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Santarelli P, Rosti V, Vivo M, Lanzuolo C. Chromatin organization of muscle stem cell. Curr Top Dev Biol 2024; 158:375-406. [PMID: 38670713 DOI: 10.1016/bs.ctdb.2024.01.014] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
The proper functioning of skeletal muscles is essential throughout life. A crucial crosstalk between the environment and several cellular mechanisms allows striated muscles to perform successfully. Notably, the skeletal muscle tissue reacts to an injury producing a completely functioning tissue. The muscle's robust regenerative capacity relies on the fine coordination between muscle stem cells (MuSCs or "satellite cells") and their specific microenvironment that dictates stem cells' activation, differentiation, and self-renewal. Critical for the muscle stem cell pool is a fine regulation of chromatin organization and gene expression. Acquiring a lineage-specific 3D genome architecture constitutes a crucial modulator of muscle stem cell function during development, in the adult stage, in physiological and pathological conditions. The context-dependent relationship between genome structure, such as accessibility and chromatin compartmentalization, and their functional effects will be analysed considering the improved 3D epigenome knowledge, underlining the intimate liaison between environmental encounters and epigenetics.
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Affiliation(s)
- Philina Santarelli
- INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Valentina Rosti
- INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy; CNR Institute of Biomedical Technologies, Milan, Italy
| | - Maria Vivo
- Università degli studi di Salerno, Fisciano, Italy.
| | - Chiara Lanzuolo
- INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy; CNR Institute of Biomedical Technologies, Milan, Italy.
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2
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Hariprakash JM, Salviato E, La Mastra F, Sebestyén E, Tagliaferri I, Silva RS, Lucini F, Farina L, Cinquanta M, Rancati I, Riboni M, Minardi SP, Roz L, Gorini F, Lanzuolo C, Casola S, Ferrari F. Leveraging Tissue-Specific Enhancer-Target Gene Regulatory Networks Identifies Enhancer Somatic Mutations That Functionally Impact Lung Cancer. Cancer Res 2024; 84:133-153. [PMID: 37855660 PMCID: PMC10758689 DOI: 10.1158/0008-5472.can-23-1129] [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: 04/13/2023] [Revised: 08/29/2023] [Accepted: 10/17/2023] [Indexed: 10/20/2023]
Abstract
Enhancers are noncoding regulatory DNA regions that modulate the transcription of target genes, often over large distances along with the genomic sequence. Enhancer alterations have been associated with various pathological conditions, including cancer. However, the identification and characterization of somatic mutations in noncoding regulatory regions with a functional effect on tumorigenesis and prognosis remain a major challenge. Here, we present a strategy for detecting and characterizing enhancer mutations in a genome-wide analysis of patient cohorts, across three lung cancer subtypes. Lung tissue-specific enhancers were defined by integrating experimental data and public epigenomic profiles, and the genome-wide enhancer-target gene regulatory network of lung cells was constructed by integrating chromatin three-dimensional architecture data. Lung cancers possessed a similar mutation burden at tissue-specific enhancers and exons but with differences in their mutation signatures. Functionally relevant alterations were prioritized on the basis of the pathway-level integration of the effect of a mutation and the frequency of mutations on individual enhancers. The genes enriched for mutated enhancers converged on the regulation of key biological processes and pathways relevant to tumor biology. Recurrent mutations in individual enhancers also affected the expression of target genes, with potential relevance for patient prognosis. Together, these findings show that noncoding regulatory mutations have a potential relevance for cancer pathogenesis and can be exploited for patient classification. SIGNIFICANCE Mapping enhancer-target gene regulatory interactions and analyzing enhancer mutations at the level of their target genes and pathways reveal convergence of recurrent enhancer mutations on biological processes involved in tumorigenesis and prognosis.
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Affiliation(s)
| | - Elisa Salviato
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Endre Sebestyén
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | | | | | - Federica Lucini
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Lorenzo Farina
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Ilaria Rancati
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | | | | | - Luca Roz
- Fondazione IRCCS—Istituto Nazionale Tumori, Milan, Italy
| | - Francesca Gorini
- INGM, National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi,” Milan, Italy
| | - Chiara Lanzuolo
- INGM, National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi,” Milan, Italy
- Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate, Italy
| | - Stefano Casola
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Francesco Ferrari
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
- Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza,” National Research Council (IGM-CNR), Pavia, Italy
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3
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Frittoli E, Palamidessi A, Iannelli F, Zanardi F, Villa S, Barzaghi L, Abdo H, Cancila V, Beznoussenko GV, Della Chiara G, Pagani M, Malinverno C, Bhattacharya D, Pisati F, Yu W, Galimberti V, Bonizzi G, Martini E, Mironov AA, Gioia U, Ascione F, Li Q, Havas K, Magni S, Lavagnino Z, Pennacchio FA, Maiuri P, Caponi S, Mattarelli M, Martino S, d'Adda di Fagagna F, Rossi C, Lucioni M, Tancredi R, Pedrazzoli P, Vecchione A, Petrini C, Ferrari F, Lanzuolo C, Bertalot G, Nader G, Foiani M, Piel M, Cerbino R, Giavazzi F, Tripodo C, Scita G. Tissue fluidification promotes a cGAS-STING cytosolic DNA response in invasive breast cancer. Nat Mater 2023; 22:644-655. [PMID: 36581770 PMCID: PMC10156599 DOI: 10.1038/s41563-022-01431-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/02/2022] [Indexed: 05/05/2023]
Abstract
The process in which locally confined epithelial malignancies progressively evolve into invasive cancers is often promoted by unjamming, a phase transition from a solid-like to a liquid-like state, which occurs in various tissues. Whether this tissue-level mechanical transition impacts phenotypes during carcinoma progression remains unclear. Here we report that the large fluctuations in cell density that accompany unjamming result in repeated mechanical deformations of cells and nuclei. This triggers a cellular mechano-protective mechanism involving an increase in nuclear size and rigidity, heterochromatin redistribution and remodelling of the perinuclear actin architecture into actin rings. The chronic strains and stresses associated with unjamming together with the reduction of Lamin B1 levels eventually result in DNA damage and nuclear envelope ruptures, with the release of cytosolic DNA that activates a cGAS-STING (cyclic GMP-AMP synthase-signalling adaptor stimulator of interferon genes)-dependent cytosolic DNA response gene program. This mechanically driven transcriptional rewiring ultimately alters the cell state, with the emergence of malignant traits, including epithelial-to-mesenchymal plasticity phenotypes and chemoresistance in invasive breast carcinoma.
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Affiliation(s)
| | | | - Fabio Iannelli
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Stefano Villa
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, Italy
- Max Plank Institute for Dynamics and Self-Organization, Göttingen, Germany
| | | | - Hind Abdo
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Valeria Cancila
- Department of Health Sciences, Human Pathology Section, University of Palermo School of Medicine, Palermo, Italy
| | | | | | - Massimiliano Pagani
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, Italy
| | | | | | - Federica Pisati
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Weimiao Yu
- Institute of Molecular and Cell Biology, A*STAR, Singapore, & Bioinformatics Institute, A*STAR, Singapore, Singapore
| | | | | | | | | | - Ubaldo Gioia
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Flora Ascione
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Qingsen Li
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Kristina Havas
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Serena Magni
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Zeno Lavagnino
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Paolo Maiuri
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Silvia Caponi
- Istituto Officina dei Materiali, National Research Council (IOM-CNR), Unit of Perugia, c/o Department of Physics and Geology, University of Perugia, Perugia, Italy
| | | | - Sabata Martino
- Department of Chemistry, Biology and Biotechnology, Biochemical and Biotechnological Sciences, University of Perugia, Perugia, Italy
| | - Fabrizio d'Adda di Fagagna
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
- Institute of Molecular Genetics, National Research Council, Pavia, Italy
| | - Chiara Rossi
- Unit of Anatomic Pathology, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
| | - Marco Lucioni
- Unit of Anatomic Pathology, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
| | - Richard Tancredi
- Medical Oncology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- S.C. Oncologia Medica, ASST Melegnano e della Martesana, Ospedale Uboldo, Cernusco sul Naviglio, Milan, Italy
| | - Paolo Pedrazzoli
- Medical Oncology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Internal Medicine and Medical Therapy, University of Pavia, Pavia, Italy
| | - Andrea Vecchione
- Department of Clinical and Molecular Medicine, University of Roma, La Sapienza, Rome, Italy
| | | | - Francesco Ferrari
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
- Institute of Molecular Genetics, National Research Council, Pavia, Italy
| | - Chiara Lanzuolo
- Institute of Biomedical Technologies, National Research Council, Milan, Italy
- National Institute of Molecular Genetics Romeo and Enrica Invernizzi, INGM, Milan, Italy
| | - Giovanni Bertalot
- Department of Pathology, S. Chiara Hospital, Azienda Provinciale per i Servizi Sanitari, Trento, Italy
- CISMed University of Trento, University of Trento, Trento, Italy
| | - Guilherme Nader
- Institut Curie and Institut Pierre Gilles de Gennes, PSL Research University, CNRS, UMR-144, Paris, France
- Cell Pathology Children's Hospital of Philadelphia, Research Institute Department of Pathology and Laboratory Medicine University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Marco Foiani
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
- Department of Oncology and Haemato-Oncology, University of Milan, Milan, Italy
| | - Matthieu Piel
- Institut Curie and Institut Pierre Gilles de Gennes, PSL Research University, CNRS, UMR-144, Paris, France
| | - Roberto Cerbino
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, Italy
- Faculty of Physics, University of Vienna, Vienna, Austria
| | - Fabio Giavazzi
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, Italy.
| | - Claudio Tripodo
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.
- Department of Health Sciences, Human Pathology Section, University of Palermo School of Medicine, Palermo, Italy.
| | - Giorgio Scita
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.
- Department of Oncology and Haemato-Oncology, University of Milan, Milan, Italy.
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4
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Frittoli E, Palamidessi A, Iannelli F, Zanardi F, Villa S, Barzaghi L, Abdo H, Cancila V, Beznoussenko GV, Della Chiara G, Pagani M, Malinverno C, Bhattacharya D, Pisati F, Yu W, Galimberti V, Bonizzi G, Martini E, Mironov AA, Gioia U, Ascione F, Li Q, Havas K, Magni S, Lavagnino Z, Pennacchio FA, Maiuri P, Caponi S, Mattarelli M, Martino S, d'Adda di Fagagna F, Rossi C, Lucioni M, Tancredi R, Pedrazzoli P, Vecchione A, Petrini C, Ferrari F, Lanzuolo C, Bertalot G, Nader G, Foiani M, Piel M, Cerbino R, Giavazzi F, Tripodo C, Scita G. Author Correction: Tissue fluidification promotes a cGAS-STING cytosolic DNA response in invasive breast cancer. Nat Mater 2023; 22:400. [PMID: 36702890 PMCID: PMC9981457 DOI: 10.1038/s41563-023-01479-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Affiliation(s)
| | | | - Fabio Iannelli
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Stefano Villa
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, Italy
- Max Plank Institute for Dynamics and Self-Organization, Göttingen, Germany
| | | | - Hind Abdo
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Valeria Cancila
- Department of Health Sciences, Human Pathology Section, University of Palermo School of Medicine, Palermo, Italy
| | | | | | - Massimiliano Pagani
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, Italy
| | | | | | - Federica Pisati
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Weimiao Yu
- Institute of Molecular and Cell Biology, A*STAR, Singapore, & Bioinformatics Institute, A*STAR, Singapore, Singapore
| | | | | | | | | | - Ubaldo Gioia
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Flora Ascione
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Qingsen Li
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Kristina Havas
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Serena Magni
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Zeno Lavagnino
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Paolo Maiuri
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Silvia Caponi
- Istituto Officina dei Materiali, National Research Council (IOM-CNR), Unit of Perugia, c/o Department of Physics and Geology, University of Perugia, Perugia, Italy
| | | | - Sabata Martino
- Department of Chemistry, Biology and Biotechnology, Biochemical and Biotechnological Sciences, University of Perugia, Perugia, Italy
| | - Fabrizio d'Adda di Fagagna
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
- Institute of Molecular Genetics, National Research Council, Pavia, Italy
| | - Chiara Rossi
- Unit of Anatomic Pathology, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
| | - Marco Lucioni
- Unit of Anatomic Pathology, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
| | - Richard Tancredi
- Medical Oncology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- S.C. Oncologia Medica, ASST Melegnano e della Martesana, Ospedale Uboldo, Cernusco sul Naviglio, Milan, Italy
| | - Paolo Pedrazzoli
- Medical Oncology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Internal Medicine and Medical Therapy, University of Pavia, Pavia, Italy
| | - Andrea Vecchione
- Department of Clinical and Molecular Medicine, University of Roma, La Sapienza, Rome, Italy
| | | | - Francesco Ferrari
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
- Institute of Molecular Genetics, National Research Council, Pavia, Italy
| | - Chiara Lanzuolo
- Institute of Biomedical Technologies, National Research Council, Milan, Italy
- National Institute of Molecular Genetics Romeo and Enrica Invernizzi, INGM, Milan, Italy
| | - Giovanni Bertalot
- Department of Pathology, S. Chiara Hospital, Azienda Provinciale per i Servizi Sanitari, Trento, Italy
- CISMed University of Trento, University of Trento, Trento, Italy
| | - Guilherme Nader
- Institut Curie and Institut Pierre Gilles de Gennes, PSL Research University, CNRS, UMR-144, Paris, France
- Cell Pathology Children's Hospital of Philadelphia, Research Institute Department of Pathology and Laboratory Medicine University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Marco Foiani
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
- Department of Oncology and Haemato-Oncology, University of Milan, Milan, Italy
| | - Matthieu Piel
- Institut Curie and Institut Pierre Gilles de Gennes, PSL Research University, CNRS, UMR-144, Paris, France
| | - Roberto Cerbino
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, Italy
- Faculty of Physics, University of Vienna, Vienna, Austria
| | - Fabio Giavazzi
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, Italy.
| | - Claudio Tripodo
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.
- Department of Health Sciences, Human Pathology Section, University of Palermo School of Medicine, Palermo, Italy.
| | - Giorgio Scita
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.
- Department of Oncology and Haemato-Oncology, University of Milan, Milan, Italy.
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5
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Gregoretti F, Lucini F, Cesarini E, Oliva G, Lanzuolo C, Antonelli L. Segmentation, 3D Reconstruction, and Analysis of PcG Proteins in Fluorescence Microscopy Images in Different Cell Culture Conditions. Methods Mol Biol 2023; 2655:147-169. [PMID: 37212995 DOI: 10.1007/978-1-0716-3143-0_12] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Polycomb-group (PcG) of proteins are evolutionarily conserved transcription factors necessary for the regulation of gene expression during the development and the safeguard of cell identity in adulthood. In the nucleus, they form aggregates whose positioning and dimension are fundamental for their function. We present an algorithm, and its MATLAB implementation, based on mathematical methods to detect and analyze PcG proteins in fluorescence cell image z-stacks. Our algorithm provides a method to measure the number, the size, and the relative positioning of the PcG bodies in the nucleus for a better understanding of their spatial distribution, and thus of their role for a correct genome conformation and function.
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Affiliation(s)
- Francesco Gregoretti
- Institute for High Performance Computing and Networking, ICAR-CNR, Naples, Italy.
| | - Federica Lucini
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
- IFOM, Institute Foundation of Molecular Oncology, Milan, Italy
| | - Elisa Cesarini
- Institute of Biochemistry and Cellular Biology, IBBC-CNR, Rome, Italy
| | - Gennaro Oliva
- Institute for High Performance Computing and Networking, ICAR-CNR, Naples, Italy
| | - Chiara Lanzuolo
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
- Institute of Biomedical Technologies, ITB-CNR, Milan, Italy
| | - Laura Antonelli
- Institute for High Performance Computing and Networking, ICAR-CNR, Naples, Italy.
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6
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Rosti V, Gorini F, Santarelli P, Sarnicola ML, Magnani S, Lanzuolo C. Polycomb Bodies Detection in Murine Fibromuscular Stroma from Skin, Skeletal Muscles, and Aortic Tissues. Methods Mol Biol 2023; 2655:125-146. [PMID: 37212994 DOI: 10.1007/978-1-0716-3143-0_11] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The regulation of chromatin structure depends on a dynamic, multiple mechanisms that modulate gene expression and constitute the epigenome. The Polycomb group (PcG) of proteins are epigenetic factors involved in the transcriptional repression. Among their multilevel, chromatin-associated functions, PcG proteins mediate the establishment and maintenance of higher-order structures at target genes, allowing the transmission of transcriptional programs throughout the cell cycle.In the nucleus, PcG proteins localize close to the pericentric heterochromatin forming microscopically foci, called Polycomb bodies. Here, to visualize the tissue-specific PcG distribution in the aorta, dorsal skin and hindlimb muscles, we combine a fluorescence-activated cell sorter (FACS)-based method with an immunofluorescence staining.
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Affiliation(s)
- Valentina Rosti
- Institute of Biomedical Technologies, National Research Council, Milan, Italy
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", INGM, Milan, Italy
| | - Francesca Gorini
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", INGM, Milan, Italy
| | - Philina Santarelli
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", INGM, Milan, Italy
| | - Maria Lucia Sarnicola
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", INGM, Milan, Italy
| | | | - Chiara Lanzuolo
- Institute of Biomedical Technologies, National Research Council, Milan, Italy.
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", INGM, Milan, Italy.
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7
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Fallatah B, Shuaib M, Adroub S, Paytuví-Gallart A, Della Valle F, Nadeef S, Lanzuolo C, Orlando V. Ago1 controls myogenic differentiation by regulating eRNA-mediated CBP-guided epigenome reprogramming. Cell Rep 2021; 37:110066. [PMID: 34852230 DOI: 10.1016/j.celrep.2021.110066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 04/28/2020] [Revised: 10/05/2021] [Accepted: 11/08/2021] [Indexed: 01/03/2023] Open
Abstract
The role of chromatin-associated RNAi components in the nucleus of mammalian cells and in particular in the context of developmental programs remains to be elucidated. Here, we investigate the function of nuclear Argonaute 1 (Ago1) in gene expression regulation during skeletal muscle differentiation. We show that Ago1 is required for activation of the myogenic program by supporting chromatin modification mediated by developmental enhancer activation. Mechanistically, we demonstrate that Ago1 directly controls global H3K27 acetylation (H3K27ac) by regulating enhancer RNA (eRNA)-CREB-binding protein (CBP) acetyltransferase interaction, a key step in enhancer-driven gene activation. In particular, we show that Ago1 is specifically required for myogenic differentiation 1 (MyoD) and downstream myogenic gene activation, whereas its depletion leads to failure of CBP acetyltransferase activation and blocking of the myogenic program. Our work establishes a role of the mammalian enhancer-associated RNAi component Ago1 in epigenome regulation and activation of developmental programs.
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Affiliation(s)
- Bodor Fallatah
- King Abdullah University of Science and Technology, KAUST Environmental Epigenetics Research Program, Biological and Environmental Sciences and Engineering Division, Thuwal 23955, Saudi Arabia
| | - Muhammad Shuaib
- King Abdullah University of Science and Technology, KAUST Environmental Epigenetics Research Program, Biological and Environmental Sciences and Engineering Division, Thuwal 23955, Saudi Arabia
| | - Sabir Adroub
- King Abdullah University of Science and Technology, KAUST Environmental Epigenetics Research Program, Biological and Environmental Sciences and Engineering Division, Thuwal 23955, Saudi Arabia
| | | | - Francesco Della Valle
- King Abdullah University of Science and Technology, KAUST Environmental Epigenetics Research Program, Biological and Environmental Sciences and Engineering Division, Thuwal 23955, Saudi Arabia
| | - Seba Nadeef
- King Abdullah University of Science and Technology, KAUST Environmental Epigenetics Research Program, Biological and Environmental Sciences and Engineering Division, Thuwal 23955, Saudi Arabia
| | - Chiara Lanzuolo
- Institute of Biomedical Technologies, National Research Council, 20090 Milan, Italy; National Institute of Molecular Genetics (INGM) "Romeo ed Enrica Invernizzi," Chromatin and Nuclear Architecture Laboratory, 20122 Milan, Italy
| | - Valerio Orlando
- King Abdullah University of Science and Technology, KAUST Environmental Epigenetics Research Program, Biological and Environmental Sciences and Engineering Division, Thuwal 23955, Saudi Arabia.
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8
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Albo G, Ripa F, Rosti V, Petrini C, Lembo G, Hariprakash J, Ferrari F, De Lorenzis E, Lanzuolo C, Montanari E. Chromatin texture remodeling underlying the epigenomic dysfunction in prostate cancer. EUR UROL SUPPL 2021. [DOI: 10.1016/s2666-1683(21)00873-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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9
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Amrute‐Nayak M, Pegoli G, Holler T, Lopez‐Davila AJ, Lanzuolo C, Nayak A. Chemotherapy triggers cachexia by deregulating synergetic function of histone-modifying enzymes. J Cachexia Sarcopenia Muscle 2021; 12:159-176. [PMID: 33305533 PMCID: PMC7890149 DOI: 10.1002/jcsm.12645] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 08/10/2020] [Accepted: 10/12/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Chemotherapy is the first line of treatment for cancer patients. However, the side effects cause severe muscle atrophy or chemotherapy-induced cachexia. Previously, the NF-κB/MuRF1-dependent pathway was shown to induce chemotherapy-induced cachexia. We hypothesized that acute collateral toxic effects of chemotherapy on muscles might involve other unknown pathways promoting chemotherapy-induced muscle atrophy. In this study, we investigated differential effects of chemotherapeutic drugs and probed whether alternative molecular mechanisms lead to cachexia. METHODS We employed mouse satellite stem cell-derived primary muscle cells and mouse C2C12 progenitor cell-derived differentiated myotubes as model systems to test the effect of drugs. The widely used chemotherapeutic drugs, such as daunorubicin (Daun), etoposide (Etop), and cytarabine (Ara-C), were tested. Molecular mechanisms by which drug affects the muscle cell organization at epigenetic, transcriptional, and protein levels were measured by employing chromatin immunoprecipitations, endogenous gene expression profiling, co-immunoprecipitation, complementation assays, and confocal microscopy. Myotube function was examined using the electrical stimulation of myotubes to monitor contractile ability (excitation-contraction coupling) post drug treatment. RESULTS Here, we demonstrate that chemotherapeutic drugs disrupt sarcomere organization and thereby the contractile ability of skeletal muscle cells. The sarcomere disorganization results from severe loss of molecular motor protein MyHC-II upon drug treatment. We identified that drugs impede chromatin targeting of SETD7 histone methyltransferase and disrupt association and synergetic function of SETD7 with p300 histone acetyltransferase. The compromised transcriptional activity of histone methyltransferase and acetyltransferase causes reduced histone acetylation and low occupancy of active RNA polymerase II on MyHC-II, promoting drastic down-regulation of MyHC-II expression (~3.6-fold and ~4.5-fold reduction of MyHC-IId mRNA levels in Daun and Etop treatment, respectively. P < 0.0001). For MyHC-IIa, gene expression was down-regulated by ~2.6-fold and ~4.5-fold in Daun and Etop treatment, respectively (P < 0.0001). Very interestingly, the drugs destabilize SUMO deconjugase SENP3. Reduction in SENP3 protein level leads to deregulation of SETD7-p300 function. Importantly, we identified that SUMO deconjugation independent role of SENP3 regulates SETD7-p300 functional axis. CONCLUSIONS The results show that the drugs critically alter SENP3-dependent synergistic action of histone-modifying enzymes in muscle cells. Collectively, we defined a unique epigenetic mechanism targeted by distinct chemotherapeutic drugs, triggering chemotherapy-induced cachexia.
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Affiliation(s)
- Mamta Amrute‐Nayak
- Institute of Molecular and Cell PhysiologyHannover Medical SchoolHannoverGermany
| | - Gloria Pegoli
- Institute of Biomedical TechnologiesNational Research CouncilMilanItaly
- Istituto Nazionale Genetica Molecolare ‘Romeo ed Enrica Invernizzi’MilanItaly
| | - Tim Holler
- Institute of Molecular and Cell PhysiologyHannover Medical SchoolHannoverGermany
| | | | - Chiara Lanzuolo
- Institute of Biomedical TechnologiesNational Research CouncilMilanItaly
- Istituto Nazionale Genetica Molecolare ‘Romeo ed Enrica Invernizzi’MilanItaly
| | - Arnab Nayak
- Institute of Molecular and Cell PhysiologyHannover Medical SchoolHannoverGermany
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10
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Bianchi A, Mozzetta C, Pegoli G, Lucini F, Valsoni S, Rosti V, Petrini C, Cortesi A, Gregoretti F, Antonelli L, Oliva G, De Bardi M, Rizzi R, Bodega B, Pasini D, Ferrari F, Bearzi C, Lanzuolo C. Dysfunctional polycomb transcriptional repression contributes to lamin A/C-dependent muscular dystrophy. J Clin Invest 2021; 130:2408-2421. [PMID: 31999646 DOI: 10.1172/jci128161] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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: 02/14/2019] [Accepted: 01/22/2020] [Indexed: 12/25/2022] Open
Abstract
Lamin A is a component of the inner nuclear membrane that, together with epigenetic factors, organizes the genome in higher order structures required for transcriptional control. Mutations in the lamin A/C gene cause several diseases belonging to the class of laminopathies, including muscular dystrophies. Nevertheless, molecular mechanisms involved in the pathogenesis of lamin A-dependent dystrophies are still largely unknown. The polycomb group (PcG) of proteins are epigenetic repressors and lamin A interactors, primarily involved in the maintenance of cell identity. Using a murine model of Emery-Dreifuss muscular dystrophy (EDMD), we show here that lamin A loss deregulated PcG positioning in muscle satellite stem cells, leading to derepression of non-muscle-specific genes and p16INK4a, a senescence driver encoded in the Cdkn2a locus. This aberrant transcriptional program caused impairment in self-renewal, loss of cell identity, and premature exhaustion of the quiescent satellite cell pool. Genetic ablation of the Cdkn2a locus restored muscle stem cell properties in lamin A/C-null dystrophic mice. Our findings establish a direct link between lamin A and PcG epigenetic silencing and indicate that lamin A-dependent muscular dystrophy can be ascribed to intrinsic epigenetic dysfunctions of muscle stem cells.
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Affiliation(s)
- Andrea Bianchi
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi," Milan, Italy.,Institute of Cell Biology and Neurobiology, National Research Council (CNR), Rome, Italy
| | - Chiara Mozzetta
- Institute of Cell Biology and Neurobiology, National Research Council (CNR), Rome, Italy
| | - Gloria Pegoli
- Santa Lucia Foundation, Scientific Institute for Research, Hospitalization and Healthcare (IRCCS), Rome, Italy
| | - Federica Lucini
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi," Milan, Italy
| | - Sara Valsoni
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi," Milan, Italy.,Santa Lucia Foundation, Scientific Institute for Research, Hospitalization and Healthcare (IRCCS), Rome, Italy
| | | | | | - Alice Cortesi
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi," Milan, Italy
| | | | - Laura Antonelli
- Institute for High Performance Computing and Networking, CNR, Naples, Italy
| | - Gennaro Oliva
- Institute for High Performance Computing and Networking, CNR, Naples, Italy
| | - Marco De Bardi
- Santa Lucia Foundation, Scientific Institute for Research, Hospitalization and Healthcare (IRCCS), Rome, Italy
| | - Roberto Rizzi
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi," Milan, Italy.,Institute of Biomedical Technologies, CNR, Milan, Italy
| | - Beatrice Bodega
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi," Milan, Italy
| | - Diego Pasini
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Milan, Italy.,Department of Health Sciences, University of Milan, Milan, Italy
| | - Francesco Ferrari
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.,Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza," CNR, Pavia, Italy
| | - Claudia Bearzi
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi," Milan, Italy.,Institute of Biochemistry and Cell Biology, CNR, Rome, Italy
| | - Chiara Lanzuolo
- Santa Lucia Foundation, Scientific Institute for Research, Hospitalization and Healthcare (IRCCS), Rome, Italy.,Institute of Biomedical Technologies, CNR, Milan, Italy
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11
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Sebestyén E, Marullo F, Lucini F, Petrini C, Bianchi A, Valsoni S, Olivieri I, Antonelli L, Gregoretti F, Oliva G, Ferrari F, Lanzuolo C. SAMMY-seq reveals early alteration of heterochromatin and deregulation of bivalent genes in Hutchinson-Gilford Progeria Syndrome. Nat Commun 2020; 11:6274. [PMID: 33293552 PMCID: PMC7722762 DOI: 10.1038/s41467-020-20048-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 11/05/2020] [Indexed: 12/14/2022] Open
Abstract
Hutchinson-Gilford progeria syndrome is a genetic disease caused by an aberrant form of Lamin A resulting in chromatin structure disruption, in particular by interfering with lamina associated domains. Early molecular alterations involved in chromatin remodeling have not been identified thus far. Here, we present SAMMY-seq, a high-throughput sequencing-based method for genome-wide characterization of heterochromatin dynamics. Using SAMMY-seq, we detect early stage alterations of heterochromatin structure in progeria primary fibroblasts. These structural changes do not disrupt the distribution of H3K9me3 in early passage cells, thus suggesting that chromatin rearrangements precede H3K9me3 alterations described at later passages. On the other hand, we observe an interplay between changes in chromatin accessibility and Polycomb regulation, with site-specific H3K27me3 variations and transcriptional dysregulation of bivalent genes. We conclude that the correct assembly of lamina associated domains is functionally connected to the Polycomb repression and rapidly lost in early molecular events of progeria pathogenesis.
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Affiliation(s)
- Endre Sebestyén
- IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Fabrizia Marullo
- Institute of Cell Biology and Neurobiology, National Research Council, Rome, Italy
| | - Federica Lucini
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | | | - Andrea Bianchi
- Institute of Cell Biology and Neurobiology, National Research Council, Rome, Italy
- IRCCS Santa Lucia Foundation, Rome, Italy
| | - Sara Valsoni
- IRCCS Santa Lucia Foundation, Rome, Italy
- Institute for High Performance Computing and Networking, National Research Council, Naples, Italy
| | - Ilaria Olivieri
- Institute of Cell Biology and Neurobiology, National Research Council, Rome, Italy
| | - Laura Antonelli
- Institute for High Performance Computing and Networking, National Research Council, Naples, Italy
| | - Francesco Gregoretti
- Institute for High Performance Computing and Networking, National Research Council, Naples, Italy
| | - Gennaro Oliva
- Institute for High Performance Computing and Networking, National Research Council, Naples, Italy
| | - Francesco Ferrari
- IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy.
- Institute of Molecular Genetics, National Research Council, Pavia, Italy.
| | - Chiara Lanzuolo
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy.
- Institute of Biomedical Technologies, National Research Council, Milan, Italy.
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12
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Pegoli G, Lucini F, Mozzetta C, Lanzuolo C. Single Myofiber Isolation and Culture from a Murine Model of Emery-Dreifuss Muscular Dystrophy in Early Post-Natal Development. J Vis Exp 2020. [PMID: 32716379 DOI: 10.3791/61516] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Autosomal dominant Emery-Dreifuss muscular dystrophy (EDMD) is caused by mutations in the LMNA gene, which encodes the A-type nuclear lamins, intermediate filament proteins that sustain the nuclear envelope and the components of the nucleoplasm. We recently reported that muscle wasting in EDMD can be ascribed to intrinsic epigenetic dysfunctions affecting muscle (satellite) stem cells regenerative capacity. Isolation and culture of single myofibers is one of the most physiological ex-vivo approaches to monitor satellite cells behavior within their niche, as they remain between the basal lamina surrounding the fiber and the sarcolemma. Therefore, it represents an invaluable experimental paradigm to study satellite cells from a variety of murine models. Here, we describe a re-adapted method to isolate intact and viable single myofibers from post-natal hindlimb muscles (Tibialis Anterior, Extensor Digitorum Longus, Gastrocnemius and Soleus). Following this protocol, we were able to study satellite cells from Lamin Δ8-11 -/- mice, a severe EDMD murine model, at only 19 days after birth. We detail the isolation procedure, as well as the culture conditions for obtaining a good amount of myofibers and their associated satellite-cells-derived progeny. When cultured in growth-factors rich medium, satellite cells derived from wild type mice activate, proliferate, and eventually differentiate or undergo self-renewal. In homozygous Lamin Δ8-11 -/- mutant mice these capabilities are severely impaired. This technique, if strictly followed, allows to study all processes linked to the myofiber-associated satellite cell even in early post-natal developmental stages and in fragile muscles.
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Affiliation(s)
- Gloria Pegoli
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi"; IRCCS Santa Lucia Foundation
| | - Federica Lucini
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi"; IRCCS Santa Lucia Foundation
| | - Chiara Mozzetta
- Department of Biology and Biotechnology, "C. Darwin" Sapienza University, CNR - IBPM;
| | - Chiara Lanzuolo
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi"; IRCCS Santa Lucia Foundation; CNR - Institute of Biomedical Technologies (ITB);
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13
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Albo G, Ripa F, Rocchini L, Gallioli A, Rosti V, Petrini C, Ferrari F, Montanari E, Lanzuolo C. Sequential Analysis of MacroMolecules accessibility-sequencing (SAMMY-seq) of chromatin organisation in normal and cancerous prostatic tissues. EUR UROL SUPPL 2020. [DOI: 10.1016/s2666-1683(20)33014-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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14
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Baci D, Chirivì M, Pace V, Maiullari F, Milan M, Rampin A, Somma P, Presutti D, Garavelli S, Bruno A, Cannata S, Lanzuolo C, Gargioli C, Rizzi R, Bearzi C. Extracellular Vesicles from Skeletal Muscle Cells Efficiently Promote Myogenesis in Induced Pluripotent Stem Cells. Cells 2020; 9:cells9061527. [PMID: 32585911 PMCID: PMC7349204 DOI: 10.3390/cells9061527] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/13/2020] [Accepted: 06/15/2020] [Indexed: 12/11/2022] Open
Abstract
The recent advances, offered by cell therapy in the regenerative medicine field, offer a revolutionary potential for the development of innovative cures to restore compromised physiological functions or organs. Adult myogenic precursors, such as myoblasts or satellite cells, possess a marked regenerative capacity, but the exploitation of this potential still encounters significant challenges in clinical application, due to low rate of proliferation in vitro, as well as a reduced self-renewal capacity. In this scenario, induced pluripotent stem cells (iPSCs) can offer not only an inexhaustible source of cells for regenerative therapeutic approaches, but also a valuable alternative for in vitro modeling of patient-specific diseases. In this study we established a reliable protocol to induce the myogenic differentiation of iPSCs, generated from pericytes and fibroblasts, exploiting skeletal muscle-derived extracellular vesicles (EVs), in combination with chemically defined factors. This genetic integration-free approach generates functional skeletal myotubes maintaining the engraftment ability in vivo. Our results demonstrate evidence that EVs can act as biological "shuttles" to deliver specific bioactive molecules for a successful transgene-free differentiation offering new opportunities for disease modeling and regenerative approaches.
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Affiliation(s)
- Denisa Baci
- Institute of Biochemistry and Cell Biology, National Research Council, 00015 Rome, Italy; (D.B.); (M.C.); (V.P.); (M.M.); (A.R.); (D.P.)
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
| | - Maila Chirivì
- Institute of Biochemistry and Cell Biology, National Research Council, 00015 Rome, Italy; (D.B.); (M.C.); (V.P.); (M.M.); (A.R.); (D.P.)
| | - Valentina Pace
- Institute of Biochemistry and Cell Biology, National Research Council, 00015 Rome, Italy; (D.B.); (M.C.); (V.P.); (M.M.); (A.R.); (D.P.)
| | | | - Marika Milan
- Institute of Biochemistry and Cell Biology, National Research Council, 00015 Rome, Italy; (D.B.); (M.C.); (V.P.); (M.M.); (A.R.); (D.P.)
| | - Andrea Rampin
- Institute of Biochemistry and Cell Biology, National Research Council, 00015 Rome, Italy; (D.B.); (M.C.); (V.P.); (M.M.); (A.R.); (D.P.)
| | - Paolo Somma
- Flow Cytometry Core, Humanitas Clinical and Research Center, 20089 Milan, Italy;
| | - Dario Presutti
- Institute of Biochemistry and Cell Biology, National Research Council, 00015 Rome, Italy; (D.B.); (M.C.); (V.P.); (M.M.); (A.R.); (D.P.)
| | - Silvia Garavelli
- Institute for Endocrinology and Oncology “Gaetano Salvatore”, National Research Council, 80131 Naples, Italy;
| | | | - Stefano Cannata
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; (S.C.); (C.G.)
| | - Chiara Lanzuolo
- Institute of Biomedical Technologies, National Research Council, 20090 Milan, Italy;
- Fondazione Istituto Nazionale di Genetica Molecolare, 20122 Milan, Italy
| | - Cesare Gargioli
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; (S.C.); (C.G.)
| | - Roberto Rizzi
- Institute of Biomedical Technologies, National Research Council, 20090 Milan, Italy;
- Fondazione Istituto Nazionale di Genetica Molecolare, 20122 Milan, Italy
- Correspondence: (R.R.); (C.B.); Tel.: +39-02-0066-0230 (R.R.); +39-02-0066-0230 (C.B.)
| | - Claudia Bearzi
- Institute of Biochemistry and Cell Biology, National Research Council, 00015 Rome, Italy; (D.B.); (M.C.); (V.P.); (M.M.); (A.R.); (D.P.)
- Fondazione Istituto Nazionale di Genetica Molecolare, 20122 Milan, Italy
- Correspondence: (R.R.); (C.B.); Tel.: +39-02-0066-0230 (R.R.); +39-02-0066-0230 (C.B.)
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15
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Fabbrizio P, Apolloni S, Bianchi A, Salvatori I, Valle C, Lanzuolo C, Bendotti C, Nardo G, Volonté C. P2X7 activation enhances skeletal muscle metabolism and regeneration in SOD1G93A mouse model of amyotrophic lateral sclerosis. Brain Pathol 2020; 30:272-282. [PMID: 31376190 PMCID: PMC7065186 DOI: 10.1111/bpa.12774] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/26/2019] [Indexed: 12/11/2022] Open
Abstract
Muscle weakness plays an important role in neuromuscular disorders comprising amyotrophic lateral sclerosis (ALS). However, it is not established whether muscle denervation originates from the motor neurons, the muscles or more likely both. Previous studies have shown that the expression of the SOD1G93A mutation in skeletal muscles causes denervation of the neuromuscular junctions, inability to regenerate and consequent atrophy, all clear symptoms of ALS. In this work, we used SOD1G93A mice, a model that best mimics some pathological features of both familial and sporadic ALS, and we investigated some biological effects induced by the activation of the P2X7 receptor in the skeletal muscles. The P2X7, belonging to the ionotropic family of purinergic receptors for extracellular ATP, is abundantly expressed in the healthy skeletal muscles, where it controls cell duplication, differentiation, regeneration or death. In particular, we evaluated whether an in vivo treatment in SOD1G93A mice with the P2X7 specific agonist 2'(3')-O-(4-Benzoylbenzoyl) adenosine5'-triphosphate (BzATP) just before the onset of a pathological neuromuscular phenotype could exert beneficial effects in the skeletal muscles. Our findings indicate that stimulation of P2X7 improves the innervation and metabolism of myofibers, moreover elicits the proliferation/differentiation of satellite cells, thus preventing the denervation atrophy of skeletal muscles in SOD1G93A mice. Overall, this study suggests that a P2X7-targeted and site-specific modulation might be a strategy to interfere with the complex multifactorial and multisystem nature of ALS.
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Affiliation(s)
- Paola Fabbrizio
- Laboratory of Molecular Neurobiology, Department of NeuroscienceIstituto di Ricerche Farmacologiche Mario Negri IRCCSMilanItaly
| | | | | | | | - Cristiana Valle
- IRCCS Fondazione Santa LuciaRomeItaly
- National Research Council, Institute of Translational PharmacologyRomeItaly
| | - Chiara Lanzuolo
- IRCCS Fondazione Santa LuciaRomeItaly
- National Research Council, Institute of Biomedical TechnologiesMilanItaly
| | - Caterina Bendotti
- Laboratory of Molecular Neurobiology, Department of NeuroscienceIstituto di Ricerche Farmacologiche Mario Negri IRCCSMilanItaly
| | - Giovanni Nardo
- Laboratory of Molecular Neurobiology, Department of NeuroscienceIstituto di Ricerche Farmacologiche Mario Negri IRCCSMilanItaly
| | - Cinzia Volonté
- IRCCS Fondazione Santa LuciaRomeItaly
- National Research Council, Institute for Systems Analysis and Computer ScienceRomeItaly
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16
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Bernasconi P, Carboni N, Ricci G, Siciliano G, Politano L, Maggi L, Mongini T, Vercelli L, Rodolico C, Biagini E, Boriani G, Ruggiero L, Santoro L, Schena E, Prencipe S, Evangelisti C, Pegoraro E, Morandi L, Columbaro M, Lanzuolo C, Sabatelli P, Cavalcante P, Cappelletti C, Bonne G, Muchir A, Lattanzi G. Elevated TGF β2 serum levels in Emery-Dreifuss Muscular Dystrophy: Implications for myocyte and tenocyte differentiation and fibrogenic processes. Nucleus 2019; 9:292-304. [PMID: 29693488 PMCID: PMC5973167 DOI: 10.1080/19491034.2018.1467722] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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] [Indexed: 01/05/2023] Open
Abstract
Among rare diseases caused by mutations in LMNA gene, Emery-Dreifuss Muscular Dystrophy type 2 and Limb-Girdle muscular Dystrophy 1B are characterized by muscle weakness and wasting, joint contractures, cardiomyopathy with conduction system disorders. Circulating biomarkers for these pathologies have not been identified. Here, we analyzed the secretome of a cohort of patients affected by these muscular laminopathies in the attempt to identify a common signature. Multiplex cytokine assay showed that transforming growth factor beta 2 (TGF β2) and interleukin 17 serum levels are consistently elevated in the vast majority of examined patients, while interleukin 6 and basic fibroblast growth factor are altered in subgroups of patients. Levels of TGF β2 are also increased in fibroblast and myoblast cultures established from patient biopsies as well as in serum from mice bearing the H222P Lmna mutation causing Emery-Dreifuss Muscular Dystrophy in humans. Both patient serum and fibroblast conditioned media activated a TGF β2-dependent fibrogenic program in normal human myoblasts and tenocytes and inhibited myoblast differentiation. Consistent with these results, a TGF β2 neutralizing antibody avoided fibrogenic marker activation and myogenesis impairment. Cell intrinsic TGF β2-dependent mechanisms were also determined in laminopathic cells, where TGF β2 activated AKT/mTOR phosphorylation. These data show that TGF β2 contributes to the pathogenesis of Emery-Dreifuss Muscular Dystrophy type 2 and Limb-Girdle muscular Dystrophy 1B and can be considered a potential biomarker of those diseases. Further, the evidence of TGF β2 pathogenetic effects in tenocytes provides the first mechanistic insight into occurrence of joint contractures in muscular laminopathies.
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Affiliation(s)
- Pia Bernasconi
- a Neurology IV - Neuroimmunology and Neuromuscular Diseases Unit , Foundation IRCCS Neurological Institute "Carlo Besta" , Milan , Italy
| | - Nicola Carboni
- b Neurology Department , Hospital San Francesco of Nuoro , Nuoro , Italy
| | - Giulia Ricci
- c Department of Clinical and Experimental Medicine , University of Pisa , Pisa , Italy
| | - Gabriele Siciliano
- c Department of Clinical and Experimental Medicine , University of Pisa , Pisa , Italy
| | - Luisa Politano
- d Cardiomyology and Medical Genetics, Department of Experimental Medicine , Campania University "Luigi Vanvitelli" (former denomination: Second University of Naples) , Italy
| | - Lorenzo Maggi
- a Neurology IV - Neuroimmunology and Neuromuscular Diseases Unit , Foundation IRCCS Neurological Institute "Carlo Besta" , Milan , Italy
| | - Tiziana Mongini
- e Department of Neurosciences "Rita Levi Montalcini" , University of Turin , Turin , Italy
| | - Liliana Vercelli
- e Department of Neurosciences "Rita Levi Montalcini" , University of Turin , Turin , Italy
| | - Carmelo Rodolico
- f Institute of Applied Sciences and Intelligent Systems "ISASI Edoardo Caianello", National Research Council of Italy , Messina , Italy
| | - Elena Biagini
- g Istituto di Cardiologia, Università di Bologna, Policlinico S.Orsola-Malpighi , Bologna , Italy
| | - Giuseppe Boriani
- h Cardiology Division, Department of Diagnostics , Clinical and Public Health Medicine, University of Modena and Reggio Emilia, Policlinico di Modena , Modena , Italy
| | - Lucia Ruggiero
- i Department of Neurosciences , Odontostomatological and Reproductive Sciences, University of Naples "Federico II" , Naples , Italy
| | - Lucio Santoro
- i Department of Neurosciences , Odontostomatological and Reproductive Sciences, University of Naples "Federico II" , Naples , Italy
| | - Elisa Schena
- j Institute of Molecular Genetics (IGM)-CNR, Unit of Bologna , Bologna , Italy.,k Laboratory of Musculoskeletal Cell Biology , Rizzoli Orthopaedic Institute , Bologna , Italy
| | - Sabino Prencipe
- j Institute of Molecular Genetics (IGM)-CNR, Unit of Bologna , Bologna , Italy.,k Laboratory of Musculoskeletal Cell Biology , Rizzoli Orthopaedic Institute , Bologna , Italy
| | - Camilla Evangelisti
- j Institute of Molecular Genetics (IGM)-CNR, Unit of Bologna , Bologna , Italy.,k Laboratory of Musculoskeletal Cell Biology , Rizzoli Orthopaedic Institute , Bologna , Italy
| | - Elena Pegoraro
- l Department of Neurosciences , Neuromuscular Center, University of Padova , Padova , Italy
| | - Lucia Morandi
- a Neurology IV - Neuroimmunology and Neuromuscular Diseases Unit , Foundation IRCCS Neurological Institute "Carlo Besta" , Milan , Italy
| | - Marta Columbaro
- k Laboratory of Musculoskeletal Cell Biology , Rizzoli Orthopaedic Institute , Bologna , Italy
| | - Chiara Lanzuolo
- m Istituto Nazionale di Genetica Molecolare "Romeo and Enrica Invernizzi" , Milan , Italy.,n Institute of Cell Biology and Neurobiology, IRCCS Santa Lucia Foundation , Rome , Italy
| | - Patrizia Sabatelli
- j Institute of Molecular Genetics (IGM)-CNR, Unit of Bologna , Bologna , Italy.,k Laboratory of Musculoskeletal Cell Biology , Rizzoli Orthopaedic Institute , Bologna , Italy
| | - Paola Cavalcante
- a Neurology IV - Neuroimmunology and Neuromuscular Diseases Unit , Foundation IRCCS Neurological Institute "Carlo Besta" , Milan , Italy
| | - Cristina Cappelletti
- a Neurology IV - Neuroimmunology and Neuromuscular Diseases Unit , Foundation IRCCS Neurological Institute "Carlo Besta" , Milan , Italy
| | - Gisèle Bonne
- o Sorbonne Universités , UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Institut de Myologie, G.H. Pitié Salpêtrière , Paris Cedex 13, France
| | - Antoine Muchir
- o Sorbonne Universités , UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, Institut de Myologie, G.H. Pitié Salpêtrière , Paris Cedex 13, France
| | - Giovanna Lattanzi
- j Institute of Molecular Genetics (IGM)-CNR, Unit of Bologna , Bologna , Italy.,k Laboratory of Musculoskeletal Cell Biology , Rizzoli Orthopaedic Institute , Bologna , Italy
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Bianchi A, Manti PG, Lucini F, Lanzuolo C. Mechanotransduction, nuclear architecture and epigenetics in Emery Dreifuss Muscular Dystrophy: tous pour un, un pour tous. Nucleus 2019; 9:276-290. [PMID: 29619865 PMCID: PMC5973142 DOI: 10.1080/19491034.2018.1460044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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] [Indexed: 02/07/2023] Open
Abstract
The alteration of the several roles that Lamin A/C plays in the mammalian cell leads to a broad spectrum of pathologies that – all together – are named laminopathies. Among those, the Emery Dreifuss Muscular Dystrophy (EDMD) is of particular interest as, despite the several known mutations of Lamin A/C, the genotype–phenotype correlation still remains poorly understood; this suggests that the epigenetic background of patients might play an important role during the time course of the disease. Historically, both a mechanical role of Lamin A/C and a regulative one have been suggested as the driving force of laminopathies; however, those two hypotheses are not mutually exclusive. Recent scientific evidence shows that Lamin A/C sustains the correct gene expression at the epigenetic level thanks to the Lamina Associated Domains (LADs) reorganization and the crosstalk with the Polycomb Group of Proteins (PcG). Furthermore, the PcG-dependent histone mark H3K27me3 increases under mechanical stress, finally pointing out the link between the mechano-properties of the nuclear lamina and epigenetics. Here, we summarize the emerging mechanisms that could explain the high variability seen in Emery Dreifuss muscular dystrophy.
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Affiliation(s)
- Andrea Bianchi
- a CNR Institute of Cell Biology and Neurobiology, Istituto di Ricovero e Cura a Carattere Scientifico Fondazione Santa Lucia , Rome , Italy.,b Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi , Milan , Italy
| | | | - Federica Lucini
- b Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi , Milan , Italy
| | - Chiara Lanzuolo
- a CNR Institute of Cell Biology and Neurobiology, Istituto di Ricovero e Cura a Carattere Scientifico Fondazione Santa Lucia , Rome , Italy.,b Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi , Milan , Italy.,c Istituto di Ricovero e Cura a Carattere Scientifico Fondazione Santa Lucia , Rome , Italy
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Marullo F, Cesarini E, Antonelli L, Gregoretti F, Oliva G, Lanzuolo C. Nucleoplasmic Lamin A/C and Polycomb group of proteins: An evolutionarily conserved interplay. Nucleus 2016; 7:103-11. [PMID: 26930442 PMCID: PMC4916880 DOI: 10.1080/19491034.2016.1157675] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [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] [Indexed: 11/09/2022] Open
Abstract
Nuclear lamins are the main components of the nuclear lamina at the nuclear periphery, providing mechanical support to the nucleus. However, recent findings suggest that lamins also reside in the nuclear interior, as a distinct and dynamic pool with critical roles in transcriptional regulation. In our work we found a functional and evolutionary conserved crosstalk between Lamin A/C and the Polycomb group (PcG) of proteins, this being required for the maintenance of the PcG repressive functions. Indeed, Lamin A/C knock-down causes PcG foci dispersion and defects in PcG-mediated higher order structures, thereby leading to impaired PcG mediated transcriptional repression. By using ad-hoc algorithms for image analysis and PLA approaches we hereby show that PcG proteins are preferentially located in the nuclear interior where they interact with nucleoplasmic Lamin A/C. Taken together, our findings suggest that nuclear components, such as Lamin A/C, functionally interact with epigenetic factors to ensure the correct transcriptional program maintenance.
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Affiliation(s)
- F Marullo
- a CNR Institute of Cell Biology and Neurobiology, IRCCS Santa Lucia Foundation , Rome , Italy
| | - E Cesarini
- a CNR Institute of Cell Biology and Neurobiology, IRCCS Santa Lucia Foundation , Rome , Italy
| | - L Antonelli
- b CNR Institute for High Performance Computing and Networking (ICAR) , Naples, Italy
| | - F Gregoretti
- b CNR Institute for High Performance Computing and Networking (ICAR) , Naples, Italy
| | - G Oliva
- b CNR Institute for High Performance Computing and Networking (ICAR) , Naples, Italy
| | - C Lanzuolo
- a CNR Institute of Cell Biology and Neurobiology, IRCCS Santa Lucia Foundation , Rome , Italy.,c Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi , Milan , Italy
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Cesarini E, Mozzetta C, Marullo F, Gregoretti F, Gargiulo A, Columbaro M, Cortesi A, Antonelli L, Di Pelino S, Squarzoni S, Palacios D, Zippo A, Bodega B, Oliva G, Lanzuolo C. Lamin A/C sustains PcG protein architecture, maintaining transcriptional repression at target genes. J Cell Biol 2016; 211:533-51. [PMID: 26553927 PMCID: PMC4639869 DOI: 10.1083/jcb.201504035] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [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] [Indexed: 12/31/2022] Open
Abstract
Reduction of lamin A/C, which is evolutionarily required for the modulation of Polycomb group (PcG) protein–dependent transcriptional repression by sustaining PcG protein nuclear architecture, leads to PcG protein diffusion and to muscle differentiation. Beyond its role in providing structure to the nuclear envelope, lamin A/C is involved in transcriptional regulation. However, its cross talk with epigenetic factors—and how this cross talk influences physiological processes—is still unexplored. Key epigenetic regulators of development and differentiation are the Polycomb group (PcG) of proteins, organized in the nucleus as microscopically visible foci. Here, we show that lamin A/C is evolutionarily required for correct PcG protein nuclear compartmentalization. Confocal microscopy supported by new algorithms for image analysis reveals that lamin A/C knock-down leads to PcG protein foci disassembly and PcG protein dispersion. This causes detachment from chromatin and defects in PcG protein–mediated higher-order structures, thereby leading to impaired PcG protein repressive functions. Using myogenic differentiation as a model, we found that reduced levels of lamin A/C at the onset of differentiation led to an anticipation of the myogenic program because of an alteration of PcG protein–mediated transcriptional repression. Collectively, our results indicate that lamin A/C can modulate transcription through the regulation of PcG protein epigenetic factors.
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Affiliation(s)
- Elisa Cesarini
- Consiglio Nazionale delle Ricerche Institute of Cellular Biology and Neurobiology, Istituto di Ricovero e Cura a Carattere Scientifico Fondazione Santa Lucia, 00143 Rome, Italy
| | - Chiara Mozzetta
- Consiglio Nazionale delle Ricerche Institute of Cellular Biology and Neurobiology, Istituto di Ricovero e Cura a Carattere Scientifico Fondazione Santa Lucia, 00143 Rome, Italy
| | - Fabrizia Marullo
- Consiglio Nazionale delle Ricerche Institute of Cellular Biology and Neurobiology, Istituto di Ricovero e Cura a Carattere Scientifico Fondazione Santa Lucia, 00143 Rome, Italy
| | - Francesco Gregoretti
- Consiglio Nazionale delle Ricerche Institute for High Performance Computing and Networking, 80131 Naples, Italy
| | - Annagiusi Gargiulo
- Consiglio Nazionale delle Ricerche Institute of Cellular Biology and Neurobiology, Istituto di Ricovero e Cura a Carattere Scientifico Fondazione Santa Lucia, 00143 Rome, Italy
| | - Marta Columbaro
- Struttura Complessa Laboratorio Biologia Cellulare Muscoloscheletrica, Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Alice Cortesi
- Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy
| | - Laura Antonelli
- Consiglio Nazionale delle Ricerche Institute for High Performance Computing and Networking, 80131 Naples, Italy
| | - Simona Di Pelino
- Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy
| | - Stefano Squarzoni
- Struttura Complessa Laboratorio Biologia Cellulare Muscoloscheletrica, Istituto Ortopedico Rizzoli, 40136 Bologna, Italy Consiglio Nazionale delle Ricerche Institute of Molecular Genetics, 40136 Bologna, Italy
| | - Daniela Palacios
- Istituto di Ricovero e Cura a Carattere Scientifico Fondazione Santa Lucia, 00143 Rome, Italy
| | - Alessio Zippo
- Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy
| | - Beatrice Bodega
- Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy
| | - Gennaro Oliva
- Consiglio Nazionale delle Ricerche Institute for High Performance Computing and Networking, 80131 Naples, Italy
| | - Chiara Lanzuolo
- Consiglio Nazionale delle Ricerche Institute of Cellular Biology and Neurobiology, Istituto di Ricovero e Cura a Carattere Scientifico Fondazione Santa Lucia, 00143 Rome, Italy
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Gregoretti F, Cesarini E, Lanzuolo C, Oliva G, Antonelli L. An Automatic Segmentation Method Combining an Active Contour Model and a Classification Technique for Detecting Polycomb-group Proteinsin High-Throughput Microscopy Images. Methods Mol Biol 2016; 1480:181-197. [PMID: 27659985 DOI: 10.1007/978-1-4939-6380-5_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The large amount of data generated in biological experiments that rely on advanced microscopy can be handled only with automated image analysis. Most analyses require a reliable cell image segmentation eventually capable of detecting subcellular structures.We present an automatic segmentation method to detect Polycomb group (PcG) proteins areas isolated from nuclei regions in high-resolution fluorescent cell image stacks. It combines two segmentation algorithms that use an active contour model and a classification technique serving as a tool to better understand the subcellular three-dimensional distribution of PcG proteins in live cell image sequences. We obtained accurate results throughout several cell image datasets, coming from different cell types and corresponding to different fluorescent labels, without requiring elaborate adjustments to each dataset.
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Affiliation(s)
- Francesco Gregoretti
- Institute for High Performance Computing and Networking, ICAR-CNR, via Pietro Castellino 111, Naples, 80131, Italy
| | - Elisa Cesarini
- Institute of Cellular Biology and Neurobiology, IRCCS Santa Lucia Foundation, via del Fosso di Fiorano 64, Rome, 00143, Italy
| | - Chiara Lanzuolo
- Institute of Cellular Biology and Neurobiology, IRCCS Santa Lucia Foundation, via del Fosso di Fiorano 64, Rome, 00143, Italy
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", via Francesco Sforza 35, Milan, 20122, Italy
| | - Gennaro Oliva
- Institute for High Performance Computing and Networking, ICAR-CNR, via Pietro Castellino 111, Naples, 80131, Italy
| | - Laura Antonelli
- Institute for High Performance Computing and Networking, ICAR-CNR, via Pietro Castellino 111, Naples, 80131, Italy.
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Lanzuolo C. Impairment of Lamin A/C-Polycomb crosstalk as a possible epigenetic cause of Emery Dreifuss Muscular Dystrophy (EDMD). Orphanet J Rare Dis 2015. [PMCID: PMC4652450 DOI: 10.1186/1750-1172-10-s2-o10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Lo Sardo F, Lanzuolo C, Comoglio F, De Bardi M, Paro R, Orlando V. PcG-mediated higher-order chromatin structures modulate replication programs at the Drosophila BX-C. PLoS Genet 2013; 9:e1003283. [PMID: 23437006 PMCID: PMC3578750 DOI: 10.1371/journal.pgen.1003283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [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: 05/03/2012] [Accepted: 12/14/2012] [Indexed: 12/03/2022] Open
Abstract
Polycomb group proteins (PcG) exert conserved epigenetic functions that convey maintenance of repressed transcriptional states, via post-translational histone modifications and high order structure formation. During S-phase, in order to preserve cell identity, in addition to DNA information, PcG-chromatin-mediated epigenetic signatures need to be duplicated requiring a tight coordination between PcG proteins and replication programs. However, the interconnection between replication timing control and PcG functions remains unknown. Using Drosophila embryonic cell lines, we find that, while presence of specific PcG complexes and underlying transcription state are not the sole determinants of cellular replication timing, PcG-mediated higher-order structures appear to dictate the timing of replication and maintenance of the silenced state. Using published datasets we show that PRC1, PRC2, and PhoRC complexes differently correlate with replication timing of their targets. In the fully repressed BX-C, loss of function experiments revealed a synergistic role for PcG proteins in the maintenance of replication programs through the mediation of higher-order structures. Accordingly, replication timing analysis performed on two Drosophila cell lines differing for BX-C gene expression states, PcG distribution, and chromatin domain conformation revealed a cell-type-specific replication program that mirrors lineage-specific BX-C higher-order structures. Our work suggests that PcG complexes, by regulating higher-order chromatin structure at their target sites, contribute to the definition and the maintenance of genomic structural domains where genes showing the same epigenetic state replicate at the same time. DNA replication is a tightly orchestrated process that precisely duplicates the entire genome during cell division to ensure that daughter cells inherit the same genetic information. The genome is replicated following a specific temporal program, where different segments replicate in distinct moments of the S phase correlating with active (early) and repressed (late) transcriptional state of resident genes. Moreover, replicating chromosomal domains are organized in the nuclear space, perhaps to guarantee the conservation of the same topological order in daughter cells. Epigenetic mechanisms, acting via chromatin organization, determine transcriptional states and must be maintained through cell division. Here, we analyzed in detail the link between Polycomb Group (PcG) proteins, higher-order chromatin structure, and replication timing in Drosophila. By using bioinformatic analyses combined with functional experiments, we show that Polycomb Repressive Complex 1 (PRC1), PRC2, and PhoRC differently correlate with replication timing of their targets and that transcription per se does not determine replication timing. Strikingly, by analyzing the PcG-regulated Bithorax Complex, where PRC1, PRC2, and PhoRC complexes are bound to repressed targets, we provide evidence for a synergistic role of PcG proteins in the modulation and maintenance of replication timing through the definition of specific, topologically distinct genomic domains.
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Affiliation(s)
- Federica Lo Sardo
- Dulbecco Telethon Institute, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Chiara Lanzuolo
- Dulbecco Telethon Institute, IRCCS Santa Lucia Foundation, Rome, Italy
- CNR Institute of Cellular Biology and Neurobiology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Federico Comoglio
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology Zürich, Basel, Switzerland
| | - Marco De Bardi
- Neuroimmunology Unit, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Renato Paro
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology Zürich, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Valerio Orlando
- Dulbecco Telethon Institute, IRCCS Santa Lucia Foundation, Rome, Italy
- Neuroimmunology Unit, IRCCS Santa Lucia Foundation, Rome, Italy
- * E-mail:
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24
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Abstract
The first genes composing the Polycomb group (PcG) were identified 50 years ago in Drosophila melanogaster as essential developmental functions that regulate the correct segmental expression of homeotic selector genes. In the past two decades, what was initially described as a large family of chromatin-associated proteins involved in the maintenance of transcriptional repression to maintain cellular memory of homeotic genes turned out to be a highly conserved and sophisticated network of epigenetic regulators that play key roles in multiple aspects of cell physiology and identity, including regulation of all developmental genes, cell differentiation, stem and somatic cell reprogramming and response to environmental stimuli. These myriad phenotypes further spread interest for the contribution that PcG proteins revealed in the pathogenesis and progression of cancer and other complex diseases. Recent novel insights have increasingly clarified the molecular regulatory mechanisms at the basis of PcG-mediated epigenetic silencing and opened new visions about PcG functions in cells. In this review, we focus on the multiple modes of action of the PcG complexes and describe their biological roles.
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Affiliation(s)
- Chiara Lanzuolo
- Dulbecco Telethon Institute, Epigenetics and Genome Reprogramming, IRCCS Santa Lucia Foundation, 00143 Rome, Italy
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25
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Abstract
Epigenetic mechanisms, acting via chromatin organization, fix in time and space different transcriptional programs and contribute to the quality, stability, and heritability of cell-specific transcription programs. In the last years, great advances have been made in our understanding of mechanisms by which this occurs in normal subjects. However, only a small part of the complete picture has been revealed. Abnormal gene expression patterns are often implicated in the development of different diseases, and thus epigenetic studies from patients promise to fill an important lack of knowledge, deciphering aberrant molecular mechanisms at the basis of pathogenesis and diseases progression. The identification of epigenetic modifications that could be used as targets for therapeutic interventions could be particularly timely in the light of pharmacologically reversion of pathological perturbations, avoiding changes in DNA sequences. Here I discuss the available information on epigenetic mechanisms that, altered in neuromuscular disorders, could contribute to the progression of the disease.
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Affiliation(s)
- Chiara Lanzuolo
- CNR Institute of Cellular Biology and Neurobiology, IRCCS Santa Lucia Foundation, Via Del Fosso di Fiorano 64, 00143 Rome, Italy
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26
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Abstract
Polycomb group of proteins (PcG), by controlling gene silencing transcriptional programs through cell cycle, lock cell identity and memory. Recent chromatin genome-wide studies indicate that PcG targets sites are bivalent domains with overlapping repressive H3K27me3 and active H3K4me3 mark domains. During S phase, the stability of epigenetic signatures is challenged by the replication fork passage. Hence, specific mechanisms of epigenetic inheritance might be provided to preserve epigenome structures. Recently, we have identified a critical time window before replication, during which high levels of PcG binding and histone marks on BX-C PRE target sites set the stage for subsequent dilution of epigenomic components, allowing proper transmission of epigenetic signatures to the next generation. Here, we extended this analysis to promoter elements, showing the same mechanism of inheritance. Furthermore, to gain insight into the inheritance of PREs bivalent marks, we analyzed dynamics of H3K4me3 deposition, a mark that correlates with transcriptionally active chromatin. Likewise, we found an early S-phase enrichment of H3K4me3 mark preceding the replication-dependent dilution. This evidence suggests that all epigenetic marks are inherited simultaneously to ensure their correct propagation through replication and to protect the “bivalency” of PREs.
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Affiliation(s)
- Chiara Lanzuolo
- Dulbecco Telethon Institute at IRCCS Santa Lucia Foundation, Epigenetics and Genome Reprogramming, Rome, Italy.
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De Zio D, Bordi M, Tino E, Lanzuolo C, Ferraro E, Mora E, Ciccosanti F, Fimia GM, Orlando V, Cecconi F. The DNA repair complex Ku70/86 modulates Apaf1 expression upon DNA damage. Cell Death Differ 2010; 18:516-27. [PMID: 20966962 DOI: 10.1038/cdd.2010.125] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Apaf1 is a key regulator of the mitochondrial intrinsic pathway of apoptosis, as it activates executioner caspases by forming the apoptotic machinery apoptosome. Its genetic regulation and its post-translational modification are crucial under the various conditions where apoptosis occurs. Here we describe Ku70/86, a mediator of non-homologous end-joining pathway of DNA repair, as a novel regulator of Apaf1 transcription. Through analysing different Apaf1 promoter mutants, we identified an element repressing the Apaf1 promoter. We demonstrated that Ku70/86 is a nuclear factor able to bind this repressing element and downregulating Apaf1 transcription. We also found that Ku70/86 interaction with Apaf1 promoter is dynamically modulated upon DNA damage. The effect of this binding is a downregulation of Apaf1 expression immediately following the damage to DNA; conversely, we observed Apaf1 upregulation and apoptosis activation when Ku70/86 unleashes the Apaf1-repressing element. Therefore, besides regulating DNA repair, our results suggest that Ku70/86 binds to the Apaf1 promoter and represses its activity. This may help to inhibit the apoptosome pathway of cell death and contribute to regulate cell survival.
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Affiliation(s)
- D De Zio
- Department of Biology, Dulbecco Telethon Institute, University of Rome Tor Vergata, 00133 Rome, Italy
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Lanzuolo C, Roure V, Dekker J, Bantignies F, Orlando V. Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex. Nat Cell Biol 2007; 9:1167-74. [PMID: 17828248 DOI: 10.1038/ncb1637] [Citation(s) in RCA: 227] [Impact Index Per Article: 13.4] [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: 03/12/2007] [Accepted: 07/26/2007] [Indexed: 12/12/2022]
Abstract
In Drosophila, the function of the Polycomb group genes (PcGs) and their target sequences (Polycomb response elements (PREs)) is to convey mitotic heritability of transcription programmes--in particular, gene silencing. As part of the mechanisms involved, PREs are thought to mediate this transcriptional memory function by building up higher-order structures in the nucleus. To address this question, we analysed in vivo the three-dimensional structure of the homeotic locus bithorax complex (BX-C) by combining chromosome conformation capture (3C) with fluorescent in situ hybridization (FISH) and FISH immunostaining (FISH-I) analysis. We found that, in the repressed state, all major elements that have been shown to bind PcG proteins, including PREs and core promoters, interact at a distance, giving rise to a topologically complex structure. We show that this structure is important for epigenetic silencing of the BX-C, as we find that major changes in higher-order structures must occur to stably maintain alternative transcription states, whereas histone modification and reduced levels of PcG proteins determine an epigenetic switch that is only partially heritable.
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Affiliation(s)
- Chiara Lanzuolo
- Dulbecco Telethon Institute at IGB CNR, Epigenetics and Genome Reprogramming, Via Pietro Castellino 111, 80131 Naples, Italy
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Abstract
During cell differentiation or metabolic switch, cells undergo profound changes in gene expression. These events are accompanied by complex modifications of chromosomal components and nuclear structures, including covalent modifications of DNA and chromatin up to topological reorganization of chromosomes and genes in the nucleus. To various extents, all these levels of organization appear to contribute to the stability and heritability of transcription programmes and define what is meant as the epigenomic level of gene regulation. Indeed, damage or perturbation of epigenome components may lead to deviations from a determined cellular programme, resulting in severe developmental disorders and tumour progression. Most recent data also suggest that tissue regeneration and transdifferentiation are controlled by epigenetic functions. Thus, the epigenome provides the molecular basis for the preservation and also for the plasticity of cell identity.
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Affiliation(s)
- C Lanzuolo
- Dulbecco Telethon Institute at Institute of Genetics and Biophysics CNR, Via Pietro Castellino 111, 80131 Naples, Italy
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Florio C, Moscariello M, Ederle S, Fasano R, Lanzuolo C, Pulitzer JF. A study of biochemical and functional interactions of Htl1p, a putative component of the Saccharomyces cerevisiae, Rsc chromatin-remodeling complex. Gene 2007; 395:72-85. [PMID: 17400406 DOI: 10.1016/j.gene.2007.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2006] [Revised: 01/23/2007] [Accepted: 02/05/2007] [Indexed: 12/14/2022]
Abstract
HTL1, a small gene of Saccharomyces cerevisiae, encodes a 78-aminoacid peptide that influences the performance of a wide range of cellular processes [Lanzuolo, C., Ederle, S., Pollice, A., Russo, F., Storlazzi, A., Pulitzer, J.F., 2001. The HTL1 gene,YCR020W-b of Saccharomyces cerevisiae is necessary for growth at 37 degrees C, and for the conservation of chromosome stability and fertility. Yeast, 18, 1317-1330]. Genetic interactions and co-immunoprecipitation experiments indicate a role for Htl1p in functions controlled by RSC, a multiprotein, ATP-dependent, chromatin-remodeling complex [Lu, Y.M., Lin, Y.R., Tsai, A., Hsao, Y.S., Li, C.C., Cheng, M.Y., 2003. Dissecting the pet18 mutation in Saccharomyces cerevisiae: HTL1 encodes a 7-kDa polypeptide that interacts with components of the RSC complex. Mol. Genet. Genomics., 269, 321-330] [Romeo, M.J., Angus-Hill, M.L., Sobering, A.K., Kamada, Y., Cairns, B.R., Levin, D.E., 2002. HTL1 encodes a novel factor that interacts with the Rsc chromatin-remodeling complex in Saccharomyces cerevisiae. Mol. Cell. Biol., 22, 8165-8174]. Htl1p and RSC components, share the property of associating with TBP a component of general multiprotein transcription factor TFIID [Sanders, S.L., Jennings, J., Canutescu, A., Link, A.J., Weil, P.A., 2002. Proteomics of the eukaryotic transcription machinery: identification of proteins associated with components of yeast TFIID by multidimensional mass spectrometry. Mol. Cell. Biol. 22, 4723-4738]. We confirm, by integrating genetic and biochemical experiments, that Htl1p binding to the RSC complex is direct and physiologically relevant and show that it is mediated by Rsc8p, a core component of the RSC complex. Deletion of HTL1, like depletion of RSC core subunits [Moreira, J.M., Holmberg, S., 1999. Transcriptional repression of the yeast CHA1 gene requires the chromatin-remodeling complex Rsc. Embo J., 18, 2836-2844], leads to constitutive transcription of the CHA1 locus. This transcriptional phenotype exhibits variable penetrance. Deletion of HTL1 also leads to hydroxyurea hypersensitivity at 30 degrees C, suggesting a defect in replication/repair. This defect leads, during cell growth, to selection of mutations at the SIR3 locus that suppress hydroxyurea sensitivity.
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Affiliation(s)
- Carolina Florio
- Università degli Studi di Napoli Federico II, Dipartimento di Biologia, Via Cinthia-80126-Naples, Italy
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Eugster A, Lanzuolo C, Bonneton M, Luciano P, Pollice A, Pulitzer JF, Stegberg E, Berthiau AS, Förstemann K, Corda Y, Lingner J, Géli V, Gilson E. The finger subdomain of yeast telomerase cooperates with Pif1p to limit telomere elongation. Nat Struct Mol Biol 2006; 13:734-9. [PMID: 16878131 DOI: 10.1038/nsmb1126] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2006] [Accepted: 07/05/2006] [Indexed: 11/09/2022]
Abstract
Telomere synthesis depends on telomerase, which contains an RNA subunit linked to a specialized reverse transcriptase subunit and several associated proteins. Here we report the characterization of four mutations in the yeast reverse transcriptase subunit Est2p that cause an overelongation of telomeres and an increase in the association of Est1p with telomeres during S phase. These 'up-mutations' are clustered in the finger subdomain of the reverse transcriptase. We show that the catalytic properties of the up-mutant telomerases are not improved in vitro. In vivo, the up-mutations neither bypass the activation step governed by Cdc13p nor do they uncouple telomerase from the Rap1p inhibition pathway. In the presence of the up-mutations, however, the ability of the Pif1p helicase to decrease telomere length and to inhibit the association of Est1p with telomeres is impaired. In addition, Pif1p associates in vivo with the telomerase RNA (TLC1) in a way that depends on the finger subdomain. We propose that, in addition to its catalytic role, the finger subdomain of Est2p facilitates the action of Pif1p at telomeres.
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Affiliation(s)
- Anne Eugster
- Laboratoire de Biologie Moléculaire et Cellulaire, UMR5161, IFR128, Centre National de la Recherche Scientifique, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
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Lanzuolo C, Ederle S, Pollice A, Russo F, Storlazzi A, Pulitzer JF. The HTL1 gene (YCR020W-b) of Saccharomyces cerevisiae is necessary for growth at 37 degrees C, and for the conservation of chromosome stability and fertility. Yeast 2001; 18:1317-30. [PMID: 11571756 DOI: 10.1002/yea.778] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A small 78 codon ORF, named HTL1 (Chen et al., unpublished results), situated between loci MAK31 and HSP30 on chromosome III of Saccharomyces cerevisiae, is required for growth at 37 degrees C. In this communication, we characterize the ORF and show that disruption of HTL1, besides preventing growth at 37 degrees C, causes genetic and/or epigenetic instability at 26 degrees C: ploidy increases in about 10% of cells grown from individual disruptants and a fraction of disruptant clones are predestined to a rapid and progressive loss of fertility during growth at 26 degrees C.
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Affiliation(s)
- C Lanzuolo
- Università degli Studi di Napoli Federico II, Dipartimento di Genetica, Biologia Generale e Molecolare, via Mezzocannone 8, 80134, Napoli, Italy
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