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Huber J, Tanasie NL, Zernia S, Stigler J. Single-molecule imaging reveals a direct role of CTCF's zinc fingers in SA interaction and cluster-dependent RNA recruitment. Nucleic Acids Res 2024; 52:6490-6506. [PMID: 38742641 PMCID: PMC11194110 DOI: 10.1093/nar/gkae391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/21/2024] [Accepted: 05/01/2024] [Indexed: 05/16/2024] Open
Abstract
CTCF is a zinc finger protein associated with transcription regulation that also acts as a barrier factor for topologically associated domains (TADs) generated by cohesin via loop extrusion. These processes require different properties of CTCF-DNA interaction, and it is still unclear how CTCF's structural features may modulate its diverse roles. Here, we employ single-molecule imaging to study both full-length CTCF and truncation mutants. We show that CTCF enriches at CTCF binding sites (CBSs), displaying a longer lifetime than observed previously. We demonstrate that the zinc finger domains mediate CTCF clustering and that clustering enables RNA recruitment, possibly creating a scaffold for interaction with RNA-binding proteins like cohesin's subunit SA. We further reveal a direct recruitment and an increase of SA residence time by CTCF bound at CBSs, suggesting that CTCF-SA interactions are crucial for cohesin stability on chromatin at TAD borders. Furthermore, we establish a single-molecule T7 transcription assay and show that although a transcribing polymerase can remove CTCF from CBSs, transcription is impaired. Our study shows that context-dependent nucleic acid binding determines the multifaceted CTCF roles in genome organization and transcription regulation.
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Affiliation(s)
- Jonas Huber
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Sarah Zernia
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Johannes Stigler
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
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2
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Del Moral-Morales A, Salgado-Albarrán M, Sánchez-Pérez Y, Wenke NK, Baumbach J, Soto-Reyes E. CTCF and Its Multi-Partner Network for Chromatin Regulation. Cells 2023; 12:1357. [PMID: 37408191 DOI: 10.3390/cells12101357] [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: 03/31/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 07/07/2023] Open
Abstract
Architectural proteins are essential epigenetic regulators that play a critical role in organizing chromatin and controlling gene expression. CTCF (CCCTC-binding factor) is a key architectural protein responsible for maintaining the intricate 3D structure of chromatin. Because of its multivalent properties and plasticity to bind various sequences, CTCF is similar to a Swiss knife for genome organization. Despite the importance of this protein, its mechanisms of action are not fully elucidated. It has been hypothesized that its versatility is achieved through interaction with multiple partners, forming a complex network that regulates chromatin folding within the nucleus. In this review, we delve into CTCF's interactions with other molecules involved in epigenetic processes, particularly histone and DNA demethylases, as well as several long non-coding RNAs (lncRNAs) that are able to recruit CTCF. Our review highlights the importance of CTCF partners to shed light on chromatin regulation and pave the way for future exploration of the mechanisms that enable the finely-tuned role of CTCF as a master regulator of chromatin.
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Affiliation(s)
- Aylin Del Moral-Morales
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City 05348, Mexico
- Institute for Computational Systems Biology, University of Hamburg, D-22607 Hamburg, Germany
| | - Marisol Salgado-Albarrán
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City 05348, Mexico
- Institute for Computational Systems Biology, University of Hamburg, D-22607 Hamburg, Germany
| | - Yesennia Sánchez-Pérez
- Subdirección de Investigación, Instituto Nacional de Cancerología, Mexico City 14080, Mexico
| | - Nina Kerstin Wenke
- Institute for Computational Systems Biology, University of Hamburg, D-22607 Hamburg, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, D-22607 Hamburg, Germany
- Computational BioMedicine Lab., University of Southern Denmark, DK-5230 Odense, Denmark
| | - Ernesto Soto-Reyes
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City 05348, Mexico
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Li R, Song J, Zhao A, Diao X, Zhang T, Qi X, Guan Z, An Y, Ren L, Wang C, He Y. Association of APP gene polymorphisms and promoter methylation with essential hypertension in Guizhou: a case-control study. Hum Genomics 2023; 17:25. [PMID: 36941702 PMCID: PMC10026478 DOI: 10.1186/s40246-023-00462-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 02/16/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Single-nucleotide polymorphisms (SNPs) and DNA methylation are crucial regulators of essential hypertension (EH). Amyloid precursor protein (APP) mutations are implicated in hypertension development. Nonetheless, studies on the association of APP gene polymorphism and promoter methylation with hypertension are limited. Therefore, this case-control aims to evaluate the genetic association of APP gene polymorphism and promoter methylation with EH in Guizhou populations. OBJECTIVE AND METHODS We conducted a case-control study on 343 EH patients and 335 healthy controls (including Miao, Buyi, and Han populations) in the Guizhou province of China to analyze 11 single-nucleotide polymorphisms (rs2040273, rs63750921, rs2211772, rs2830077, rs467021, rs368196, rs466433, rs364048, rs364051, rs438031, rs463946) in the APP gene via MassARRAY SNP. The MassARRAY EpiTYPER was employed to detect the methylation levels of the promoters. RESULTS In the Han population, the rs2211772 genotype distribution was significantly different between disease and control groups (χ2 = 6.343, P = 0.039). The CC genotype reduced the risk of hypertension compared to the TT or TC genotype (OR 0.105, 95%CI 0.012-0.914, P = 0.041). For rs2040273 in the Miao population, AG or GG genotype reduced the hypertension risk compared with the AA genotype (OR 0.533, 95%CI 0.294-0.965, P = 0.038). Haplotype TCC (rs364051-rs438031-rs463946) increased the risk of EH in Guizhou (OR 1.427, 95%CI 1.020-1.996, P = 0.037). Each 1% increase in CpG_19 (- 613 bp) methylation level was associated with a 4.1% increase in hypertension risk (OR 1.041, 95%CI 1.002-1.081, P = 0.039). Each 1% increase in CpG_1 (- 296 bp) methylation level was associated with an 8% decrease in hypertension risk in women (OR 0.920, 95%CI 0.860-0.984, P = 0.015). CpG_19 significantly correlated with systolic blood pressure (r = 0.2, P = 0.03). The methylation levels of CpG_19 in hypertensive patients with rs466433, rs364048, and rs364051 minor alleles were lower than that with wild-type alleles (P < 0.05). Moreover, rs467021 and rs364051 showed strong synergistic interaction with EH (χ2 = 7.633, P = 0.006). CpG_11, CpG_19, and rs364051 showed weak synergistic interaction with EH (χ2 = 19.874, P < 0.001). CONCLUSION In summary, rs2211772 polymorphism and promoter methylation level of APP gene may be linked to EH in Guizhou populations. Our findings will provide novel insights for genetic research of hypertension and Alzheimer's disease.
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Affiliation(s)
- Ruichao Li
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, & Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Juhui Song
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, & Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Ansu Zhao
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, & Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Xiaoyan Diao
- Department of Cardiovascular Medicine, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Ting Zhang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, & Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Xiaolan Qi
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, & Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Zhizhong Guan
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, & Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Yu An
- The Clinical Laboratory Center, Guizhou Provincial People's Hospital, Guiyang, China
| | - Lingyan Ren
- Antenatal Diagnosis Centre, Guizhou Provincial People's Hospital, Guiyang, China.
| | - Chanjuan Wang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, & Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, 550004, Guizhou, China.
| | - Yan He
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, & Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, 550004, Guizhou, China.
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Dinami R, Petti E, Porru M, Rizzo A, Ganci F, Sacconi A, Ostano P, Chiorino G, Trusolino L, Blandino G, Ciliberto G, Zizza P, Biroccio A. TRF2 cooperates with CTCF for controlling the oncomiR-193b-3p in colorectal cancer. Cancer Lett 2022; 533:215607. [PMID: 35240232 DOI: 10.1016/j.canlet.2022.215607] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/11/2022] [Accepted: 02/24/2022] [Indexed: 12/14/2022]
Abstract
The Telomeric Repeat binding Factor 2 (TRF2), a key protein involved in telomere integrity, is over-expressed in several human cancers and promotes tumor formation and progression. Recently, TRF2 has been also found outside telomeres where it can affect gene expression. Here we provide evidence that TRF2 is able to modulate the expression of microRNAs (miRNAs), small non-coding RNAs altered in human tumors. Among the miRNAs regulated by TRF2, we focused on miR-193b-3p, an oncomiRNA that positively correlates with TRF2 expression in human colorectal cancer patients from The Cancer Genome Atlas dataset. At the mechanistic level, the control of miR-193b-3p expression requires the cooperative activity between TRF2 and the chromatin organization factor CTCF. We found that CTCF physically interacts with TRF2, thus driving the proper positioning of TRF2 on a binding site located upstream the miR-193b-3p host-gene. The binding of TRF2 on the identified region is necessary for promoting the expression of miR-193b3p which, in turn, inhibits the translation of the onco-suppressive methyltransferase SUV39H1 and promotes tumor cell proliferation. The translational relevance of the oncogenic properties of miR-193b-3p was confirmed in patients, in whom the association between TRF2 and miR-193b-3p has a prognostic value.
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Affiliation(s)
- Roberto Dinami
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, Rome, 00144, Italy
| | - Eleonora Petti
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, Rome, 00144, Italy
| | - Manuela Porru
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, Rome, 00144, Italy
| | - Angela Rizzo
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, Rome, 00144, Italy
| | - Federica Ganci
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, Rome, 00144, Italy
| | - Andrea Sacconi
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, Rome, 00144, Italy
| | - Paola Ostano
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, via Malta 3, Biella, 13900, Italy
| | - Giovanna Chiorino
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, via Malta 3, Biella, 13900, Italy
| | - Livio Trusolino
- Department of Oncology, University of Torino, Strada Provinciale 142, Candiolo, TO, 10060, Italy; Laboratory of Translational Cancer Medicine, Candiolo Cancer Institute, FPO - IRCCS, Strada Provinciale 142, Candiolo, TO, 10060, Italy
| | - Giovanni Blandino
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, Rome, 00144, Italy
| | - Gennaro Ciliberto
- Scientific Direction, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, Rome, 00144, Italy
| | - Pasquale Zizza
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, Rome, 00144, Italy.
| | - Annamaria Biroccio
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, Rome, 00144, Italy.
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5
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Hua J, Chen Y, Fu B, Chen X, Xu XJ, Yang SH, Chen C, Xu YJ. Downregulation of p53 by Insufficient CTCF in CD4 + T Cells Is an Important Factor Inducing Acute Graft-Versus-Host Disease. Front Immunol 2020; 11:568637. [PMID: 33133081 PMCID: PMC7550539 DOI: 10.3389/fimmu.2020.568637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/26/2020] [Indexed: 01/10/2023] Open
Abstract
Recent evidence indicates that p53 plays a protective role against various systemic autoimmune diseases by suppressing pro-inflammatory cytokine production and reducing the number of pathogenic T cells. However, whether abnormal p53 expression participates in the development of acute graft-versus-host disease (aGVHD) remains unclear. In this study, we demonstrated that p53 was downregulated in CD4+ T cells from patients with aGVHD compared with the non-aGVHD group. Furthermore, we confirmed that low expression of CCCTC-binding factor (CTCF) in CD4+ T cells from aGVHD cases is an important factor affecting histone H3K9/K14 hypoacetylation in the p53 promoter and p53 downregulation. Restoring CTCF expression in CD4+ T cells from aGVHD patients increased p53 amounts and corrected the imbalance of Th17 cells/Tregs. Taken together, these results provide novel insights into p53 downregulation in CD4+ T cells from aGVHD patients.
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Affiliation(s)
- Juan Hua
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
| | - Yan Chen
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
| | - Bin Fu
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
| | - Xu Chen
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
| | - Xue-Jun Xu
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
| | - Shuang-Hui Yang
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
| | - Cong Chen
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
| | - Ya-Jing Xu
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
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6
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Wu Q, Liu P, Wang L. Many facades of CTCF unified by its coding for three-dimensional genome architecture. J Genet Genomics 2020; 47:407-424. [PMID: 33187878 DOI: 10.1016/j.jgg.2020.06.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/15/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023]
Abstract
CCCTC-binding factor (CTCF) is a multifunctional zinc finger protein that is conserved in metazoan species. CTCF is consistently found to play an important role in many diverse biological processes. CTCF/cohesin-mediated active chromatin 'loop extrusion' architects three-dimensional (3D) genome folding. The 3D architectural role of CTCF underlies its multifarious functions, including developmental regulation of gene expression, protocadherin (Pcdh) promoter choice in the nervous system, immunoglobulin (Ig) and T-cell receptor (Tcr) V(D)J recombination in the immune system, homeobox (Hox) gene control during limb development, as well as many other aspects of biology. Here, we review the pleiotropic functions of CTCF from the perspective of its essential role in 3D genome architecture and topological promoter/enhancer selection. We envision the 3D genome as an enormous complex architecture, with tens of thousands of CTCF sites as connecting nodes and CTCF proteins as mysterious bonds that glue together genomic building parts with distinct articulation joints. In particular, we focus on the internal mechanisms by which CTCF controls higher order chromatin structures that manifest its many façades of physiological and pathological functions. We also discuss the dichotomic role of CTCF sites as intriguing 3D genome nodes for seemingly contradictory 'looping bridges' and 'topological insulators' to frame a beautiful magnificent house for a cell's nuclear home.
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Affiliation(s)
- Qiang Wu
- MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Center for Comparative Biomedicine, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China.
| | - Peifeng Liu
- MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Center for Comparative Biomedicine, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China
| | - Leyang Wang
- MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Center for Comparative Biomedicine, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China
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7
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Abstract
In eukaryotes, DNA is highly compacted within the nucleus into a structure known as chromatin. Modulation of chromatin structure allows for precise regulation of gene expression, and thereby controls cell fate decisions. Specific chromatin organization is established and preserved by numerous factors to generate desired cellular outcomes. In embryonic stem (ES) cells, chromatin is precisely regulated to preserve their two defining characteristics: self-renewal and pluripotent state. This action is accomplished by a litany of nucleosome remodelers, histone variants, epigenetic marks, and other chromatin regulatory factors. These highly dynamic regulatory factors come together to precisely define a chromatin state that is conducive to ES cell maintenance and development, where dysregulation threatens the survival and fitness of the developing organism.
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Affiliation(s)
- David C Klein
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States.
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DNA methylation analysis on purified neurons and glia dissects age and Alzheimer's disease-specific changes in the human cortex. Epigenetics Chromatin 2018; 11:41. [PMID: 30045751 PMCID: PMC6058387 DOI: 10.1186/s13072-018-0211-3] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/17/2018] [Indexed: 12/30/2022] Open
Abstract
Background Epigenome-wide association studies (EWAS) based on human brain samples allow a deep and direct understanding of epigenetic dysregulation in Alzheimer’s disease (AD). However, strong variation of cell-type proportions across brain tissue samples represents a significant source of data noise. Here, we report the first EWAS based on sorted neuronal and non-neuronal (mostly glia) nuclei from postmortem human brain tissues. Results We show that cell sorting strongly enhances the robust detection of disease-related DNA methylation changes even in a relatively small cohort. We identify numerous genes with cell-type-specific methylation signatures and document differential methylation dynamics associated with aging specifically in neurons such as CLU, SYNJ2 and NCOR2 or in glia RAI1,CXXC5 and INPP5A. Further, we found neuron or glia-specific associations with AD Braak stage progression at genes such as MCF2L, ANK1, MAP2, LRRC8B, STK32C and S100B. A comparison of our study with previous tissue-based EWAS validates multiple AD-associated DNA methylation signals and additionally specifies their origin to neuron, e.g., HOXA3 or glia (ANK1). In a meta-analysis, we reveal two novel previously unrecognized methylation changes at the key AD risk genes APP and ADAM17. Conclusions Our data highlight the complex interplay between disease, age and cell-type-specific methylation changes in AD risk genes thus offering new perspectives for the validation and interpretation of large EWAS results. Electronic supplementary material The online version of this article (10.1186/s13072-018-0211-3) contains supplementary material, which is available to authorized users.
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Abstract
This paper provides a brief introductory review of the most recent advances in our knowledge about the structural and functional aspects of two transcriptional regulators: MeCP2, a protein whose mutated forms are involved in Rett syndrome; and CTCF, a constitutive transcriptional insulator. This is followed by a description of the PTMs affecting these two proteins and an analysis of their known interacting partners. A special emphasis is placed on the recent studies connecting these two proteins, focusing on the still poorly understood potential structural and functional interactions between the two of them on the chromatin substrate. An overview is provided for some of the currently known genes that are dually regulated by these two proteins. Finally, a model is put forward to account for their possible involvement in their regulation of gene expression.
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Affiliation(s)
- Juan Ausió
- a Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada.,b Center for Biomedical Research, University of Victoria, Victoria, BC V8W 3N5, Canada
| | - Philippe T Georgel
- c Department of Biological Sciences, Marshall University, Huntington, WV 25755, USA.,d Cell Differentiation and Development Center, Marshall University, Huntington, WV 25755, USA
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10
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Kim S, Yu NK, Kaang BK. CTCF as a multifunctional protein in genome regulation and gene expression. Exp Mol Med 2015; 47:e166. [PMID: 26045254 PMCID: PMC4491725 DOI: 10.1038/emm.2015.33] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/08/2015] [Accepted: 02/27/2015] [Indexed: 12/18/2022] Open
Abstract
CCCTC-binding factor (CTCF) is a highly conserved zinc finger protein and is best known as a transcription factor. It can function as a transcriptional activator, a repressor or an insulator protein, blocking the communication between enhancers and promoters. CTCF can also recruit other transcription factors while bound to chromatin domain boundaries. The three-dimensional organization of the eukaryotic genome dictates its function, and CTCF serves as one of the core architectural proteins that help establish this organization. The mapping of CTCF-binding sites in diverse species has revealed that the genome is covered with CTCF-binding sites. Here we briefly describe the diverse roles of CTCF that contribute to genome organization and gene expression.
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Affiliation(s)
- Somi Kim
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, Korea
| | - Nam-Kyung Yu
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, Korea
| | - Bong-Kiun Kaang
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, Korea
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11
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Genome-wide targeting of the epigenetic regulatory protein CTCF to gene promoters by the transcription factor TFII-I. Proc Natl Acad Sci U S A 2015; 112:E677-86. [PMID: 25646466 DOI: 10.1073/pnas.1416674112] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
CCCTC-binding factor (CTCF) is a key regulator of nuclear chromatin structure and gene regulation. The impact of CTCF on transcriptional output is highly varied, ranging from repression to transcriptional pausing and transactivation. The multifunctional nature of CTCF may be directed solely through remodeling chromatin architecture. However, another hypothesis is that the multifunctional nature of CTCF is mediated, in part, through differential association with protein partners having unique functions. Consistent with this hypothesis, our mass spectrometry analyses of CTCF interacting partners reveal a previously undefined association with the transcription factor general transcription factor II-I (TFII-I). Biochemical fractionation of CTCF indicates that a distinct CTCF complex incorporating TFII-I is assembled on DNA. Unexpectedly, we found that the interaction between CTCF and TFII-I is essential for directing CTCF to the promoter proximal regulatory regions of target genes across the genome, particularly at genes involved in metabolism. At genes coregulated by CTCF and TFII-I, we find knockdown of TFII-I results in diminished CTCF binding, lack of cyclin-dependent kinase 8 (CDK8) recruitment, and an attenuation of RNA polymerase II phosphorylation at serine 5. Phenotypically, knockdown of TFII-I alters the cellular response to metabolic stress. Our data indicate that TFII-I directs CTCF binding to target genes, and in turn the two proteins cooperate to recruit CDK8 and enhance transcription initiation.
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12
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Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding sites in the human genome. PLoS One 2012; 7:e41374. [PMID: 22829947 PMCID: PMC3400636 DOI: 10.1371/journal.pone.0041374] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 06/20/2012] [Indexed: 12/17/2022] Open
Abstract
Chromatin insulators are DNA elements that regulate the level of gene expression either by preventing gene silencing through the maintenance of heterochromatin boundaries or by preventing gene activation by blocking interactions between enhancers and promoters. CCCTC-binding factor (CTCF), a ubiquitously expressed 11-zinc-finger DNA-binding protein, is the only protein implicated in the establishment of insulators in vertebrates. While CTCF has been implicated in diverse regulatory functions, CTCF has only been studied in a limited number of cell types across human genome. Thus, it is not clear whether the identified cell type-specific differences in CTCF-binding sites are functionally significant. Here, we identify and characterize cell type-specific and ubiquitous CTCF-binding sites in the human genome across 38 cell types designated by the Encyclopedia of DNA Elements (ENCODE) consortium. These cell type-specific and ubiquitous CTCF-binding sites show uniquely versatile transcriptional functions and characteristic chromatin features. In addition, we confirm the insulator barrier function of CTCF-binding and explore the novel function of CTCF in DNA replication. These results represent a critical step toward the comprehensive and systematic understanding of CTCF-dependent insulators and their versatile roles in the human genome.
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13
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Lee BK, Bhinge AA, Battenhouse A, McDaniell RM, Liu Z, Song L, Ni Y, Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR. Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome Res 2011; 22:9-24. [PMID: 22090374 DOI: 10.1101/gr.127597.111] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cell-type diversity is governed in part by differential gene expression programs mediated by transcription factor (TF) binding. However, there are few systematic studies of the genomic binding of different types of TFs across a wide range of human cell types, especially in relation to gene expression. In the ENCODE Project, we have identified the genomic binding locations across 11 different human cell types of CTCF, RNA Pol II (RNAPII), and MYC, three TFs with diverse roles. Our data and analysis revealed how these factors bind in relation to genomic features and shape gene expression and cell-type specificity. CTCF bound predominantly in intergenic regions while RNAPII and MYC preferentially bound to core promoter regions. CTCF sites were relatively invariant across diverse cell types, while MYC showed the greatest cell-type specificity. MYC and RNAPII co-localized at many of their binding sites and putative target genes. Cell-type specific binding sites, in particular for MYC and RNAPII, were associated with cell-type specific functions. Patterns of binding in relation to gene features were generally conserved across different cell types. RNAPII occupancy was higher over exons than adjacent introns, likely reflecting a link between transcriptional elongation and splicing. TF binding was positively correlated with the expression levels of their putative target genes, but combinatorial binding, in particular of MYC and RNAPII, was even more strongly associated with higher gene expression. These data illuminate how combinatorial binding of transcription factors in diverse cell types is associated with gene expression and cell-type specific biology.
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Affiliation(s)
- Bum-Kyu Lee
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas 78712, USA
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14
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Weth O, Renkawitz R. CTCF function is modulated by neighboring DNA binding factors. Biochem Cell Biol 2011; 89:459-68. [PMID: 21895576 DOI: 10.1139/o11-033] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The zinc-finger protein CTCF was originally identified in the context of gene silencing and gene repression (Baniahmad et al. 1990; Lobanenkov et al. 1990). CTCF was later shown to be involved in several transcriptional mechanisms such as gene activation (Vostrov et al. 2002) and enhancer blocking (Filippova et al. 2001; Hark et al. 2000; Kanduri et al. 2000; Lutz et al. 2003; Szabó et al. 2000; Tanimoto et al. 2003; Phillips and Corces 2009; Bell et al. 1999; Zlatanova and Caiafa 2009a, 2009b). Insulators block the action of enhancers when positioned between enhancer and promoter. CTCF was found to be required in almost all cases of enhancer blocking tested in vertebrates. This CTCF-mediated enhancer blocking is in many instances conferred by constitutive CTCF action. For some examples however, a modulation of the enhancer blocking activity was documented (Lutz et al. 2003; Weth et al. 2010). One mechanism is achieved by regulation of binding to DNA. It was shown that CTCF is not able to bind to those binding-sites containing methylated CpG sequences. At the imprinting control region (ICR) of the Igf2/H19 locus the binding-site for CTCF on the paternal allele is methylated. This prevents DNA-binding of CTCF, resulting in the loss of enhancer blocking (Bell and Felsenfeld 2000; Chao et al. 2002; Filippova et al. 2001; Hark et al. 2000; Kanduri et al. 2000, 2002; Szabó et al. 2000; Takai et al. 2001). Not only can DNA methylation interfere with CTCF binding to DNA, it was also shown in one report that RNA transcription through the CTCF binding site results in CTCF eviction (Lefevre et al. 2008). In contrast to these cases most of the DNA sites are not differentially bound by CTCF. Even CTCF interaction with its cofactor cohesin does not seem to differ in different cell types (Schmidt et al. 2010). These results indicate that regulation of CTCF activity might be achieved by neighboring factors bound to DNA. In fact, whole genome analyses of CTCF binding sites identified several classes of neighboring sequences (Dickson et al. 2010; Boyle et al. 2010; Essien et al. 2009). Therefore, in this review we will summarize those results for which a combined action of CTCF with factors bound adjacently was found. These neighboring factors include the RNA polymerases I, II and III, another zinc finger factor VEZF1 and the factors YY1, SMAD, TR and Oct4. Each of these seems to influence, modulate or determine the function of CTCF. Thereby, at least some of the pleiotropic effects of CTCF can be explained.
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Affiliation(s)
- Oliver Weth
- Institute for Genetics, Justus-Liebig-University Giessen, D35392 Giessen, Germany.
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15
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Choi NM, Majumder P, Boss JM. Regulation of major histocompatibility complex class II genes. Curr Opin Immunol 2010; 23:81-7. [PMID: 20970972 DOI: 10.1016/j.coi.2010.09.007] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Accepted: 09/23/2010] [Indexed: 12/11/2022]
Abstract
The major histocompatibility complex class II (MHC-II) genes are regulated at the level of transcription. Recent studies have shown that chromatin modification is critical for efficient transcription of these genes, and a number of chromatin modifying complexes recruited to MHC-II genes have been described. The MHC-II genes are segregated from each other by a series of chromatin elements, termed MHC-II insulators. Interactions between MHC-insulators and the promoters of MHC-II genes are mediated by the insulator factor CCCTC-binding factor and are critical for efficient expression. This regulatory mechanism provides a novel view of how the entire MHC-II locus is assembled architecturally and can be coordinately controlled.
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Affiliation(s)
- Nancy M Choi
- Department of Microbiology & Immunology, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, United States
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16
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Cleary JD, Tomé S, López Castel A, Panigrahi GB, Foiry L, Hagerman KA, Sroka H, Chitayat D, Gourdon G, Pearson CE. Tissue- and age-specific DNA replication patterns at the CTG/CAG-expanded human myotonic dystrophy type 1 locus. Nat Struct Mol Biol 2010; 17:1079-87. [DOI: 10.1038/nsmb.1876] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Accepted: 06/24/2010] [Indexed: 01/30/2023]
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17
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Kitchen NS, Schoenherr CJ. Sumoylation modulates a domain in CTCF that activates transcription and decondenses chromatin. J Cell Biochem 2010; 111:665-75. [DOI: 10.1002/jcb.22751] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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18
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Bowers SR, Mirabella F, Calero-Nieto FJ, Valeaux S, Hadjur S, Baxter EW, Merkenschlager M, Cockerill PN. A conserved insulator that recruits CTCF and cohesin exists between the closely related but divergently regulated interleukin-3 and granulocyte-macrophage colony-stimulating factor genes. Mol Cell Biol 2009; 29:1682-93. [PMID: 19158269 PMCID: PMC2655614 DOI: 10.1128/mcb.01411-08] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Revised: 11/05/2008] [Accepted: 01/09/2009] [Indexed: 01/07/2023] Open
Abstract
The human interleukin-3 (IL-3) and granulocyte-macrophage colony-stimulating-factor (GM-CSF, or CSF2) gene cluster arose by duplication of an ancestral gene. Although just 10 kb apart and responsive to the same signals, the IL-3 and GM-CSF genes are nevertheless regulated independently by separate, tissue-specific enhancers. To understand the differential regulation of the IL-3 and GM-CSF genes we have investigated a cluster of three ubiquitous DNase I-hypersensitive sites (DHSs) located between the two genes. We found that each site contains a conserved CTCF consensus sequence, binds CTCF, and recruits the cohesin subunit Rad21 in vivo. The positioning of these sites relative to the IL-3 and GM-CSF genes and their respective enhancers is conserved between human and mouse, suggesting a functional role in the organization of the locus. We found that these sites effectively block functional interactions between the GM-CSF enhancer and either the IL-3 or the GM-CSF promoter in reporter gene assays. These data argue that the regulation of the IL-3 and the GM-CSF promoters depends on the positions of their enhancers relative to the conserved CTCF/cohesin-binding sites. We suggest that one important role of these sites is to enable the independent regulation of the IL-3 and GM-CSF genes.
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Affiliation(s)
- Sarion R Bowers
- Experimental Haematology, Leeds Institute of Molecular Medicine, University of Leeds, St. James's University Hospital, Leeds LS9 7TF, United Kingdom
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19
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Smith ST, Wickramasinghe P, Olson A, Loukinov D, Lin L, Deng J, Xiong Y, Rux J, Sachidanandam R, Sun H, Lobanenkov V, Zhou J. Genome wide ChIP-chip analyses reveal important roles for CTCF in Drosophila genome organization. Dev Biol 2009; 328:518-28. [PMID: 19210964 DOI: 10.1016/j.ydbio.2008.12.039] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Revised: 11/26/2008] [Accepted: 12/22/2008] [Indexed: 01/27/2023]
Abstract
Insulators or chromatin boundary elements are defined by their ability to block transcriptional activation by an enhancer and to prevent the spread of active or silenced chromatin. Recent studies have increasingly suggested that insulator proteins play a role in large-scale genome organization. To better understand insulator function on the global scale, we conducted a genome-wide analysis of the binding sites for the insulator protein CTCF in Drosophila by Chromatin Immunoprecipitation (ChIP) followed by a tiling-array analysis. The analysis revealed CTCF binding to many known domain boundaries within the Abd-B gene of the BX-C including previously characterized Fab-8 and MCP insulators, and the Fab-6 region. Based on this finding, we characterized the Fab-6 insulator element. In genome-wide analysis, we found that dCTCF-binding sites are often situated between closely positioned gene promoters, consistent with the role of CTCF as an insulator protein. Importantly, CTCF tends to bind gene promoters just upstream of transcription start sites, in contrast to the predicted binding sites of the insulator protein Su(Hw). These findings suggest that CTCF plays more active roles in regulating gene activity and it functions differently from other insulator proteins in organizing the Drosophila genome.
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Affiliation(s)
- Sheryl T Smith
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
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20
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Soshnev AA, Li X, Wehling MD, Geyer PK. Context differences reveal insulator and activator functions of a Su(Hw) binding region. PLoS Genet 2008; 4:e1000159. [PMID: 18704163 PMCID: PMC2493044 DOI: 10.1371/journal.pgen.1000159] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2008] [Accepted: 07/10/2008] [Indexed: 11/19/2022] Open
Abstract
Insulators are DNA elements that divide chromosomes into independent transcriptional domains. The Drosophila genome contains hundreds of binding sites for the Suppressor of Hairy-wing [Su(Hw)] insulator protein, corresponding to locations of the retroviral gypsy insulator and non-gypsy binding regions (BRs). The first non-gypsy BR identified, 1A-2, resides in cytological region 1A. Using a quantitative transgene system, we show that 1A-2 is a composite insulator containing enhancer blocking and facilitator elements. We discovered that 1A-2 separates the yellow (y) gene from a previously unannotated, non-coding RNA gene, named yar for y-achaete (ac) intergenic RNA. The role of 1A-2 was elucidated using homologous recombination to excise these sequences from the natural location, representing the first deletion of any Su(Hw) BR in the genome. Loss of 1A-2 reduced yar RNA accumulation, without affecting mRNA levels from the neighboring y and ac genes. These data indicate that within the 1A region, 1A-2 acts an activator of yar transcription. Taken together, these studies reveal that the properties of 1A-2 are context-dependent, as this element has both insulator and enhancer activities. These findings imply that the function of non-gypsy Su(Hw) BRs depends on the genomic environment, predicting that Su(Hw) BRs represent a diverse collection of genomic regulatory elements.
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Affiliation(s)
- Alexey A. Soshnev
- Program in Molecular and Cellular Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Xingguo Li
- Department of Biochemistry, University of Iowa, Iowa City, Iowa, United States of America
| | - Misty D. Wehling
- Program in Molecular and Cellular Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Pamela K. Geyer
- Program in Molecular and Cellular Biology, University of Iowa, Iowa City, Iowa, United States of America
- Department of Biochemistry, University of Iowa, Iowa City, Iowa, United States of America
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21
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Renda M, Baglivo I, Burgess-Beusse B, Esposito S, Fattorusso R, Felsenfeld G, Pedone PV. Critical DNA binding interactions of the insulator protein CTCF: a small number of zinc fingers mediate strong binding, and a single finger-DNA interaction controls binding at imprinted loci. J Biol Chem 2007; 282:33336-33345. [PMID: 17827499 DOI: 10.1074/jbc.m706213200] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The DNA-binding protein CTCF (CCCTC binding factor) mediates enhancer blocking insulation at sites throughout the genome and plays an important role in regulating allele-specific expression at the Igf2/H19 locus and at other imprinted loci. Evidence is also accumulating that CTCF is involved in large scale organization of genomic chromatin. Although CTCF has 11 zinc fingers, we show here that only 4 of these are essential to strong binding and that they recognize a core 12-bp DNA sequence common to most CTCF sites. By deleting individual fingers and mutating individual sites, we determined the orientation of binding. Furthermore, we were able to identify the specific finger and its point of DNA interaction that are responsible for the loss of CTCF binding when CpG residues are methylated in the imprinted Igf2/H19 locus. This single interaction appears to be critical for allele-specific binding and insulation by CTCF.
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Affiliation(s)
- Mario Renda
- Dipartimento di Scienze Ambientali, Seconda Università degli Studi di Napoli via Vivaldi 43, 81100 Caserta, Italy
| | - Ilaria Baglivo
- Dipartimento di Scienze Ambientali, Seconda Università degli Studi di Napoli via Vivaldi 43, 81100 Caserta, Italy
| | - Bonnie Burgess-Beusse
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0540
| | - Sabrina Esposito
- Dipartimento di Scienze Ambientali, Seconda Università degli Studi di Napoli via Vivaldi 43, 81100 Caserta, Italy
| | - Roberto Fattorusso
- Dipartimento di Scienze Ambientali, Seconda Università degli Studi di Napoli via Vivaldi 43, 81100 Caserta, Italy
| | - Gary Felsenfeld
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0540.
| | - Paolo V Pedone
- Dipartimento di Scienze Ambientali, Seconda Università degli Studi di Napoli via Vivaldi 43, 81100 Caserta, Italy.
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22
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Lv H, Jia L, Jia J. Promoter polymorphisms which modulate APP expression may increase susceptibility to Alzheimer's disease. Neurobiol Aging 2006; 29:194-202. [PMID: 17112637 DOI: 10.1016/j.neurobiolaging.2006.10.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2006] [Revised: 09/17/2006] [Accepted: 10/02/2006] [Indexed: 10/23/2022]
Abstract
Increasing evidence indicates that variants in promoter of the beta-amyloid precursor protein (APP) gene could up-regulate the APP gene expression and aggravate the amyloid beta protein (A beta) accumulation, thus contributing to the development of Alzheimer's disease (AD). In Chinese Han populations we found three polymorphisms in APP promoter: -877T/C(rs466433), -955A/G(rs364048) and -9G/C. The -877T and -955A alleles were over-represented in 209 sporadic AD (SAD) patients when compared to those in 437 healthy individuals. Furthermore, -877T/C and -955A/G were in strong linkage disequilibrium and they constructed a relatively risky -877T/-955A and a relatively protective -877C/-955G. Luciferase reporter assay indicated -877T/-955A had four times higher transcriptional activity than -877C/-955G. A more marked increase in -877T/-955A transcriptional activity was seen when under A beta(25-35) treatment. As for the -9G/C polymorphism, significant differences between the two alleles were not observed either in genetic evaluation or in functional assay. The present study provides strong evidence that APP promoter polymorphisms that significantly increase APP expression levels are associated with development of SAD.
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Affiliation(s)
- Haiyan Lv
- Department of Neurology, Xuanwu Hospital of the Capital University of Medical Sciences, Beijing 100053, PR China
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23
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El-Kady A, Klenova E. Regulation of the transcription factor, CTCF, by phosphorylation with protein kinase CK2. FEBS Lett 2005; 579:1424-34. [PMID: 15733852 DOI: 10.1016/j.febslet.2005.01.044] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2004] [Revised: 12/10/2004] [Accepted: 01/13/2005] [Indexed: 01/30/2023]
Abstract
CTCF is a transcription factor involved in various aspects of gene regulation. We previously reported that CTCF function is modulated by protein kinase CK2. In this report we investigate further the role of CK2 in regulating the transcriptional properties of CTCF. We demonstrate that coexpression of CTCF with CK2 switches function of CTCF from repressor to activator. The non-phosphorylatable mutant increases repression by CTCF and potentiates the growth-suppressive ability of the protein, whereas the phospho-mimetic mutant behaves in the opposite fashion. Mutation of the individual serines reveals that Serine 612 is a critical residue in regulation of CTCF by CK2.
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Affiliation(s)
- Ayman El-Kady
- Genetics Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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24
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Klenova E, Scott AC, Roberts J, Shamsuddin S, Lovejoy EA, Bergmann S, Bubb VJ, Royer HD, Quinn JP. YB-1 and CTCF differentially regulate the 5-HTT polymorphic intron 2 enhancer which predisposes to a variety of neurological disorders. J Neurosci 2004; 24:5966-73. [PMID: 15229244 PMCID: PMC6729234 DOI: 10.1523/jneurosci.1150-04.2004] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The serotonin transporter (5-HTT) gene contains a variable number tandem repeat (VNTR) domain within intron 2 that is often associated with a number of neurological conditions, including affective disorders. The implications of this polymorphism are not yet understood, however, we have previously demonstrated that the 5-HTT VNTR is a transcriptional regulatory domain, and the allelic variation supports differential reporter gene expression in vivo and in vitro. The aim of this study was to identify transcription factors responsible for the regulation of this VNTR. Using a yeast one-hybrid screen, we found the transcription factor Y box binding protein 1 (YB-1) interacts with the 5-HTT VNTR. Consistent with this, we demonstrate in a reporter gene assay that the polymorphic VNTR domains differentially respond to exogenous YB-1 and that YB-1 will bind to the VNTR in vitro in a sequence-specific manner. Interestingly, the transcription factor CCTC-binding factor (CTCF), previously shown to interact with YB-1, interferes with the ability of the VNTR to support YB-1-directed reporter gene expression. In addition, CTCF blocks the binding of YB-1 to its DNA recognition sequences in vitro, thus providing a possible mechanism of regulation of YB-1 activation of the VNTR by CTCF. Therefore, we have identified YB-1 and CTCF as transcription factors responsible, at least in part, for modulation of VNTR function as a transcriptional regulatory domain. Our data suggest a novel mechanism that explains, in part, the ability of the distinct VNTR copy numbers to support differential reporter gene expression based on YB-1 binding sites.
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Affiliation(s)
- Elena Klenova
- Department of Biological Sciences, University of Essex, Essex CO4 3SQ, United Kingdom.
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25
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Abstract
The nuclear factor CTCF was first identified as one of the factors binding to the regulatory regions of the c-myc gene. Further study of this protein revealed roles in transcriptional repression, insulator function, and imprinting genetic information. Recent studies have provided new insight into the mechanism through which this factor acts at various levels of gene regulation.
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Affiliation(s)
- Katherine L Dunn
- Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, Canada
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26
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Defossez PA, Gilson E. The vertebrate protein CTCF functions as an insulator in Saccharomyces cerevisiae. Nucleic Acids Res 2002; 30:5136-41. [PMID: 12466537 PMCID: PMC137948 DOI: 10.1093/nar/gkf629] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Insulators are elements that shelter genes from the effects of silencers or enhancers. CTCF is the only vertebrate protein that has a recognized role in transcriptional insulation, but how it exerts its effect is unknown. In an attempt to better understand how CTCF functions, we have used an insulation assay in Saccharomyces cerevisiae. We show that CTCF acts as an insulator in yeast, where it can efficiently block the spreading of repressive telomeric chromatin. We identify two domains of the protein that are responsible for this activity: a short and very potent N-terminal domain, as well as the C-terminus of the protein.
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Affiliation(s)
- Pierre-Antoine Defossez
- CNRS UMR 5665, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France.
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27
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Burton T, Liang B, Dibrov A, Amara F. Transforming growth factor-beta-induced transcription of the Alzheimer beta-amyloid precursor protein gene involves interaction between the CTCF-complex and Smads. Biochem Biophys Res Commun 2002; 295:713-23. [PMID: 12099698 DOI: 10.1016/s0006-291x(02)00725-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Transforming growth factor-beta-1 (TGF-beta), a key regulator of the brain responses to injury and inflammation, has been implicated in upregulating the expression of the Alzheimer amyloid precursor protein (APP) and Alzheimer's disease (AD) pathogenesis. However, little is known about the mechanisms underlying the effects of TGF-beta on APP expression. Analysis of APP promoter activity upstream of the chloramphenicol acetyltransferase reporter gene in normal human astrocytes (NHAs), revealed that the APP promoter binding beta (APBbeta) site (-93/-82) is responsive to TGF-beta. This site interacts with the zinc finger nuclear factor CTCF, involved in APP transcriptional activity. As determined by gel shift assay, there was no significant difference in the CTCF-APBbeta complex binding activity in the presence or absence of TGF-beta treatment of NHAs. To further investigate the contributions of the CTCF-complex and Smad proteins to the TGF-beta induced APP promoter activity, we examined the distribution of these factors and their DNA binding activity. Interestingly, upon TGF-beta treatment both Smads 3 and 4 were translocated to the nuclei in contrast to Smad 2, which was cytoplasmic. However, CTCF was predominantly localized in the nuclei irrespective of TGF-beta treatment. Gel super shift assay coupled with Western blot analysis showed that Smads 3 and 4 specifically associated with the CTCF-APBbeta complex. In addition, AD brain sections showed increased expression and nuclear localization of Smad 4, which correlated with higher levels of APP and TGF-beta. However, over expression of Smad 4 on its own was not sufficient to affect APP expression. These results demonstrate that TGF-beta activation of Smad protein complexes promotes transcription of the APP gene. Increased synthesis of APP may in part determine Abeta production and deposition in affected AD brain.
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Affiliation(s)
- Teralee Burton
- The Dr. John Foerster Centre for Health Research on Aging. St. Boniface General Hospital Research Centre, 351 Taché Avenue, Winnipeg, MB, Canada R3E 0W3
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28
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Loukinov DI, Pugacheva E, Vatolin S, Pack SD, Moon H, Chernukhin I, Mannan P, Larsson E, Kanduri C, Vostrov AA, Cui H, Niemitz EL, Rasko JEJ, Docquier FM, Kistler M, Breen JJ, Zhuang Z, Quitschke WW, Renkawitz R, Klenova EM, Feinberg AP, Ohlsson R, Morse HC, Lobanenkov VV. BORIS, a novel male germ-line-specific protein associated with epigenetic reprogramming events, shares the same 11-zinc-finger domain with CTCF, the insulator protein involved in reading imprinting marks in the soma. Proc Natl Acad Sci U S A 2002; 99:6806-11. [PMID: 12011441 PMCID: PMC124484 DOI: 10.1073/pnas.092123699] [Citation(s) in RCA: 262] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
CTCF, a conserved, ubiquitous, and highly versatile 11-zinc-finger factor involved in various aspects of gene regulation, forms methylation-sensitive insulators that regulate X chromosome inactivation and expression of imprinted genes. We document here the existence of a paralogous gene with the same exons encoding the 11-zinc-finger domain as mammalian CTCF genes and thus the same DNA-binding potential, but with distinct amino and carboxy termini. We named this gene BORIS for Brother of the Regulator of Imprinted Sites. BORIS is present only in the testis, and expressed in a mutually exclusive manner with CTCF during male germ cell development. We show here that erasure of methylation marks during male germ-line development is associated with dramatic up-regulation of BORIS and down-regulation of CTCF expression. Because BORIS bears the same DNA-binding domain that CTCF employs for recognition of methylation marks in soma, BORIS is a candidate protein for the elusive epigenetic reprogramming factor acting in the male germ line.
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Affiliation(s)
- Dmitri I Loukinov
- Laboratory of Immunopathology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-0760, USA
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