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YY1 interacts with guanine quadruplexes to regulate DNA looping and gene expression. Nat Chem Biol 2021; 17:161-168. [PMID: 33199912 PMCID: PMC7854983 DOI: 10.1038/s41589-020-00695-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/30/2020] [Accepted: 10/14/2020] [Indexed: 01/28/2023]
Abstract
The DNA guanine quadruplexes (G4) play important roles in multiple cellular processes, including DNA replication, transcription and maintenance of genome stability. Here, we showed that Yin and Yang 1 (YY1) can bind directly to G4 structures. ChIP-seq results revealed that YY1-binding sites overlap extensively with G4 structure loci in chromatin. We also observed that the dimerization of YY1 and its binding with G4 structures contribute to YY1-mediated long-range DNA looping. Displacement of YY1 from G4 structure sites disrupts substantially the YY1-mediated DNA looping. Moreover, treatment with G4-stabilizing ligands modulates the expression of not only those genes with G4 structures in their promoters, but also those associated with distal G4 structures that are brought to close proximity via YY1-mediated DNA looping. Together, we identified YY1 as a DNA G4-binding protein, and revealed that YY1-mediated long-range DNA looping requires its dimerization and occurs, in part, through its recognition of G4 structure.
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Verheul TCJ, van Hijfte L, Perenthaler E, Barakat TS. The Why of YY1: Mechanisms of Transcriptional Regulation by Yin Yang 1. Front Cell Dev Biol 2020; 8:592164. [PMID: 33102493 PMCID: PMC7554316 DOI: 10.3389/fcell.2020.592164] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022] Open
Abstract
First described in 1991, Yin Yang 1 (YY1) is a transcription factor that is ubiquitously expressed throughout mammalian cells. It regulates both transcriptional activation and repression, in a seemingly context-dependent manner. YY1 has a well-established role in the development of the central nervous system, where it is involved in neurogenesis and maintenance of homeostasis in the developing brain. In neurodevelopmental and neurodegenerative disease, the crucial role of YY1 in cellular processes in the central nervous system is further underscored. In this mini-review, we discuss the various mechanisms leading to the transcriptional activating and repressing roles of YY1, including its role as a traditional transcription factor, its interactions with cofactors and chromatin modifiers, the role of YY1 in the non-coding genome and 3D chromatin organization and the possible implications of the phase-separation mechanism on YY1 function. We provide examples on how these processes can be involved in normal development and how alterations can lead to various diseases.
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Affiliation(s)
- Thijs C J Verheul
- Department of Cell Biology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Levi van Hijfte
- Department of Neurology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Elena Perenthaler
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, Netherlands
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Kwon JE, Lee SY, Seo HB, Moon YM, Ryu JG, Jung KA, Jhun JY, Park JS, Hwang SS, Kim JM, Lee GR, Park SH, Cho ML. YinYang1 deficiency ameliorates joint inflammation in a murine model of rheumatoid arthritis by modulating Th17 cell activation. Immunol Lett 2018; 197:63-69. [DOI: 10.1016/j.imlet.2018.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 03/04/2018] [Accepted: 03/10/2018] [Indexed: 12/11/2022]
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Palstra RJ, de Crignis E, Röling MD, van Staveren T, Kan TW, van Ijcken W, Mueller YM, Katsikis PD, Mahmoudi T. Allele-specific long-distance regulation dictates IL-32 isoform switching and mediates susceptibility to HIV-1. SCIENCE ADVANCES 2018; 4:e1701729. [PMID: 29507875 PMCID: PMC5833994 DOI: 10.1126/sciadv.1701729] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 01/19/2018] [Indexed: 06/08/2023]
Abstract
We integrated data obtained from HIV-1 genome-wide association studies with T cell-derived epigenome data and found that the noncoding intergenic variant rs4349147, which is statistically associated with HIV-1 acquisition, is located in a CD4+ T cell-specific deoxyribonuclease I hypersensitive region, suggesting regulatory potential for this variant. Deletion of the rs4349147 element in Jurkat cells strongly reduced expression of interleukin-32 (IL-32), approximately 10-kb upstream, and chromosome conformation capture assays identified a chromatin loop between rs4349147 and the IL-32 promoter validating its function as a long-distance enhancer. We generated single rs4349147-A or rs4349147-G allele clones and demonstrated that IL-32 enhancer activity and interaction with the IL-32 promoter are strongly allele dependent; rs4349147 -/A cells display reduced IL-32 expression and altered chromatin conformation as compared to rs4349147 G/- cells. Moreover, RNA sequencing demonstrated that rs4349147 G/- cells express a lower relative ratio of IL-32α to non-α isoforms than rs4349147 -/A cells and display increased expression of lymphocyte activation factors rendering them more prone to infection with HIV-1. In agreement, in primary CD4+ T cells, both treatment with recombinant IL-32γ (rIL-32γ) but not rIL-32α, and exogenous lentiviral overexpression of IL-32γ or IL-32β but not IL-32α resulted in a proinflammatory T cell cytokine environment concomitant with increased susceptibility to HIV infection. Our data demonstrate that rs4349147-G promotes transcription of non-IL-32α isoforms, generating a proinflammatory environment more conducive to HIV infection. This study provides a mechanistic link between a HIV-associated noncoding DNA variant and the expression of different IL-32 isoforms that display discrete anti-HIV properties.
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Affiliation(s)
- Robert-Jan Palstra
- Department of Biochemistry, Erasmus University Medical Center, Ee-634, PO Box 2040, 3000CA Rotterdam, Netherlands
| | - Elisa de Crignis
- Department of Biochemistry, Erasmus University Medical Center, Ee-634, PO Box 2040, 3000CA Rotterdam, Netherlands
| | - Michael D. Röling
- Department of Biochemistry, Erasmus University Medical Center, Ee-634, PO Box 2040, 3000CA Rotterdam, Netherlands
| | - Thomas van Staveren
- Department of Biochemistry, Erasmus University Medical Center, Ee-634, PO Box 2040, 3000CA Rotterdam, Netherlands
| | - Tsung Wai Kan
- Department of Biochemistry, Erasmus University Medical Center, Ee-634, PO Box 2040, 3000CA Rotterdam, Netherlands
| | - Wilfred van Ijcken
- Erasmus Center for Biomics, Erasmus University Medical Center, Ee-671, PO Box 2040, 3000CA Rotterdam, Netherlands
| | - Yvonne M. Mueller
- Department of Immunology, Erasmus University Medical Center, Na-1218, PO Box 2040, 3000CA Rotterdam, Netherlands
| | - Peter D. Katsikis
- Department of Immunology, Erasmus University Medical Center, Na-1218, PO Box 2040, 3000CA Rotterdam, Netherlands
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, Ee-634, PO Box 2040, 3000CA Rotterdam, Netherlands
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CHOI GUNHO, KO KIHAN, KIM JUNGOH, KIM JINKWON, OH SEUNGHUN, HAN INBO, CHO KYUNGGI, KIM OKJOON, BAE JINKUN, KIM NAMKEUN. Association of miR-34a, miR-130a, miR-150 and miR-155 polymorphisms with the risk of ischemic stroke. Int J Mol Med 2016; 38:345-56. [DOI: 10.3892/ijmm.2016.2609] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 05/11/2016] [Indexed: 11/06/2022] Open
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Wang J, Meng X, Chen H, Yuan C, Li X, Zhou Y, Chen M. Exploring the mechanisms of genome-wide long-range interactions: interpreting chromosome organization. Brief Funct Genomics 2016; 15:385-95. [PMID: 26769147 DOI: 10.1093/bfgp/elv062] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Developments in chromosome conformation capture (3C) technologies have revealed that the three-dimensional organization of a genome leads widely separated functional elements to reside in close proximity. However, the mechanisms responsible for mediating long-range interactions are still not completely known. In this review, we firstly evaluate and compare the current seven 3C-based methods, summarize their advantages and discuss their limitations to our current understanding of genome structure. Then, software packages available to perform the analysis of 3C-based data are described. Moreover, we review the insights into the two main mechanisms of long-range interactions, which regulate gene expression by bringing together promoters and distal regulatory elements and by creating structural domains that contain functionally related genes with similar expression landscape. At last, we summarize what is known about the mediating factors involved in stimulation/repression of long-range interactions, such as transcription factors and noncoding RNAs.
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