bonferroni P-value: 0.039). We further assessed the effect of rs3888188 polymorphism on IFITM3 transcription in vitro. As based on luciferase promoter assays, the promoter activity of haplotypes with rs3888188 G allele was lower than that of haplotypes with rs3888188 T allele. Moreover, peripheral-blood mononuclear cells carrying rs3888188 GG genotype showed a reduced IFITM3 mRNA level compared to cells carrying TT or GT genotype. In conclusion, rs3888188, a functional promoter polymorphism of IFITM3, was identified to influence the risk for pediatric TB in Han Chinese population.
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Affiliation(s)
- Chen Shen
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Xi-rong Wu
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Wei-wei Jiao
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Lin Sun
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Wei-xing Feng
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Jing Xiao
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Qing Miao
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Fang Liu
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Qing-qin Yin
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Chen-guang Zhang
- Department of Cell Biology, Capital Medical University, Beijing, China
| | - Ya-jie Guo
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - A-dong Shen
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
- * E-mail:
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Cardon M, Loot G, Grenouillet G, Blanchet S. Host characteristics and environmental factors differentially drive the burden and pathogenicity of an ectoparasite: a multilevel causal analysis. J Anim Ecol 2011; 80:657-67. [PMID: 21303365 DOI: 10.1111/j.1365-2656.2011.01804.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
1. Understanding the ecological factors driving the burden and pathogenicity of parasites is challenging. Indeed, the dynamics of host-parasite interactions is driven by factors organized across nested hierarchical levels (e.g. hosts, localities), and indirect effects are expected owing to interactions between levels. 2. In this study, we combined Bayesian multilevel models, path analyses and a model selection procedure to account for these complexities and to decipher the relative effects of host- and environment-related factors on the burden and the pathogenicity of an ectoparasite (Tracheliastes polycolpus) on its fish host (Leuciscus leuciscus). We also tested the year-to-year consistency of the relationships linking these factors to the burden and the pathogenic effects of T. polycolpus. 3. We found significant relationships between the parasite burden and host-related factors: body length and age were positively related to parasite burden and heterozygous hosts displayed a higher parasite burden. In contrast, both host- and environment-related factors were linked to pathogenic effects. Pathogenicity was correlated negatively with host body length and positively with age; this illustrates that some factors (e.g. body length) showed inverse relationships with parasite burden and pathogenicity. Pathogenic effects were stronger in cooler upstream sites and where host density was lower. Path analyses revealed that these relationships between environment-related factors and pathogenic effects were direct and were not indirect relationships mediated by the host characteristics. Finally, we found that the strength and the shape of certain relationships were consistent across years, while they were clearly not for some others. 4. Our study illustrates that considering conjointly causal relationships among factors and the hierarchical structure of host-parasite interactions is appropriate for dissecting the complex links between hosts, parasites and their common environment.
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Affiliation(s)
- Maxime Cardon
- Laboratoire Evolution et Diversité Biologique, UMR 5174, CNRS - Université Paul Sabatier, 118 route de Narbonne, F-31062 Toulouse Cedex 4, France
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Siegrist F, Ebeling M, Certa U. The small interferon-induced transmembrane genes and proteins. J Interferon Cytokine Res 2010; 31:183-97. [PMID: 21166591 DOI: 10.1089/jir.2010.0112] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Interferon-induced transmembrane (IFITM) genes are transcribed in most tissues and are with the exception of IFITM5 interferon inducible. They are involved in early development, cell adhesion, and control of cell growth. Most IFITM genes are activated in response to bacterial and viral infections, and the exact host immune defense mechanisms are still unknown. Elevated gene expression triggered by past or chronic inflammation could prevent spreading of pathogens by limiting host cell proliferation. Accordingly, induction in cells with low basal protein levels is sufficient to drive growth arrest and a senescence-like morphology. On the other hand, loss of IFITM levels in cancer is correlated with pronounced malignancy; thus, these genes are considered as tumor suppressors. However, several cancer cells have deregulated high levels of IFITM transcripts, indicating a tumor progression stage where at least one of the interferon-controlled antiproliferative pathways has been silenced. Phylogenetic analyses of the protein coding genomic sequences suggest a single interferon-inducible gene in the common ancestor of rodents and primates. Biological functions studied so far may have evolved in parallel, and functional characterization of IFITM proteins will provide insight into innate immune defense, cancer development, and other pathways.
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Affiliation(s)
- Fredy Siegrist
- Non-Clinical Safety, F. Hoffmann-La Roche Ltd., Basel, Switzerland
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The cellular antiviral protein viperin is attenuated by proteasome-mediated protein degradation in Japanese encephalitis virus-infected cells. J Virol 2008; 82:10455-64. [PMID: 18768981 DOI: 10.1128/jvi.00438-08] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Viperin is identified as an antiviral protein induced by interferon (IFN), viral infections, and pathogen-associated molecules. In this study, we found that viperin is highly induced at the RNA level by Japanese encephalitis virus (JEV) and Sindbis virus (SIN) and that viperin protein is degraded in JEV-infected cells through a proteasome-dependent mechanism. Promoter analysis revealed that SIN induces viperin expression in an IFN-dependent manner but that JEV by itself activates the viperin promoter through IFN regulatory factor-3 and AP-1. The overexpression of viperin significantly decreased the production of SIN, but not of JEV, whereas the proteasome inhibitor MG132 sustained the protein level and antiviral effect of viperin in JEV-infected cells. Knockdown of viperin expression by RNA interference also enhanced the replication of SIN, but not that of JEV. Our results suggest that even though viperin gene expression is highly induced by JEV, it is negatively regulated at the protein level to counteract its antiviral effect. In contrast, SIN induces viperin through the action of IFN, and viperin exhibits potent antiviral activity against SIN.
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Xu X, Xing S, Du ZQ, Rothschild MF, Yerle M, Liu B. Porcine TEF1 and RTEF1: molecular characterization and association analyses with growth traits. Comp Biochem Physiol B Biochem Mol Biol 2008; 150:447-53. [PMID: 18558506 DOI: 10.1016/j.cbpb.2008.05.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Revised: 04/28/2008] [Accepted: 05/05/2008] [Indexed: 11/15/2022]
Abstract
TEA domain transcription factors play vital roles in myogenesis by binding the M-CAT motif in the promoter of the muscle-specific genes. In the present study, we cloned two porcine TEA domain family genes, TEF1 and RTEF1, and identified two different variants respectively. RT-PCR revealed that the TEF1-a variant was highly expressed and up-regulated with the development of the porcine skeletal muscle, indicating its potential regulatory function for muscle development. Promoter analysis revealed porcine TEF1 was regulated, in a TATA-independent manner, by a specific intact initiator element, and numerous binding motifs of multiple transcription factors, including SP1, CREB/ATF and AREB6. A substitution G93A was identified in the 5'-flanking sequence and used for the linkage mapping of TEF1. Association analyses in a BerkshirexYorkshire F(2) population revealed that the substitution of G93A has a significant effect on average daily gain from birth to weaning (p<0.05) and 16-day weight (p<0.05), and a suggestive effect on loin eye area (p<0.06), average back fat (p<0.07) and lumbar back fat (p<0.08). The association analyses results are in agreement with the gene's localization demonstrated by linkage analysis, SCHP and RH mapping to the QTL region of growth and carcass traits on chromosome 2p14-17.
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Affiliation(s)
- Xuewen Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
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