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Villaman C, Pollastri G, Saez M, Martin AJ. Benefiting from the intrinsic role of epigenetics to predict patterns of CTCF binding. Comput Struct Biotechnol J 2023; 21:3024-3031. [PMID: 37266407 PMCID: PMC10229758 DOI: 10.1016/j.csbj.2023.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 06/03/2023] Open
Abstract
Motivation One of the most relevant mechanisms involved in the determination of chromatin structure is the formation of structural loops that are also related with the conservation of chromatin states. Many of these loops are stabilized by CCCTC-binding factor (CTCF) proteins at their base. Despite the relevance of chromatin structure and the key role of CTCF, the role of the epigenetic factors that are involved in the regulation of CTCF binding, and thus, in the formation of structural loops in the chromatin, is not thoroughly understood. Results Here we describe a CTCF binding predictor based on Random Forest that employs different epigenetic data and genomic features. Importantly, given the ability of Random Forests to determine the relevance of features for the prediction, our approach also shows how the different types of descriptors impact the binding of CTCF, confirming previous knowledge on the relevance of chromatin accessibility and DNA methylation, but demonstrating the effect of epigenetic modifications on the activity of CTCF. We compared our approach against other predictors and found improved performance in terms of areas under PR and ROC curves (PRAUC-ROCAUC), outperforming current state-of-the-art methods.
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Affiliation(s)
- Camilo Villaman
- Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Escuela de Ingeniería, Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | | | - Mauricio Saez
- Centro de Oncología de Precisión, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago, Chile
- Laboratorio de Investigación en Salud de Precisión, Departamento de Procesos Diagnósticos y Evaluación, Facultad de Ciencias de la Salud, Universidad Católica de Temuco, Chile
| | - Alberto J.M. Martin
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Escuela de Ingeniería, Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
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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: 3] [Impact Index Per Article: 3.0] [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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3
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Sun X, Zhang J, Cao C. CTCF and Its Partners: Shaper of 3D Genome during Development. Genes (Basel) 2022; 13:genes13081383. [PMID: 36011294 PMCID: PMC9407368 DOI: 10.3390/genes13081383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 02/06/2023] Open
Abstract
The 3D genome organization and its dynamic modulate genome function, playing a pivotal role in cell differentiation and development. CTCF and cohesin, acting as the core architectural components involved in chromatin looping and genome folding, can also recruit other protein or RNA partners to fine-tune genome structure during development. Moreover, systematic screening for partners of CTCF has been performed through high-throughput approaches. In particular, several novel protein and RNA partners, such as BHLHE40, WIZ, MAZ, Aire, MyoD, YY1, ZNF143, and Jpx, have been identified, and these partners are mostly implicated in transcriptional regulation and chromatin remodeling, offering a unique opportunity for dissecting their roles in higher-order chromatin organization by collaborating with CTCF and cohesin. Here, we review the latest advancements with an emphasis on features of CTCF partners and also discuss the specific functions of CTCF-associated complexes in chromatin structure modulation, which may extend our understanding of the functions of higher-order chromatin architecture in developmental processes.
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Affiliation(s)
- Xiaoyue Sun
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Jing Zhang
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Chunwei Cao
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Guangzhou Laboratory, Guangzhou 510320, China
- Correspondence:
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4
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Segueni J, Noordermeer D. CTCF: a misguided jack-of-all-trades in cancer cells. Comput Struct Biotechnol J 2022; 20:2685-2698. [PMID: 35685367 PMCID: PMC9166472 DOI: 10.1016/j.csbj.2022.05.044] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/20/2022] [Accepted: 05/21/2022] [Indexed: 12/13/2022] Open
Abstract
The emergence and progression of cancers is accompanied by a dysregulation of transcriptional programs. The three-dimensional (3D) organization of the human genome has emerged as an important multi-level mediator of gene transcription and regulation. In cancer cells, this organization can be restructured, providing a framework for the deregulation of gene activity. The CTCF protein, initially identified as the product from a tumor suppressor gene, is a jack-of-all-trades for the formation of 3D genome organization in normal cells. Here, we summarize how CTCF is involved in the multi-level organization of the human genome and we discuss emerging insights into how perturbed CTCF function and DNA binding causes the activation of oncogenes in cancer cells, mostly through a process of enhancer hijacking. Moreover, we highlight non-canonical functions of CTCF that can be relevant for the emergence of cancers as well. Finally, we provide guidelines for the computational identification of perturbed CTCF binding and reorganized 3D genome structure in cancer cells.
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5
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Alharbi AB, Schmitz U, Bailey CG, Rasko JEJ. CTCF as a regulator of alternative splicing: new tricks for an old player. Nucleic Acids Res 2021; 49:7825-7838. [PMID: 34181707 PMCID: PMC8373115 DOI: 10.1093/nar/gkab520] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/01/2021] [Accepted: 06/10/2021] [Indexed: 12/15/2022] Open
Abstract
Three decades of research have established the CCCTC-binding factor (CTCF) as a ubiquitously expressed chromatin organizing factor and master regulator of gene expression. A new role for CTCF as a regulator of alternative splicing (AS) has now emerged. CTCF has been directly and indirectly linked to the modulation of AS at the individual transcript and at the transcriptome-wide level. The emerging role of CTCF-mediated regulation of AS involves diverse mechanisms; including transcriptional elongation, DNA methylation, chromatin architecture, histone modifications, and regulation of splicing factor expression and assembly. CTCF thereby appears to not only co-ordinate gene expression regulation but contributes to the modulation of transcriptomic complexity. In this review, we highlight previous discoveries regarding the role of CTCF in AS. In addition, we summarize detailed mechanisms by which CTCF mediates AS regulation. We propose opportunities for further research designed to examine the possible fate of CTCF-mediated alternatively spliced genes and associated biological consequences. CTCF has been widely acknowledged as the 'master weaver of the genome'. Given its multiple connections, further characterization of CTCF's emerging role in splicing regulation might extend its functional repertoire towards a 'conductor of the splicing orchestra'.
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Affiliation(s)
- Adel B Alharbi
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, NSW 2006, Australia
- Cancer & Gene Regulation Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Ulf Schmitz
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, NSW 2006, Australia
| | - Charles G Bailey
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, NSW 2006, Australia
- Cancer & Gene Regulation Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
| | - John E J Rasko
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, NSW 2006, Australia
- Cell & Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
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6
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Valletta M, Russo R, Baglivo I, Russo V, Ragucci S, Sandomenico A, Iaccarino E, Ruvo M, De Feis I, Angelini C, Iachettini S, Biroccio A, Pedone PV, Chambery A. Exploring the Interaction between the SWI/SNF Chromatin Remodeling Complex and the Zinc Finger Factor CTCF. Int J Mol Sci 2020; 21:E8950. [PMID: 33255744 PMCID: PMC7728349 DOI: 10.3390/ijms21238950] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/19/2020] [Accepted: 11/22/2020] [Indexed: 12/18/2022] Open
Abstract
The transcription factor CCCTC-binding factor (CTCF) modulates pleiotropic functions mostly related to gene expression regulation. The role of CTCF in large scale genome organization is also well established. A unifying model to explain relationships among many CTCF-mediated activities involves direct or indirect interactions with numerous protein cofactors recruited to specific binding sites. The co-association of CTCF with other architectural proteins such as cohesin, chromodomain helicases, and BRG1, further supports the interplay between master regulators of mammalian genome folding. Here, we report a comprehensive LC-MS/MS mapping of the components of the switch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex co-associated with CTCF including subunits belonging to the core, signature, and ATPase modules. We further show that the localization patterns of representative SWI/SNF members significantly overlap with CTCF sites on transcriptionally active chromatin regions. Moreover, we provide evidence of a direct binding of the BRK-BRG1 domain to the zinc finger motifs 4-8 of CTCF, thus, suggesting that these domains mediate the interaction of CTCF with the SWI/SNF complex. These findings provide an updated view of the cooperative nature between CTCF and the SWI/SNF ATP-dependent chromatin remodeling complexes, an important step for understanding how these architectural proteins collaborate to shape the genome.
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Affiliation(s)
- Mariangela Valletta
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy; (M.V.); (R.R.); (I.B.); (V.R.); (S.R.)
| | - Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy; (M.V.); (R.R.); (I.B.); (V.R.); (S.R.)
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy; (M.V.); (R.R.); (I.B.); (V.R.); (S.R.)
| | - Veronica Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy; (M.V.); (R.R.); (I.B.); (V.R.); (S.R.)
| | - Sara Ragucci
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy; (M.V.); (R.R.); (I.B.); (V.R.); (S.R.)
| | - Annamaria Sandomenico
- Istituto di Biostrutture e Bioimmagini IBB, National Research Council, 80134 Napoli, Italy; (A.S.); (E.I.); (M.R.)
| | - Emanuela Iaccarino
- Istituto di Biostrutture e Bioimmagini IBB, National Research Council, 80134 Napoli, Italy; (A.S.); (E.I.); (M.R.)
| | - Menotti Ruvo
- Istituto di Biostrutture e Bioimmagini IBB, National Research Council, 80134 Napoli, Italy; (A.S.); (E.I.); (M.R.)
| | - Italia De Feis
- Istituto per le Applicazioni del Calcolo IAC ‘M. Picone’, National Research Council, 80131 Napoli, Italy; (I.D.F.); (C.A.)
| | - Claudia Angelini
- Istituto per le Applicazioni del Calcolo IAC ‘M. Picone’, National Research Council, 80131 Napoli, Italy; (I.D.F.); (C.A.)
| | - Sara Iachettini
- Oncogenomic and Epigenetic Unit, IRCCS-Regina Elena National Cancer Institute, 00144 Roma, Italy; (S.I.); (A.B.)
| | - Annamaria Biroccio
- Oncogenomic and Epigenetic Unit, IRCCS-Regina Elena National Cancer Institute, 00144 Roma, Italy; (S.I.); (A.B.)
| | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy; (M.V.); (R.R.); (I.B.); (V.R.); (S.R.)
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy; (M.V.); (R.R.); (I.B.); (V.R.); (S.R.)
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Chandradoss KR, Chawla B, Dhuppar S, Nayak R, Ramachandran R, Kurukuti S, Mazumder A, Sandhu KS. CTCF-Mediated Genome Architecture Regulates the Dosage of Mitotically Stable Mono-allelic Expression of Autosomal Genes. Cell Rep 2020; 33:108302. [PMID: 33113374 DOI: 10.1016/j.celrep.2020.108302] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 07/31/2020] [Accepted: 09/30/2020] [Indexed: 11/30/2022] Open
Abstract
The mechanisms that guide the clonally stable random mono-allelic expression of autosomal genes remain enigmatic. We show that (1) mono-allelically expressed (MAE) genes are assorted and insulated from bi-allelically expressed (BAE) genes through CTCF-mediated chromatin loops; (2) the cell-type-specific dynamics of mono-allelic expression coincides with the gain and loss of chromatin insulator sites; (3) dosage of MAE genes is more sensitive to the loss of chromatin insulation than that of BAE genes; and (4) inactive alleles of MAE genes are significantly more insulated than active alleles and are de-repressed upon CTCF depletion. This alludes to a topology wherein the inactive alleles of MAE genes are insulated from the spatial interference of transcriptional states from the neighboring bi-allelic domains via CTCF-mediated loops. We propose that CTCF functions as a typical insulator on inactive alleles, but facilitates transcription through enhancer-linking on active allele of MAE genes, indicating widespread allele-specific regulatory roles of CTCF.
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Affiliation(s)
- Keerthivasan Raanin Chandradoss
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, Knowledge City, Sector 81, SAS Nagar 140306, India
| | - Bindia Chawla
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, Knowledge City, Sector 81, SAS Nagar 140306, India
| | - Shivnarayan Dhuppar
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research (TIFR) Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal, Hyderabad 500046, India
| | - Rakhee Nayak
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Gachibowli, Hyderabad 500046, India
| | - Rajesh Ramachandran
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, Knowledge City, Sector 81, SAS Nagar 140306, India
| | - Sreenivasulu Kurukuti
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Gachibowli, Hyderabad 500046, India
| | - Aprotim Mazumder
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research (TIFR) Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal, Hyderabad 500046, India
| | - Kuljeet Singh Sandhu
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, Knowledge City, Sector 81, SAS Nagar 140306, India.
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Hwang SY, Kang MA, Baik CJ, Lee Y, Hang NT, Kim BG, Han JS, Jeong JH, Park D, Myung K, Lee JS. CTCF cooperates with CtIP to drive homologous recombination repair of double-strand breaks. Nucleic Acids Res 2019; 47:9160-9179. [PMID: 31340001 PMCID: PMC6753481 DOI: 10.1093/nar/gkz639] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/01/2019] [Accepted: 07/15/2019] [Indexed: 01/09/2023] Open
Abstract
The pleiotropic CCCTC-binding factor (CTCF) plays a role in homologous recombination (HR) repair of DNA double-strand breaks (DSBs). However, the precise mechanistic role of CTCF in HR remains largely unclear. Here, we show that CTCF engages in DNA end resection, which is the initial, crucial step in HR, through its interactions with MRE11 and CtIP. Depletion of CTCF profoundly impairs HR and attenuates CtIP recruitment at DSBs. CTCF physically interacts with MRE11 and CtIP and promotes CtIP recruitment to sites of DNA damage. Subsequently, CTCF facilitates DNA end resection to allow HR, in conjunction with MRE11–CtIP. Notably, the zinc finger domain of CTCF binds to both MRE11 and CtIP and enables proficient CtIP recruitment, DNA end resection and HR. The N-terminus of CTCF is able to bind to only MRE11 and its C-terminus is incapable of binding to MRE11 and CtIP, thereby resulting in compromised CtIP recruitment, DSB resection and HR. Overall, this suggests an important function of CTCF in DNA end resection through the recruitment of CtIP at DSBs. Collectively, our findings identify a critical role of CTCF at the first control point in selecting the HR repair pathway.
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Affiliation(s)
- Soon Young Hwang
- Department of Life Sciences and Cellulomics Institute Ajou University, Suwon 16499, Korea
| | - Mi Ae Kang
- Department of Life Sciences and Cellulomics Institute Ajou University, Suwon 16499, Korea
| | - Chul Joon Baik
- Department of Life Sciences and Cellulomics Institute Ajou University, Suwon 16499, Korea
| | - Yejin Lee
- Department of Life Sciences and Cellulomics Institute Ajou University, Suwon 16499, Korea
| | - Ngo Thanh Hang
- Department of Life Sciences and Cellulomics Institute Ajou University, Suwon 16499, Korea
| | - Byung-Gyu Kim
- Center for Genomic Integrity, Institute for Basic Science, UNIST, Ulsan 44919, Korea
| | - Joo Seok Han
- Center for Genomic Integrity, Institute for Basic Science, UNIST, Ulsan 44919, Korea
| | - Jae-Hoon Jeong
- Division of Applied Radiation Bioscience, Korea Institute of Radiological and Medical Science, Seoul 01812, Korea
| | - Daechan Park
- Department of Life Sciences and Cellulomics Institute Ajou University, Suwon 16499, Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, UNIST, Ulsan 44919, Korea
| | - Jong-Soo Lee
- Department of Life Sciences and Cellulomics Institute Ajou University, Suwon 16499, Korea
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9
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Interaction network analysis of YBX1 for identification of therapeutic targets in adenocarcinomas. J Biosci 2019. [DOI: 10.1007/s12038-019-9848-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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A stress-induced response complex (SIRC) shuttles miRNAs, siRNAs, and oligonucleotides to the nucleus. Proc Natl Acad Sci U S A 2018; 115:E5756-E5765. [PMID: 29866826 PMCID: PMC6016802 DOI: 10.1073/pnas.1721346115] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The deregulation of miRNA function is critical in the pathogenesis of cancer and other diseases. miRNAs and other noncoding RNAs (ncRNAs) tightly regulate gene expression, often in the cell nucleus. Heretofore, there has been no understanding that there exists a general shuttling mechanism that brings miRNAs, in addition to therapeutic oligonucleotides and siRNAs, from the cytoplasm into the nucleus. We have identified this shuttling mechanism, which occurs in response to cell stress. Nuclear imported miRNAs are functional, can potentially alter gene expression, and participate in cell stress response mechanisms. This shuttling mechanism can be augmented to target specific RNAs, including miRNA sponges, and long ncRNAs like Malat-1, which have been implicated in promoting tumor metastasis. Although some information is available for specific subsets of miRNAs and several factors have been shown to bind oligonucleotides (ONs), no general transport mechanism for these molecules has been identified to date. In this work, we demonstrate that the nuclear transport of ONs, siRNAs, and miRNAs responds to cellular stress. Furthermore, we have identified a stress-induced response complex (SIRC), which includes Ago-1 and Ago-2 in addition to the transcription and splicing regulators YB1, CTCF, FUS, Smad1, Smad3, and Smad4. The SIRC transports endogenous miRNAs, siRNAs, and ONs to the nucleus. We show that cellular stress can significantly increase ON- or siRNA-directed splicing switch events and endogenous miRNA targeting of nuclear RNAs.
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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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12
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Hilmi K, Jangal M, Marques M, Zhao T, Saad A, Zhang C, Luo VM, Syme A, Rejon C, Yu Z, Krum A, Fabian MR, Richard S, Alaoui-Jamali M, Orthwein A, McCaffrey L, Witcher M. CTCF facilitates DNA double-strand break repair by enhancing homologous recombination repair. SCIENCE ADVANCES 2017; 3:e1601898. [PMID: 28560323 PMCID: PMC5443639 DOI: 10.1126/sciadv.1601898] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 03/29/2017] [Indexed: 05/06/2023]
Abstract
The repair of DNA double-strand breaks (DSBs) is mediated via two major pathways, nonhomologous end joining (NHEJ) and homologous recombination (HR) repair. DSB repair is vital for cell survival, genome stability, and tumor suppression. In contrast to NHEJ, HR relies on extensive homology and templated DNA synthesis to restore the sequence surrounding the break site. We report a new role for the multifunctional protein CCCTC-binding factor (CTCF) in facilitating HR-mediated DSB repair. CTCF is recruited to DSB through its zinc finger domain independently of poly(ADP-ribose) polymers, known as PARylation, catalyzed by poly(ADP-ribose) polymerase 1 (PARP-1). CTCF ensures proper DSB repair kinetics in response to γ-irradiation, and the loss of CTCF compromises HR-mediated repair. Consistent with its role in HR, loss of CTCF results in hypersensitivity to DNA damage, inducing agents and inhibitors of PARP. Mechanistically, CTCF acts downstream of BRCA1 in the HR pathway and associates with BRCA2 in a PARylation-dependent manner, enhancing BRCA2 recruitment to DSB. In contrast, CTCF does not influence the recruitment of the NHEJ protein 53BP1 or LIGIV to DSB. Together, our findings establish for the first time that CTCF is an important regulator of the HR pathway.
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Affiliation(s)
- Khalid Hilmi
- Departments of Oncology and Experimental Medicine, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, McGill University, 3755 Chemin Côte-Ste-Catherine, Montréal, Quebec H3T 1E2, Canada
| | - Maïka Jangal
- Departments of Oncology and Experimental Medicine, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, McGill University, 3755 Chemin Côte-Ste-Catherine, Montréal, Quebec H3T 1E2, Canada
| | - Maud Marques
- Departments of Oncology and Experimental Medicine, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, McGill University, 3755 Chemin Côte-Ste-Catherine, Montréal, Quebec H3T 1E2, Canada
| | - Tiejun Zhao
- Departments of Oncology and Experimental Medicine, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, McGill University, 3755 Chemin Côte-Ste-Catherine, Montréal, Quebec H3T 1E2, Canada
| | - Amine Saad
- Departments of Oncology and Experimental Medicine, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, McGill University, 3755 Chemin Côte-Ste-Catherine, Montréal, Quebec H3T 1E2, Canada
| | - Chenxi Zhang
- Departments of Oncology and Experimental Medicine, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, McGill University, 3755 Chemin Côte-Ste-Catherine, Montréal, Quebec H3T 1E2, Canada
| | - Vincent M. Luo
- Departments of Oncology and Experimental Medicine, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, McGill University, 3755 Chemin Côte-Ste-Catherine, Montréal, Quebec H3T 1E2, Canada
- Department of Microbiology and Immunology, McGill University, 3775 University Street, Montréal, Quebec H3A 2B4, Canada
| | - Alasdair Syme
- Department of Radiation Oncology, Medical Physics Unit, Jewish General Hospital, McGill University, Montréal, Quebec H3T 1E2, Canada
| | - Carlis Rejon
- Department of Oncology, Rosalind and Morris Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue West, Montréal, Quebec H3A 1A3, Canada
| | - Zhenbao Yu
- Departments of Oncology and Experimental Medicine, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, McGill University, 3755 Chemin Côte-Ste-Catherine, Montréal, Quebec H3T 1E2, Canada
| | - Asiev Krum
- Department of Radiation Oncology, Medical Physics Unit, Jewish General Hospital, McGill University, Montréal, Quebec H3T 1E2, Canada
| | - Marc R. Fabian
- Departments of Oncology and Experimental Medicine, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, McGill University, 3755 Chemin Côte-Ste-Catherine, Montréal, Quebec H3T 1E2, Canada
| | - Stéphane Richard
- Departments of Oncology and Experimental Medicine, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, McGill University, 3755 Chemin Côte-Ste-Catherine, Montréal, Quebec H3T 1E2, Canada
| | - Moulay Alaoui-Jamali
- Departments of Oncology and Experimental Medicine, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, McGill University, 3755 Chemin Côte-Ste-Catherine, Montréal, Quebec H3T 1E2, Canada
| | - Alexander Orthwein
- Departments of Oncology and Experimental Medicine, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, McGill University, 3755 Chemin Côte-Ste-Catherine, Montréal, Quebec H3T 1E2, Canada
- Department of Microbiology and Immunology, McGill University, 3775 University Street, Montréal, Quebec H3A 2B4, Canada
| | - Luke McCaffrey
- Department of Oncology, Rosalind and Morris Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue West, Montréal, Quebec H3A 1A3, Canada
| | - Michael Witcher
- Departments of Oncology and Experimental Medicine, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, McGill University, 3755 Chemin Côte-Ste-Catherine, Montréal, Quebec H3T 1E2, Canada
- Corresponding author.
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13
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Zhu L, Gomez-Duran A, Saretzki G, Jin S, Tilgner K, Melguizo-Sanchis D, Anyfantis G, Al-Aama J, Vallier L, Chinnery P, Lako M, Armstrong L. The mitochondrial protein CHCHD2 primes the differentiation potential of human induced pluripotent stem cells to neuroectodermal lineages. J Cell Biol 2016; 215:187-202. [PMID: 27810911 PMCID: PMC5084643 DOI: 10.1083/jcb.201601061] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 09/19/2016] [Indexed: 01/09/2023] Open
Abstract
Human induced pluripotent stem cell (hiPSC) utility is limited by variations in the ability of these cells to undergo lineage-specific differentiation. We have undertaken a transcriptional comparison of human embryonic stem cell (hESC) lines and hiPSC lines and have shown that hiPSCs are inferior in their ability to undergo neuroectodermal differentiation. Among the differentially expressed candidates between hESCs and hiPSCs, we identified a mitochondrial protein, CHCHD2, whose expression seems to correlate with neuroectodermal differentiation potential of pluripotent stem cells. We provide evidence that hiPSC variability with respect to CHCHD2 expression and differentiation potential is caused by clonal variation during the reprogramming process and that CHCHD2 primes neuroectodermal differentiation of hESCs and hiPSCs by binding and sequestering SMAD4 to the mitochondria, resulting in suppression of the activity of the TGFβ signaling pathway. Using CHCHD2 as a marker for assessing and comparing the hiPSC clonal and/or line differentiation potential provides a tool for large scale differentiation and hiPSC banking studies.
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Affiliation(s)
- Lili Zhu
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, England, UK
| | - Aurora Gomez-Duran
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, England, UK.,Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, England, UK
| | - Gabriele Saretzki
- Institute for Ageing and Health, Newcastle University, Newcastle NE1 3BZ, England, UK
| | - Shibo Jin
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, England, UK
| | - Katarzyna Tilgner
- Wellcome Trust-Medical Research Council Stem Cell Institute, Hinxton, Cambridge CB10 1SA, England, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, England, UK
| | | | - Georgios Anyfantis
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, England, UK
| | - Jumana Al-Aama
- Princess Al Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ludovic Vallier
- Wellcome Trust-Medical Research Council Stem Cell Institute, Hinxton, Cambridge CB10 1SA, England, UK
| | - Patrick Chinnery
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, England, UK
| | - Majlinda Lako
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, England, UK
| | - Lyle Armstrong
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, England, UK
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14
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Lake RJ, Boetefuer EL, Won KJ, Fan HY. The CSB chromatin remodeler and CTCF architectural protein cooperate in response to oxidative stress. Nucleic Acids Res 2015; 44:2125-35. [PMID: 26578602 PMCID: PMC4797267 DOI: 10.1093/nar/gkv1219] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/28/2015] [Indexed: 12/11/2022] Open
Abstract
Cockayne syndrome is a premature aging disease associated with numerous developmental and neurological abnormalities, and elevated levels of reactive oxygen species have been found in cells derived from Cockayne syndrome patients. The majority of Cockayne syndrome cases contain mutations in the ATP-dependent chromatin remodeler CSB; however, how CSB protects cells from oxidative stress remains largely unclear. Here, we demonstrate that oxidative stress alters the genomic occupancy of the CSB protein and increases CSB occupancy at promoters. Additionally, we found that the long-range chromatin-structure regulator CTCF plays a pivotal role in regulating sites of genomic CSB occupancy upon oxidative stress. We show that CSB directly interacts with CTCF in vitro and that oxidative stress enhances the CSB-CTCF interaction in cells. Reciprocally, we demonstrate that CSB facilitates CTCF-DNA interactions in vitro and regulates CTCF-chromatin interactions in oxidatively stressed cells. Together, our results indicate that CSB and CTCF can regulate each other's chromatin association, thereby modulating chromatin structure and coordinating gene expression in response to oxidative stress.
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Affiliation(s)
- Robert J Lake
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104,USA Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erica L Boetefuer
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104,USA Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA Biology Graduate Program, Graduate School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kyoung-Jae Won
- Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hua-Ying Fan
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104,USA Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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15
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CTCF cooperates with noncoding RNA MYCNOS to promote neuroblastoma progression through facilitating MYCN expression. Oncogene 2015; 35:3565-76. [PMID: 26549029 DOI: 10.1038/onc.2015.422] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 07/26/2015] [Accepted: 10/05/2015] [Indexed: 12/11/2022]
Abstract
Previous studies have indicated the important roles of MYCN in tumorigenesis and progression of neuroblastoma (NB), the most common extracranial solid tumor derived from neural crest in childhood. However, the regulatory mechanisms of MYCN expression in NB still remain largely unknown. In this study, through mining public microarray databases and analyzing the cis-regulatory elements and chromatin immunoprecipitation data sets, we identified CCCTC-binding factor (CTCF) as a crucial transcription factor facilitating the MYCN expression in NB. RNA immunoprecipitation, RNA electrophoretic mobility shift assay, RNA pull down and in vitro binding assay indicated the physical interaction between CTCF and MYCN opposite strand (MYCNOS), a natural noncoding RNA surrounding the MYNC promoter. Gain- and loss-of-function studies revealed that MYCNOS facilitated the recruitment of CTCF to its binding sites within the MYCN promoter to induce chromatin remodeling, resulting in enhanced MYCN levels and altered downstream gene expression, in cultured NB cell lines. CTCF cooperated with MYCNOS to suppress the differentiation and promote the growth, invasion and metastasis of NB cells in vitro and in vivo. In clinical NB tissues and cell lines, CTCF and MYCNOS were upregulated and positively correlated with MYCN expression. CTCF was an independent prognostic factor for unfavorable outcome of NB, and patients with high MYCNOS expression had lower survival probability. Taken together, these results demonstrate that CTCF cooperates with noncoding RNA MYCNOS to exhibit oncogenic activity that affects the aggressiveness and progression of NB through transcriptional upregulation of MYCN.
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16
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Pugacheva EM, Rivero-Hinojosa S, Espinoza CA, Méndez-Catalá CF, Kang S, Suzuki T, Kosaka-Suzuki N, Robinson S, Nagarajan V, Ye Z, Boukaba A, Rasko JEJ, Strunnikov AV, Loukinov D, Ren B, Lobanenkov VV. Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions. Genome Biol 2015; 16:161. [PMID: 26268681 PMCID: PMC4562119 DOI: 10.1186/s13059-015-0736-8] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 07/31/2015] [Indexed: 12/22/2022] Open
Abstract
Background CTCF and BORIS (CTCFL), two paralogous mammalian proteins sharing nearly identical DNA binding domains, are thought to function in a mutually exclusive manner in DNA binding and transcriptional regulation. Results Here we show that these two proteins co-occupy a specific subset of regulatory elements consisting of clustered CTCF binding motifs (termed 2xCTSes). BORIS occupancy at 2xCTSes is largely invariant in BORIS-positive cancer cells, with the genomic pattern recapitulating the germline-specific BORIS binding to chromatin. In contrast to the single-motif CTCF target sites (1xCTSes), the 2xCTS elements are preferentially found at active promoters and enhancers, both in cancer and germ cells. 2xCTSes are also enriched in genomic regions that escape histone to protamine replacement in human and mouse sperm. Depletion of the BORIS gene leads to altered transcription of a large number of genes and the differentiation of K562 cells, while the ectopic expression of this CTCF paralog leads to specific changes in transcription in MCF7 cells. Conclusions We discover two functionally and structurally different classes of CTCF binding regions, 2xCTSes and 1xCTSes, revealed by their predisposition to bind BORIS. We propose that 2xCTSes play key roles in the transcriptional program of cancer and germ cells. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0736-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elena M Pugacheva
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Samuel Rivero-Hinojosa
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Celso A Espinoza
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA, 92093, USA.,Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, San Diego School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Claudia Fabiola Méndez-Catalá
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Sungyun Kang
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Teruhiko Suzuki
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA.,Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo, Japan
| | - Natsuki Kosaka-Suzuki
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Susan Robinson
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Vijayaraj Nagarajan
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Zhen Ye
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Abdelhalim Boukaba
- Guangzhou Institutes of Biomedicine and Health, Molecular Epigenetics Laboratory, 190 Kai Yuan Avenue, Science Park, Guangzhou, 510530, China
| | - John E J Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW, 2050, Australia
| | - Alexander V Strunnikov
- Guangzhou Institutes of Biomedicine and Health, Molecular Epigenetics Laboratory, 190 Kai Yuan Avenue, Science Park, Guangzhou, 510530, China
| | - Dmitri Loukinov
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA, 92093, USA. .,Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, San Diego School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Victor V Lobanenkov
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA.
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17
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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: 58] [Impact Index Per Article: 6.4] [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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18
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Franco MM, Prickett AR, Oakey RJ. The role of CCCTC-binding factor (CTCF) in genomic imprinting, development, and reproduction. Biol Reprod 2014; 91:125. [PMID: 25297545 DOI: 10.1095/biolreprod.114.122945] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
CCCTC-binding factor (CTCF) is the major protein involved in insulator activity in vertebrates, with widespread DNA binding sites in the genome. CTCF participates in many processes related to global chromatin organization and remodeling, contributing to the repression or activation of gene transcription. It is also involved in epigenetic reprogramming and is essential during gametogenesis and embryo development. Abnormal DNA methylation patterns at CTCF motifs may impair CTCF binding to DNA, and are related to fertility disorders in mammals. Therefore, CTCF and its binding sites are important candidate regions to be investigated as molecular markers for gamete and embryo quality. This article reviews the role of CTCF in genomic imprinting, gametogenesis, and early embryo development and, moreover, highlights potential opportunities for environmental influences associated with assisted reproductive techniques (ARTs) to affect CTCF-mediated processes. We discuss the potential use of CTCF as a molecular marker for assessing gamete and embryo quality in the context of improving the efficiency and safety of ARTs.
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Affiliation(s)
- Maurício M Franco
- Embrapa Genetic Resources & Biotechnology, Laboratory of Animal Reproduction, Parque Estação Biológica, Brasília, Brazil
| | - Adam R Prickett
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London, United Kingdom
| | - Rebecca J Oakey
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London, United Kingdom
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19
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Kotova ES, Sorokina IV, Akopov SB, Nikolaev LG, Sverdlov ED. Expression of chicken CTCF gene in COS-1 cells and partial purification of CTCF protein. BIOCHEMISTRY (MOSCOW) 2014; 78:879-83. [PMID: 24228875 DOI: 10.1134/s0006297913080038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The chicken gene for transcription factor CTCF was expressed in COS-1 mammalian cells. The CTCF protein containing polyhistidine tag was partially purified using metallo-affinity and ion-exchange chromatography. The expressed protein localized in the cell nucleus and was shown to be functionally active in the electrophoretic mobility shift assay and specifically interacted with anti-CTCF antibodies.
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Affiliation(s)
- E S Kotova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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20
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Liu Q, Yang B, Xie X, Wei L, Liu W, Yang W, Ge Y, Zhu Q, Zhang J, Jiang L, Yu X, Shen W, Li R, Shi X, Li B, Qin Y. Vigilin interacts with CCCTC-binding factor (CTCF) and is involved in CTCF-dependent regulation of the imprinted genes Igf2 and H19. FEBS J 2014; 281:2713-25. [PMID: 24725430 DOI: 10.1111/febs.12816] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 04/07/2014] [Accepted: 04/10/2014] [Indexed: 11/26/2022]
Abstract
CCCTC-binding factor (CTCF), a highly conserved zinc finger protein, is a master organizer of genome spatial organization and has multiple functions in gene regulation. Mounting evidence indicates that CTCF regulates the imprinted genes Igf2 and H19 by organizing chromatin at the Igf2/H19 locus, although the mechanism by which CTCF carries out this function is not fully understood. By yeast two-hybrid screening, we identified vigilin, a multi-KH-domain protein, as a new partner of CTCF. Subsequent coimmunoprecipitation and glutathione S-transferase pulldown experiments confirmed that vigilin interacts with CTCF. Moreover, vigilin is present at several known CTCF target sites, such as the promoter regions of c-myc and BRCA1, the locus control region of β-globin, and several regions within the Igf2/H19 locus. In vivo depletion of vigilin did not affect CTCF binding; however, knockdown of CTCF reduced vigilin binding to the H19 imprinting control region. Furthermore, ectopic expression of vigilin significantly downregulated Igf2 and upregulated H19, whereas depletion of vigilin upregulated Igf2 and downregulated H19, in HepG2, CNE1 and HeLa cells. These results reveal the functional relevance of vigilin and CTCF, and show that the CTCF-vigilin complex contributes to regulation of Igf2/H19.
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Affiliation(s)
- Qiuying Liu
- Department of Biochemistry and Molecular Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, China
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21
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Shi J, Marconett CN, Duan J, Hyland PL, Li P, Wang Z, Wheeler W, Zhou B, Campan M, Lee DS, Huang J, Zhou W, Triche T, Amundadottir L, Warner A, Hutchinson A, Chen PH, Chung BSI, Pesatori AC, Consonni D, Bertazzi PA, Bergen AW, Freedman M, Siegmund KD, Berman BP, Borok Z, Chatterjee N, Tucker MA, Caporaso NE, Chanock SJ, Laird-Offringa IA, Landi MT. Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue. Nat Commun 2014; 5:3365. [PMID: 24572595 PMCID: PMC3982882 DOI: 10.1038/ncomms4365] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 01/31/2014] [Indexed: 12/17/2022] Open
Abstract
The genetic regulation of the human epigenome is not fully appreciated. Here we describe the effects of genetic variants on the DNA methylome in human lung based on methylation-quantitative trait loci (meQTL) analyses. We report 34,304 cis- and 585 trans-meQTLs, a genetic-epigenetic interaction of surprising magnitude, including a regulatory hotspot. These findings are replicated in both breast and kidney tissues and show distinct patterns: cis-meQTLs mostly localize to CpG sites outside of genes, promoters and CpG islands (CGIs), while trans-meQTLs are over-represented in promoter CGIs. meQTL SNPs are enriched in CTCF-binding sites, DNaseI hypersensitivity regions and histone marks. Importantly, four of the five established lung cancer risk loci in European ancestry are cis-meQTLs and, in aggregate, cis-meQTLs are enriched for lung cancer risk in a genome-wide analysis of 11,587 subjects. Thus, inherited genetic variation may affect lung carcinogenesis by regulating the human methylome.
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Affiliation(s)
- Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
| | - Crystal N Marconett
- 1] Department of Surgery, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA [2] Department of Biochemistry and Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA
| | - Jubao Duan
- Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, North Shore University Health System Research Institute, University of Chicago Pritzker School of Medicine, Evanston, Illinois 60201, USA
| | - Paula L Hyland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
| | - Peng Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
| | - William Wheeler
- Information Management Services Inc., Rockville, Maryland 20852, USA
| | - Beiyun Zhou
- Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, USC Keck School of Medicine, Los Angeles, California 90089, USA
| | - Mihaela Campan
- 1] Department of Surgery, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA [2] Department of Biochemistry and Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA
| | - Diane S Lee
- 1] Department of Surgery, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA [2] Department of Biochemistry and Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA
| | - Jing Huang
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
| | - Tim Triche
- Bioinformatics Division, Department of Preventive Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Laufey Amundadottir
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
| | - Andrew Warner
- Pathology/Histotechnology Laboratory, Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
| | - Po-Han Chen
- 1] Department of Surgery, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA [2] Department of Biochemistry and Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA
| | - Brian S I Chung
- 1] Department of Surgery, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA [2] Department of Biochemistry and Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA
| | - Angela C Pesatori
- Unit of Epidemiology, IRCCS Fondazione Ca' Granda Ospedale Maggiore Policlinico, Department of Clinical Sciences and Community Health, University of Milan, Milan 20122, Italy
| | - Dario Consonni
- Unit of Epidemiology, IRCCS Fondazione Ca' Granda Ospedale Maggiore Policlinico, Department of Clinical Sciences and Community Health, University of Milan, Milan 20122, Italy
| | - Pier Alberto Bertazzi
- Unit of Epidemiology, IRCCS Fondazione Ca' Granda Ospedale Maggiore Policlinico, Department of Clinical Sciences and Community Health, University of Milan, Milan 20122, Italy
| | - Andrew W Bergen
- Molecular Genetics Program, Center for Health Sciences, SRI, Menlo Park, California 94025, USA
| | - Mathew Freedman
- 1] Program in Medical and Population Genetics, The Broad Institute, Cambridge, Massachusetts 02142, USA [2] Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Kimberly D Siegmund
- Bioinformatics Division, Department of Preventive Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Benjamin P Berman
- 1] Bioinformatics Division, Department of Preventive Medicine, University of Southern California, Los Angeles, California 90089, USA [2] USC Epigenome Center and USC/Norris Comprehensive Cancer Center, Los Angeles, California 90089, USA
| | - Zea Borok
- 1] Department of Biochemistry and Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA [2] Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, USC Keck School of Medicine, Los Angeles, California 90089, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
| | - Ite A Laird-Offringa
- 1] Department of Surgery, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA [2] Department of Biochemistry and Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
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22
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Maksimenko O, Georgiev P. Mechanisms and proteins involved in long-distance interactions. Front Genet 2014; 5:28. [PMID: 24600469 PMCID: PMC3927085 DOI: 10.3389/fgene.2014.00028] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 01/25/2014] [Indexed: 12/28/2022] Open
Abstract
Due to advances in genome-wide technologies, consistent distant interactions within chromosomes of higher eukaryotes have been revealed. In particular, it has been shown that enhancers can specifically and directly interact with promoters by looping out intervening sequences, which can be up to several hundred kilobases long. This review is focused on transcription factors that are supposed to be involved in long-range interactions. Available data are in agreement with the model that several known transcription factors and insulator proteins belong to an abundant but poorly studied class of proteins that are responsible for chromosomal architecture.
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Affiliation(s)
- Oksana Maksimenko
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences Moscow, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences Moscow, Russia
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23
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The DNA-binding factor Ctcf critically controls gene expression in macrophages. Cell Mol Immunol 2013; 11:58-70. [PMID: 24013844 DOI: 10.1038/cmi.2013.41] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 07/11/2013] [Accepted: 07/21/2013] [Indexed: 12/18/2022] Open
Abstract
Macrophages play an important role in immunity and homeostasis. Upon pathogen recognition via specific receptors, they rapidly induce inflammatory responses. This process is tightly controlled at the transcriptional level. The DNA binding zinc-finger protein CCCTC-binding factor (Ctcf) is a crucial regulator of long-range chromatin interactions and coordinates specific communication between transcription factors and gene expression processes. In this study, the Ctcf gene was specifically deleted in myeloid cells by making use of the transgenic Cre-LoxP system. Conditional deletion of the Ctcf gene in myeloid cells induced a mild phenotype in vivo. Ctcf-deficient mice exhibited significantly reduced expression of major histocompatibility complex (MHC) class II in the liver. Ctcf-deficient macrophages demonstrated a normal surface phenotype and phagocytosis capacity. Upon Toll-like receptor (TLR) stimulation, they produced normal levels of the pro-inflammatory cytokines IL-12 and IL-6, but manifested a strongly impaired capacity to produce tumor-necrosis factor (TNF) and IL-10, as well as to express the IL-10 family members IL-19, IL-20 and IL-24. Taken together, our data demonstrate a role of Ctcf that involves fine-tuning of macrophage function.
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24
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Identification of a new Schistosoma mansoni SMYB1 partner: putative roles in RNA metabolism. Parasitology 2013; 140:1085-95. [PMID: 23673212 DOI: 10.1017/s0031182013000413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
SMYB1 is a Schistosoma mansoni protein highly similar to members of the Y-box binding protein family. Similar to other homologues, SMYB1 is able to bind double- and single-stranded DNA, as well as RNA molecules. The characterization of proteins involved in the regulation of gene expression in S. mansoni is of great importance for the understanding of molecular events that control morphological and physiological changes in this parasite. Here we demonstrate that SMYB1 is located in the cytoplasm of cells from different life-cycle stages of S. mansoni, suggesting that this protein is probably acting in mRNA metabolism in the cytoplasm and corroborating previous findings from our group that showed its ability to bind RNA. Protein-protein interactions are important events in all biological processes, since most proteins execute their functions through large supramolecular structures. Yeast two-hybrid screenings using SMYB1 as bait identified a partner in S. mansoni similar to the SmD3 protein of Drosophila melanogaster (SmRNP), which is important in the assembly of small nuclear ribonucleoprotein complexes. Also, pull-down assays were conducted using immobilized GST-SMYB1 proteins and confirmed the SMYB1-SmRNP interaction. The interaction of SMYB1 with a protein involved in mRNA processing suggests that it may act in processes such as turnover, transport and stabilization of RNA molecules.
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25
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Eliseeva IA, Kim ER, Guryanov SG, Ovchinnikov LP, Lyabin DN. Y-box-binding protein 1 (YB-1) and its functions. BIOCHEMISTRY (MOSCOW) 2012; 76:1402-33. [PMID: 22339596 DOI: 10.1134/s0006297911130049] [Citation(s) in RCA: 250] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review describes the structure and functions of Y-box binding protein 1 (YB-1) and its homologs. Interactions of YB-1 with DNA, mRNAs, and proteins are considered. Data on the participation of YB-1 in DNA reparation and transcription, mRNA splicing and translation are systematized. Results on interactions of YB-1 with cytoskeleton components and its possible role in mRNA localization are discussed. Data on intracellular distribution of YB-1, its redistribution between the nucleus and the cytoplasm, and its secretion and extracellular functions are summarized. The effect of YB-1 on cell differentiation, its involvement in extra- and intracellular signaling pathways, and its role in early embryogenesis are described. The mechanisms of regulation of YB-1 expression in the cell are presented. Special attention is paid to the involvement of YB-1 in oncogenic cell transformation, multiple drug resistance, and dissemination of tumors. Both the oncogenic and antioncogenic activities of YB-1 are reviewed. The potential use of YB-1 in diagnostics and therapy as an early cancer marker and a molecular target is discussed.
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Affiliation(s)
- I A Eliseeva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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26
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Cheng YC, Chen TA, Chen CY, Liang CM, Liang SM. 3'poly-G-tailed ODNs inhibit F-spondin to induce cell death and neurite retraction in rat embryonic neurons. Mol Neurobiol 2012; 45:536-49. [PMID: 22592270 DOI: 10.1007/s12035-012-8275-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Accepted: 05/01/2012] [Indexed: 10/28/2022]
Abstract
The effects and mechanism of action of oligodeoxyribonucleotides containing CpG motif (CpG-ODNs) on neuron cells are largely unexamined. Here, we found that CpG-A ODNs but not other types of CpG-ODNs induced neurite retraction and cell apoptosis of rat embryonic neurons in a TLR9-independent manner. These effects of CpG-A ODNs were primarily due to the poly-guanosine at the 3' terminus (3'G-ODNs). Pull-down analysis showed that 3'G-ODNs associated with transcription factor Y-BOX1 (YB-1) to facilitate the translocation of YB-1 into the nucleus via the nuclear localizing sequence of YB-1. YB-1 then interacted with the promoter of F-spondin directly at -45 and -1,375 sites as demonstrated by chromatin immunoprecipitation (ChIP) analysis. Binding of YB-1 to F-spondin promoter resulted in downregulation of F-spondin expression. Overexpression of F-spondin rescued the cell death and neurite retraction induced by 3'G-ODNs in embryonic neuron cells. Taken together, these findings suggest that 3'G-ODNs enhance nucleus YB-1 to inhibit F-spondin leading to cell death and neurite retraction of embryonic neuron cells.
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Affiliation(s)
- Yung-Chih Cheng
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
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27
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Inoue I, Matsumoto K, Yu Y, Bay BH. Surmounting Chemoresistance by Targeting the Y-Box Binding Protein-1. Anat Rec (Hoboken) 2011; 295:215-22. [DOI: 10.1002/ar.22401] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 06/30/2011] [Indexed: 12/23/2022]
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28
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de Necochea-Campion R, Ghochikyan A, Josephs SF, Zacharias S, Woods E, Karimi-Busheri F, Alexandrescu DT, Chen CS, Agadjanyan MG, Carrier E. Expression of the epigenetic factor BORIS (CTCFL) in the human genome. J Transl Med 2011; 9:213. [PMID: 22168535 PMCID: PMC3264669 DOI: 10.1186/1479-5876-9-213] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 12/14/2011] [Indexed: 11/10/2022] Open
Abstract
BORIS, or CTCFL, the so called Brother of the Regulator of Imprinted Sites because of the extensive homology in the central DNA binding region of the protein to the related regulator, CTCF, is expressed in early gametogenesis and in multiple cancers but not in differentiated somatic cells. Thus it is a member of the cancer testes antigen group (CTAs). Since BORIS and CTCF target common DNA binding sites, these proteins function on two levels, the first level is their regulation via the methylation context of the DNA target site and the second level is their distinct and different epigenetic associations due to differences in the non-homologous termini of the proteins. The regulation on both of these levels is extensive and complex and the sphere of influence of each of these proteins is associated with vastly different cellular signaling processes. On the level of gene expression, BORIS has three known promoters and multiple spliced mRNAs which adds another level of complexity to this intriguing regulator. BORIS expression is observed in the majority of cancer tissues and cell lines analyzed up to today. The expression profile and essential role of BORIS in cancer make this molecule very attractive target for cancer immunotherapy. This review summarizes what is known about BORIS regarding its expression, structure, and function and then presents some theoretical considerations with respect to its genome wide influence and its potential for use as a vaccine for cancer immunotherapy.
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29
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Abstract
Chromatin insulators are DNA-protein complexes with broad functions in nuclear biology. Based on the ability of insulator proteins to interact with each other, it was originally found that insulators form loops that bring together distant regions of the genome. Data from genome-wide localization studies indicate that insulator proteins can be present in intergenic regions as well as at the 5', introns or 3' of genes, suggesting a variety of roles for insulator loops in chromosome biology. Recent results suggest that insulators mediate intra- and interchromosomal interactions to affect transcription, imprinting, and recombination. Cells have developed mechanisms to control insulator activity by recruiting specialized proteins or by covalent modification of core components. It is then possible that insulator-mediated interactions set up cell-specific blueprints of nuclear organization that may contribute to the establishment of different patterns of gene expression during cell differentiation and development. As a consequence, disruption of insulator activity could result in the development of cancer or other disease states.
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Affiliation(s)
- Jingping Yang
- Department of Biology, Emory University, Atlanta, GA, USA
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30
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Nikolaev LG, Akopov SB, Didych DA, Sverdlov ED. Vertebrate Protein CTCF and its Multiple Roles in a Large-Scale Regulation of Genome Activity. Curr Genomics 2011; 10:294-302. [PMID: 20119526 PMCID: PMC2729993 DOI: 10.2174/138920209788921038] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 06/15/2009] [Accepted: 06/18/2009] [Indexed: 11/24/2022] Open
Abstract
The CTCF transcription factor is an 11 zinc fingers multifunctional protein that uses different zinc finger combinations to recognize and bind different sites within DNA. CTCF is thought to participate in various gene regulatory networks including transcription activation and repression, formation of independently functioning chromatin domains and regulation of imprinting. Sequencing of human and other genomes opened up a possibility to ascertain the genomic distribution of CTCF binding sites and to identify CTCF-dependent cis-regulatory elements, including insulators. In the review, we summarized recent data on genomic distribution of CTCF binding sites in the human and other genomes within a framework of the loop domain hypothesis of large-scale regulation of the genome activity. We also tried to formulate possible lines of studies on a variety of CTCF functions which probably depend on its ability to specifically bind DNA, interact with other proteins and form di- and multimers. These three fundamental properties allow CTCF to serve as a transcription factor, an insulator and a constitutive dispersed genome-wide demarcation tool able to recruit various factors that emerge in response to diverse external and internal signals, and thus to exert its signal-specific function(s).
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Affiliation(s)
- L G Nikolaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya, 117997, Moscow, Russia
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31
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Jin Y, Oomah K, Cattini PA. Enhancer-blocking activity is associated with hypersensitive site V sequences in the human growth hormone locus control region. DNA Cell Biol 2011; 30:995-1005. [PMID: 21711161 DOI: 10.1089/dna.2011.1268] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Activation of the human growth hormone gene (hGH-N) is linked to a locus control region (LCR) containing four (I-III, V) hypersensitive sites (HS). Pit-1 binding to HS I/II is required for efficient pituitary expression. However, inclusion of HS III and V, located about 28 and 32 kb upstream of the hGH-N gene, respectively, is also required for consistent hGH-N expression levels in vivo. HS V is referred to as a boundary for the hGH LCR, but no specific enhancer blocking or barrier function is reported. We examined a 547 bp fragment containing HS V sequences (nucleotides -32,718/-32,172 relative to hGH-N) for enhancer-blocking activity using a well-established transient gene transfer system and assessed these sequences for CCCTC binding factor (CTCF), which is linked to enhancer-blocking activity. The 547 bp HS V fragment decreased enhancer activity with a reverse-orientation preference when inserted between HS III enhancer sequences and a minimal thymidine kinase promoter (TKp). These sequences are associated with CTCF in human pituitary and nonpituitary chromatin. Enhancer-blocking activity with an orientation preference was further localized to a 45 bp sub-fragment, with evidence of CTCF and upstream binding factor 1 (USF1) binding; USF1 is linked more closely with barrier function. The presence of yin and yang 1 (Yy1) that cooperates with CTCF in the regulation of X-chromosome inactivation was also seen. A decrease in CTCF and Yy1 RNA levels was associated with a significant reduction in enhancer-blocking activity. Assessment of CpG-dinucleotides in the TKp indicates that the presence of HS V sequences are associated with an increased incidence of CpG-dinucleotide methylation of the GC box region. These data support association of CTCF and enhancer-blocking activity with HS V that is consistent with a role as a (LCR) boundary element and also implicates Yy1 in this process.
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Affiliation(s)
- Yan Jin
- Department of Physiology, University of Manitoba, Winnipeg, Manitoba, Canada
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32
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Soshnikova N, Montavon T, Leleu M, Galjart N, Duboule D. Functional analysis of CTCF during mammalian limb development. Dev Cell 2011; 19:819-30. [PMID: 21145498 DOI: 10.1016/j.devcel.2010.11.009] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 10/17/2010] [Accepted: 11/15/2010] [Indexed: 10/18/2022]
Abstract
CCCTC-binding factor (CTCF) is a nuclear zinc-finger protein that displays insulating activity in a variety of biological assays. For example, CTCF-binding sites have been suggested to isolate Hox gene clusters from neighboring transcriptional interference. We investigated this issue during limb development, where Hoxd genes must remain isolated from long-range effects to allow essential regulation within independent sub-groups. We used conditional Ctcf inactivation in incipient forelimbs and show that the overall pattern of Hoxd gene expression remains unchanged. Transcriptome analysis using tiling arrays covering chromosomes 2 and X confirmed the weak effect of CTCF depletion on global gene regulation. However, Ctcf deletion caused massive apoptosis, leading to a nearly complete loss of limb structure at a later stage. We conclude that, at least in this physiological context, rather than being an insulator, CTCF is required for cell survival via the direct transcriptional regulation of target genes critical for cellular homeostasis.
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Affiliation(s)
- Natalia Soshnikova
- Department of Zoology and Animal Biology, University of Geneva, Switzerland
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33
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Farrar D, Rai S, Chernukhin I, Jagodic M, Ito Y, Yammine S, Ohlsson R, Murrell A, Klenova E. Mutational analysis of the poly(ADP-ribosyl)ation sites of the transcription factor CTCF provides an insight into the mechanism of its regulation by poly(ADP-ribosyl)ation. Mol Cell Biol 2010; 30:1199-216. [PMID: 20038529 PMCID: PMC2820893 DOI: 10.1128/mcb.00827-09] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Revised: 08/02/2009] [Accepted: 12/10/2009] [Indexed: 12/13/2022] Open
Abstract
Poly(ADP-ribosyl)ation of the conserved multifunctional transcription factor CTCF was previously identified as important to maintain CTCF insulator and chromatin barrier functions. However, the molecular mechanism of this regulation and also the necessity of this modification for other CTCF functions remain unknown. In this study, we identified potential sites of poly(ADP-ribosyl)ation within the N-terminal domain of CTCF and generated a mutant deficient in poly(ADP-ribosyl)ation. Using this CTCF mutant, we demonstrated the requirement of poly(ADP-ribosyl)ation for optimal CTCF function in transcriptional activation of the p19ARF promoter and inhibition of cell proliferation. By using a newly generated isogenic insulator reporter cell line, the CTCF insulator function at the mouse Igf2-H19 imprinting control region (ICR) was found to be compromised by the CTCF mutation. The association and simultaneous presence of PARP-1 and CTCF at the ICR, confirmed by single and serial chromatin immunoprecipitation assays, were found to be independent of CTCF poly(ADP-ribosyl)ation. These results suggest a model of CTCF regulation by poly(ADP-ribosyl)ation whereby CTCF and PARP-1 form functional complexes at sites along the DNA, producing a dynamic reversible modification of CTCF. By using bioinformatics tools, numerous sites of CTCF and PARP-1 colocalization were demonstrated, suggesting that such regulation of CTCF may take place at the genome level.
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Affiliation(s)
- Dawn Farrar
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom, Box 280, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Sushma Rai
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom, Box 280, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Igor Chernukhin
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom, Box 280, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Maja Jagodic
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom, Box 280, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Yoko Ito
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom, Box 280, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Samer Yammine
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom, Box 280, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Rolf Ohlsson
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom, Box 280, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Adele Murrell
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom, Box 280, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Elena Klenova
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom, Box 280, Karolinska Institute, SE-171 77 Stockholm, Sweden
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34
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Abstract
The multifunctional zinc-finger protein CCCTC-binding factor (CTCF) is a very strong candidate for the role of coordinating the expression level of coding sequences with their three-dimensional position in the nucleus, apparently responding to a "code" in the DNA itself. Dynamic interactions between chromatin fibers in the context of nuclear architecture have been implicated in various aspects of genome functions. However, the molecular basis of these interactions still remains elusive and is a subject of intense debate. Here we discuss the nature of CTCF-DNA interactions, the CTCF-binding specificity to its binding sites and the relationship between CTCF and chromatin, and we examine data linking CTCF with gene regulation in the three-dimensional nuclear space. We discuss why these features render CTCF a very strong candidate for the role and propose a unifying model, the "CTCF code," explaining the mechanistic basis of how the information encrypted in DNA may be interpreted by CTCF into diverse nuclear functions.
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Affiliation(s)
- Rolf Ohlsson
- Department of Microbiology, Tumor and Cell Biology, Nobels väg 16, Box 280, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Victor Lobanenkov
- Molecular Pathology Section, Laboratory of Immunopathology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (LIP/NIAID/NIH), Twinbrook Building, Room 1329, MSC-8152, 5640 Fisher Lane, Rockville, MD 20852, USA
| | - Elena Klenova
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
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35
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Ali FR, Vasiliou SA, Haddley K, Paredes UM, Roberts JC, Miyajima F, Klenova E, Bubb VJ, Quinn JP. Combinatorial interaction between two human serotonin transporter gene variable number tandem repeats and their regulation by CTCF. J Neurochem 2009; 112:296-306. [PMID: 19860858 PMCID: PMC2848977 DOI: 10.1111/j.1471-4159.2009.06453.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two distinct variable number tandem repeats (VNTRs) within the human serotonin transporter gene (SLC6A4) have been implicated as predisposing factors for CNS disorders. The linked polymorphic region in the 5′-promoter exists as short (s) and long (l) alleles of a 22 or 23 bp elements. The second within intron 2 (Stin2) exists as three variants containing 9, 10 or 12 copies of a 16 or 17 bp element. These VNTRs, individually or in combination, supported differential reporter gene expression in rat neonate prefrontal cortical cultures. The level of reporter gene activity from the dual VNTR constructs indicated combinatorial action between the two domains. Chromatin immunoprecipitation demonstrated that both these VNTR domains can bind the CCCTC-binding factor and this correlated with the ability of exogenously supplied CCCTC-binding factor to modulate the expression supported by these reporter gene constructs. We suggest that the potential for interaction between multiple polymorphic domains should be incorporated into genetic association studies. J. Neurochem. (2010) 112, 296–306.
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Affiliation(s)
- Fahad R Ali
- School of Biomedical Sciences, University of Liverpool, Liverpool, UK
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36
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Mishiro T, Ishihara K, Hino S, Tsutsumi S, Aburatani H, Shirahige K, Kinoshita Y, Nakao M. Architectural roles of multiple chromatin insulators at the human apolipoprotein gene cluster. EMBO J 2009; 28:1234-45. [PMID: 19322193 PMCID: PMC2683055 DOI: 10.1038/emboj.2009.81] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2008] [Accepted: 03/04/2009] [Indexed: 12/31/2022] Open
Abstract
Long-range regulatory elements and higher-order chromatin structure coordinate the expression of multiple genes in cluster, and CTCF/cohesin-mediated chromatin insulator may be a key in this regulation. The human apolipoprotein (APO) A1/C3/A4/A5 gene region, whose alterations increase the risk of dyslipidemia and atherosclerosis, is partitioned at least by three CTCF-enriched sites and three cohesin protein RAD21-enriched sites (two overlap with the CTCF sites), resulting in the formation of two transcribed chromatin loops by interactions between insulators. The C3 enhancer and APOC3/A4/A5 promoters reside in the same loop, where the APOC3/A4 promoters are pointed towards the C3 enhancer, whereas the APOA1 promoter is present in the different loop. The depletion of either CTCF or RAD21 disrupts the chromatin loop structure, together with significant changes in the APO expression and the localization of transcription factor hepatocyte nuclear factor (HNF)-4alpha and transcriptionally active form of RNA polymerase II at the APO promoters. Thus, CTCF/cohesin-mediated insulators maintain the chromatin loop formation and the localization of transcriptional apparatus at the promoters, suggesting an essential role of chromatin insulation in controlling the expression of clustered genes.
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Affiliation(s)
- Tsuyoshi Mishiro
- Department of Regeneration Medicine, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
- Department of Gastroenterology and Hepatology, Shimane University School of Medicine, Izumo, Japan
| | - Ko Ishihara
- Department of Regeneration Medicine, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Shinjiro Hino
- Department of Regeneration Medicine, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Shuichi Tsutsumi
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Komaba, Meguro-ku, Tokyo, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Komaba, Meguro-ku, Tokyo, Japan
| | - Katsuhiko Shirahige
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama City, Kanagawa, Japan
| | - Yoshikazu Kinoshita
- Department of Gastroenterology and Hepatology, Shimane University School of Medicine, Izumo, Japan
| | - Mitsuyoshi Nakao
- Department of Regeneration Medicine, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
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37
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Abstract
CTCF is a ubiquitous transcription factor that is involved in numerous, seemingly unrelated functions. These functions include, but are not limited to, positive or negative regulation of transcription, enhancer-blocking activities at developmentally regulated gene clusters and at imprinted loci, and X-chromosome inactivation. Here, we review recent data acquired with state-of-the-art technologies that illuminate possible mechanisms behind the diversity of CTCF functions. CTCF interacts with numerous protein partners, including cohesin, nucleophosmin, PARP1, Yy1 and RNA polymerase II. We propose that CTCF interacts with one or two different partners according to the biological context, applying the Roman principle of governance, 'divide and rule' (divide et impera).
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Affiliation(s)
- Jordanka Zlatanova
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA.
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Onishi H, Kino Y, Morita T, Futai E, Sasagawa N, Ishiura S. MBNL1 associates with YB-1 in cytoplasmic stress granules. J Neurosci Res 2008; 86:1994-2002. [PMID: 18335541 DOI: 10.1002/jnr.21655] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The muscleblind-like (MBNL) protein family is thought to be involved in the molecular mechanism of myotonic dystrophy (DM). Although it has been shown to have splicing activity, a broader function in cellular RNA metabolism has been implicated. In this study, we attempted to find the binding proteins of MBNL1 in order to elucidate its physiological function. First, we performed a GST pull-down assay using GST-MBNL1-6xHis as bait. Several proteins were identified, including YB-1, a multifunctional DNA/RNA-binding protein, and DDX1, a DEAD box RNA helicase. MBNL1 formed an RNP complex with YB-1 and DDX1 in binding assays. YB-1 also showed a weak but significant effect on alpha-actinin splice site selection. Interestingly, in response to stress, MBNL1 moved to cytoplasmic stress granules, where it colocalized with YB-1, which was previously reported to be a component of stress granules. We found that DDX1 also colocalized with MBNL1 at stress granules. These results provide new insight into the dynamics of MBNL1 in response to stress, and they suggest a role for MBNL1 in mRNA metabolism in the cytoplasm.
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Affiliation(s)
- Hayato Onishi
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan
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Brayer KJ, Segal DJ. Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains. Cell Biochem Biophys 2008; 50:111-31. [PMID: 18253864 DOI: 10.1007/s12013-008-9008-5] [Citation(s) in RCA: 220] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Accepted: 12/28/2007] [Indexed: 11/28/2022]
Abstract
Cys2-His2 (C2H2) zinc finger domains (ZFs) were originally identified as DNA-binding domains, and uncharacterized domains are typically assumed to function in DNA binding. However, a growing body of evidence suggests an important and widespread role for these domains in protein binding. There are even examples of zinc fingers that support both DNA and protein interactions, which can be found in well-known DNA-binding proteins such as Sp1, Zif268, and Ying Yang 1 (YY1). C2H2 protein-protein interactions (PPIs) are proving to be more abundant than previously appreciated, more plastic than their DNA-binding counterparts, and more variable and complex in their interactions surfaces. Here we review the current knowledge of over 100 C2H2 zinc finger-mediated PPIs, focusing on what is known about the binding surface, contributions of individual fingers to the interaction, and function. An accurate understanding of zinc finger biology will likely require greater insights into the potential protein interaction capabilities of C2H2 ZFs.
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Affiliation(s)
- Kathryn J Brayer
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA
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41
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Li Y, Li G, Ivanova A, Aaron S, Simm M. The critical role of human transcriptional repressor CTCF mRNA up-regulation in the induction of anti-HIV-1 responses in CD4(+) T cells. Immunol Lett 2007; 117:35-44. [PMID: 18207574 DOI: 10.1016/j.imlet.2007.11.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Revised: 11/26/2007] [Accepted: 11/26/2007] [Indexed: 12/26/2022]
Abstract
We have employed our CD4(+) T cell model named HIV-1 resistance factor (HRF(+)) to study the inducible anti-HIV-1 responses mediated through novel soluble molecules. We found that exposure to the soluble products of HRF(+) cells activated CCCTC-binding factor (CTCF) mRNA expression in HIV-1 susceptible primary and transformed CD4(+) T cells and overlapped with their acquisition of transient resistance to virus. Conversely, the interference with the expression of CTCF gene in HRF(+) cells reversed the resistant phenotype and eliminated the biological potential of their cell culture supernatant to induce "HRF-like" activity in target cells. Band-shift analysis upon the nuclear fractions from HIV-1 resistant cells showed that CTCF protein bound to HIV-1 promoter and this binding prevented the formation of NF-kappaB/LTR complex. This evidence suggests that CTCF is an intracellular effector of HRF activity and that the acquisition of resistance to HIV-1 in CD4(+) T cells is a consequence of the prior activation of CTCF gene by the soluble entity secreted by HRF(+) cells.
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Affiliation(s)
- Yuchang Li
- Molecular Virology Division, St. Luke's-Roosevelt Hospital Center, Columbia University Medical Center, New York, NY 10019, USA
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42
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Wallace JA, Felsenfeld G. We gather together: insulators and genome organization. Curr Opin Genet Dev 2007; 17:400-7. [PMID: 17913488 PMCID: PMC2215060 DOI: 10.1016/j.gde.2007.08.005] [Citation(s) in RCA: 310] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Revised: 07/20/2007] [Accepted: 08/17/2007] [Indexed: 12/21/2022]
Abstract
When placed between an enhancer and promoter, certain DNA sequence elements inhibit enhancer-stimulated gene expression. The best characterized of these enhancer-blocking insulators, gypsy in Drosophila and the CTCF-binding element in vertebrates and flies, stabilize contacts between distant genomic regulatory sites leading to the formation of loop domains. Current results show that CTCF mediates long-range contacts in the mouse beta-globin locus and at the Igf2/H19-imprinted locus. Recently described active chromatin hubs and transcription factories also involve long-range interactions; it is likely that CTCF interferes with their formation when acting as an insulator. The properties of CTCF, and its newly described genomic distribution, suggest that it may play an important role in large-scale nuclear architecture, perhaps mediated by the co-factors with which it interacts in vivo.
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Affiliation(s)
- Julie A Wallace
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892-0540, United States
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Komura JI, Ikehata H, Ono T. Chromatin fine structure of the c-MYC insulator element/DNase I-hypersensitive site I is not preserved during mitosis. Proc Natl Acad Sci U S A 2007; 104:15741-6. [PMID: 17890321 PMCID: PMC2000435 DOI: 10.1073/pnas.0702363104] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During mitosis in higher eukaryotic cells, transcription is silenced and transcription complexes are absent from promoters in the condensed chromosomes; however, epigenetic information concerning the pattern of expressed and silent genes must be preserved. Recently, it has been reported that CTCF, a major protein in vertebrate insulator elements, remains associated with mitotic chromatin. If the structure of insulators is preserved during mitosis, then it is possible that insulators can function as components or elements of the mechanism involved in the transfer of epigenetic information through the mitotic phase and can help guide the reconstitution of domain structure and nuclear organization after the completion of this phase. We have studied the chromatin structure of the insulator upstream of the c-MYC gene in mitotic HeLa cells. The region of the insulator corresponds to the DNase I hypersensitive site I, but Southern blot analysis revealed that hypersensitivity was lost during mitosis. High resolution in vivo footprinting analysis using dimethyl sulfate, UV light, psoralen, and DNase I also demonstrated the disappearance of the sequence-specific direct binding of CTCF and the absence of detectable structures during mitosis. Thus, it appears that the nucleoprotein complex involving this insulator element must be reassembled de novo with each new cell generation.
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Affiliation(s)
- Jun-Ichiro Komura
- Department of Cell Biology, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan.
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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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Roberts J, Scott AC, Howard MR, Breen G, Bubb VJ, Klenova E, Quinn JP. Differential regulation of the serotonin transporter gene by lithium is mediated by transcription factors, CCCTC binding protein and Y-box binding protein 1, through the polymorphic intron 2 variable number tandem repeat. J Neurosci 2007; 27:2793-801. [PMID: 17360901 PMCID: PMC6672559 DOI: 10.1523/jneurosci.0892-06.2007] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The serotoninergic pathways are possible targets for the action of lithium, a therapeutic agent for treatment of bipolar affective disorders. This study aimed to investigate the molecular mechanisms regulating human serotonin transporter gene (SLC6A4) expression by lithium and, specifically, the role of the variable number tandem repeat (VNTR) polymorphic region in intron 2, which is potentially a predisposing genetic factor for bipolar affective disorders. We demonstrated that addition of lithium to human JAr cells led to changes in the levels of SLC6A4 mRNA and protein. Additional investigations revealed that the intron 2 VNTR domain was a potential target for mediation of a transcriptional response to lithium. Properties of two transcription factors, CCCTC binding protein (CTCF) and Y-box binding protein 1 (YB-1), previously shown to be involved in the regulation of SLC6A4 VNTR, were found to be modulated by LiCl. Thus, levels of CTCF and YB-1 mRNA and protein were altered in vivo in response to LiCl. Furthermore, CTCF and YB-1 showed differential binding to the polymorphic alleles of the VNTR on exposure to LiCl. Our data suggest a model in which differential binding of CTCF and YB-1 to the allelic variants of the intron 2 VNTR can be regulated by lithium and in part result in differential and even aberrant expression of SLC6A4. Our study of the regulation of the SLC6A4 VNTR by lithium may improve the understanding of psychiatric disorders and enable the development of novel therapies for conditions such as bipolar affective disorder to target only the at-risk allele.
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Affiliation(s)
- Julian Roberts
- Physiology Laboratory, School of Biomedical Science
- Department of Human Anatomy and Cell Biology, School of Biomedical Science, and
- Neurological Science, Medical School, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - Alison C. Scott
- Physiology Laboratory, School of Biomedical Science
- Department of Human Anatomy and Cell Biology, School of Biomedical Science, and
| | - Mark R. Howard
- Physiology Laboratory, School of Biomedical Science
- Department of Human Anatomy and Cell Biology, School of Biomedical Science, and
| | - Gerome Breen
- Medical Research Council Social Genetic and Developmental Psychiatry Research Centre, Institute of Psychiatry, King's College London, London SE5 8AF, United Kingdom, and
| | - Vivien J. Bubb
- Department of Human Anatomy and Cell Biology, School of Biomedical Science, and
- Neurological Science, Medical School, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - Elena Klenova
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
| | - John P. Quinn
- Physiology Laboratory, School of Biomedical Science
- Department of Human Anatomy and Cell Biology, School of Biomedical Science, and
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46
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Kantidze OL, Iarovaia OV, Philonenko ES, Yakutenko II, Razin SV. Unusual compartmentalization of CTCF and other transcription factors in the course of terminal erythroid differentiation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2007; 1773:924-33. [PMID: 17467075 DOI: 10.1016/j.bbamcr.2007.03.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2006] [Revised: 03/06/2007] [Accepted: 03/21/2007] [Indexed: 01/31/2023]
Abstract
It is demonstrated that in chicken embryonic and mature erythrocyte nuclei the distribution of a versatile transcription factor CTCF differs drastically from its distribution in nuclei of proliferating erythroid and non-erythroid cells. In the latter case CTCF was distributed throughout the whole nucleus volume, being concentrated in many small compartments (punctuate nuclear staining). In contrast, in embryonic and mature erythrocytes CTCF was concentrated in a limited number of large compartments. These large CTCF-containing compartments were not observed in other cells. Occasionally, but not in all cells, some of these compartments were localized close to nucleoli but did not colocalize with them. In mature erythrocytes a clear exclusion of CTCF-containing compartments from the chromatin domain was observed. This exclusion correlated with a tight association of CTCF with the nuclear matrix. Concentration in relatively large compartments and exclusion from the chromatin domain in nuclei of mature erythrocytes were also observed for RNA polymerase II and several transcription factors. The data are discussed in the context of a hypothesis postulating that relocalization of different components of the transcriptional machinery from the chromatin domain into the interchromatin compartment is an important step of the terminal inactivation of chicken erythrocyte nuclei.
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Affiliation(s)
- Omar L Kantidze
- Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology RAS, 34/5 Vavilov Street, 119334 Moscow, Russia
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Donohoe ME, Zhang LF, Xu N, Shi Y, Lee JT. Identification of a Ctcf cofactor, Yy1, for the X chromosome binary switch. Mol Cell 2007; 25:43-56. [PMID: 17218270 DOI: 10.1016/j.molcel.2006.11.017] [Citation(s) in RCA: 189] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Revised: 10/13/2006] [Accepted: 11/16/2006] [Indexed: 11/27/2022]
Abstract
In mammals, inactivation of one X chromosome in the female equalizes gene dosages between XX females and XY males. Two noncoding loci, Tsix and Xite, together regulate X chromosome fate by controlling homologous chromosome pairing, counting, and mutually exclusive choice. Following choice, the asymmetry of Xite and Tsix expression drives divergent chromosome fates, but how this pattern becomes established is currently unknown. Although no proven trans-acting factors have been identified, a likely candidate is Ctcf, a chromatin insulator with essential function in autosomal imprinting. Here, we search for trans-factors and identify Yy1 as a required cofactor for Ctcf. Paired Ctcf-Yy1 elements are highly clustered within the counting/choice and imprinting domain of Tsix. A deficiency of Yy1 leads to aberrant Tsix and Xist expression, resulting in a deficit of male and female embryos. Yy1 and Ctcf associate through specific protein-protein interactions and together transactivate Tsix. We propose that the Ctcf-Yy1-Tsix complex functions as a key component of the X chromosome binary switch.
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Chernukhin I, Shamsuddin S, Kang SY, Bergström R, Kwon YW, Yu W, Whitehead J, Mukhopadhyay R, Docquier F, Farrar D, Morrison I, Vigneron M, Wu SY, Chiang CM, Loukinov D, Lobanenkov V, Ohlsson R, Klenova E. CTCF interacts with and recruits the largest subunit of RNA polymerase II to CTCF target sites genome-wide. Mol Cell Biol 2007; 27:1631-48. [PMID: 17210645 PMCID: PMC1820452 DOI: 10.1128/mcb.01993-06] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
CTCF is a transcription factor with highly versatile functions ranging from gene activation and repression to the regulation of insulator function and imprinting. Although many of these functions rely on CTCF-DNA interactions, it is an emerging realization that CTCF-dependent molecular processes involve CTCF interactions with other proteins. In this study, we report the association of a subpopulation of CTCF with the RNA polymerase II (Pol II) protein complex. We identified the largest subunit of Pol II (LS Pol II) as a protein significantly colocalizing with CTCF in the nucleus and specifically interacting with CTCF in vivo and in vitro. The role of CTCF as a link between DNA and LS Pol II has been reinforced by the observation that the association of LS Pol II with CTCF target sites in vivo depends on intact CTCF binding sequences. "Serial" chromatin immunoprecipitation (ChIP) analysis revealed that both CTCF and LS Pol II were present at the beta-globin insulator in proliferating HD3 cells but not in differentiated globin synthesizing HD3 cells. Further, a single wild-type CTCF target site (N-Myc-CTCF), but not the mutant site deficient for CTCF binding, was sufficient to activate the transcription from the promoterless reporter gene in stably transfected cells. Finally, a ChIP-on-ChIP hybridization assay using microarrays of a library of CTCF target sites revealed that many intergenic CTCF target sequences interacted with both CTCF and LS Pol II. We discuss the possible implications of our observations with respect to plausible mechanisms of transcriptional regulation via a CTCF-mediated direct link of LS Pol II to the DNA.
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Affiliation(s)
- Igor Chernukhin
- Department of Biological Sciences, Central Campus, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
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49
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Abstract
Recent advances in studying long-range chromatin interactions have shifted focus from the transcriptional regulation by nearby regulatory elements to recognition of the role of higher-order chromatin organization within the nucleus. These advances have also suggested that CCCTC-binding factor (CTCF), a known chromatin insulator protein, may play a central role in mediating long-range chromatin interactions, directing DNA segments into transcription factories and/or facilitating interactions with other DNA regions. Several models that describe possible mechanisms for multiple functions of CTCF in establishment and maintenance of epigenetic programs are now emerging. Epigenetics plays an important role in normal development and disease including cancer. CTCF involvement in multiple aspects of epigenetic regulation, including regulation of genomic imprinting and X-chromosome inactivation, has been well established. More recently, CTCF was found to play a role in regulation of noncoding transcription and establishing local chromatin structure at the repetitive elements in mammalian genomes, suggesting a new epigenetic basis for several repeat-associated genetic disorders. Emerging evidence also points to the role of CTCF deregulation in the epigenetic imbalance in cancer. These studies provide some of the important missing links in our understanding of epigenetic control of both development and cancer.
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Affiliation(s)
- Galina N Filippova
- Human Biology Division, Fred Hutchinson Cancer Research Center Seattle, Washington 98109, USA
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50
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Ishihara K, Oshimura M, Nakao M. CTCF-dependent chromatin insulator is linked to epigenetic remodeling. Mol Cell 2006; 23:733-42. [PMID: 16949368 DOI: 10.1016/j.molcel.2006.08.008] [Citation(s) in RCA: 182] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2006] [Revised: 06/17/2006] [Accepted: 08/10/2006] [Indexed: 10/24/2022]
Abstract
Chromatin insulators are boundary elements between distinctly regulated, neighboring chromosomal domains, and they function by blocking the effects of nearby enhancers in a position-dependent manner. Here, we show that the SNF2-like chromodomain helicase protein CHD8 interacts with the insulator binding protein CTCF. Chromatin immunoprecipitation analysis revealed that CHD8 was present at known CTCF target sites, such as the differentially methylated region (DMR) of H19, the locus control region of beta-globin, and the promoter region of BRCA1 and c-myc genes. RNA interference-mediated knockdown of CHD8 significantly abolished the H19 DMR insulator activity that depends highly on CTCF, leading to reactivation of imprinted IGF2 from chromosome of maternal origin. Further, the lack of CHD8 affected CpG methylation and histone acetylation around the CTCF binding sites, adjacent to heterochromatin, of BRCA1 and c-myc genes. These findings provide insight into the role of CTCF-CHD8 complex in insulation and epigenetic regulation at active insulator sites.
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Affiliation(s)
- Ko Ishihara
- Department of Regeneration Medicine, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Kumamoto 860-0811, Japan
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