1
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Cecalev D, Viçoso B, Galupa R. Compensation of gene dosage on the mammalian X. Development 2024; 151:dev202891. [PMID: 39140247 PMCID: PMC11361640 DOI: 10.1242/dev.202891] [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] [Indexed: 08/15/2024]
Abstract
Changes in gene dosage can have tremendous evolutionary potential (e.g. whole-genome duplications), but without compensatory mechanisms, they can also lead to gene dysregulation and pathologies. Sex chromosomes are a paradigmatic example of naturally occurring gene dosage differences and their compensation. In species with chromosome-based sex determination, individuals within the same population necessarily show 'natural' differences in gene dosage for the sex chromosomes. In this Review, we focus on the mammalian X chromosome and discuss recent new insights into the dosage-compensation mechanisms that evolved along with the emergence of sex chromosomes, namely X-inactivation and X-upregulation. We also discuss the evolution of the genetic loci and molecular players involved, as well as the regulatory diversity and potentially different requirements for dosage compensation across mammalian species.
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Affiliation(s)
- Daniela Cecalev
- Molecular, Cellular and Developmental Biology (MCD) Unit, Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062, Toulouse, France
| | - Beatriz Viçoso
- Institute of Science and Technology Austria (ISTA), Am Campus 1, Klosterneuburg 3400, Austria
| | - Rafael Galupa
- Molecular, Cellular and Developmental Biology (MCD) Unit, Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062, Toulouse, France
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2
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Dror I, Tan T, Plath K. A critical role for X-chromosome architecture in mammalian X-chromosome dosage compensation. Curr Opin Genet Dev 2024; 87:102235. [PMID: 39053028 DOI: 10.1016/j.gde.2024.102235] [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: 04/20/2024] [Revised: 07/02/2024] [Accepted: 07/05/2024] [Indexed: 07/27/2024]
Abstract
To regulate gene expression, the macromolecular components of the mammalian interphase nucleus are spatially organized into a myriad of functional compartments. Over the past decade, increasingly sophisticated genomics, microscopy, and functional approaches have probed this organization in unprecedented detail. These investigations have linked chromatin-associated noncoding RNAs to specific nuclear compartments and uncovered mechanisms by which these RNAs establish such domains. In this review, we focus on the long non-coding RNA Xist and summarize new evidence demonstrating the significance of chromatin reconfiguration in creating the inactive X-chromosome compartment. Differences in chromatin compaction correlate with distinct levels of gene repression on the X-chromosome, potentially explaining how human XIST can induce chromosome-wide dampening and silencing of gene expression at different stages of human development.
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Affiliation(s)
- Iris Dror
- Department of Biological Chemistry, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Tiao Tan
- Department of Biological Chemistry, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, Jonsson Comprehensive Cancer Center, Brain Research Institute, Graduate Program in the Biosciences, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA.
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3
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Martitz A, Schulz EG. Spatial orchestration of the genome: topological reorganisation during X-chromosome inactivation. Curr Opin Genet Dev 2024; 86:102198. [PMID: 38663040 DOI: 10.1016/j.gde.2024.102198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/21/2024] [Accepted: 04/05/2024] [Indexed: 06/11/2024]
Abstract
Genomes are organised through hierarchical structures, ranging from local kilobase-scale cis-regulatory contacts to large chromosome territories. Most notably, (sub)-compartments partition chromosomes according to transcriptional activity, while topologically associating domains (TADs) define cis-regulatory landscapes. The inactive X chromosome in mammals has provided unique insights into the regulation and function of the three-dimensional (3D) genome. Concurrent with silencing of the majority of genes and major alterations of its chromatin state, the X chromosome undergoes profound spatial rearrangements at multiple scales. These include the emergence of megadomains, alterations of the compartment structure and loss of the majority of TADs. Moreover, the Xist locus, which orchestrates X-chromosome inactivation, has provided key insights into regulation and function of regulatory domains. This review provides an overview of recent insights into the control of these structural rearrangements and contextualises them within a broader understanding of 3D genome organisation.
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Affiliation(s)
- Alexandra Martitz
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Edda G Schulz
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
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4
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Gillis A, Berry S. Global control of RNA polymerase II. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195024. [PMID: 38552781 DOI: 10.1016/j.bbagrm.2024.195024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
RNA polymerase II (Pol II) is the multi-protein complex responsible for transcribing all protein-coding messenger RNA (mRNA). Most research on gene regulation is focused on the mechanisms controlling which genes are transcribed when, or on the mechanics of transcription. How global Pol II activity is determined receives comparatively less attention. Here, we follow the life of a Pol II molecule from 'assembly of the complex' to nuclear import, enzymatic activity, and degradation. We focus on how Pol II spends its time in the nucleus, and on the two-way relationship between Pol II abundance and activity in the context of homeostasis and global transcriptional changes.
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Affiliation(s)
- Alexander Gillis
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, Australia; UNSW RNA Institute, University of New South Wales, Sydney, Australia; Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Scott Berry
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, Australia; UNSW RNA Institute, University of New South Wales, Sydney, Australia; Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
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5
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Hayward-Lara G, Fischer MD, Mir M. Dynamic microenvironments shape nuclear organization and gene expression. Curr Opin Genet Dev 2024; 86:102177. [PMID: 38461773 PMCID: PMC11162947 DOI: 10.1016/j.gde.2024.102177] [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: 12/05/2023] [Revised: 02/11/2024] [Accepted: 02/14/2024] [Indexed: 03/12/2024]
Abstract
Live imaging has revealed that the regulation of gene expression is largely driven by transient interactions. For example, many regulatory proteins bind chromatin for just seconds, and loop-like genomic contacts are rare and last only minutes. These discoveries have been difficult to reconcile with our canonical models that are predicated on stable and hierarchical interactions. Proteomic microenvironments that concentrate nuclear factors may explain how brief interactions can still mediate gene regulation by creating conditions where reactions occur more frequently. Here, we summarize new imaging technologies and recent discoveries implicating microenvironments as a potential driver of nuclear function. Finally, we propose that key properties of proteomic microenvironments, such as their size, enrichment, and lifetimes, are directly linked to regulatory function.
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Affiliation(s)
- Gabriela Hayward-Lara
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania. Philadelphia, PA 19104
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia. Philadelphia, PA 19104
- Developmental, Stem Cell, and Regenerative Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania. Philadelphia, PA 19104
| | - Matthew D. Fischer
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania. Philadelphia, PA 19104
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia. Philadelphia, PA 19104
| | - Mustafa Mir
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania. Philadelphia, PA 19104
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia. Philadelphia, PA 19104
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania. Philadelphia, PA 19104
- Howard Hughes Medical Institute, Children’s Hospital of Philadelphia. Philadelphia, PA 19104
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6
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Zacco E, Broglia L, Kurihara M, Monti M, Gustincich S, Pastore A, Plath K, Nagakawa S, Cerase A, Sanchez de Groot N, Tartaglia GG. RNA: The Unsuspected Conductor in the Orchestra of Macromolecular Crowding. Chem Rev 2024; 124:4734-4777. [PMID: 38579177 PMCID: PMC11046439 DOI: 10.1021/acs.chemrev.3c00575] [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: 08/14/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 04/07/2024]
Abstract
This comprehensive Review delves into the chemical principles governing RNA-mediated crowding events, commonly referred to as granules or biological condensates. We explore the pivotal role played by RNA sequence, structure, and chemical modifications in these processes, uncovering their correlation with crowding phenomena under physiological conditions. Additionally, we investigate instances where crowding deviates from its intended function, leading to pathological consequences. By deepening our understanding of the delicate balance that governs molecular crowding driven by RNA and its implications for cellular homeostasis, we aim to shed light on this intriguing area of research. Our exploration extends to the methodologies employed to decipher the composition and structural intricacies of RNA granules, offering a comprehensive overview of the techniques used to characterize them, including relevant computational approaches. Through two detailed examples highlighting the significance of noncoding RNAs, NEAT1 and XIST, in the formation of phase-separated assemblies and their influence on the cellular landscape, we emphasize their crucial role in cellular organization and function. By elucidating the chemical underpinnings of RNA-mediated molecular crowding, investigating the role of modifications, structures, and composition of RNA granules, and exploring both physiological and aberrant phase separation phenomena, this Review provides a multifaceted understanding of the intriguing world of RNA-mediated biological condensates.
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Affiliation(s)
- Elsa Zacco
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Laura Broglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Misuzu Kurihara
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Michele Monti
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Stefano Gustincich
- Central
RNA Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Annalisa Pastore
- UK
Dementia Research Institute at the Maurice Wohl Institute of King’s
College London, London SE5 9RT, U.K.
| | - Kathrin Plath
- Department
of Biological Chemistry, David Geffen School
of Medicine at the University of California Los Angeles, Los Angeles, California 90095, United States
| | - Shinichi Nagakawa
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Andrea Cerase
- Blizard
Institute,
Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, U.K.
- Unit
of Cell and developmental Biology, Department of Biology, Università di Pisa, 56123 Pisa, Italy
| | - Natalia Sanchez de Groot
- Unitat
de Bioquímica, Departament de Bioquímica i Biologia
Molecular, Universitat Autònoma de
Barcelona, 08193 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
- Catalan
Institution for Research and Advanced Studies, ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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7
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Lin Z, Li D, Zheng J, Yao C, Liu D, Zhang H, Feng H, Chen C, Li P, Zhang Y, Jiang B, Hu Z, Zhao Y, Shi F, Cao D, Rodriguez-Wallberg KA, Li Z, Yeung WSB, Chow LT, Wang H, Liu K. The male pachynema-specific protein MAPS drives phase separation in vitro and regulates sex body formation and chromatin behaviors in vivo. Cell Rep 2024; 43:113651. [PMID: 38175751 DOI: 10.1016/j.celrep.2023.113651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 08/12/2023] [Accepted: 12/19/2023] [Indexed: 01/06/2024] Open
Abstract
Dynamic chromosome remodeling and nuclear compartmentalization take place during mammalian meiotic prophase I. We report here that the crucial roles of male pachynema-specific protein (MAPS) in pachynema progression might be mediated by its liquid-liquid phase separation in vitro and in cellulo. MAPS forms distinguishable liquid phases, and deletion or mutations of its N-terminal amino acids (aa) 2-9 disrupt its secondary structure and charge properties, impeding phase separation. Maps-/- pachytene spermatocytes exhibit defects in nucleus compartmentalization, including defects in forming sex bodies, altered nucleosome composition, and disordered chromatin accessibility. MapsΔ2-9/Δ2-9 male mice expressing MAPS protein lacking aa 2-9 phenocopy Maps-/- mice. Moreover, a frameshift mutation in C3orf62, the human counterpart of Maps, is correlated with nonobstructive azoospermia in a patient exhibiting pachynema arrest in spermatocyte development. Hence, the phase separation property of MAPS seems essential for pachynema progression in mouse and human spermatocytes.
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Affiliation(s)
- Zexiong Lin
- Department of Obstetrics and Gynecology, Li Ka Shing Faculty of Medicine; Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong-Shenzhen Hospital, The University of Hong Kong, Hong Kong, China
| | - Dongliang Li
- Department of Obstetrics and Gynecology, Li Ka Shing Faculty of Medicine; Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong-Shenzhen Hospital, The University of Hong Kong, Hong Kong, China
| | - Jiahuan Zheng
- Department of Obstetrics and Gynecology, Li Ka Shing Faculty of Medicine; Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong-Shenzhen Hospital, The University of Hong Kong, Hong Kong, China
| | - Chencheng Yao
- Department of Andrology, Center for Men's Health, Department of ART, Institute of Urology, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Dongteng Liu
- Department of Obstetrics and Gynecology, Li Ka Shing Faculty of Medicine; Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong-Shenzhen Hospital, The University of Hong Kong, Hong Kong, China
| | - Hao Zhang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Haiwei Feng
- Department of Obstetrics and Gynecology, Li Ka Shing Faculty of Medicine; Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong-Shenzhen Hospital, The University of Hong Kong, Hong Kong, China
| | - Chunxu Chen
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA; Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Massey Cancer Institute, Virginia Commonwealth University, Richmond, VA, USA
| | - Peng Li
- Department of Andrology, Center for Men's Health, Department of ART, Institute of Urology, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Yuxiang Zhang
- Department of Andrology, Center for Men's Health, Department of ART, Institute of Urology, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Binjie Jiang
- Department of Obstetrics and Gynecology, Li Ka Shing Faculty of Medicine; Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong-Shenzhen Hospital, The University of Hong Kong, Hong Kong, China
| | - Zhe Hu
- Department of Obstetrics and Gynecology, Li Ka Shing Faculty of Medicine; Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong-Shenzhen Hospital, The University of Hong Kong, Hong Kong, China
| | - Yu Zhao
- Department of Obstetrics and Gynecology, Li Ka Shing Faculty of Medicine; Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong-Shenzhen Hospital, The University of Hong Kong, Hong Kong, China
| | - Fu Shi
- Department of Obstetrics and Gynecology, Li Ka Shing Faculty of Medicine; Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong-Shenzhen Hospital, The University of Hong Kong, Hong Kong, China
| | - Dandan Cao
- Department of Obstetrics and Gynecology, Li Ka Shing Faculty of Medicine; Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong-Shenzhen Hospital, The University of Hong Kong, Hong Kong, China
| | | | - Zheng Li
- Department of Andrology, Center for Men's Health, Department of ART, Institute of Urology, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - William S B Yeung
- Department of Obstetrics and Gynecology, Li Ka Shing Faculty of Medicine; Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong-Shenzhen Hospital, The University of Hong Kong, Hong Kong, China
| | - Louise T Chow
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Hengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA; Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Massey Cancer Institute, Virginia Commonwealth University, Richmond, VA, USA.
| | - Kui Liu
- Department of Obstetrics and Gynecology, Li Ka Shing Faculty of Medicine; Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong-Shenzhen Hospital, The University of Hong Kong, Hong Kong, China.
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8
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Pinto-Pinho P, Soares J, Esteves P, Pinto-Leite R, Fardilha M, Colaço B. Comparative Bioinformatic Analysis of the Proteomes of Rabbit and Human Sex Chromosomes. Animals (Basel) 2024; 14:217. [PMID: 38254386 PMCID: PMC10812427 DOI: 10.3390/ani14020217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/18/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
Studying proteins associated with sex chromosomes can provide insights into sex-specific proteins. Membrane proteins accessible through the cell surface may serve as excellent targets for diagnostic, therapeutic, or even technological purposes, such as sperm sexing technologies. In this context, proteins encoded by sex chromosomes have the potential to become targets for X- or Y-chromosome-bearing spermatozoa. Due to the limited availability of proteomic studies on rabbit spermatozoa and poorly annotated databases for rabbits compared to humans, a bioinformatic analysis of the available rabbit X chromosome proteome (RX), as well as the human X (HX) and Y (HY) chromosomes proteome, was conducted to identify potential targets that could be accessible from the cell surface and predict which of the potential targets identified in humans might also exist in rabbits. We identified 100, 211, and 3 proteins associated with the plasma membrane or cell surface for RX, HX, and HY, respectively, of which 61, 132, and 3 proteins exhibit potential as targets as they were predicted to be accessible from the cell surface. Cross-referencing the potential HX targets with the rabbit proteome revealed an additional 60 proteins with the potential to be RX targets, resulting in a total of 121 potential RX targets. In addition, at least 53 possible common HX and RX targets have been previously identified in human spermatozoa, emphasizing their potential as targets of X-chromosome-bearing spermatozoa. Further proteomic studies on rabbit sperm will be essential to identify and validate the usefulness of these proteins for application in rabbit sperm sorting techniques as targets of X-chromosome-bearing spermatozoa.
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Affiliation(s)
- Patrícia Pinto-Pinho
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal;
- Laboratory of Signal Transduction, Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal;
- Laboratory of Genetics and Andrology, Hospital Center of Trás-os-Montes and Alto Douro, E.P.E., 5000-508 Vila Real, Portugal;
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center, Portuguese Institute of Oncology of Porto Francisco Gentil, E.P.E., 4200-072 Porto, Portugal
| | - João Soares
- Department of Computer Science, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal; (J.S.); (P.E.)
- Center for Research in Advanced Computing Systems, Institute for Systems and Computer Engineering, Technology and Science (CRACS—INESC TEC), 4150-179 Porto, Portugal
| | - Pedro Esteves
- Department of Computer Science, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal; (J.S.); (P.E.)
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
- CIBIO—Research Centre in Biodiversity and Genetic Resources, InBIO Associate Laboratory, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Research Centre in Biodiversity and Genetic Resources, 4485-661 Vairão, Portugal
| | - Rosário Pinto-Leite
- Laboratory of Genetics and Andrology, Hospital Center of Trás-os-Montes and Alto Douro, E.P.E., 5000-508 Vila Real, Portugal;
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center, Portuguese Institute of Oncology of Porto Francisco Gentil, E.P.E., 4200-072 Porto, Portugal
| | - Margarida Fardilha
- Laboratory of Signal Transduction, Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Bruno Colaço
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal;
- Animal and Veterinary Research Centre, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal
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9
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Sofi S, Coverley D. CIZ1 in Xist seeded assemblies at the inactive X chromosome. Front Cell Dev Biol 2023; 11:1296600. [PMID: 38155839 PMCID: PMC10753822 DOI: 10.3389/fcell.2023.1296600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/04/2023] [Indexed: 12/30/2023] Open
Abstract
There is growing evidence that X-chromosome inactivation is driven by phase-separated supramolecular assemblies. However, among the many proteins recruited to the inactive X chromosome by Xist long non-coding RNA, so far only a minority (CIZ1, CELF1, SPEN, TDP-43, MATR3, PTBP1, PCGF5) have been shown to form Xist-seeded protein assemblies, and of these most have not been analyzed in detail. With focus on CIZ1, here we describe 1) the contribution of intrinsically disordered regions in RNA-dependent protein assembly formation at the inactive X chromosome, and 2) enrichment, distribution, and function of proteins within Xist-seeded assemblies.
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Affiliation(s)
- Sajad Sofi
- Department of Biology, University of York, York, United Kingdom
| | - Dawn Coverley
- Department of Biology, University of York, York, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom
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10
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Weinmann R, Frank L, Rippe K. Approaches to characterize chromatin subcompartment organization in the cell nucleus. Curr Opin Struct Biol 2023; 83:102695. [PMID: 37722292 DOI: 10.1016/j.sbi.2023.102695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/05/2023] [Accepted: 08/07/2023] [Indexed: 09/20/2023]
Abstract
The mechanism of self-organization of chromatin subcompartments on the 0.1-1 μm scale and their impact on genome-associated activities has long been a key aspect of research on nuclear organization. Understanding the underlying structure-function relationship, however, remains challenging due to the complex hierarchical structure of chromatin and the polymorphic organization of subcompartments that assemble around it. Towards this goal, approaches to measure local properties and compositional dynamics of chromatin in its endogenous cellular environment are instrumental. Here, we discuss recent advancements in studying these features and their functional implications in protein and RNA enrichment and genome accessibility.
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Affiliation(s)
- Robin Weinmann
- German Cancer Research Center (DKFZ) Heidelberg, Division of Chromatin Networks, Germany; Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, Germany; Faculty of Biosciences, Heidelberg University, Germany
| | - Lukas Frank
- German Cancer Research Center (DKFZ) Heidelberg, Division of Chromatin Networks, Germany; Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, Germany
| | - Karsten Rippe
- German Cancer Research Center (DKFZ) Heidelberg, Division of Chromatin Networks, Germany; Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, Germany.
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11
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Peeters SB, Posynick BJ, Brown CJ. Out of the Silence: Insights into How Genes Escape X-Chromosome Inactivation. EPIGENOMES 2023; 7:29. [PMID: 38131901 PMCID: PMC10742877 DOI: 10.3390/epigenomes7040029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023] Open
Abstract
The silencing of all but one X chromosome in mammalian cells is a remarkable epigenetic process leading to near dosage equivalence in X-linked gene products between the sexes. However, equally remarkable is the ability of a subset of genes to continue to be expressed from the otherwise inactive X chromosome-in some cases constitutively, while other genes are variable between individuals, tissues or cells. In this review we discuss the advantages and disadvantages of the approaches that have been used to identify escapees. The identity of escapees provides important clues to mechanisms underlying escape from XCI, an arena of study now moving from correlation to functional studies. As most escapees show greater expression in females, the not-so-inactive X chromosome is a substantial contributor to sex differences in humans, and we highlight some examples of such impact.
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Affiliation(s)
| | | | - Carolyn J. Brown
- Molecular Epigenetics Group, Department of Medical Genetics, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
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12
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Moyano Rodriguez Y, Borensztein M. X-chromosome inactivation: a historic topic that's still hot. Development 2023; 150:dev202072. [PMID: 37997921 DOI: 10.1242/dev.202072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
The last edition of the X-chromosome inactivation (XCI) meeting was held as an EMBO workshop in Berlin on 19-22 June 2023. The conference took place at the Harnack-haus in the Dahlem district, birthplace of the first modern research campus, where notable scientists such as Lise Meitner, Hans Krebs and, briefly, Albert Einstein conducted their research. This special edition, also accessible online, was organized by Rafael Galupa (Centre for Integrative Biology of Toulouse, France), Joost Gribnau (Erasmus MC Rotterdam, The Netherlands), Claire Rougeulle (Université Paris Cité/CNRS, Epigenetics and Cell Fate Center, Paris, France), Edda Schulz (Max Planck Institute for Molecular Genetics, Berlin, Germany) and James Turner (The Francis Crick Institute, London, UK). Originally scheduled for 2021, to commemorate the 60th anniversary of Mary Lyon's hypothesis on X-chromosome inactivation in mammals and the 30th anniversary of XIST/Xist discovery, the meeting had to be postponed because of the COVID-19 pandemic. Seven years after the latest XCI meeting in London, the enthusiasm and expectations of the community were at their highest, bringing together over 160 scientists from around the world to share and discuss their research. Eighty posters and more than 40 talks were presented at this event, in a collegial and collaborative atmosphere. A historical session and several breakout discussions were also organized, as well as the now traditional boat trip, all thanks to great organization. Here, we debrief readers on this fantastic conference.
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Affiliation(s)
| | - Maud Borensztein
- IGMM, University of Montpellier, CNRS, 34090 Montpellier, France
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Keniry A, Blewitt ME. Chromatin-mediated silencing on the inactive X chromosome. Development 2023; 150:dev201742. [PMID: 37991053 DOI: 10.1242/dev.201742] [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] [Indexed: 11/23/2023]
Abstract
In mammals, the second X chromosome in females is silenced to enable dosage compensation between XX females and XY males. This essential process involves the formation of a dense chromatin state on the inactive X (Xi) chromosome. There is a wealth of information about the hallmarks of Xi chromatin and the contribution each makes to silencing, leaving the tantalising possibility of learning from this knowledge to potentially remove silencing to treat X-linked diseases in females. Here, we discuss the role of each chromatin feature in the establishment and maintenance of the silent state, which is of crucial relevance for such a goal.
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Affiliation(s)
- Andrew Keniry
- Epigenetics and Development Division, The Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Marnie E Blewitt
- Epigenetics and Development Division, The Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
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Zimmer F, Basilicata MF, Keller Valsecchi CI. Transcription and replication meet the silent X chromosome territory. Nat Struct Mol Biol 2023; 30:1054-1056. [PMID: 37563441 DOI: 10.1038/s41594-023-01054-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Affiliation(s)
- Frederic Zimmer
- Institute of Molecular Biology (IMB), Mainz, Germany
- DFG-Research Training Group 2526 'GenEvo', Mainz, Germany
| | - M Felicia Basilicata
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
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Dossin F, Heard E. The Molecular and Nuclear Dynamics of X-Chromosome Inactivation. Cold Spring Harb Perspect Biol 2022; 14:a040196. [PMID: 34312245 PMCID: PMC9121902 DOI: 10.1101/cshperspect.a040196] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In female eutherian mammals, dosage compensation of X-linked gene expression is achieved during development through transcriptional silencing of one of the two X chromosomes. Following X chromosome inactivation (XCI), the inactive X chromosome remains faithfully silenced throughout somatic cell divisions. XCI is dependent on Xist, a long noncoding RNA that coats and silences the X chromosome from which it is transcribed. Xist coating triggers a cascade of chromosome-wide changes occurring at the levels of transcription, chromatin composition, chromosome structure, and spatial organization within the nucleus. XCI has emerged as a paradigm for the study of such crucial nuclear processes and the dissection of their functional interplay. In the past decade, the advent of tools to characterize and perturb these processes have provided an unprecedented understanding into their roles during XCI. The mechanisms orchestrating the initiation of XCI as well as its maintenance are thus being unraveled, although many questions still remain. Here, we introduce key aspects of the XCI process and review the recent discoveries about its molecular basis.
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Affiliation(s)
- François Dossin
- European Molecular Biology Laboratory, Director's Unit, 69117 Heidelberg, Germany
| | - Edith Heard
- European Molecular Biology Laboratory, Director's Unit, 69117 Heidelberg, Germany
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