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Bussey-Sutton CR, Ward A, Fox JA, Turner AMW, Peterson JJ, Emery A, Longoria AR, Gomez-Martinez I, Jones C, Hepperla A, Margolis DM, Strahl BD, Browne EP. The histone methyltransferase SETD2 regulates HIV expression and latency. PLoS Pathog 2024; 20:e1012281. [PMID: 38848441 PMCID: PMC11189200 DOI: 10.1371/journal.ppat.1012281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 06/20/2024] [Accepted: 05/22/2024] [Indexed: 06/09/2024] Open
Abstract
Understanding the mechanisms that drive HIV expression and latency is a key goal for achieving an HIV cure. Here we investigate the role of the SETD2 histone methyltransferase, which deposits H3K36 trimethylation (H3K36me3), in HIV infection. We show that prevention of H3K36me3 by a potent and selective inhibitor of SETD2 (EPZ-719) leads to reduced post-integration viral gene expression and accelerated emergence of latently infected cells. CRISPR/Cas9-mediated knockout of SETD2 in primary CD4 T cells confirmed the role of SETD2 in HIV expression. Transcriptomic profiling of EPZ-719-exposed HIV-infected cells identified numerous pathways impacted by EPZ-719. Notably, depletion of H3K36me3 prior to infection did not prevent HIV integration but resulted in a shift of integration sites from highly transcribed genes to quiescent chromatin regions and to polycomb repressed regions. We also observed that SETD2 inhibition did not apparently affect HIV RNA levels, indicating a post-transcriptional mechanism affecting HIV expression. Viral RNA splicing was modestly reduced in the presence of EPZ-719. Intriguingly, EPZ-719 exposure enhanced responsiveness of latent HIV to the HDAC inhibitor vorinostat, suggesting that H3K36me3 can contribute to a repressive chromatin state at the HIV locus. These results identify SETD2 and H3K36me3 as novel regulators of HIV integration, expression and latency.
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Affiliation(s)
- Cameron R. Bussey-Sutton
- Department of Biochemistry, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Airlie Ward
- Department of Medicine, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- UNC HIV Cure Center, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Joshua A. Fox
- Department of Medicine, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- UNC HIV Cure Center, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Anne-Marie W. Turner
- Department of Medicine, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- UNC HIV Cure Center, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jackson J. Peterson
- UNC HIV Cure Center, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ann Emery
- Lineberger Comprehensive Cancer Center, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Arturo R. Longoria
- Department of Medicine, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- UNC HIV Cure Center, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ismael Gomez-Martinez
- Department of Genetics, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Corbin Jones
- Department of Genetics, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Austin Hepperla
- Department of Genetics, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - David M. Margolis
- Department of Medicine, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- UNC HIV Cure Center, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Brian D. Strahl
- Department of Biochemistry, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Edward P. Browne
- Department of Medicine, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- UNC HIV Cure Center, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, UNC Chapel Hill, Chapel Hill, North Carolina, United States of America
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2
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Zocher S, McCloskey A, Karasinsky A, Schulte R, Friedrich U, Lesche M, Rund N, Gage FH, Hetzer MW, Toda T. Lifelong persistence of nuclear RNAs in the mouse brain. Science 2024; 384:53-59. [PMID: 38574132 PMCID: PMC7615865 DOI: 10.1126/science.adf3481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 02/02/2024] [Indexed: 04/06/2024]
Abstract
Genomic DNA that resides in the nuclei of mammalian neurons can be as old as the organism itself. The life span of nuclear RNAs, which are critical for proper chromatin architecture and transcription regulation, has not been determined in adult tissues. In this work, we identified and characterized nuclear RNAs that do not turn over for at least 2 years in a subset of postnatally born cells in the mouse brain. These long-lived RNAs were stably retained in nuclei in a neural cell type-specific manner and were required for the maintenance of heterochromatin. Thus, the life span of neural cells may depend on both the molecular longevity of DNA for the storage of genetic information and also the extreme stability of RNA for the functional organization of chromatin.
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Affiliation(s)
- Sara Zocher
- Nuclear Architecture in Neural Plasticity and Aging, German Center for Neurodegenerative Diseases (DZNE), Dresden 01307, Germany
| | - Asako McCloskey
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
- Kura Oncology, Inc., 5510 Morehouse Dr., San Diego, CA 92121, USA
| | - Anne Karasinsky
- Nuclear Architecture in Neural Plasticity and Aging, German Center for Neurodegenerative Diseases (DZNE), Dresden 01307, Germany
| | - Roberta Schulte
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ulrike Friedrich
- DRESDEN-concept Genome Center, Technology Platform at the Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Fetscherstr. 105, Dresden 01307, Germany
- German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany
- Paul Langerhans Institute Dresden of the Helmholtz Center Munich, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Mathias Lesche
- DRESDEN-concept Genome Center, Technology Platform at the Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Fetscherstr. 105, Dresden 01307, Germany
| | - Nicole Rund
- Nuclear Architecture in Neural Plasticity and Aging, German Center for Neurodegenerative Diseases (DZNE), Dresden 01307, Germany
| | - Fred H. Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Martin W. Hetzer
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
| | - Tomohisa Toda
- Nuclear Architecture in Neural Plasticity and Aging, German Center for Neurodegenerative Diseases (DZNE), Dresden 01307, Germany
- Laboratory of Neural Epigenomics, Institute of Medical Physics and Micro-tissue Engineering, Faculty of Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
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3
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Michelatti D, Beyes S, Bernardis C, Negri ML, Morelli L, Bediaga NG, Poli V, Fagnocchi L, Lago S, D'Annunzio S, Cona N, Gaspardo I, Bianchi A, Jovetic J, Gianesello M, Turdo A, D'Accardo C, Gaggianesi M, Dori M, Forcato M, Crispatzu G, Rada-Iglesias A, Sosa MS, Timmers HTM, Bicciato S, Todaro M, Tiberi L, Zippo A. Oncogenic enhancers prime quiescent metastatic cells to escape NK immune surveillance by eliciting transcriptional memory. Nat Commun 2024; 15:2198. [PMID: 38503727 PMCID: PMC10951355 DOI: 10.1038/s41467-024-46524-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/29/2024] [Indexed: 03/21/2024] Open
Abstract
Metastasis arises from disseminated tumour cells (DTCs) that are characterized by intrinsic phenotypic plasticity and the capability of seeding to secondary organs. DTCs can remain latent for years before giving rise to symptomatic overt metastasis. In this context, DTCs fluctuate between a quiescent and proliferative state in response to systemic and microenvironmental signals including immune-mediated surveillance. Despite its relevance, how intrinsic mechanisms sustain DTCs plasticity has not been addressed. By interrogating the epigenetic state of metastatic cells, we find that tumour progression is coupled with the activation of oncogenic enhancers that are organized in variable interconnected chromatin domains. This spatial chromatin context leads to the activation of a robust transcriptional response upon repeated exposure to retinoic acid (RA). We show that this adaptive mechanism sustains the quiescence of DTCs through the activation of the master regulator SOX9. Finally, we determine that RA-stimulated transcriptional memory increases the fitness of metastatic cells by supporting the escape of quiescent DTCs from NK-mediated immune surveillance. Overall, these findings highlight the contribution of oncogenic enhancers in establishing transcriptional memories as an adaptive mechanism to reinforce cancer dormancy and immune escape, thus amenable for therapeutic intervention.
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Affiliation(s)
- Daniela Michelatti
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Sven Beyes
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Chiara Bernardis
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Maria Luce Negri
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Leonardo Morelli
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Naiara Garcia Bediaga
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
- The South Australian Immunogenomics Cancer Institute, Faculty of Medicine Nursing and Medical Sciences, The University of Adelaide, Adelaide, Australia
| | - Vittoria Poli
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
- Istituto Italiano di Tecnologia IIT, Milan, Italy
| | - Luca Fagnocchi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
- Department of Epigenetics Van Andel Institute, Grand Rapids, MI, USA
| | - Sara Lago
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Sarah D'Annunzio
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Nicole Cona
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Ilaria Gaspardo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Aurora Bianchi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Jovana Jovetic
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Matteo Gianesello
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Alice Turdo
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy
| | - Caterina D'Accardo
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy
| | - Miriam Gaggianesi
- Department of Surgical, Oncological and Stomatological Sciences (DICHIRONS), University of Palermo, Palermo, Italy
| | - Martina Dori
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Mattia Forcato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Giuliano Crispatzu
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Alvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Santander, Spain
| | - Maria Soledad Sosa
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - H T Marc Timmers
- Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Matilde Todaro
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy
| | - Luca Tiberi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Alessio Zippo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy.
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4
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Fourneaux C, Racine L, Koering C, Dussurgey S, Vallin E, Moussy A, Parmentier R, Brunard F, Stockholm D, Modolo L, Picard F, Gandrillon O, Paldi A, Gonin-Giraud S. Differentiation is accompanied by a progressive loss in transcriptional memory. BMC Biol 2024; 22:58. [PMID: 38468285 DOI: 10.1186/s12915-024-01846-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 02/13/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND Cell differentiation requires the integration of two opposite processes, a stabilizing cellular memory, especially at the transcriptional scale, and a burst of gene expression variability which follows the differentiation induction. Therefore, the actual capacity of a cell to undergo phenotypic change during a differentiation process relies upon a modification in this balance which favors change-inducing gene expression variability. However, there are no experimental data providing insight on how fast the transcriptomes of identical cells would diverge on the scale of the very first two cell divisions during the differentiation process. RESULTS In order to quantitatively address this question, we developed different experimental methods to recover the transcriptomes of related cells, after one and two divisions, while preserving the information about their lineage at the scale of a single cell division. We analyzed the transcriptomes of related cells from two differentiation biological systems (human CD34+ cells and T2EC chicken primary erythrocytic progenitors) using two different single-cell transcriptomics technologies (scRT-qPCR and scRNA-seq). CONCLUSIONS We identified that the gene transcription profiles of differentiating sister cells are more similar to each other than to those of non-related cells of the same type, sharing the same environment and undergoing similar biological processes. More importantly, we observed greater discrepancies between differentiating sister cells than between self-renewing sister cells. Furthermore, a progressive increase in this divergence from first generation to second generation was observed when comparing differentiating cousin cells to self renewing cousin cells. Our results are in favor of a gradual erasure of transcriptional memory during the differentiation process.
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Affiliation(s)
- Camille Fourneaux
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - Laëtitia Racine
- Ecole Pratique des Hautes Etudes, PSL Research University, Sorbonne Université, INSERM, CRSA, Paris, 75012, France
| | - Catherine Koering
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - Sébastien Dussurgey
- Plateforme AniRA-Cytométrie, Université Claude Bernard Lyon 1, CNRS UAR3444, Inserm US8, ENS de Lyon, SFR Biosciences, Lyon, F-69007, France
| | - Elodie Vallin
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - Alice Moussy
- Ecole Pratique des Hautes Etudes, PSL Research University, Sorbonne Université, INSERM, CRSA, Paris, 75012, France
| | - Romuald Parmentier
- Ecole Pratique des Hautes Etudes, PSL Research University, Sorbonne Université, INSERM, CRSA, Paris, 75012, France
| | - Fanny Brunard
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - Daniel Stockholm
- Ecole Pratique des Hautes Etudes, PSL Research University, Sorbonne Université, INSERM, CRSA, Paris, 75012, France
| | - Laurent Modolo
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - Franck Picard
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - Olivier Gandrillon
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard Lyon 1, Lyon, France
- Inria Center, Grenoble Rhone-Alpes, Equipe Dracula, Villeurbanne, F69100, France
| | - Andras Paldi
- Ecole Pratique des Hautes Etudes, PSL Research University, Sorbonne Université, INSERM, CRSA, Paris, 75012, France
| | - Sandrine Gonin-Giraud
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard Lyon 1, Lyon, France.
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5
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Chen ZS, Ou M, Taylor S, Dafinca R, Peng SI, Talbot K, Chan HYE. Mutant GGGGCC RNA prevents YY1 from binding to Fuzzy promoter which stimulates Wnt/β-catenin pathway in C9ALS/FTD. Nat Commun 2023; 14:8420. [PMID: 38110419 PMCID: PMC10728118 DOI: 10.1038/s41467-023-44215-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/05/2023] [Indexed: 12/20/2023] Open
Abstract
The GGGGCC hexanucleotide repeat expansion mutation in the chromosome 9 open reading frame 72 (C9orf72) gene is a major genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia (C9ALS/FTD). In this study, we demonstrate that the zinc finger (ZF) transcriptional regulator Yin Yang 1 (YY1) binds to the promoter region of the planar cell polarity gene Fuzzy to regulate its transcription. We show that YY1 interacts with GGGGCC repeat RNA via its ZF and that this interaction compromises the binding of YY1 to the FuzzyYY1 promoter sites, resulting in the downregulation of Fuzzy transcription. The decrease in Fuzzy protein expression in turn activates the canonical Wnt/β-catenin pathway and induces synaptic deficits in C9ALS/FTD neurons. Our findings demonstrate a C9orf72 GGGGCC RNA-initiated perturbation of YY1-Fuzzy transcriptional control that implicates aberrant Wnt/β-catenin signalling in C9ALS/FTD-associated neurodegeneration. This pathogenic cascade provides a potential new target for disease-modifying therapy.
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Affiliation(s)
- Zhefan Stephen Chen
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
- Oxford Motor Neuron Disease Centre, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Mingxi Ou
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Stephanie Taylor
- Oxford Motor Neuron Disease Centre, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Ruxandra Dafinca
- Oxford Motor Neuron Disease Centre, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK
| | - Shaohong Isaac Peng
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Kevin Talbot
- Oxford Motor Neuron Disease Centre, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK.
| | - Ho Yin Edwin Chan
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.
- Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.
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6
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Croci O, Campaner S. ChroKit: a Shiny-based framework for interactive analysis, visualization and integration of genomic data. Nucleic Acids Res 2023:7152871. [PMID: 37144464 DOI: 10.1093/nar/gkad345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/06/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023] Open
Abstract
We developed ChroKit (the Chromatin toolKit), an interactive web-based framework written in R that enables intuitive exploration, multidimensional analyses, and visualization of genomic data from ChIP-Seq, DNAse-Seq or any other NGS experiment that reports the enrichment of aligned reads over genomic regions. This program takes preprocessed NGS data and performs operations on genomic regions of interest, including resetting their boundaries, their annotation based on proximity to genomic features, the association to gene ontologies, and signal enrichment calculations. Genomic regions can be further refined or subsetted by user-defined logical operations and unsupervised classification algorithms. ChroKit generates a full range of plots that are easily manipulated by point and click operations, thus allowing 'on the fly' re-analysis and fast exploration of the data. Working sessions can be exported for reproducibility, accountability, and easy sharing within the bioinformatics community. ChroKit is multiplatform and can be deployed on a server to enhance computational speed and provide simultaneous access by multiple users. ChroKit is a fast and intuitive genomic analysis tool suited for a wide range of users due to its architecture and its user-friendly graphical interface. ChroKit source code is available at https://github.com/ocroci/ChroKit and the Docker image at https://hub.docker.com/r/ocroci/chrokit.
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Affiliation(s)
- Ottavio Croci
- Center for Genomic Science of CGS@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan20139, Italy
| | - Stefano Campaner
- Center for Genomic Science of CGS@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan20139, Italy
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7
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Zhu Y, Saribas AS, Liu J, Lin Y, Bodnar B, Zhao R, Guo Q, Ting J, Wei Z, Ellis A, Li F, Wang X, Yang X, Wang H, Ho WZ, Yang L, Hu W. Protein expression/secretion boost by a novel unique 21-mer cis-regulatory motif (Exin21) via mRNA stabilization. Mol Ther 2023; 31:1136-1158. [PMID: 36793212 PMCID: PMC9927791 DOI: 10.1016/j.ymthe.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 10/24/2022] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Boosting protein production is invaluable in both industrial and academic applications. We discovered a novel expression-increasing 21-mer cis-regulatory motif (Exin21) that inserts between SARS-CoV-2 envelope (E) protein-encoding sequence and luciferase reporter gene. This unique Exin21 (CAACCGCGGTTCGCGGCCGCT), encoding a heptapeptide (QPRFAAA, designated as Qα), significantly (34-fold on average) boosted E production. Both synonymous and nonsynonymous mutations within Exin21 diminished its boosting capability, indicating the exclusive composition and order of 21 nucleotides. Further investigations demonstrated that Exin21/Qα addition could boost the production of multiple SARS-CoV-2 structural proteins (S, M, and N) and accessory proteins (NSP2, NSP16, and ORF3), and host cellular gene products such as IL-2, IFN-γ, ACE2, and NIBP. Exin21/Qα enhanced the packaging yield of S-containing pseudoviruses and standard lentivirus. Exin21/Qα addition on the heavy and light chains of human anti-SARS-CoV monoclonal antibody robustly increased antibody production. The extent of such boosting varied with protein types, cellular density/function, transfection efficiency, reporter dosage, secretion signaling, and 2A-mediated auto-cleaving efficiency. Mechanistically, Exin21/Qα increased mRNA synthesis/stability, and facilitated protein expression and secretion. These findings indicate that Exin21/Qα has the potential to be used as a universal booster for protein production, which is of importance for biomedicine research and development of bioproducts, drugs, and vaccines.
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Affiliation(s)
- Yuanjun Zhu
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - A. Sami Saribas
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Jinbiao Liu
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Yuan Lin
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Brittany Bodnar
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Ruotong Zhao
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Qian Guo
- Department of Medical Genetics & Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Julia Ting
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Zhengyu Wei
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Aidan Ellis
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Fang Li
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Xu Wang
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Xiaofeng Yang
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Hong Wang
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Wen-Zhe Ho
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Ling Yang
- Department of Medical Genetics & Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Wenhui Hu
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA; Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA.
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Chen H, Good MC. Nascent transcriptome reveals orchestration of zygotic genome activation in early embryogenesis. Curr Biol 2022; 32:4314-4324.e7. [PMID: 36007528 PMCID: PMC9560990 DOI: 10.1016/j.cub.2022.07.078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/25/2022] [Accepted: 07/29/2022] [Indexed: 12/14/2022]
Abstract
Early embryo development requires maternal-to-zygotic transition, during which transcriptionally silent nuclei begin widespread gene expression during zygotic genome activation (ZGA).1-3 ZGA is vital for early cell fating and germ-layer specification,3,4 and ZGA timing is regulated by multiple mechanisms.1-5 However, controversies remain about whether these mechanisms are interrelated and vary among species6-10 and whether the timing of germ-layer-specific gene activation is temporally ordered.11,12 In some embryonic models, widespread ZGA onset is spatiotemporally graded,13,14 yet it is unclear whether the transcriptome follows this pattern. A major challenge in addressing these questions is to accurately measure the timing of each gene activation. Here, we metabolically label and identify the nascent transcriptome using 5-ethynyl uridine (5-EU) in Xenopus blastula embryos. We find that EU-RNA-seq outperforms total RNA-seq in detecting the ZGA transcriptome, which is dominated by transcription from maternal-zygotic genes, enabling improved ZGA timing determination. We uncover discrete spatiotemporal patterns for individual gene activation, a majority following a spatial pattern of ZGA that is correlated with a cell size gradient.14 We further reveal that transcription necessitates a period of developmental progression and that ZGA can be precociously induced by cycloheximide, potentially through elongation of interphase. Finally, most ectodermal genes are activated earlier than endodermal genes, suggesting a temporal orchestration of germ-layer-specific genes, potentially linked to the spatially graded pattern of ZGA. Together, our study provides fundamental new insights into the composition and dynamics of the ZGA transcriptome, mechanisms regulating ZGA timing, and its role in the onset of early cell fating.
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Affiliation(s)
- Hui Chen
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew C Good
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Abstract
Virtually all cell types have the same DNA, yet each type exhibits its own cell-specific pattern of gene expression. During the brief period of mitosis, the chromosomes exhibit changes in protein composition and modifications, a marked condensation, and a consequent reduction in transcription. Yet as cells exit mitosis, they reactivate their cell-specific programs with high fidelity. Initially, the field focused on the subset of transcription factors that are selectively retained in, and hence bookmark, chromatin in mitosis. However, recent studies show that many transcription factors can be retained in mitotic chromatin and that, surprisingly, such retention can be due to nonspecific chromatin binding. Here, we review the latest studies focusing on low-level transcription via promoters, rather than enhancers, as contributing to mitotic memory, as well as new insights into chromosome structure dynamics, histone modifications, cell cycle signaling, and nuclear envelope proteins that together ensure the fidelity of gene expression through a round of mitosis.
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Affiliation(s)
- Kenji Ito
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
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Soares MAF, Oliveira RA, Castro DS. Function and regulation of transcription factors during mitosis-to-G1 transition. Open Biol 2022; 12:220062. [PMID: 35642493 PMCID: PMC9157305 DOI: 10.1098/rsob.220062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
During cell division, drastic cellular changes characteristic of mitosis result in the inactivation of the transcriptional machinery, and global downregulation of transcription. Sequence-specific transcription factors (TFs) have thus been considered mere bystanders, devoid of any regulatory function during mitosis. This view changed significantly in recent years, upon the conclusion that many TFs associate with condensed chromosomes during cell division, even occupying a fraction of their genomic target sites in mitotic chromatin. This finding was at the origin of the concept of mitotic bookmarking by TFs, proposed as a mechanism to propagate gene regulatory information across cell divisions, by facilitating the reactivation of specific bookmarked genes. While the underlying mechanisms and biological significance of this model remain elusive, recent developments in this fast-moving field have cast new light into TF activity during mitosis, beyond a bookmarking role. Here, we start by reviewing the most recent findings on the complex nature of TF-chromatin interactions during mitosis, and on mechanisms that may regulate them. Next, and in light of recent reports describing how transcription is reinitiated in temporally distinct waves during mitosis-to-G1 transition, we explore how TFs may contribute to defining this hierarchical gene expression process. Finally, we discuss how TF activity during mitotic exit may impact the acquisition of cell identity upon cell division, and propose a model that integrates dynamic changes in TF-chromatin interactions during this cell-cycle period, with the execution of cell-fate decisions.
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Affiliation(s)
- Mário A. F. Soares
- i3S Instituto de Investigação e Inovação em Saúde, IBMC Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | | | - Diogo S. Castro
- i3S Instituto de Investigação e Inovação em Saúde, IBMC Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
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