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Chachoua I, Tzelepis I, Dai H, Lim JP, Lewandowska-Ronnegren A, Casagrande FB, Wu S, Vestlund J, Mallet de Lima CD, Bhartiya D, Scholz BA, Martino M, Mehmood R, Göndör A. Canonical WNT signaling-dependent gating of MYC requires a noncanonical CTCF function at a distal binding site. Nat Commun 2022; 13:204. [PMID: 35017527 PMCID: PMC8752836 DOI: 10.1038/s41467-021-27868-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 12/19/2021] [Indexed: 01/21/2023] Open
Abstract
Abnormal WNT signaling increases MYC expression in colon cancer cells in part via oncogenic super-enhancer-(OSE)-mediated gating of the active MYC to the nuclear pore in a poorly understood process. We show here that the principal tenet of the WNT-regulated MYC gating, facilitating nuclear export of the MYC mRNA, is regulated by a CTCF binding site (CTCFBS) within the OSE to confer growth advantage in HCT-116 cells. To achieve this, the CTCFBS directs the WNT-dependent trafficking of the OSE to the nuclear pore from intra-nucleoplasmic positions in a stepwise manner. Once the OSE reaches a peripheral position, which is triggered by a CTCFBS-mediated CCAT1 eRNA activation, its final stretch (≤0.7 μm) to the nuclear pore requires the recruitment of AHCTF1, a key nucleoporin, to the CTCFBS. Thus, a WNT/ß-catenin-AHCTF1-CTCF-eRNA circuit enables the OSE to promote pathological cell growth by coordinating the trafficking of the active MYC gene within the 3D nuclear architecture. Gene-gating of a MYC oncogenic super-enhancer (OSE) increases its expression in colon cancer cells in a poorly understood process. Here the authors show that MYC gating requires a CTCF binding site (CTCFBS) within the OSE that directs the stepwise trafficking of the OSE to the nuclear pore to facilitate increased nuclear export of MYC mRNA, which results in a growth advantage.
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Affiliation(s)
- Ilyas Chachoua
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Ilias Tzelepis
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Hao Dai
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden.,Department of Breast Disease, Henan Breast Cancer Center, The affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Jia Pei Lim
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Anna Lewandowska-Ronnegren
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Felipe Beccaria Casagrande
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Shuangyang Wu
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Johanna Vestlund
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Carolina Diettrich Mallet de Lima
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Deeksha Bhartiya
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Barbara A Scholz
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Mirco Martino
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Rashid Mehmood
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Anita Göndör
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden.
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Sumida N, Sifakis EG, Kiani NA, Ronnegren AL, Scholz BA, Vestlund J, Gomez-Cabrero D, Tegner J, Göndör A, Ohlsson R. MYC as a driver of stochastic chromatin networks: implications for the fitness of cancer cells. Nucleic Acids Res 2020; 48:10867-10876. [PMID: 33051686 PMCID: PMC7641766 DOI: 10.1093/nar/gkaa817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/09/2020] [Accepted: 10/11/2020] [Indexed: 11/20/2022] Open
Abstract
The relationship between stochastic transcriptional bursts and dynamic 3D chromatin states is not well understood. Using an innovated, ultra-sensitive technique, we address here enigmatic features underlying the communications between MYC and its enhancers in relation to the transcriptional process. MYC thus interacts with its flanking enhancers in a mutually exclusive manner documenting that enhancer hubs impinging on MYC detected in large cell populations likely do not exist in single cells. Dynamic encounters with pathologically activated enhancers responsive to a range of environmental cues, involved <10% of active MYC alleles at any given time in colon cancer cells. Being the most central node of the chromatin network, MYC itself likely drives its communications with flanking enhancers, rather than vice versa. We submit that these features underlie an acquired ability of MYC to become dynamically activated in response to a diverse range of environmental cues encountered by the cell during the neoplastic process.
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Affiliation(s)
- Noriyuki Sumida
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Z1:00, SE-171 76 Stockholm, Sweden
| | - Emmanouil G Sifakis
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Z1:00, SE-171 76 Stockholm, Sweden
| | - Narsis A Kiani
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Z1:00, SE-171 76 Stockholm, Sweden
| | - Anna Lewandowska Ronnegren
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Z1:00, SE-171 76 Stockholm, Sweden
| | - Barbara A Scholz
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Z1:00, SE-171 76 Stockholm, Sweden
| | - Johanna Vestlund
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Z1:00, SE-171 76 Stockholm, Sweden.,Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, L8:05, SE-171 76, Stockholm, Sweden
| | - David Gomez-Cabrero
- Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, L8:05, SE-171 76, Stockholm, Sweden.,Mucosal and Salivary Biology Division, King's College London Dental Institute, London SE1 9RT, UK
| | - Jesper Tegner
- Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, L8:05, SE-171 76, Stockholm, Sweden.,Science for Life Laboratory, Tomtebodavägen 23A, SE-17165, Solna, Sweden.,Biological and Environmental Sciences and Engineering Division, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Anita Göndör
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Z1:00, SE-171 76 Stockholm, Sweden
| | - Rolf Ohlsson
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Z1:00, SE-171 76 Stockholm, Sweden
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Scholz BA, Sumida N, de Lima CDM, Chachoua I, Martino M, Tzelepis I, Nikoshkov A, Zhao H, Mehmood R, Sifakis EG, Bhartiya D, Göndör A, Ohlsson R. WNT signaling and AHCTF1 promote oncogenic MYC expression through super-enhancer-mediated gene gating. Nat Genet 2019; 51:1723-1731. [DOI: 10.1038/s41588-019-0535-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 10/23/2019] [Indexed: 01/10/2023]
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Ruiz FM, Scholz BA, Buzamet E, Kopitz J, André S, Menéndez M, Romero A, Solís D, Gabius HJ. Natural single amino acid polymorphism (F19Y) in human galectin-8: detection of structural alterations and increased growth-regulatory activity on tumor cells. FEBS J 2014; 281:1446-1464. [DOI: 10.1111/febs.12716] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 01/02/2014] [Accepted: 01/05/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Federico M. Ruiz
- Departamento de Biología Físico-Química; Centro de Investigaciones Biológicas; Madrid Spain
| | - Barbara A. Scholz
- Institut für Physiologische Chemie; Tierärztliche Fakultät; Ludwig-Maximilians-Universität München; Germany
| | - Eliza Buzamet
- Departamento de Química-Física Biológica; Instituto de Química Física Rocasolano; CSIC, and Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES); Madrid Spain
| | - Jürgen Kopitz
- Abteilung Angewandte Tumorbiologie; Universitätsklinikum Heidelberg; Germany
| | - Sabine André
- Institut für Physiologische Chemie; Tierärztliche Fakultät; Ludwig-Maximilians-Universität München; Germany
| | - Margarita Menéndez
- Departamento de Química-Física Biológica; Instituto de Química Física Rocasolano; CSIC, and Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES); Madrid Spain
| | - Antonio Romero
- Departamento de Biología Físico-Química; Centro de Investigaciones Biológicas; Madrid Spain
| | - Dolores Solís
- Departamento de Química-Física Biológica; Instituto de Química Física Rocasolano; CSIC, and Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES); Madrid Spain
| | - Hans-Joachim Gabius
- Institut für Physiologische Chemie; Tierärztliche Fakultät; Ludwig-Maximilians-Universität München; Germany
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Harth-Hertle ML, Scholz BA, Erhard F, Glaser LV, Dölken L, Zimmer R, Kempkes B. Inactivation of intergenic enhancers by EBNA3A initiates and maintains polycomb signatures across a chromatin domain encoding CXCL10 and CXCL9. PLoS Pathog 2013; 9:e1003638. [PMID: 24068939 PMCID: PMC3777872 DOI: 10.1371/journal.ppat.1003638] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 08/03/2013] [Indexed: 01/28/2023] Open
Abstract
Epstein-Barr virus (EBV) causes a persistent infection in human B cells by establishing specific transcription programs to control B cell activation and differentiation. Transcriptional reprogramming of EBV infected B cells is predominantly driven by the action of EBV nuclear antigens, among them the transcriptional repressor EBNA3A. By comparing gene expression profiles of wt and EBNA3A negative EBV infected B cells, we have previously identified a broad array of cellular genes controlled by EBNA3A. We now find that genes repressed by EBNA3A in these cells are significantly enriched for the repressive histone mark H3K27me3, which is installed by Polycomb group (PcG) proteins. This PcG-controlled subset of genes also carries H3K27me3 marks in a variety of other tissues, suggesting that the commitment to PcG silencing is an intrinsic feature of these gene loci that can be used by EBNA3A. In addition, EBNA3A targets frequently reside in co-regulated gene clusters. To study the mechanism of gene repression by EBNA3A and to evaluate the relative contribution of PcG proteins during this process, we have selected the genomic neighbors CXCL10 and CXCL9 as a model for co-repressed and PcG-controlled genes. We show that EBNA3A binds to CBF1 occupied intergenic enhancers located between CXCL10 and CXCL9 and displaces the transactivator EBNA2. This impairs enhancer activity, resulting in a rapid transcriptional shut-down of both genes in a CBF1-dependent manner and initiation of a delayed gain of H3K27me3 marks covering an extended chromatin domain. H3K27me3 marks increase gradually and are maintained by EBNA3A. Our study provides direct evidence that repression by EBNA3A requires CBF1 and that EBNA3A and EBNA2 compete for access to CBF1 at identical genomic sites. Most importantly, our results demonstrate that transcriptional silencing by EBNA3A precedes the appearance of repressive PcG marks and indicate that both events are triggered by loss of enhancer activity. Epstein-Barr virus (EBV) is a γ-herpesvirus which establishes a latent infection in human B cells and is associated with the pathogenesis of several types of cancer. Here, we report that cellular genes repressed by the EBV nuclear antigen 3A (EBNA3A) in EBV infected B cells frequently form contiguous clusters in the human genome and are committed to epigenetic silencing by Polycomb group (PcG) proteins. The chemokine genes CXCL10 and CXCL9 and their receptors on NK and T cells are critical weapons of the infected host to control herpesvirus infections. CXCL10 and CXCL9 are close neighbors within an extended PcG-controlled domain. We show that EBNA3A binds to intergenic enhancers located between CXCL10 and CXCL9 and displaces the transactivator EBNA2. This process impairs enhancer activity, resulting in a rapid transcriptional shut-down of both genes followed by a delayed gain of PcG histone marks. These PcG marks increase within the following weeks and are maintained by EBNA3A. Our results show that rapid transcriptional shut-down of distal genes and domain-wide PcG silencing is triggered by loss of enhancer activity and suggest that EBNA3A can reprogram the cellular genome in order to escape the immune surveillance of the host.
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Affiliation(s)
- Marie L. Harth-Hertle
- Department of Gene Vectors, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany
| | - Barbara A. Scholz
- Department of Gene Vectors, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany
| | - Florian Erhard
- Institut für Informatik, Ludwig-Maximilians-Universität München, München, Germany
| | - Laura V. Glaser
- Department of Gene Vectors, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany
| | - Lars Dölken
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Ralf Zimmer
- Institut für Informatik, Ludwig-Maximilians-Universität München, München, Germany
| | - Bettina Kempkes
- Department of Gene Vectors, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany
- * E-mail:
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Scholz BA, Harth-Hertle ML, Malterer G, Haas J, Ellwart J, Schulz TF, Kempkes B. Abortive lytic reactivation of KSHV in CBF1/CSL deficient human B cell lines. PLoS Pathog 2013; 9:e1003336. [PMID: 23696732 PMCID: PMC3656114 DOI: 10.1371/journal.ppat.1003336] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 03/20/2013] [Indexed: 11/25/2022] Open
Abstract
Since Kaposi's sarcoma associated herpesvirus (KSHV) establishes a persistent infection in human B cells, B cells are a critical compartment for viral pathogenesis. RTA, the replication and transcription activator of KSHV, can either directly bind to DNA or use cellular DNA binding factors including CBF1/CSL as DNA adaptors. In addition, the viral factors LANA1 and vIRF4 are known to bind to CBF1/CSL and modulate RTA activity. To analyze the contribution of CBF1/CSL to reactivation in human B cells, we have successfully infected DG75 and DG75 CBF1/CSL knock-out cell lines with recombinant KSHV.219 and selected for viral maintenance by selective medium. Both lines maintained the virus irrespective of their CBF1/CSL status. Viral reactivation could be initiated in both B cell lines but viral genome replication was attenuated in CBF1/CSL deficient lines, which also failed to produce detectable levels of infectious virus. Induction of immediate early, early and late viral genes was impaired in CBF1/CSL deficient cells at multiple stages of the reactivation process but could be restored to wild-type levels by reintroduction of CBF1/CSL. To identify additional viral RTA target genes, which are directly controlled by CBF1/CSL, we analyzed promoters of a selected subset of viral genes. We show that the induction of the late viral genes ORF29a and ORF65 by RTA is strongly enhanced by CBF1/CSL. Orthologs of ORF29a in other herpesviruses are part of the terminase complex required for viral packaging. ORF65 encodes the small capsid protein essential for capsid shell assembly. Our study demonstrates for the first time that in human B cells viral replication can be initiated in the absence of CBF1/CSL but the reactivation process is severely attenuated at all stages and does not lead to virion production. Thus, CBF1/CSL acts as a global hub which is used by the virus to coordinate the lytic cascade. Kaposi's sarcoma associated herpesvirus (KSHV) establishes a life-long persistent infection in B cells, which constitute the viral reservoir for reactivation and production of progeny virus. Viral reactivation is associated with multiple AIDS related malignancies including Kaposi's sarcoma, an endothelial tumor, and two B cell lymphoproliferative malignancies, the primary effusion lymphoma and the multicentric Castleman's disease. CBF1/CSL is a cellular DNA binding protein that can recruit transactivators or repressors to regulatory sites in the viral and cellular genome. The replication and transcription activator (RTA) plays an essential role in the switch between latency and lytic reactivation. RTA can either bind to DNA directly or is recruited to DNA via anchor proteins like CBF1/CSL and activates transcription. In this study we used a novel cell culture model to analyze the contribution of the CBF1/CSL protein to the process of viral reactivation in human B cells. Two isogenic CBF1/CSL proficient or deficient B cell lines were latently infected with recombinant KSHV. Lytic viral gene expression, viral replication and virus production were compared. Our results suggest that viral lytic gene expression is severely attenuated but not abolished at multiple stages before and after the onset of lytic replication while virus production is below detection levels in CBF1/CSL deficient B cells.
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Affiliation(s)
- Barbara A. Scholz
- Department of Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Marie L. Harth-Hertle
- Department of Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Georg Malterer
- Division of Pathway Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Juergen Haas
- Division of Pathway Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Joachim Ellwart
- Institute of Molecular Immunology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Thomas F. Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Bettina Kempkes
- Department of Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- * E-mail:
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