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Figliozzi RW, Chen F, Hsia SV. Reversing thyroid-hormone-mediated repression of a HSV-1 promoter via computationally guided mutagenesis. J Cell Sci 2017; 130:3740-3748. [PMID: 28916515 DOI: 10.1242/jcs.204222] [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: 03/22/2017] [Accepted: 09/12/2017] [Indexed: 11/20/2022] Open
Abstract
Thyroid hormones (THs) and their DNA-binding nuclear receptors (TRs) direct transcriptional regulation in diverse ways depending on the host cell environment and specific promoter characteristics of TH-sensitive genes. This study sought to elucidate the impact on transcriptional repression of nucleotide sequence or orientation within TR binding sites - the TH response elements (TREs) of TH-sensitive promoters - to better understand ligand-dependent transcriptional repression of wild-type promoters. Computational analysis of the HSV-1 thymidine kinase (TK) gene TRE bound by TR and retinoid X receptor (RXR) revealed a single TRE point mutation sufficient to reverse the TRE orientation. In vitro experiments showed that the TRE point mutation had distinct impacts on promoter activity, sufficient to reverse the TH-dependent negative regulation in neuroendocrine differentiated cells. This point mutation altered the promoter's regulatory mechanism by discrete changes in transcription factor TR occupancy and altered enrichment of the repressive chromatin modification of histone-3-lysine-9-trimethyl (H3K9Me3). Insights relating to this negative TRE (nTRE) mechanism aids our understanding of other nTREs and TRE mutations associated with TH and herpes diseases.
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Affiliation(s)
- Robert W Figliozzi
- Department of Pharmaceutical Sciences, School of Pharmacy and Health Professions, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA.,Department of Natural Sciences, School of Agriculture and Natural Sciences, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA
| | - Feng Chen
- Department of Pharmaceutical Sciences, School of Pharmacy and Health Professions, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA
| | - Shaochung V Hsia
- Department of Pharmaceutical Sciences, School of Pharmacy and Health Professions, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA .,Department of Natural Sciences, School of Agriculture and Natural Sciences, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA
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Wang YL, Feng SH, Guo SC, Wei WJ, Li DS, Wang Y, Wang X, Wang ZY, Ma YY, Jin L, Ji QH, Wang JC. Confirmation of papillary thyroid cancer susceptibility loci identified by genome-wide association studies of chromosomes 14q13, 9q22, 2q35 and 8p12 in a Chinese population. J Med Genet 2013; 50:689-95. [DOI: 10.1136/jmedgenet-2013-101687] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Paul S, Kim SJ, Park HW, Lee SY, An YR, Oh MJ, Jung JW, Ryu JC, Hwang SY. Impact of miRNA deregulation on mRNA expression profiles in response to environmental toxicant, nonylphenol. Mol Cell Toxicol 2011. [DOI: 10.1007/s13273-011-0032-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Gillen AE, Harris A. The role of CTCF in coordinating the expression of single gene loci. Biochem Cell Biol 2011; 89:489-94. [PMID: 21916612 DOI: 10.1139/o11-040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The CCCTC-binding factor (CTCF), which binds insulator elements in vertebrates, also facilitates coordinated gene expression at several gene clusters, including the β-globin, Igf2/H19 (insulin like growth factor 2/H19 noncoding RNA), and major histocompatibility complex (MHC) class II loci. CTCF controls expression of these genes both by enabling insulator function and facilitating higher order chromatin interactions. While the role of CTCF in gene regulation is best studied at these multi-gene loci, there is also evidence that CTCF contributes to the regulated expression of single genes. Here, we discuss how CTCF participates in coordinating gene expression at the CFTR (cystic fibrosis transmembrane conductance regulator) and IFNG (interferon-gamma) loci. We consider the structural similarities between the loci with regard to CTCF-binding elements, the possible interaction between nuclear receptors and CTCF, and the role of CTCF in chromatin looping at these genes. These comparisons reveal a functional model that may be applicable to other single-gene loci that require CTCF for coordinated gene expression.
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Affiliation(s)
- Austin E Gillen
- Human Molecular Genetics Program, Children's Memorial Research Center, Department of Pediatrics, Northwestern University Feinberg School of Medicine Chicago, IL 60614, USA
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Abstract
Various factors/pathways including hormonal regulation have been suggested to control HSV-1 latency and reactivation. Our computer analysis identified a DNA repeat containing thyroid hormone response elements (TRE) in the regulatory region of HSV-1 LAT. Thyroid hormone (T3) exerts its function via its receptor (TR), a transcriptional factor. Present study investigated the roles of TR and T3 on HSV-1 gene expression using cultured neuoroblastoma cell lines. We demonstrated that liganded TR activated LAT transcription but repressed ICP0 transcription in the presence of LAT TRE. The chromatin immunoprecipitation (ChIP) assays showed that TRs were recruited to LAT TREs independently of T3 and hyperacetylated H4 was associated with promoters that were transcriptionally active. In addition, ChIP results showed that a chromatin insulator protein CTCF was enriched at the LAT TREs in the presence of TR and T3. In addition, chromatin remodeling factor BRG1 complex is found to participate in the T3/TR-mediated LAT activation since overexpression of BRG1 enhanced the LAT transcription and the dominant negative mutant K785R abolished the activation. This is the first report revealing that TR exerted epigenetic regulation on HSV-1 ICP0 expression in neuronal cells and could have a role in the complex processes of HSV-1 latency/reactivation.
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Canto-Soler MV, Huang H, Romero MS, Adler R. Transcription factors CTCF and Pax6 are segregated to different cell types during retinal cell differentiation. Dev Dyn 2008; 237:758-67. [PMID: 18224715 DOI: 10.1002/dvdy.21420] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
We have hypothesized that the transcription factor CTCF may influence retinal cell differentiation by controlling Pax6 expression, because (1) CTCF has been shown to repress Pax6 expression in some tissues, and (2) Pax6 blocks the differentiation of retinal progenitor cells as photoreceptors and promotes their differentiation as nonphotoreceptor neurons. Our results show that, as predicted by this hypothesis, CTCF and Pax6 become segregated to different retinal cell types. The factors are initially coexpressed in the undifferentiated neuroepithelium, but already at that time they show complementary periphery-to-fundus gradients of distribution. As the retina laminates, Pax6 becomes restricted to ganglion and amacrine cells, and CTCF to the bipolar/Muller cell layer and the outer nuclear layer. Polymerase chain reaction analysis of laser capture microdissection samples and dissociated cells showed that both immature and differentiated photoreceptors are CTCF (+)/ Pax6 (-). Functional studies are now under way to further analyze the role of CTCF in retinal cell differentiation.
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Affiliation(s)
- M Valeria Canto-Soler
- The Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287-9257, USA.
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Blackledge N, Carter E, Evans J, Lawson V, Rowntree R, Harris A. CTCF mediates insulator function at the CFTR locus. Biochem J 2007; 408:267-75. [PMID: 17696881 PMCID: PMC2267356 DOI: 10.1042/bj20070429] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Regulatory elements that lie outside the basal promoter of a gene may be revealed by local changes in chromatin structure and histone modifications. The promoter of the CFTR (cystic fibrosis transmembrane conductance regulator) gene is not responsible for its complex pattern of expression. To identify important regulatory elements for CFTR we have previously mapped DHS (DNase I-hypersensitive sites) across 400 kb spanning the locus. Of particular interest were two DHS that flank the CFTR gene, upstream at -20.9 kb with respect to the translational start site, and downstream at +15.6 kb. In the present study we show that these two DHS possess enhancer-blocking activity and bind proteins that are characteristic of known insulator elements. The DHS core at -20.9 kb binds CTCF (CCCTC-binding factor) both in vitro and in vivo; however, the +15.6 kb core appears to bind other factors. Histone-modification analysis across the CFTR locus highlights structural differences between the -20.9 kb and +15.6 kb DHS, further suggesting that these two insulator elements may operate by distinct mechanisms. We propose that these two DHS mark the boundaries of the CFTR gene functional unit and establish a chromatin domain within which the complex profile of CFTR expression is maintained.
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Affiliation(s)
- Neil P. Blackledge
- *Paediatric Molecular Genetics, Weatherall Institute of Molecular Medicine, Oxford University, John Radcliffe Hospital, Oxford OX3 9DS, U.K
- †Children's Memorial Research Center, Northwestern University Feinberg School of Medicine, 2300 Children's Plaza, Chicago, IL 60614, U.S.A
| | - Emma J. Carter
- *Paediatric Molecular Genetics, Weatherall Institute of Molecular Medicine, Oxford University, John Radcliffe Hospital, Oxford OX3 9DS, U.K
| | - Joanne R. Evans
- *Paediatric Molecular Genetics, Weatherall Institute of Molecular Medicine, Oxford University, John Radcliffe Hospital, Oxford OX3 9DS, U.K
| | | | - Rebecca K. Rowntree
- §Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, U.S.A
| | - Ann Harris
- *Paediatric Molecular Genetics, Weatherall Institute of Molecular Medicine, Oxford University, John Radcliffe Hospital, Oxford OX3 9DS, U.K
- †Children's Memorial Research Center, Northwestern University Feinberg School of Medicine, 2300 Children's Plaza, Chicago, IL 60614, U.S.A
- To whom correspondence should be addressed at Children's Memorial Research Center, Northwestern University Feinberg School of Medicine, 2300 Children's Plaza #211, Chicago, IL 60614, U.S.A. (email )
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Chau CM, Zhang XY, McMahon SB, Lieberman PM. Regulation of Epstein-Barr virus latency type by the chromatin boundary factor CTCF. J Virol 2006; 80:5723-32. [PMID: 16731911 PMCID: PMC1472585 DOI: 10.1128/jvi.00025-06] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Epstein Barr virus (EBV) can establish distinct latency types with different growth-transforming properties. Type I latency and type III latency can be distinguished by the expression of EBNA2, which has been shown to be regulated, in part, by the EBNA1-dependent enhancer activity of the origin of replication (OriP). Here, we report that CTCF, a chromatin boundary factor with well-established enhancer-blocking activity, binds to EBV sequences between the OriP and the RBP-Jkappa response elements of the C promoter (Cp) and regulates transcription levels of EBNA2 mRNA. Using DNA affinity, electrophoretic mobility shift assay, DNase I footprinting, and chromatin immunoprecipitation (ChIP), we found that CTCF binds both in vitro and in vivo to the EBV genome between OriP and Cp, with an approximately 50-bp footprint at EBV coordinates 10515 to 10560. Deletion of this CTCF binding site in a recombinant EBV bacterial artificial chromosome (BAC) increased EBNA2 transcription by 3.5-fold compared to a wild-type EBV BAC. DNA affinity and ChIP showed more CTCF binding at this site in type I latency cell lines (MutuI and KemI) than in type III latency cell lines (LCL3456 and Raji). CTCF protein and mRNA expression levels were higher in type I than type III cell lines. Short interfering RNA depletion of CTCF in type I MutuI cells stimulated EBNA2 mRNA levels, while overexpression of CTCF in type III Raji cells inhibited EBNA2 mRNA levels. These results indicate that increased CTCF can repress EBNA2 transcription. We also show that c-MYC, as well as EBNA2, can stimulate CTCF mRNA levels, suggesting that CTCF levels may contribute to B-cell differentiation as well as EBV latency type determination.
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