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Rupasinghe M, Bersaglieri C, Leslie Pedrioli DM, Pedrioli PG, Panatta M, Hottiger MO, Cinelli P, Santoro R. PRAMEL7 and CUL2 decrease NuRD stability to establish ground-state pluripotency. EMBO Rep 2024; 25:1453-1468. [PMID: 38332149 PMCID: PMC10933316 DOI: 10.1038/s44319-024-00083-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 02/10/2024] Open
Abstract
Pluripotency is established in E4.5 preimplantation epiblast. Embryonic stem cells (ESCs) represent the immortalization of pluripotency, however, their gene expression signature only partially resembles that of developmental ground-state. Induced PRAMEL7 expression, a protein highly expressed in the ICM but lowly expressed in ESCs, reprograms developmentally advanced ESC+serum into ground-state pluripotency by inducing a gene expression signature close to developmental ground-state. However, how PRAMEL7 reprograms gene expression remains elusive. Here we show that PRAMEL7 associates with Cullin2 (CUL2) and this interaction is required to establish ground-state gene expression. PRAMEL7 recruits CUL2 to chromatin and targets regulators of repressive chromatin, including the NuRD complex, for proteasomal degradation. PRAMEL7 antagonizes NuRD-mediated repression of genes implicated in pluripotency by decreasing NuRD stability and promoter association in a CUL2-dependent manner. Our data link proteasome degradation pathways to ground-state gene expression, offering insights to generate in vitro models to reproduce the in vivo ground-state pluripotency.
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Affiliation(s)
- Meneka Rupasinghe
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, 8057, Zurich, Switzerland
- Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, 8057, Zurich, Switzerland
| | - Cristiana Bersaglieri
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, 8057, Zurich, Switzerland
| | - Deena M Leslie Pedrioli
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, 8057, Zurich, Switzerland
| | - Patrick Ga Pedrioli
- Department of Health Sciences and Technology, ETH Zurich, 8093, Zurich, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Martina Panatta
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, 8057, Zurich, Switzerland
- RNA Biology Program, Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, 8057, Zurich, Switzerland
| | - Paolo Cinelli
- Department of Trauma Surgery, University Hospital Zurich, University of Zurich, Rämistrasse 100, 8091, Zurich, Switzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, 8057, Zurich, Switzerland.
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Roganowicz M, Bär D, Bersaglieri C, Aprigliano R, Santoro R. BAZ2A-RNA mediated association with TOP2A and KDM1A represses genes implicated in prostate cancer. Life Sci Alliance 2023; 6:e202301950. [PMID: 37184661 PMCID: PMC10130768 DOI: 10.26508/lsa.202301950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 05/16/2023] Open
Abstract
BAZ2A represses rRNA genes (rDNA) that are transcribed by RNA polymerase I. In prostate cancer (PCa), BAZ2A function goes beyond this role because it represses genes frequently silenced in metastatic disease. However, the mechanisms of this BAZ2A-mediated repression remain elusive. Here, we show that BAZ2A represses genes through its RNA-binding TAM domain using mechanisms differing from rDNA silencing. Although the TAM domain mediates BAZ2A recruitment to rDNA, in PCa, this is not required for BAZ2A association with target genes. Instead, the BAZ2A-TAM domain in association with RNA mediates the interaction with topoisomerase 2A (TOP2A) and histone demethylase KDM1A, whose expression positively correlates with BAZ2A levels in localized and metastatic PCa. TOP2A and KDM1A pharmacological inhibition up-regulate BAZ2A-repressed genes that are regulated by inactive enhancers bound by BAZ2A, whereas rRNA genes are not affected. Our findings showed a novel RNA-based mechanism of gene regulation in PCa. Furthermore, we determined that RNA-mediated interactions between BAZ2A and TOP2A and KDM1A repress genes critical to PCa and may prove to be useful to stratify prostate cancer risk and treatment in patients.
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Affiliation(s)
- Marcin Roganowicz
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland
- RNA Biology Program, Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Dominik Bär
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland
| | - Cristiana Bersaglieri
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland
| | - Rossana Aprigliano
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland
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Bersaglieri C, Santoro R. Methods for mapping 3D-chromosome architecture around nucleoli. Curr Opin Cell Biol 2023; 81:102171. [PMID: 37230037 DOI: 10.1016/j.ceb.2023.102171] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/03/2023] [Accepted: 04/23/2023] [Indexed: 05/27/2023]
Abstract
The nucleolus is the largest subcompartment of the nucleus, known to be the place of ribosome biogenesis. Emerging evidence has started to implicate the nucleolus in the organization of chromosomes in the nucleus. Genomic domains contacting the nucleolus are defined as nucleolar associated domains (NADs) and are generally characterized by repressive chromatin states. However, the role of the nucleolus in genome architecture remains still not fully understood mainly because the lack of a membrane has challenged the establishment of methods for accurate identification of NADs. Here, we will discuss recent advances on methods to identify and characterize NADs, discuss their improvements relative to old methods, and highlight future perspectives.
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Affiliation(s)
- Cristiana Bersaglieri
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland.
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Dalcher D, Tan JY, Bersaglieri C, Peña‐Hernández R, Vollenweider E, Zeyen S, Schmid MW, Bianchi V, Butz S, Roganowicz M, Kuzyakiv R, Baubec T, Marques AC, Santoro R. BAZ2A safeguards genome architecture of ground-state pluripotent stem cells. EMBO J 2020; 39:e105606. [PMID: 33433018 PMCID: PMC7705451 DOI: 10.15252/embj.2020105606] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 12/30/2022] Open
Abstract
Chromosomes have an intrinsic tendency to segregate into compartments, forming long-distance contacts between loci of similar chromatin states. How genome compartmentalization is regulated remains elusive. Here, comparison of mouse ground-state embryonic stem cells (ESCs) characterized by open and active chromatin, and advanced serum ESCs with a more closed and repressed genome, reveals distinct regulation of their genome organization due to differential dependency on BAZ2A/TIP5, a component of the chromatin remodeling complex NoRC. On ESC chromatin, BAZ2A interacts with SNF2H, DNA topoisomerase 2A (TOP2A) and cohesin. BAZ2A associates with chromatin sub-domains within the active A compartment, which intersect through long-range contacts. We found that ground-state chromatin selectively requires BAZ2A to limit the invasion of active domains into repressive compartments. BAZ2A depletion increases chromatin accessibility at B compartments. Furthermore, BAZ2A regulates H3K27me3 genome occupancy in a TOP2A-dependent manner. Finally, ground-state ESCs require BAZ2A for growth, differentiation, and correct expression of developmental genes. Our results uncover the propensity of open chromatin domains to invade repressive domains, which is counteracted by chromatin remodeling to establish genome partitioning and preserve cell identity.
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Affiliation(s)
- Damian Dalcher
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
- Molecular Life Science ProgramLife Science Zurich Graduate SchoolUniversity of ZurichZurichSwitzerland
| | - Jennifer Yihong Tan
- Department of Computational BiologyUniversity of LausanneLausanneSwitzerland
| | - Cristiana Bersaglieri
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
- Molecular Life Science ProgramLife Science Zurich Graduate SchoolUniversity of ZurichZurichSwitzerland
| | - Rodrigo Peña‐Hernández
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
- Molecular Life Science ProgramLife Science Zurich Graduate SchoolUniversity of ZurichZurichSwitzerland
| | - Eva Vollenweider
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
- Molecular Life Science ProgramLife Science Zurich Graduate SchoolUniversity of ZurichZurichSwitzerland
| | - Stefan Zeyen
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
- Molecular Life Science ProgramLife Science Zurich Graduate SchoolUniversity of ZurichZurichSwitzerland
| | - Marc W Schmid
- Service and Support for Science ITUniversity of ZurichZurichSwitzerland
| | - Valerio Bianchi
- Oncode InstituteHubrecht Institute‐KNAWUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Stefan Butz
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
- Molecular Life Science ProgramLife Science Zurich Graduate SchoolUniversity of ZurichZurichSwitzerland
| | - Marcin Roganowicz
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
- Molecular Life Science ProgramLife Science Zurich Graduate SchoolUniversity of ZurichZurichSwitzerland
| | - Rostyslav Kuzyakiv
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
- Service and Support for Science ITUniversity of ZurichZurichSwitzerland
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
| | - Ana Claudia Marques
- Department of Computational BiologyUniversity of LausanneLausanneSwitzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
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5
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Tomasetti M, Re M, Monaco F, Gaetani S, Rubini C, Bertini A, Pasquini E, Bersaglieri C, Bracci M, Staffolani S, Colomba M, Gregorini A, Valentino M, Tagliabracci A, Bovenzi M, Neuzil J, Amati M, Santarelli L. MiR-126 in intestinal-type sinonasal adenocarcinomas: exosomal transfer of MiR-126 promotes anti-tumour responses. BMC Cancer 2018; 18:896. [PMID: 30223817 PMCID: PMC6142309 DOI: 10.1186/s12885-018-4801-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 09/05/2018] [Indexed: 12/14/2022] Open
Abstract
Background Intestinal-type sinonasal adenocarcinomas (ITACs) are aggressive malignancies related to wood dust and leather exposure. ITACs are generally associated with advanced stage at presentation due to the insidious growth pattern and non-specific symptoms. Therefore, biomarkers that can detect the switch from the benign disease to malignancy are needed. Essential for tumour growth, angiogenesis is an important step in tumour development and progression. This process is strictly regulated, and MiR-126 considered its master modulator. Methods We have investigated MiR-126 levels in ITACs and compared them to benign sinonasal lesions, such as sinonasal-inverted papillomas (SIPs) and inflammatory polyps (NIPs). The tumour-suppressive functions of MiR-126 were also evaluated. Results We found that MiR-126 can significantly distinguish malignancy from benign nasal forms. The low levels of MiR-126 in ITACs point to its role in tumour progression. In this context, restoration of MiR-126 induced metabolic changes, and inhibited cell growth and the tumorigenic potential of MNSC cells. Conclusions We report that MiR-126 delivered via exosomes from endothelial cells promotes anti-tumour responses. This paracrine transfer of MiRs may represent a new approach towards MiR-based therapy. Electronic supplementary material The online version of this article (10.1186/s12885-018-4801-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marco Tomasetti
- Department of Clinical and Molecular Sciences, Section of Occupational Medicine, Polytechnic University of Marche, Via Tronto 10/a, 60020, Ancona, Italy. .,International Society of Doctors for the Environment (ISDE), Arezzo, Italy.
| | - Massimo Re
- Department of Clinical and Molecular Sciences, Section of Otorhinolaryngology, Polytechnic University of Marche, Ancona, Italy
| | - Federica Monaco
- Department of Clinical and Molecular Sciences, Section of Occupational Medicine, Polytechnic University of Marche, Via Tronto 10/a, 60020, Ancona, Italy
| | - Simona Gaetani
- Department of Clinical and Molecular Sciences, Section of Occupational Medicine, Polytechnic University of Marche, Via Tronto 10/a, 60020, Ancona, Italy
| | - Corrado Rubini
- Department of Biomedical Sciences and Public Health, Section of Anatomical Pathology, Polytechnic University of Marche, Ancona, Italy
| | - Andrea Bertini
- Department of Clinical and Molecular Sciences, Section of Otorhinolaryngology, Polytechnic University of Marche, Ancona, Italy
| | - Ernesto Pasquini
- Surgical Department, ENT Metropolitan Unit, Bellaria & Budrio Hospital, Bologna, Italy
| | - Cristiana Bersaglieri
- Department of Clinical and Molecular Sciences, Section of Occupational Medicine, Polytechnic University of Marche, Via Tronto 10/a, 60020, Ancona, Italy
| | - Massimo Bracci
- Department of Clinical and Molecular Sciences, Section of Occupational Medicine, Polytechnic University of Marche, Via Tronto 10/a, 60020, Ancona, Italy
| | - Sara Staffolani
- Department of Clinical and Molecular Sciences, Section of Occupational Medicine, Polytechnic University of Marche, Via Tronto 10/a, 60020, Ancona, Italy
| | - Mariastella Colomba
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, PU, Italy
| | - Armando Gregorini
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, PU, Italy
| | - Matteo Valentino
- Department of Clinical and Molecular Sciences, Section of Occupational Medicine, Polytechnic University of Marche, Via Tronto 10/a, 60020, Ancona, Italy
| | - Adriano Tagliabracci
- Department of Biomedical Sciences and Public Health, Section of Legal Medicine, Polytechnic University of Marche, Ancona, Italy
| | - Massimo Bovenzi
- Department of Medical Sciences, Clinical Unit of Occupational Medicine, School of Medicine, University of Trieste, Trieste, Italy
| | - Jiri Neuzil
- School of Medical Science, Griffith University, Southport, Australia.,Institute of Biotechnology, Czech Academy of Sciences, Prague-West, Czech Republic
| | - Monica Amati
- Department of Clinical and Molecular Sciences, Section of Occupational Medicine, Polytechnic University of Marche, Via Tronto 10/a, 60020, Ancona, Italy
| | - Lory Santarelli
- Department of Clinical and Molecular Sciences, Section of Occupational Medicine, Polytechnic University of Marche, Via Tronto 10/a, 60020, Ancona, Italy.
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