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Li Q, Zhu G, Zhang L, Zeng B, Cai T, Wu J, Wei B, Xie Z, He L, Tang W, Lin X, Lu H, Wu F, Huang J, Hu H, Liu N, Fan S. Mutational landscape of head and neck cancer and cervical cancer in Chinese and Western population. Head Neck 2024; 46:528-540. [PMID: 38111234 DOI: 10.1002/hed.27603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 11/12/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND We aimed to unbiasedly map the genetic mutation profile of HNSC and CESC associated with HPV status in the Chinese population (SYSU-cohort) and compare them with Western population (TCGA-cohort). METHODS Fifty-one HNSC patients (SYSU-HNSC) and 38 CESC patients (SYSU-CESC) were enrolled in this study. Genomic alterations were examined, and the profile was produced using the YuanSuTM450 gene panel (OrigiMed, Shanghai, China). The altered genes were inferred and compared to Western patients from TCGA cohorts. RESULTS Compared to the TCGA-HNSC cohort, FGFR3 mutation was identified as a novel target in SYSU-HNSC with therapeutic potential. Compared to the TCGA-CESC cohort, some epigenetic regulation-associated genes were frequently mutated in SYSU-CESC cohort (KMT2C, KMT2D, KDM5C, KMT2A). CONCLUSION In summary, our study provides unbiased insights into the genetic landscape of HNSC and CESC in the Chinese population and highlights potential novel therapeutic targets that may benefit Chinese patients.
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Affiliation(s)
- Qunxing Li
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | - Genhai Zhu
- Department of Gynecology, Hainan General Hospital, Haikou, China
| | - Lizao Zhang
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | - Binghui Zeng
- Guanghua School of Stomatology, Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Tingting Cai
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiaying Wu
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Bin Wei
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhijun Xie
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lile He
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Wenbing Tang
- Department of Stomatology, Guangdong Agriculture and Reclamation Central Hospital, Zhanjiang, China
| | - Xinyu Lin
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Huaiwu Lu
- Department of Gynecologic Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Fan Wu
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | | | - Huijun Hu
- Department of Radiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Niu Liu
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Song Fan
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Guangzhou, China
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Xu H, Liang H. The regulation of totipotency transcription: Perspective from in vitro and in vivo totipotency. Front Cell Dev Biol 2022; 10:1024093. [DOI: 10.3389/fcell.2022.1024093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/13/2022] [Indexed: 11/13/2022] Open
Abstract
Totipotency represents the highest developmental potency. By definition, totipotent stem cells are capable of giving rise to all embryonic and extraembryonic cell types. In mammalian embryos, totipotency occurs around the zygotic genome activation period, which is around the 2-cell stage in mouse embryo or the 4-to 8-cell stage in human embryo. Currently, with the development of in vitro totipotent-like models and the advances in small-scale genomic methods, an in-depth mechanistic understanding of the totipotency state and regulation was enabled. In this review, we explored and summarized the current views about totipotency from various angles, including genetic and epigenetic aspects. This will hopefully formulate a panoramic view of totipotency from the available research works until now. It can also help delineate the scaffold and formulate new hypotheses on totipotency for future research works.
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3
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Dehingia B, Milewska M, Janowski M, Pękowska A. CTCF
shapes chromatin structure and gene expression in health and disease. EMBO Rep 2022; 23:e55146. [PMID: 35993175 PMCID: PMC9442299 DOI: 10.15252/embr.202255146] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/31/2022] [Accepted: 07/14/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Bondita Dehingia
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology Polish Academy of Sciences Warsaw Poland
| | - Małgorzata Milewska
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology Polish Academy of Sciences Warsaw Poland
| | - Marcin Janowski
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology Polish Academy of Sciences Warsaw Poland
| | - Aleksandra Pękowska
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology Polish Academy of Sciences Warsaw Poland
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4
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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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5
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Warrier T, El Farran C, Zeng Y, Ho B, Bao Q, Zheng Z, Bi X, Ng HH, Ong D, Chu J, Sanyal A, Fullwood MJ, Collins J, Li H, Xu J, Loh YH. SETDB1 acts as a topological accessory to Cohesin via an H3K9me3-independent, genomic shunt for regulating cell fates. Nucleic Acids Res 2022; 50:7326-7349. [PMID: 35776115 PMCID: PMC9303280 DOI: 10.1093/nar/gkac531] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 05/30/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
SETDB1 is a key regulator of lineage-specific genes and endogenous retroviral elements (ERVs) through its deposition of repressive H3K9me3 mark. Apart from its H3K9me3 regulatory role, SETDB1 has seldom been studied in terms of its other potential regulatory roles. To investigate this, a genomic survey of SETDB1 binding in mouse embryonic stem cells across multiple libraries was conducted, leading to the unexpected discovery of regions bereft of common repressive histone marks (H3K9me3, H3K27me3). These regions were enriched with the CTCF motif that is often associated with the topological regulator Cohesin. Further profiling of these non-H3K9me3 regions led to the discovery of a cluster of non-repeat loci that were co-bound by SETDB1 and Cohesin. These regions, which we named DiSCs (domains involving SETDB1 and Cohesin) were seen to be proximal to the gene promoters involved in embryonic stem cell pluripotency and lineage development. Importantly, it was found that SETDB1-Cohesin co-regulate target gene expression and genome topology at these DiSCs. Depletion of SETDB1 led to localized dysregulation of Cohesin binding thereby locally disrupting topological structures. Dysregulated gene expression trends revealed the importance of this cluster in ES cell maintenance as well as at gene 'islands' that drive differentiation to other lineages. The 'unearthing' of the DiSCs thus unravels a unique topological and transcriptional axis of control regulated chiefly by SETDB1.
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Affiliation(s)
- Tushar Warrier
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Chadi El Farran
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Yingying Zeng
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
| | - Benedict Shao Quan Ho
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - Qiuye Bao
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - Zi Hao Zheng
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Xuezhi Bi
- Proteomics Group, Bioprocessing Technology Institute, A*STAR, Singapore 138668, Singapore
| | - Huck Hui Ng
- Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Derrick Sek Tong Ong
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Justin Jang Hann Chu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- Infectious Disease Translational Research Programme, National University of Singapore, Singapore 117597, Singapore
| | - Amartya Sanyal
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
| | - Melissa Jane Fullwood
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
| | - James J Collins
- Howard Hughes Medical Institute, Boston, MA 02114, USA
- Institute for Medical Engineering and Science Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Jian Xu
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
- Department of Plant Systems Physiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Yuin-Han Loh
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 28 MedicalDrive, Singapore 117456, Singapore
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6
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Bellefroid M, Rodari A, Galais M, Krijger PHL, Tjalsma SJD, Nestola L, Plant E, Vos ESM, Cristinelli S, Van Driessche B, Vanhulle C, Ait-Ammar A, Burny A, Ciuffi A, de Laat W, Van Lint C. Role of the cellular factor CTCF in the regulation of bovine leukemia virus latency and three-dimensional chromatin organization. Nucleic Acids Res 2022; 50:3190-3202. [PMID: 35234910 PMCID: PMC8989512 DOI: 10.1093/nar/gkac107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 01/31/2022] [Accepted: 02/05/2022] [Indexed: 01/12/2023] Open
Abstract
Bovine leukemia virus (BLV)-induced tumoral development is a multifactorial phenomenon that remains incompletely understood. Here, we highlight the critical role of the cellular CCCTC-binding factor (CTCF) both in the regulation of BLV transcriptional activities and in the deregulation of the three-dimensional (3D) chromatin architecture surrounding the BLV integration site. We demonstrated the in vivo recruitment of CTCF to three conserved CTCF binding motifs along the provirus. Next, we showed that CTCF localized to regions of transitions in the histone modifications profile along the BLV genome and that it is implicated in the repression of the 5′Long Terminal Repeat (LTR) promoter activity, thereby contributing to viral latency, while favoring the 3′LTR promoter activity. Finally, we demonstrated that BLV integration deregulated the host cellular 3D chromatin organization through the formation of viral/host chromatin loops. Altogether, our results highlight CTCF as a new critical effector of BLV transcriptional regulation and BLV-induced physiopathology.
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Affiliation(s)
- Maxime Bellefroid
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Anthony Rodari
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Mathilde Galais
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Peter H L Krijger
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht 3584, CT, The Netherlands
| | - Sjoerd J D Tjalsma
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht 3584, CT, The Netherlands
| | - Lorena Nestola
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Estelle Plant
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Erica S M Vos
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht 3584, CT, The Netherlands
| | - Sara Cristinelli
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne 1011, Switzerland
| | - Benoit Van Driessche
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Caroline Vanhulle
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Amina Ait-Ammar
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Arsène Burny
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Angela Ciuffi
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne 1011, Switzerland
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht 3584, CT, The Netherlands
| | - Carine Van Lint
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
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7
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DNA G-Quadruplexes Contribute to CTCF Recruitment. Int J Mol Sci 2021; 22:ijms22137090. [PMID: 34209337 PMCID: PMC8269367 DOI: 10.3390/ijms22137090] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 12/12/2022] Open
Abstract
G-quadruplex (G4) sites in the human genome frequently colocalize with CCCTC-binding factor (CTCF)-bound sites in CpG islands (CGIs). We aimed to clarify the role of G4s in CTCF positioning. Molecular modeling data suggested direct interactions, so we performed in vitro binding assays with quadruplex-forming sequences from CGIs in the human genome. G4s bound CTCF with Kd values similar to that of the control duplex, while respective i-motifs exhibited no affinity for CTCF. Using ChIP-qPCR assays, we showed that G4-stabilizing ligands enhance CTCF occupancy at a G4-prone site in STAT3 gene. In view of the reportedly increased CTCF affinity for hypomethylated DNA, we next questioned whether G4s also facilitate CTCF recruitment to CGIs via protecting CpG sites from methylation. Bioinformatics analysis of previously published data argued against such a possibility. Finally, we questioned whether G4s facilitate CTCF recruitment by affecting chromatin structure. We showed that three architectural chromatin proteins of the high mobility group colocalize with G4s in the genome and recognize parallel-stranded or mixed-topology G4s in vitro. One of such proteins, HMGN3, contributes to the association between G4s and CTCF according to our bioinformatics analysis. These findings support both direct and indirect roles of G4s in CTCF recruitment.
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8
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Pauletto E, Eickhoff N, Padrão NA, Blattner C, Zwart W. TRIMming Down Hormone-Driven Cancers: The Biological Impact of TRIM Proteins on Tumor Development, Progression and Prognostication. Cells 2021; 10:1517. [PMID: 34208621 PMCID: PMC8234875 DOI: 10.3390/cells10061517] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/08/2021] [Accepted: 06/12/2021] [Indexed: 02/06/2023] Open
Abstract
The tripartite motif (TRIM) protein family is attracting increasing interest in oncology. As a protein family based on structure rather than function, a plethora of biological activities are described for TRIM proteins, which are implicated in multiple diseases including cancer. With hormone-driven cancers being among the leading causes of cancer-related death, TRIM proteins have been described to portrait tumor suppressive or oncogenic activities in these tumor types. This review describes the biological impact of TRIM proteins in relation to hormone receptor biology, as well as hormone-independent mechanisms that contribute to tumor cell biology in prostate, breast, ovarian and endometrial cancer. Furthermore, we point out common functions of TRIM proteins throughout the group of hormone-driven cancers. An improved understanding of the biological impact of TRIM proteins in cancer may pave the way for improved prognostication and novel therapeutics, ultimately improving cancer care for patients with hormone-driven cancers.
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Affiliation(s)
- Eleonora Pauletto
- Institute of Biological and Chemical Systems-Biological Information Processing, Karlsruhe Institute of Technology, PO-Box 3640, 76021 Karlsruhe, Germany;
| | - Nils Eickhoff
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands; (N.E.); (N.A.P.)
| | - Nuno A. Padrão
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands; (N.E.); (N.A.P.)
| | - Christine Blattner
- Institute of Biological and Chemical Systems-Biological Information Processing, Karlsruhe Institute of Technology, PO-Box 3640, 76021 Karlsruhe, Germany;
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands; (N.E.); (N.A.P.)
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9
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D’Arienzo V, Ferguson J, Giraud G, Chapus F, Harris JM, Wing PAC, Claydon A, Begum S, Zhuang X, Balfe P, Testoni B, McKeating JA, Parish JL. The CCCTC-binding factor CTCF represses hepatitis B virus enhancer I and regulates viral transcription. Cell Microbiol 2021; 23:e13274. [PMID: 33006186 PMCID: PMC7116737 DOI: 10.1111/cmi.13274] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/09/2020] [Accepted: 09/29/2020] [Indexed: 12/17/2022]
Abstract
Hepatitis B virus (HBV) infection is of global importance with over 2 billion people exposed to the virus during their lifetime and at risk of progressive liver disease, cirrhosis and hepatocellular carcinoma. HBV is a member of the Hepadnaviridae family that replicates via episomal copies of a covalently closed circular DNA (cccDNA) genome. The chromatinization of this small viral genome, with overlapping open reading frames and regulatory elements, suggests an important role for epigenetic pathways to regulate viral transcription. The chromatin-organising transcriptional insulator protein, CCCTC-binding factor (CTCF), has been reported to regulate transcription in a diverse range of viruses. We identified two conserved CTCF binding sites in the HBV genome within enhancer I and chromatin immunoprecipitation (ChIP) analysis demonstrated an enrichment of CTCF binding to integrated or episomal copies of the viral genome. siRNA knock-down of CTCF results in a significant increase in pre-genomic RNA levels in de novo infected HepG2 cells and those supporting episomal HBV DNA replication. Furthermore, mutation of these sites in HBV DNA minicircles abrogated CTCF binding and increased pre-genomic RNA levels, providing evidence of a direct role for CTCF in repressing HBV transcription.
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Affiliation(s)
| | - Jack Ferguson
- institute of Cancer and Genomic sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Guillaume Giraud
- CRCL INSERM and Cancer Research Center of Lyon (CRCL), Lyon, France
| | - Fleur Chapus
- CRCL INSERM and Cancer Research Center of Lyon (CRCL), Lyon, France
| | - James M. Harris
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Peter A. C. Wing
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Adam Claydon
- institute of Cancer and Genomic sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Sophia Begum
- institute of Cancer and Genomic sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Xiaodong Zhuang
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Peter Balfe
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Barbara Testoni
- CRCL INSERM and Cancer Research Center of Lyon (CRCL), Lyon, France
| | | | - Joanna L. Parish
- institute of Cancer and Genomic sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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10
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VonHandorf A, Zablon HA, Biesiada J, Zhang X, Medvedovic M, Puga A. Hexavalent chromium promotes differential binding of CTCF to its cognate sites in Euchromatin. Epigenetics 2021; 16:1361-1376. [PMID: 33319643 DOI: 10.1080/15592294.2020.1864168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Hexavalent chromium compounds are well-established respiratory carcinogens to which humans are commonly exposed in industrial and occupational settings. In addition, natural and anthropogenic sources of these compounds contribute to the exposure of global populations through multiple routes, including dermal, ingestion and inhalation that elevate the risk of cancer by largely unresolved mechanisms. Cr(VI) has genotoxic properties that include ternary adduct formation with DNA, increases in DNA damage, mostly by double-strand break formation, and altered transcriptional responses. Our previous work using ATAC-seq showed that CTCF motifs were enriched in Cr(VI)-dependent differentially accessible chromatin, suggesting that CTCF, a key transcription factor responsible for the regulation of the transcriptome, might be a chromium target. To test this hypothesis, we investigated the effect of Cr(VI) treatment on the binding of CTCF to its cognate sites and ensuing changes in transcription-related histone modifications. Differentially bound CTCF sites were enriched by Cr(VI) treatment within transcription-related regions, specifically transcription start sites and upstream genic regions. Functional annotation of the affected genes highlighted biological processes previously associated with Cr(VI) exposure. Notably, we found that differentially bound CTCF sites proximal to the promoters of this subset of genes were frequently associated with the active histone marks H3K27ac, H3K4me3, and H3K36me3, in agreement with the concept that Cr(VI) targets CTCF in euchromatic regions of the genome. Our results support the conclusion that Cr(VI) treatment promotes the differential binding of CTCF to its cognate sites in genes near transcription-active boundaries, targeting these genes for dysregulation.
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Affiliation(s)
- Andrew VonHandorf
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Hesbon A Zablon
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Jacek Biesiada
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Xiang Zhang
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Mario Medvedovic
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Alvaro Puga
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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11
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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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12
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Burchfiel ET, Vihervaara A, Guertin MJ, Gomez-Pastor R, Thiele DJ. Comparative interactomes of HSF1 in stress and disease reveal a role for CTCF in HSF1-mediated gene regulation. J Biol Chem 2020; 296:100097. [PMID: 33208463 PMCID: PMC7948500 DOI: 10.1074/jbc.ra120.015452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/10/2020] [Accepted: 11/18/2020] [Indexed: 01/09/2023] Open
Abstract
Heat shock transcription factor 1 (HSF1) orchestrates cellular stress protection by activating or repressing gene transcription in response to protein misfolding, oncogenic cell proliferation, and other environmental stresses. HSF1 is tightly regulated via intramolecular repressive interactions, post-translational modifications, and protein-protein interactions. How these HSF1 regulatory protein interactions are altered in response to acute and chronic stress is largely unknown. To elucidate the profile of HSF1 protein interactions under normal growth and chronic and acutely stressful conditions, quantitative proteomics studies identified interacting proteins in the response to heat shock or in the presence of a poly-glutamine aggregation protein cell-based model of Huntington's disease. These studies identified distinct protein interaction partners of HSF1 as well as changes in the magnitude of shared interactions as a function of each stressful condition. Several novel HSF1-interacting proteins were identified that encompass a wide variety of cellular functions, including roles in DNA repair, mRNA processing, and regulation of RNA polymerase II. One HSF1 partner, CTCF, interacted with HSF1 in a stress-inducible manner and functions in repression of specific HSF1 target genes. Understanding how HSF1 regulates gene repression is a crucial question, given the dysregulation of HSF1 target genes in both cancer and neurodegeneration. These studies expand our understanding of HSF1-mediated gene repression and provide key insights into HSF1 regulation via protein-protein interactions.
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Affiliation(s)
- Eileen T Burchfiel
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA; Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Anniina Vihervaara
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Michael J Guertin
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
| | - Rocio Gomez-Pastor
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Dennis J Thiele
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA; Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA.
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13
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Hu G, Dong X, Gong S, Song Y, Hutchins AP, Yao H. Systematic screening of CTCF binding partners identifies that BHLHE40 regulates CTCF genome-wide distribution and long-range chromatin interactions. Nucleic Acids Res 2020; 48:9606-9620. [PMID: 32885250 PMCID: PMC7515718 DOI: 10.1093/nar/gkaa705] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 07/27/2020] [Accepted: 08/14/2020] [Indexed: 11/14/2022] Open
Abstract
CTCF plays a pivotal role in mediating chromatin interactions, but it does not do so alone. A number of factors have been reported to co-localize with CTCF and regulate CTCF loops, but no comprehensive analysis of binding partners has been performed. This prompted us to identify CTCF loop participants and regulators by co-localization analysis with CTCF. We screened all factors that had ChIP-seq data in humans by co-localization analysis with human super conserved CTCF (hscCTCF) binding sites, and identified many new factors that overlapped with hscCTCF binding sites. Combined with CTCF loop information, we observed that clustered factors could promote CTCF loops. After in-depth mining of each factor, we found that many factors might have the potential to promote CTCF loops. Our data further demonstrated that BHLHE40 affected CTCF loops by regulating CTCF binding. Together, this study revealed that many factors have the potential to participate in or regulate CTCF loops, and discovered a new role for BHLHE40 in modulating CTCF loop formation.
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Affiliation(s)
- Gongcheng Hu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaotao Dong
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shixin Gong
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yawei Song
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Andrew P Hutchins
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hongjie Yao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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14
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Wang J, Wang J, Yang L, Zhao C, Wu LN, Xu L, Zhang F, Weng Q, Wegner M, Lu QR. CTCF-mediated chromatin looping in EGR2 regulation and SUZ12 recruitment critical for peripheral myelination and repair. Nat Commun 2020; 11:4133. [PMID: 32807777 PMCID: PMC7431862 DOI: 10.1038/s41467-020-17955-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 07/24/2020] [Indexed: 11/25/2022] Open
Abstract
Chromatin organization is critical for cell growth, differentiation, and disease development, however, its functions in peripheral myelination and myelin repair remain elusive. In this report, we demonstrate that the CCCTC-binding factor (CTCF), a crucial chromatin organizer, is essential for Schwann cell myelination and myelin regeneration after nerve injury. Inhibition of CTCF or its deletion blocks Schwann cell differentiation at the pro-myelinating stage, whereas overexpression of CTCF promotes the myelination program. We find that CTCF establishes chromatin interaction loops between enhancer and promoter regulatory elements and promotes expression of a key pro-myelinogenic factor EGR2. In addition, CTCF interacts with SUZ12, a component of polycomb-repressive-complex 2 (PRC2), to repress the transcriptional program associated with negative regulation of Schwann cell maturation. Together, our findings reveal a dual role of CTCF-dependent chromatin organization in promoting myelinogenic programs and recruiting chromatin-repressive complexes to block Schwann cell differentiation inhibitors to control peripheral myelination and repair. Myelination by Schwann cells (SC) in the peripheral nervous system is essential for motor function, and dysregulation of SC myelination can lead to various neuropathies. Here the authors describe a critical role of CCCTC-binding factor (CTCF)-dependent chromatin reorganization in peripheral myelination and myelin regeneration after injury.
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Affiliation(s)
- Jincheng Wang
- Center for Drug Safety Evaluation and Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jiajia Wang
- Department of Pediatrics, Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Lijun Yang
- Department of Pediatrics, Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Chuntao Zhao
- Department of Pediatrics, Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Laiman Natalie Wu
- Department of Pediatrics, Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Lingli Xu
- Department of Pediatrics, Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Feng Zhang
- Department of Pediatrics, Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Qinjie Weng
- Center for Drug Safety Evaluation and Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Michael Wegner
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Q Richard Lu
- Department of Pediatrics, Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
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15
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Akhtar MS, Akhter N, Najm MZ, Deo SVS, Shukla NK, Almalki SSR, Alharbi RA, Sindi AAA, Alruwetei A, Ahmad A, Husain SA. Association of mutation and low expression of the CTCF gene with breast cancer progression. Saudi Pharm J 2020; 28:607-614. [PMID: 32435142 PMCID: PMC7229322 DOI: 10.1016/j.jsps.2020.03.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/29/2020] [Indexed: 12/15/2022] Open
Abstract
Background CTCF encodes 11-zinc finger protein which is implicated in multiple tumors including the carcinoma of the breast. The Present study investigates the association of CTCF mutations and their expression in breast cancer cases. Methods A total of 155 breast cancer and an equal number of adjacent normal tissue samples from 155 breast cancer patients were examined for CTCF mutation(s) by PCR-SSCP and automated DNA sequencing. Immunohistochemistry (IHC) method was used to analyze CTCF expression. Molecular findings were statistically analyzed with various clinicopathological features to identify associations of clinical relevance. Results Of the total, 16.1% (25/155) cases exhibited mutation in the CTCF gene. Missense mutations Gln > His (G > T) in exon 1 and silent mutations Ser > Ser (C > T) in exon 4 of CTCF gene were analyzed. A significant association was observed between CTCF mutations and some clinicopathological parameters namely menopausal status (p = 0.02) tumor stage (p = 0.03) nodal status (p = 0.03) and ER expression (p = 0.04). Protein expression analysis showed 42.58% samples having low or no expression (+), 38.0% with moderate (++) expression and 19.35% having high (+++) expression for CTCF. A significant association was found between CTCF protein expression and clinicopathological parameters include histological grade (p = 0.04), tumor stage (p = 0.04), nodal status (p = 0.03) and ER status (p = 0.04). Conclusions The data suggest that CTCF mutations leading to its inactivation significantly contribute to the progression of breast cancer.
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Affiliation(s)
- Md Salman Akhtar
- Human Genetics Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.,Faculty of Applied Medical Sciences, Albaha University, Albaha, Saudi Arabia
| | - Naseem Akhter
- Human Genetics Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.,Faculty of Applied Medical Sciences, Albaha University, Albaha, Saudi Arabia
| | | | - S V S Deo
- Department of Surgical Oncology, DR. BRA-IRCH, AIIMS, New Delhi 110029, India
| | - N K Shukla
- Department of Surgical Oncology, DR. BRA-IRCH, AIIMS, New Delhi 110029, India
| | | | - Raed A Alharbi
- Faculty of Applied Medical Sciences, Albaha University, Albaha, Saudi Arabia
| | | | - Abdulmohsen Alruwetei
- Department of Medical Laboratory, College of Applied Medical Sciences, Qassim University, Qassim, Saudi Arabia
| | - Abrar Ahmad
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Syed Akhtar Husain
- Human Genetics Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
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16
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Ueberschär M, Wang H, Zhang C, Kondo S, Aoki T, Schedl P, Lai EC, Wen J, Dai Q. BEN-solo factors partition active chromatin to ensure proper gene activation in Drosophila. Nat Commun 2019; 10:5700. [PMID: 31836703 PMCID: PMC6911014 DOI: 10.1038/s41467-019-13558-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 11/14/2019] [Indexed: 11/08/2022] Open
Abstract
The Drosophila genome encodes three BEN-solo proteins including Insensitive (Insv), Elba1 and Elba2 that possess activities in transcriptional repression and chromatin insulation. A fourth protein-Elba3-bridges Elba1 and Elba2 to form an ELBA complex. Here, we report comprehensive investigation of these proteins in Drosophila embryos. We assess common and distinct binding sites for Insv and ELBA and their genetic interdependencies. While Elba1 and Elba2 binding generally requires the ELBA complex, Elba3 can associate with chromatin independently of Elba1 and Elba2. We further demonstrate that ELBA collaborates with other insulators to regulate developmental patterning. Finally, we find that adjacent gene pairs separated by an ELBA bound sequence become less differentially expressed in ELBA mutants. Transgenic reporters confirm the insulating activity of ELBA- and Insv-bound sites. These findings define ELBA and Insv as general insulator proteins in Drosophila and demonstrate the functional importance of insulators to partition transcription units.
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Affiliation(s)
- Malin Ueberschär
- Department of Molecular Bioscience, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Huazhen Wang
- Department of Molecular Bioscience, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Chun Zhang
- Department of Molecular Bioscience, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- State Key Laboratory of Developmental Biology of Freshwater Fish College of Life Sciences, Hunan Normal University, Changsha, China
| | - Shu Kondo
- Laboratory of Invertebrate Genetics, National Institute of Genetics, Mishima, Japan
| | - Tsutomu Aoki
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Paul Schedl
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Eric C Lai
- Department of Developmental Biology, Memorial Sloan Kettering Institute, New York, NY, USA.
| | - Jiayu Wen
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia.
| | - Qi Dai
- Department of Molecular Bioscience, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
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17
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Dutta RK, Chinnapaiyan S, Unwalla H. Aberrant MicroRNAomics in Pulmonary Complications: Implications in Lung Health and Diseases. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 18:413-431. [PMID: 31655261 PMCID: PMC6831837 DOI: 10.1016/j.omtn.2019.09.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 02/07/2023]
Abstract
Over the last few decades, evolutionarily conserved molecular networks have emerged as important regulators in the expression and function of eukaryotic genomes. Recently, miRNAs (miRNAs), a large family of small, non-coding regulatory RNAs were identified in these networks as regulators of endogenous genes by exerting post-transcriptional gene regulation activity in a broad range of eukaryotic species. Dysregulation of miRNA expression correlates with aberrant gene expression and can play an essential role in human health and disease. In the context of the lung, miRNAs have been implicated in organogenesis programming, such as proliferation, differentiation, and morphogenesis. Gain- or loss-of-function studies revealed their pivotal roles as regulators of disease development, potential therapeutic candidates/targets, and clinical biomarkers. An altered microRNAome has been attributed to several pulmonary diseases, such as asthma, chronic pulmonary obstructive disease, cystic fibrosis, lung cancer, and idiopathic pulmonary fibrosis. Considering the relevant roles and functions of miRNAs under physiological and pathological conditions, they may lead to the invention of new diagnostic and therapeutic tools. This review will focus on recent advances in understanding the role of miRNAs in lung development, lung health, and diseases, while also exploring the progress and prospects of their application as therapeutic leads or as biomarkers.
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Affiliation(s)
- Rajib Kumar Dutta
- Department of Immunology and Nano-medicine, Institute of Neuroimmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Srinivasan Chinnapaiyan
- Department of Immunology and Nano-medicine, Institute of Neuroimmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Hoshang Unwalla
- Department of Immunology and Nano-medicine, Institute of Neuroimmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA.
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18
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Iyer LM, Nagarajan S, Woelfer M, Schoger E, Khadjeh S, Zafiriou MP, Kari V, Herting J, Pang ST, Weber T, Rathjens FS, Fischer TH, Toischer K, Hasenfuss G, Noack C, Johnsen SA, Zelarayán LC. A context-specific cardiac β-catenin and GATA4 interaction influences TCF7L2 occupancy and remodels chromatin driving disease progression in the adult heart. Nucleic Acids Res 2019; 46:2850-2867. [PMID: 29394407 PMCID: PMC5887416 DOI: 10.1093/nar/gky049] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/18/2018] [Indexed: 12/17/2022] Open
Abstract
Chromatin remodelling precedes transcriptional and structural changes in heart failure. A body of work suggests roles for the developmental Wnt signalling pathway in cardiac remodelling. Hitherto, there is no evidence supporting a direct role of Wnt nuclear components in regulating chromatin landscapes in this process. We show that transcriptionally active, nuclear, phosphorylated(p)Ser675-β-catenin and TCF7L2 are upregulated in diseased murine and human cardiac ventricles. We report that inducible cardiomyocytes (CM)-specific pSer675-β-catenin accumulation mimics the disease situation by triggering TCF7L2 expression. This enhances active chromatin, characterized by increased H3K27ac and TCF7L2 occupancies to cardiac developmental and remodelling genes in vivo. Accordingly, transcriptomic analysis of β-catenin stabilized hearts shows a strong recapitulation of cardiac developmental processes like cell cycling and cytoskeletal remodelling. Mechanistically, TCF7L2 co-occupies distal genomic regions with cardiac transcription factors NKX2–5 and GATA4 in stabilized-β-catenin hearts. Validation assays revealed a previously unrecognized function of GATA4 as a cardiac repressor of the TCF7L2/β-catenin complex in vivo, thereby defining a transcriptional switch controlling disease progression. Conversely, preventing β-catenin activation post-pressure-overload results in a downregulation of these novel TCF7L2-targets and rescues cardiac function. Thus, we present a novel role for TCF7L2/β-catenin in CMs-specific chromatin modulation, which could be exploited for manipulating the ubiquitous Wnt pathway.
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Affiliation(s)
- Lavanya M Iyer
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen, Georg-August University, Goettingen 37075, Germany.,German Center for Cardiovascular Research (DZHK) partner site Goettingen, Goettingen 37075, Germany
| | - Sankari Nagarajan
- Clinic for General, Visceral and Pediatric Surgery, University Medical Center Goettingen, Georg-August University, Goettingen 37075, Germany.,Cancer Research UK (CRUK-CI), Cambridge CB2 0RE, UK
| | - Monique Woelfer
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen, Georg-August University, Goettingen 37075, Germany.,German Center for Cardiovascular Research (DZHK) partner site Goettingen, Goettingen 37075, Germany
| | - Eric Schoger
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen, Georg-August University, Goettingen 37075, Germany.,German Center for Cardiovascular Research (DZHK) partner site Goettingen, Goettingen 37075, Germany
| | - Sara Khadjeh
- German Center for Cardiovascular Research (DZHK) partner site Goettingen, Goettingen 37075, Germany.,Department of Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University, Goettingen 37075, Germany
| | - Maria Patapia Zafiriou
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen, Georg-August University, Goettingen 37075, Germany.,German Center for Cardiovascular Research (DZHK) partner site Goettingen, Goettingen 37075, Germany
| | - Vijayalakshmi Kari
- Clinic for General, Visceral and Pediatric Surgery, University Medical Center Goettingen, Georg-August University, Goettingen 37075, Germany
| | - Jonas Herting
- German Center for Cardiovascular Research (DZHK) partner site Goettingen, Goettingen 37075, Germany.,Department of Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University, Goettingen 37075, Germany
| | - Sze Ting Pang
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen, Georg-August University, Goettingen 37075, Germany.,German Center for Cardiovascular Research (DZHK) partner site Goettingen, Goettingen 37075, Germany
| | - Tobias Weber
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen, Georg-August University, Goettingen 37075, Germany.,German Center for Cardiovascular Research (DZHK) partner site Goettingen, Goettingen 37075, Germany
| | - Franziska S Rathjens
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen, Georg-August University, Goettingen 37075, Germany.,German Center for Cardiovascular Research (DZHK) partner site Goettingen, Goettingen 37075, Germany
| | - Thomas H Fischer
- German Center for Cardiovascular Research (DZHK) partner site Goettingen, Goettingen 37075, Germany.,Department of Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University, Goettingen 37075, Germany
| | - Karl Toischer
- German Center for Cardiovascular Research (DZHK) partner site Goettingen, Goettingen 37075, Germany.,Department of Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University, Goettingen 37075, Germany
| | - Gerd Hasenfuss
- German Center for Cardiovascular Research (DZHK) partner site Goettingen, Goettingen 37075, Germany.,Department of Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University, Goettingen 37075, Germany
| | - Claudia Noack
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen, Georg-August University, Goettingen 37075, Germany.,German Center for Cardiovascular Research (DZHK) partner site Goettingen, Goettingen 37075, Germany
| | - Steven A Johnsen
- Clinic for General, Visceral and Pediatric Surgery, University Medical Center Goettingen, Georg-August University, Goettingen 37075, Germany
| | - Laura C Zelarayán
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen, Georg-August University, Goettingen 37075, Germany.,German Center for Cardiovascular Research (DZHK) partner site Goettingen, Goettingen 37075, Germany
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19
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Steuernagel L, Meckbach C, Heinrich F, Zeidler S, Schmitt AO, Gültas M. Computational identification of tissue-specific transcription factor cooperation in ten cattle tissues. PLoS One 2019; 14:e0216475. [PMID: 31095599 PMCID: PMC6522001 DOI: 10.1371/journal.pone.0216475] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 04/22/2019] [Indexed: 01/01/2023] Open
Abstract
Transcription factors (TFs) are a special class of DNA-binding proteins that orchestrate gene transcription by recruiting other TFs, co-activators or co-repressors. Their combinatorial interplay in higher organisms maintains homeostasis and governs cell identity by finely controlling and regulating tissue-specific gene expression. Despite the rich literature on the importance of cooperative TFs for deciphering the mechanisms of individual regulatory programs that control tissue specificity in several organisms such as human, mouse, or Drosophila melanogaster, to date, there is still need for a comprehensive study to detect specific TF cooperations in regulatory processes of cattle tissues. To address the needs of knowledge about specific combinatorial gene regulation in cattle tissues, we made use of three publicly available RNA-seq datasets and obtained tissue-specific gene (TSG) sets for ten tissues (heart, lung, liver, kidney, duodenum, muscle tissue, adipose tissue, colon, spleen and testis). By analyzing these TSG-sets, tissue-specific TF cooperations of each tissue have been identified. The results reveal that similar to the combinatorial regulatory events of model organisms, TFs change their partners depending on their biological functions in different tissues. Particularly with regard to preferential partner choice of the transcription factors STAT3 and NR2C2, this phenomenon has been highlighted with their five different specific cooperation partners in multiple tissues. The information about cooperative TFs could be promising: i) to understand the molecular mechanisms of regulating processes; and ii) to extend the existing knowledge on the importance of single TFs in cattle tissues.
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Affiliation(s)
- Lukas Steuernagel
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
| | - Cornelia Meckbach
- Institute of Medical Bioinformatics, Goldschmidtstraße 1, University Medical Center Göttingen, Georg-August-University, 37077 Göttingen, Germany
| | - Felix Heinrich
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
| | - Sebastian Zeidler
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
| | - Armin O. Schmitt
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075, Göttingen, Germany
| | - Mehmet Gültas
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075, Göttingen, Germany
- * E-mail:
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20
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Sodium valproate rescues expression of TRANK1 in iPSC-derived neural cells that carry a genetic variant associated with serious mental illness. Mol Psychiatry 2019; 24:613-624. [PMID: 30135510 PMCID: PMC6894932 DOI: 10.1038/s41380-018-0207-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 05/19/2018] [Accepted: 06/08/2018] [Indexed: 01/07/2023]
Abstract
Biological characterization of genetic variants identified in genome-wide association studies (GWAS) remains a substantial challenge. Here we used human-induced pluripotent stem cells (iPSC) and their neural derivatives to characterize common variants on chromosome 3p22 that have been associated by GWAS with major mental illnesses. IPSC-derived neural progenitor cells carrying the risk allele of the single nucleotide polymorphism (SNP), rs9834970, displayed lower baseline TRANK1 expression that was rescued by chronic treatment with therapeutic dosages of valproic acid (VPA). VPA had the greatest effects on TRANK1 expression in iPSC, NPC, and astrocytes. Although rs9834970 has no known function, we demonstrated that a nearby SNP, rs906482, strongly affects binding by the transcription factor, CTCF, and that the high-affinity allele usually occurs on haplotypes carrying the rs9834970 risk allele. Decreased expression of TRANK1 perturbed expression of many genes involved in neural development and differentiation. These findings have important implications for the pathophysiology of major mental illnesses and the development of novel therapeutics.
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21
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Roles of CTCF in conformation and functions of chromosome. Semin Cell Dev Biol 2018; 90:168-173. [PMID: 30031212 DOI: 10.1016/j.semcdb.2018.07.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 07/17/2018] [Indexed: 02/08/2023]
Abstract
CCCTC-binding factor (CTCF) plays indispensable roles in transcriptional inhibition/activation, insulation, gene imprinting, and regulation of 3Dchromatin structure. CTCF contributes to formation of genome multi-dimensions, regulation of dimensional changes, or control of central signals to transcriptional networks. A large number of factors affect CTCF binding, methylation/demethylation, base mutation, or poly(adp-ribosyl)ation. CTCF is one of the most important elements in the regulation of chromatin folding by combining with CBSs in TADs in a positive-reverse or reverse-positive orders. CTCF acts as a versatile nuclear factor, a transcriptional activator or repressor, an insulator binding factor, or a regulator of genomic imprinting as required for various biological procedures. Although molecular regulatory mechanisms of CTCF in cell differentiation and disease development remains unclear, roles of CTCF in carcinogenesis have been intensively explored. There is little understanding about regulatory roles of CTCF in inflammation-associated transcriptional signaling, cell injury, organ dysfunction, and systemic responses. It is also highly expected that further in-depth studies of CTCF control mechanisms can provide better understanding of disease development and potential disease-specific biomarkers and therapeutic targets.
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22
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Matthews BJ, Waxman DJ. Computational prediction of CTCF/cohesin-based intra-TAD loops that insulate chromatin contacts and gene expression in mouse liver. eLife 2018; 7:e34077. [PMID: 29757144 PMCID: PMC5986275 DOI: 10.7554/elife.34077] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 04/30/2018] [Indexed: 12/18/2022] Open
Abstract
CTCF and cohesin are key drivers of 3D-nuclear organization, anchoring the megabase-scale Topologically Associating Domains (TADs) that segment the genome. Here, we present and validate a computational method to predict cohesin-and-CTCF binding sites that form intra-TAD DNA loops. The intra-TAD loop anchors identified are structurally indistinguishable from TAD anchors regarding binding partners, sequence conservation, and resistance to cohesin knockdown; further, the intra-TAD loops retain key functional features of TADs, including chromatin contact insulation, blockage of repressive histone mark spread, and ubiquity across tissues. We propose that intra-TAD loops form by the same loop extrusion mechanism as the larger TAD loops, and that their shorter length enables finer regulatory control in restricting enhancer-promoter interactions, which enables selective, high-level expression of gene targets of super-enhancers and genes located within repressive nuclear compartments. These findings elucidate the role of intra-TAD cohesin-and-CTCF binding in nuclear organization associated with widespread insulation of distal enhancer activity.
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Affiliation(s)
- Bryan J Matthews
- Department of Biology and Bioinformatics ProgramBoston UniversityBostonUnited States
| | - David J Waxman
- Department of Biology and Bioinformatics ProgramBoston UniversityBostonUnited States
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23
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Guerra-Calderas L, González-Barrios R, Patiño CC, Alcaraz N, Salgado-Albarrán M, de León DC, Hernández CC, Sánchez-Pérez Y, Maldonado-Martínez HA, De la Rosa-Velazquez IA, Vargas-Romero F, Herrera LA, García-Carrancá A, Soto-Reyes E. CTCF-KDM4A complex correlates with histone modifications that negatively regulate CHD5 gene expression in cancer cell lines. Oncotarget 2018; 9:17028-17042. [PMID: 29682202 PMCID: PMC5908303 DOI: 10.18632/oncotarget.24798] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 02/26/2018] [Indexed: 11/25/2022] Open
Abstract
Histone demethylase KDM4A is involved in H3K9me3 and H3K36me3 demethylation, which are epigenetic modifications associated with gene silencing and RNA Polymerase II elongation, respectively. KDM4A is abnormally expressed in cancer, affecting the expression of multiple targets, such as the CHD5 gene. This enzyme localizes at the first intron of CHD5, and the dissociation of KDM4A increases gene expression. In vitro assays showed that KDM4A-mediated demethylation is enhanced in the presence of CTCF, suggesting that CTCF could increase its enzymatic activity in vivo, however the specific mechanism by which CTCF and KDM4A might be involved in the CHD5 gene repression is poorly understood. Here, we show that CTCF and KDM4A form a protein complex, which is recruited into the first intron of CHD5. This is related to a decrease in H3K36me3/2 histone marks and is associated with its transcriptional downregulation. Depletion of CTCF or KDM4A by siRNA, triggered the reactivation of CHD5 expression, suggesting that both proteins are involved in the negative regulation of this gene. Furthermore, the knockout of KDM4A restored the CHD5 expression and H3K36me3 and H3K36me2 histone marks. Such mechanism acts independently of CHD5 promoter DNA methylation. Our findings support a novel mechanism of epigenetic repression at the gene body that does not involve promoter silencing.
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Affiliation(s)
- Lissania Guerra-Calderas
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Rodrigo González-Barrios
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Carlos César Patiño
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Nicolás Alcaraz
- The Bioinformatics Centre, Section for RNA and Computational Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Marisol Salgado-Albarrán
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - David Cantú de León
- Clinical Research, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Clementina Castro Hernández
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.,Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Yesennia Sánchez-Pérez
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | | | - Inti A De la Rosa-Velazquez
- Genomics Lab, Universidad Nacional Autónoma de México, Red de Apoyo a la Investigación-CIC and Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán", Mexico City, Mexico
| | - Fernanda Vargas-Romero
- Instituto de Fisiologia Celular-Neurociencias, Universidad Nacional Autonoma de Mexico (UNAM), Mexico City, Mexico
| | - Luis A Herrera
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.,Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Alejandro García-Carrancá
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.,Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Ernesto Soto-Reyes
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
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24
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CTCF Binding Sites in the Herpes Simplex Virus 1 Genome Display Site-Specific CTCF Occupation, Protein Recruitment, and Insulator Function. J Virol 2018; 92:JVI.00156-18. [PMID: 29437965 DOI: 10.1128/jvi.00156-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 11/20/2022] Open
Abstract
There are seven conserved CTCF binding domains in the herpes simplex virus 1 (HSV-1) genome. These binding sites individually flank the latency-associated transcript (LAT) and the immediate early (IE) gene regions, suggesting that CTCF insulators differentially control transcriptional domains in HSV-1 latency. In this work, we show that two CTCF binding motifs in HSV-1 display enhancer blocking in a cell-type-specific manner. We found that CTCF binding to the latent HSV-1 genome was LAT dependent and that the quantity of bound CTCF was site specific. Following reactivation, CTCF eviction was dynamic, suggesting that each CTCF site was independently regulated. We explored whether CTCF sites recruit the polycomb-repressive complex 2 (PRC2) to establish repressive domains through a CTCF-Suz12 interaction and found that Suz12 colocalized to the CTCF insulators flanking the ICP0 and ICP4 regions and, conversely, was removed at early times postreactivation. Collectively, these data support the idea that CTCF sites in HSV-1 are independently regulated and may contribute to lytic-latent HSV-1 control in a site-specific manner.IMPORTANCE The role of chromatin insulators in DNA viruses is an area of interest. It has been shown in several beta- and gammaherpesviruses that insulators likely control the lytic transcriptional profile through protein recruitment and through the formation of three-dimensional (3D) chromatin loops. The ability of insulators to regulate alphaherpesviruses has been understudied to date. The alphaherpesvirus HSV-1 has seven conserved insulator binding motifs that flank regions of the genome known to contribute to the establishment of latency. Our work presented here contributes to the understanding of how insulators control transcription of HSV-1.
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25
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Synergistic Association of Valproate and Resveratrol Reduces Brain Injury in Ischemic Stroke. Int J Mol Sci 2018; 19:ijms19010172. [PMID: 29316653 PMCID: PMC5796121 DOI: 10.3390/ijms19010172] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 12/15/2017] [Accepted: 01/02/2018] [Indexed: 11/16/2022] Open
Abstract
Histone deacetylation, together with altered acetylation of NF-κB/RelA, encompassing the K310 residue acetylation, occur during brain ischemia. By restoring the normal acetylation condition, we previously reported that sub-threshold doses of resveratrol and entinostat (MS-275), respectively, an activator of the AMP-activated kinase (AMPK)-sirtuin 1 pathway and an inhibitor of class I histone deacetylases (HDACs), synergistically elicited neuroprotection in a mouse model of ischemic stroke. To improve the translational power of this approach, we investigated the efficacy of MS-275 replacement with valproate, the antiepileptic drug also reported to be a class I HDAC blocker. In cortical neurons previously exposed to oxygen glucose deprivation (OGD), valproate elicited neuroprotection at 100 nmol/mL concentration when used alone and at 1 nmol/mL concentration when associated with resveratrol (3 nmol/mL). Resveratrol and valproate restored the acetylation of histone H3 (K9/18), and they reduced the RelA(K310) acetylation and the Bim level in neurons exposed to OGD. Chromatin immunoprecipitation analysis showed that the synergistic drug association impaired the RelA binding to the Bim promoter, as well as the promoter-specific H3 (K9/18) acetylation. In mice subjected to 60 min of middle cerebral artery occlusion (MCAO), the association of resveratrol 680 µg/kg and valproate 200 µg/kg significantly reduced the infarct volume as well as the neurological deficits. The present study suggests that valproate and resveratrol may represent a promising ready-to-use strategy to treat post-ischemic brain damage.
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26
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Rambout X, Dequiedt F, Maquat LE. Beyond Transcription: Roles of Transcription Factors in Pre-mRNA Splicing. Chem Rev 2017; 118:4339-4364. [PMID: 29251915 DOI: 10.1021/acs.chemrev.7b00470] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Whereas individual steps of protein-coding gene expression in eukaryotes can be studied in isolation in vitro, it has become clear that these steps are intimately connected within cells. Connections not only ensure quality control but also fine-tune the gene expression process, which must adapt to environmental changes while remaining robust. In this review, we systematically present proven and potential mechanisms by which sequence-specific DNA-binding transcription factors can alter gene expression beyond transcription initiation and regulate pre-mRNA splicing, and thereby mRNA isoform production, by (i) influencing transcription elongation rates, (ii) binding to pre-mRNA to recruit splicing factors, and/or (iii) blocking the association of splicing factors with pre-mRNA. We propose various mechanistic models throughout the review, in some cases without explicit supportive evidence, in hopes of providing fertile ground for future studies.
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27
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Abstract
CCCTC-binding factor (CTCF) is a conserved, essential regulator of chromatin architecture containing a unique array of 11 zinc fingers (ZFs). Gene duplication and sequence divergence during early amniote evolution generated the CTCF paralog Brother Of the Regulator of Imprinted Sites (BORIS), which has a DNA binding specificity identical to that of CTCF but divergent N- and C-termini. While healthy somatic tissues express only CTCF, CTCF and BORIS are normally co-expressed in meiotic and post-meiotic germ cells, and aberrant activation of BORIS occurs in tumors and some cancer cell lines. This has led to a model in which CTCF and BORIS compete for binding to some but not all genomic target sites; however, regulation of CTCF and BORIS genomic co-occupancy is not well understood. We recently addressed this issue, finding evidence for two major classes of CTCF target sequences, some of which contain single CTCF target sites (1xCTSes) and others containing two adjacent CTCF motifs (2xCTSes). The functional and chromatin structural features of 2xCTSes are distinct from those of 1xCTS-containing regions bound by a CTCF monomer. We suggest that these previously overlooked classes of CTCF binding regions may have different roles in regulating diverse chromatin-based phenomena, and may impact our understanding of heritable epigenetic regulation in cancer cells and normal germ cells.
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Affiliation(s)
- Victor V Lobanenkov
- a Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health , 5601 Fishers Ln, Rockville , MD , USA
| | - Gabriel E Zentner
- b Department of Biology , Indiana University , 915 E 3rd St, Bloomington , IN 47405 , USA
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28
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Fedotova AA, Bonchuk AN, Mogila VA, Georgiev PG. C2H2 Zinc Finger Proteins: The Largest but Poorly Explored Family of Higher Eukaryotic Transcription Factors. Acta Naturae 2017; 9:47-58. [PMID: 28740726 PMCID: PMC5509000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Indexed: 12/03/2022] Open
Abstract
The emergence of whole-genome assays has initiated numerous genome-wide studies of transcription factor localizations at genomic regulatory elements (enhancers, promoters, silencers, and insulators), as well as facilitated the uncovering of some of the key principles of chromosomal organization. However, the proteins involved in the formation and maintenance of the chromosomal architecture and the organization of regulatory domains remain insufficiently studied. This review attempts to collate the available data on the abundant but still poorly understood family of proteins with clusters of the C2H2 zinc finger domains. One of the best known proteins of this family is a well conserved protein known as CTCF, which plays a key role in the establishment of the chromosomal architecture in vertebrates. The distinctive features of C2H2 zinc finger proteins include strong and specific binding to a long and unique DNA recognition target sequence and rapid expansion within various animal taxa during evolution. The reviewed data support a proposed model according to which many of the C2H2 proteins have functions that are similar to those of the CTCF in the organization of the chromatin architecture.
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Affiliation(s)
- A. A. Fedotova
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Str., 34/5, Moscow, 119334, Russia
| | - A. N. Bonchuk
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Str., 34/5, Moscow, 119334, Russia
| | - V. A. Mogila
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Str., 34/5, Moscow, 119334, Russia
| | - P. G. Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Str., 34/5, Moscow, 119334, Russia
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29
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Histone deacetylase-mediated regulation of chondroitin 4-O-sulfotransferase-1 (Chst11) gene expression by Wnt/β-catenin signaling. Biochem Biophys Res Commun 2016; 480:234-240. [PMID: 27751852 DOI: 10.1016/j.bbrc.2016.10.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 10/13/2016] [Indexed: 12/31/2022]
Abstract
Chondroitin sulfate (CS) proteoglycans are abundant extracellular and cell surface molecules that consist of a protein core to which highly sulfated CS chains are covalently attached. The CS backbone is composed of repeating disaccharide units [-GlcA-GalNAc-]n, and during synthesis the CS chains acquire structural variability due to the action of sulfotransferases. Specific sulfation patterns are recognized by a large variety of proteins, including growth factors, morphogens, and extracellular matrix proteins, and these interactions regulate key events in development and normal physiology. Therefore, it is important to understand how gene expression of CS sulfotransferases is regulated. We previously found that Wnt signaling regulates the sulfation patterns of cell-associated CS chains by suppressing expression of chondroitin 4-O-sulfotaransferase-1 (C4ST-1), a CS biosynthetic enzyme. Here we investigated the mechanism underlying the regulation of C4ST-1 gene expression by Wnt/β-catenin signaling. Although C4ST-1 mRNA of 3'-UTR contains three binding sites for microRNAs (miRNA), these miRNAs played little role in controlling C4ST-1 gene expression. In contrast, the suppression of C4ST-1 gene expression by Wnt/β-catenin signaling can be recovered by treatment with trichostatin A, but not with 5'-aza-2'-deoxycytidine. These results suggest that the Wnt/β-catenin signal pathway controls C4ST-1 gene expression mainly through histone deacetylase.
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30
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Long Non-coding RNA H19 Inhibits Adipocyte Differentiation of Bone Marrow Mesenchymal Stem Cells through Epigenetic Modulation of Histone Deacetylases. Sci Rep 2016; 6:28897. [PMID: 27349231 PMCID: PMC4924093 DOI: 10.1038/srep28897] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/10/2016] [Indexed: 02/06/2023] Open
Abstract
Bone marrow mesenchymal stem cells (BMSCs) exhibit an increased propensity toward adipocyte differentiation accompanied by a reduction in osteogenesis in osteoporotic bone marrow. However, limited knowledge is available concerning the role of long non-coding RNAs (lncRNAs) in the differentiation of BMSCs into adipocytes. In this study, we demonstrated that lncRNA H19 and microRNA-675 (miR-675) derived from H19 were significantly downregulated in BMSCs that were differentiating into adipocytes. Overexpression of H19 and miR-675 inhibited adipogenesis, while knockdown of their endogenous expression accelerated adipogenic differentiation. Mechanistically, we found that miR-675 targeted the 3' untranslated regions of the histone deacetylase (HDAC) 4-6 transcripts and resulted in deregulation of HDACs 4-6, essential molecules in adipogenesis. In turn, trichostatin A, an HDAC inhibitor, significantly reduced CCCTC-binding factor (CTCF) occupancy in the imprinting control region upstream of the H19 gene locus and subsequently downregulated the expression of H19. These results show that the CTCF/H19/miR-675/HDAC regulatory pathway plays an important role in the commitment of BMSCs into adipocytes.
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31
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Hwang SS, Kim LK, Lee GR, Flavell RA. Role of OCT-1 and partner proteins in T cell differentiation. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1859:825-31. [PMID: 27126747 DOI: 10.1016/j.bbagrm.2016.04.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/12/2016] [Accepted: 04/13/2016] [Indexed: 12/24/2022]
Abstract
The understanding of CD4 T cell differentiation gives important insights into the control of immune responses against various pathogens and in autoimmune diseases. Naïve CD4 T cells become effector T cells in response to antigen stimulation in combination with various environmental cytokine stimuli. Several transcription factors and cis-regulatory regions have been identified to regulate epigenetic processes on chromatin, to allow the production of proper effector cytokines during CD4 T cell differentiation. OCT-1 (Pou2f1) is well known as a widely expressed transcription factor in most tissues and cells. Although the importance of OCT-1 has been emphasized during development and differentiation, its detailed molecular underpinning and precise role are poorly understood. Recently, a series of studies have reported that OCT-1 plays a critical role in CD4 T cells through regulating gene expression during differentiation and mediating long-range chromosomal interactions. In this review, we will describe the role of OCT-1 in CD4 T cell differentiation and discuss how this factor orchestrates the fate and function of CD4 effector T cells.
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Affiliation(s)
- Soo Seok Hwang
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Lark Kyun Kim
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Severance Biomedical Science Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, 211 Eonjuro, Gangnam-gu, Seoul 135-720, South Korea
| | - Gap Ryol Lee
- Department of Life-Science, Sogang University, Baekbeom-ro, Seoul 121-742, South Korea
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520, USA.
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32
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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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Maksimenko O, Gasanov NB, Georgiev P. Regulatory Elements in Vectors for Efficient Generation of Cell Lines Producing Target Proteins. Acta Naturae 2015; 7:15-26. [PMID: 26483956 PMCID: PMC4610161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
To date, there has been an increasing number of drugs produced in mammalian cell cultures. In order to enhance the expression level and stability of target recombinant proteins in cell cultures, various regulatory elements with poorly studied mechanisms of action are used. In this review, we summarize and discuss the potential mechanisms of action of such regulatory elements.
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Affiliation(s)
- O. Maksimenko
- Institute of Gene Biology, Russian Academy of Sciences, Vavilova str. 34/5, 119334, Moscow, Russia
| | - N. B. Gasanov
- Institute of Gene Biology, Russian Academy of Sciences, Vavilova str. 34/5, 119334, Moscow, Russia
| | - P. Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, Vavilova str. 34/5, 119334, Moscow, Russia
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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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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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36
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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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37
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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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Holwerda SJB, de Laat W. CTCF: the protein, the binding partners, the binding sites and their chromatin loops. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120369. [PMID: 23650640 PMCID: PMC3682731 DOI: 10.1098/rstb.2012.0369] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
CTCF has it all. The transcription factor binds to tens of thousands of genomic sites, some tissue-specific, others ultra-conserved. It can act as a transcriptional activator, repressor and insulator, and it can pause transcription. CTCF binds at chromatin domain boundaries, at enhancers and gene promoters, and inside gene bodies. It can attract many other transcription factors to chromatin, including tissue-specific transcriptional activators, repressors, cohesin and RNA polymerase II, and it forms chromatin loops. Yet, or perhaps therefore, CTCF's exact function at a given genomic site is unpredictable. It appears to be determined by the associated transcription factors, by the location of the binding site relative to the transcriptional start site of a gene, and by the site's engagement in chromatin loops with other CTCF-binding sites, enhancers or gene promoters. Here, we will discuss genome-wide features of CTCF binding events, as well as locus-specific functions of this remarkable transcription factor.
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Affiliation(s)
| | - Wouter de Laat
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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Wang R, Shen J, Huang P, Zhu X. CCCTC-binding factor controls its own nuclear transport via regulating the expression of importin 13. Mol Cells 2013; 35:388-95. [PMID: 23620300 PMCID: PMC3887860 DOI: 10.1007/s10059-013-2283-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 03/07/2013] [Accepted: 03/15/2013] [Indexed: 11/25/2022] Open
Abstract
CCCTC-binding factor (CTCF), a multivalent zinc-finger protein, is involved in different aspects of regulation including promoter activation or repression, gene silencing, chromatin insulation, gene imprinting, X-chromosome inactivation, cell growth or differentiation and tumor genesis. However, the molecular mechanisms of CTCF nuclear import remains unclear. In this study, we showed that the expression of CTCF influenced the intracellular distribution of itself, which might go through transport receptor - import 13 (IPO13). We further confirmed that there is a CTCF target site in ipo13 -774∼-573 bp promoter region and CTCF regulates the expression of IPO13. Besides, GST pull-down and Co-IP experiments demonstrated that CTCF interacts with IPO13. Immunofluorescence staining showed that IPO13 influenced intracellular distribution of CTCF. In all, we conclude that CTCF regulates the expression of IPO13, which, in turn, mediates the nuclear import of CTCF.
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Affiliation(s)
- Rong Wang
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing,
China
| | - Jingjing Shen
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing,
China
| | - Peitang Huang
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing,
China
| | - Xudong Zhu
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing,
China
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Gosalia N, Leir SH, Harris A. Coordinate regulation of the gel-forming mucin genes at chromosome 11p15.5. J Biol Chem 2013; 288:6717-25. [PMID: 23303185 DOI: 10.1074/jbc.m112.437400] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Four of the genes that encode gel-forming mucins, which are major components of the mucus layer protecting many epithelial surfaces, are clustered at chromosome 11p15.5 and show both cell- and tissue-specific expression patterns. We aimed to determine whether the individual genes were coordinately regulated by mechanisms involving higher order chromatin structure. CCCTC-binding factor (CTCF) sites were predicted in silico and CTCF occupancy then evaluated by chromatin immunoprecipitation. CTCF was found at many sites across the gene cluster, and its binding was correlated with mucin gene expression. Next, siRNA-mediated depletion of CTCF was shown to increase MUC2 expression in A549 lung carcinoma cells and both MUC6 and MUC5AC expression in LS180 colon carcinoma cells. These changes correlated with loss of CTCF binding at multiple sites, although others retained occupancy. In cells actively expressing the mucins, the gene cluster was shown by chromosome conformation capture to form looped three-dimensional structures with direct interactions between the MUC2 promoter region, regions 30 kb 5' to it, close to the MUC6 promoter and others near the 3' end of MUC5AC, >170 kb away. Finally, to demonstrate the importance of CTCF binding to mucin gene expression, Calu-3 lung carcinoma cells were exposed to lipopolysaccharide (LPS). LPS increased the expression of MUC2 and MUC5AC and reduced MUC5B. CTCF occupancy was concurrently depleted at specific binding sites close to these genes. These data suggest that CTCF binding and cell type-specific long-range interactions across the 11p15.5 gene cluster are critical mechanisms for coordinating gel-forming mucin gene expression.
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Affiliation(s)
- Nehal Gosalia
- Human Molecular Genetics Program, Children's Memorial Research Center and Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60614, USA
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Muck JS, Kandasamy K, Englmann A, Günther M, Zink D. Perinuclear positioning of the inactive human cystic fibrosis gene depends on CTCF, A-type lamins and an active histone deacetylase. J Cell Biochem 2012; 113:2607-21. [PMID: 22422629 DOI: 10.1002/jcb.24136] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The nuclear positioning of mammalian genes often correlates with their functional state. For instance, the human cystic fibrosis transmembrane conductance regulator (CFTR) gene associates with the nuclear periphery in its inactive state, but occupies interior positions when active. It is not understood how nuclear gene positioning is determined. Here, we investigated trichostatin A (TSA)-induced repositioning of CFTR in order to address molecular mechanisms controlling gene positioning. Treatment with the histone deacetylase (HDAC) inhibitor TSA induced increased histone acetylation and CFTR repositioning towards the interior within 20 min. When CFTR localized in the nuclear interior (either after TSA treatment or when the gene was active) consistent histone H3 hyperacetylation was observed at a CTCF site close to the CFTR promoter. Knockdown experiments revealed that CTCF was essential for perinuclear CFTR positioning and both, CTCF knockdown as well as TSA treatment had similar and CFTR-specific effects on radial positioning. Furthermore, knockdown experiments revealed that also A-type lamins were required for the perinuclear positioning of CFTR. Together, the results showed that CTCF, A-type lamins and an active HDAC were essential for perinuclear positioning of CFTR and these components acted on a CTCF site adjacent to the CFTR promoter. The results are consistent with the idea that CTCF bound close to the CFTR promoter, A-type lamins and an active HDAC form a complex at the nuclear periphery, which becomes disrupted upon inhibition of the HDAC, leading to the observed release of CFTR.
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Affiliation(s)
- Joscha S Muck
- Institute of Bioengineering and Nanotechnology (IBN), Department of Cell and Tissue Engineering, 31 Biopolis Way, The Nanos, Singapore 138669
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CTCF occupation of the herpes simplex virus 1 genome is disrupted at early times postreactivation in a transcription-dependent manner. J Virol 2012; 86:12741-59. [PMID: 22973047 DOI: 10.1128/jvi.01655-12] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In herpes simplex virus 1 (HSV-1), binding clusters enriched in CTCF during latency have been previously identified. We hypothesized that CTCF binding to CTCF clusters in HSV-1 would be disrupted in a reactivation event. To investigate, CTCF occupation of three CTCF binding clusters in HSV-1 was analyzed following sodium butyrate (NaB)- and explant-induced reactivation in the mouse. Our data show that the CTCF domains positioned within the HSV-1 genome, specifically around the latency-associated transcript (LAT) and ICP0 and ICP4 regions of the genome, lose CTCF occupancy following the application of reactivation stimuli in wild-type virus. We also found that CTCF binding clusters upstream of the ICP0 and ICP4 promoters both function as classical insulators capable of acting as enhancer blockers of the LAT enhancer. Finally, our results suggest that CTCF occupation of domains in HSV-1 may be differentially regulated both during latency and at early times following reactivation by the presence of lytic transcripts and further implicate epigenetic regulation of HSV-1 as a critical component of the latency-reactivation transition.
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Lanzillotta A, Pignataro G, Branca C, Cuomo O, Sarnico I, Benarese M, Annunziato L, Spano P, Pizzi M. Targeted acetylation of NF-kappaB/RelA and histones by epigenetic drugs reduces post-ischemic brain injury in mice with an extended therapeutic window. Neurobiol Dis 2012; 49:177-89. [PMID: 22971966 DOI: 10.1016/j.nbd.2012.08.018] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 08/01/2012] [Accepted: 08/22/2012] [Indexed: 01/29/2023] Open
Abstract
UNLABELLED Nuclear factor-kappaB (NF-κB) p50/RelA is a key molecule with a dual effect in the progression of ischemic stroke. In harmful ischemia, but not in preconditioning insult, neurotoxic activation of p50/RelA is characterized by RelA-specific acetylation at Lys310 (K310) and deacetylation at other Lys residues. The derangement of RelA acetylation is associated with activation of Bim promoter. OBJECTIVE With the aim of producing neuroprotection by correcting altered acetylation of RelA in brain ischemia, we combined the pharmacological inhibition of histone deacetylase (HDAC) 1-3, the enzymes known to reduce global RelA acetylation, and the activation of sirtuin 1, endowed with a specific deacetylase activity on the K310 residue of RelA. To afford this aim, we tested the clinically used HDAC 1-3 inhibitor entinostat (MS-275) and the sirtuin 1 activator resveratrol. METHODS We used the mouse model of transient middle cerebral artery occlusion (MCAO) and primary cortical neurons exposed to oxygen glucose deprivation (OGD). RESULTS The combined use of MS-275 and resveratrol, by restoring normal RelA acetylation, elicited a synergistic neuroprotection in neurons exposed to OGD. This effect correlated with MS-275 capability to increase total RelA acetylation and resveratrol capability to reduce RelA K310 acetylation through the activation of an AMP-activated protein kinase-sirtuin 1 pathway. The synergistic treatment reproduced the acetylation state of RelA peculiar of preconditioning ischemia. Neurons exposed to the combined drugs totally recovered the optimal histone H3 acetylation. Neuroprotection was reproduced in mice subjected to MCAO and treated with MS-275 (20μg/kg and 200μg/kg) or resveratrol (6800μg/kg) individually. However, the administration of lowest doses of MS-275 (2μg/kg) and resveratrol (68μg/kg) synergistically reduced infarct volume and neurological deficits. Importantly, the treatment was effective even when administered 7h after the stroke onset. Chromatin immunoprecipitation analysis of cortices harvested from treated mice showed that the RelA binding and histone acetylation increased at the Bcl-xL promoter and decreased at the Bim promoter. CONCLUSION Our study reveals that epigenetic therapy shaping acetylation of both RelA and histones may be a promising strategy to limit post-ischemic injury with an extended therapeutic window.
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Affiliation(s)
- Annamaria Lanzillotta
- Division of Pharmacology and Experimental Therapeutics, Department of Biomedical Sciences & Biotechnologies and National Institute of Neuroscience, School of Medicine, University of Brescia, Italy
| | - Giuseppe Pignataro
- Division of Pharmacology, Department of Neuroscience and National Institute of Neuroscience, School of Medicine, Federico II University of Naples, Italy
| | - Caterina Branca
- Division of Pharmacology and Experimental Therapeutics, Department of Biomedical Sciences & Biotechnologies and National Institute of Neuroscience, School of Medicine, University of Brescia, Italy
| | - Ornella Cuomo
- Division of Pharmacology, Department of Neuroscience and National Institute of Neuroscience, School of Medicine, Federico II University of Naples, Italy
| | - Ilenia Sarnico
- Division of Pharmacology and Experimental Therapeutics, Department of Biomedical Sciences & Biotechnologies and National Institute of Neuroscience, School of Medicine, University of Brescia, Italy
| | - Marina Benarese
- Division of Pharmacology and Experimental Therapeutics, Department of Biomedical Sciences & Biotechnologies and National Institute of Neuroscience, School of Medicine, University of Brescia, Italy
| | - Lucio Annunziato
- Division of Pharmacology, Department of Neuroscience and National Institute of Neuroscience, School of Medicine, Federico II University of Naples, Italy; IRCCS SDN, Naples, Italy
| | - PierFranco Spano
- Division of Pharmacology and Experimental Therapeutics, Department of Biomedical Sciences & Biotechnologies and National Institute of Neuroscience, School of Medicine, University of Brescia, Italy; IRCCS, S. Camillo Hospital, Venice, Italy
| | - Marina Pizzi
- Division of Pharmacology and Experimental Therapeutics, Department of Biomedical Sciences & Biotechnologies and National Institute of Neuroscience, School of Medicine, University of Brescia, Italy; IRCCS, S. Camillo Hospital, Venice, Italy.
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Son J, Min NY, Choi JH, Ko YJ, Liang W, Rhee S, Lee KH. Direct evidence of allele-specific binding of CTCF and MeCP2 to Tsix in a HPRT-deficient female F₁ hybrid mouse cell line. Cytogenet Genome Res 2012; 138:11-8. [PMID: 22889989 DOI: 10.1159/000341503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2012] [Indexed: 11/19/2022] Open
Abstract
Mammalian dosage compensation requires silencing of one of the two X chromosomes in females and is controlled by the X inactivation center (Xic). Xic contains many of the regulatory elements for the mutual interplay of X-inactive specific transcript (Xist) and Tsix, the antisense counterpart of Xist. The regulatory elements control X chromosome inactivation (XCI) via the formation of DNA-DNA and DNA-protein complexes with cis- and trans-acting factors. However, the process-dependent regulation of Xist/Tsix by these elements in each XCI process remains largely unknown. In this study, a 6-thioguanine-resistant female F(1) hybrid mouse cell line (designated HOBMSKI2) was constructed from a cross between a female HPRT-deficient transgenic mouse (designated BM3) and a male wild type Mus spretus mouse (designated MS), which enabled the direct discrimination of both allele-specific expression of X-linked genes and allele-specific binding of proteins associated with XCI due to DNA polymorphisms between BM3 and MS. Using this cell line, we found that Tsix on the active X chromosome (Xa) was not expressed in somatic cells despite the fact that CTCF, which ensures Tsix expression in embryonic stem cells, was still bound to the 5' end of Tsix on Xa, implying that CTCF may function differently during each XCI process and its trans-activating activity for Tsix expression may be lost in the maintenance process. In addition, the monoallelic expression of Tsix on Xa was inhibited by epigenetic modification of the chromatin in the maintenance process, which was mediated by protein complexes recruited by MeCP2. The results indicate the value of HOBMSKI2 in directly detecting the allele-specific binding of CTCF and MeCP2 to the 5' end of Tsix. The HOBMSKI2 mouse line is a versatile and useful resource for studying the molecular mechanism of the XCI process.
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Affiliation(s)
- J Son
- School of Life Sciences, College of Natural Science, Chung-Ang University, Seoul, Republic of Korea
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45
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A microRNA network regulates expression and biosynthesis of wild-type and DeltaF508 mutant cystic fibrosis transmembrane conductance regulator. Proc Natl Acad Sci U S A 2012. [PMID: 22853952 DOI: 10.1073/+pnas.1210906109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Production of functional proteins requires multiple steps, including gene transcription and posttranslational processing. MicroRNAs (miRNAs) can regulate individual stages of these processes. Despite the importance of the cystic fibrosis transmembrane conductance regulator (CFTR) channel for epithelial anion transport, how its expression is regulated remains uncertain. We discovered that miRNA-138 regulates CFTR expression through its interactions with the transcriptional regulatory protein SIN3A. Treating airway epithelia with an miR-138 mimic increased CFTR mRNA and also enhanced CFTR abundance and transepithelial Cl(-) permeability independent of elevated mRNA levels. An miR-138 anti-miR had the opposite effects. Importantly, miR-138 altered the expression of many genes encoding proteins that associate with CFTR and may influence its biosynthesis. The most common CFTR mutation, ΔF508, causes protein misfolding, protein degradation, and cystic fibrosis. Remarkably, manipulating the miR-138 regulatory network also improved biosynthesis of CFTR-ΔF508 and restored Cl(-) transport to cystic fibrosis airway epithelia. This miRNA-regulated network directs gene expression from the chromosome to the cell membrane, indicating that an individual miRNA can control a cellular process more broadly than recognized previously. This discovery also provides therapeutic avenues for restoring CFTR function to cells affected by the most common cystic fibrosis mutation.
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A microRNA network regulates expression and biosynthesis of wild-type and DeltaF508 mutant cystic fibrosis transmembrane conductance regulator. Proc Natl Acad Sci U S A 2012; 109:13362-7. [PMID: 22853952 DOI: 10.1073/pnas.1210906109] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Production of functional proteins requires multiple steps, including gene transcription and posttranslational processing. MicroRNAs (miRNAs) can regulate individual stages of these processes. Despite the importance of the cystic fibrosis transmembrane conductance regulator (CFTR) channel for epithelial anion transport, how its expression is regulated remains uncertain. We discovered that miRNA-138 regulates CFTR expression through its interactions with the transcriptional regulatory protein SIN3A. Treating airway epithelia with an miR-138 mimic increased CFTR mRNA and also enhanced CFTR abundance and transepithelial Cl(-) permeability independent of elevated mRNA levels. An miR-138 anti-miR had the opposite effects. Importantly, miR-138 altered the expression of many genes encoding proteins that associate with CFTR and may influence its biosynthesis. The most common CFTR mutation, ΔF508, causes protein misfolding, protein degradation, and cystic fibrosis. Remarkably, manipulating the miR-138 regulatory network also improved biosynthesis of CFTR-ΔF508 and restored Cl(-) transport to cystic fibrosis airway epithelia. This miRNA-regulated network directs gene expression from the chromosome to the cell membrane, indicating that an individual miRNA can control a cellular process more broadly than recognized previously. This discovery also provides therapeutic avenues for restoring CFTR function to cells affected by the most common cystic fibrosis mutation.
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47
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Higher-order chromatin regulation and differential gene expression in the human tumor necrosis factor/lymphotoxin locus in hepatocellular carcinoma cells. Mol Cell Biol 2012; 32:1529-41. [PMID: 22354988 DOI: 10.1128/mcb.06478-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The three-dimensional context of endogenous chromosomal regions may contribute to the regulation of gene clusters by influencing interactions between transcriptional regulatory elements. In this study, we investigated the effects of tumor necrosis factor (TNF) signaling on spatiotemporal enhancer-promoter interactions in the human tumor necrosis factor (TNF)/lymphotoxin (LT) gene locus, mediated by CCCTC-binding factor (CTCF)-dependent chromatin insulators. The cytokine genes LTα, TNF, and LTβ are differentially regulated by NF-κB signaling in inflammatory and oncogenic responses. We identified at least four CTCF-enriched sites with enhancer-blocking activities and a TNF-responsive TE2 enhancer in the TNF/LT locus. One of the CTCF-enriched sites is located between the early-inducible LTα/TNF promoters and the late-inducible LTβ promoter. Depletion of CTCF reduced TNF expression and accelerated LTβ induction. After TNF stimulation, via intrachromosomal dynamics, these insulators mediated interactions between the enhancer and the LTα/TNF promoters, followed by interaction with the LTβ promoter. These results suggest that insulators mediate the spatiotemporal control of enhancer-promoter associations in the TNF/LT gene cluster.
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48
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Regulation of the human catalytic subunit of telomerase (hTERT). Gene 2012; 498:135-46. [PMID: 22381618 DOI: 10.1016/j.gene.2012.01.095] [Citation(s) in RCA: 199] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 01/29/2012] [Accepted: 01/30/2012] [Indexed: 12/12/2022]
Abstract
Over the past decade, there has been much interest in the regulation of telomerase, the enzyme responsible for maintaining the integrity of chromosomal ends, and its crucial role in cellular immortalization, tumorigenesis, and the progression of cancer. Telomerase activity is characterized by the expression of the telomerase reverse transcriptase (TERT) gene, suggesting that TERT serves as the major limiting agent for telomerase activity. Recent discoveries have led to characterization of various interactants that aid in the regulation of human TERT (hTERT), including numerous transcription factors; further supporting the pivotal role that transcription plays in both the expression and repression of telomerase. Several studies have suggested that epigenetic modulation of the hTERT core promoter region may provide an additional level of regulation. Although these studies have provided essential information on the regulation of hTERT, there has been ambiguity of the role of methylation within the core promoter region and the subsequent binding of various activating and repressive agents. As a result, we found it necessary to consolidate and summarize these recent developments and elucidate these discrepancies. In this review, we focus on the co-regulation of hTERT via transcriptional regulation, the presence or absence of various activators and repressors, as well as the epigenetic pathways of DNA methylation and histone modifications.
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Abstract
CTCF is an evolutionary conserved and ubiquitously expressed protein that binds thousands of sites in the human genome. Ectopic expression of CTCF in various normal and tumoral human cell lines inhibits cell division and clonogenicity, with the consequence to consider CTCF a potential tumor-suppressor factor. In this review article, we focused on the molecular mechanisms engaged by CTCF to modulate the expression of several key-regulators of differentiation, cellular senescence, cell cycle control and progression, whose expression is frequently altered in tumors. Moreover, we discussed common features of CTCF at each tumor-related DNA-binding sequence, such as protein-partners, post-translational modifications, and distinctive epigenetic marks establishment. The investigation of the molecular mechanisms engaged by CTCF to modulate tumor-related genes emphasizes the cell-type dependency of its tumor suppressor role. Indeed, the ability of CTCF to bind their promoters strictly depends by cell-type features as DNA methylation, BORIS-binding and post-translational modifications as PARYlation.
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Affiliation(s)
- Francesco Paolo Fiorentino
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, Department of Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA
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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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