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Luchsinger-Morcelle SJ, Gribnau J, Mira-Bontenbal H. Orchestrating Asymmetric Expression: Mechanisms behind Xist Regulation. Epigenomes 2024; 8:6. [PMID: 38390897 PMCID: PMC10885031 DOI: 10.3390/epigenomes8010006] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
Compensation for the gene dosage disequilibrium between sex chromosomes in mammals is achieved in female cells by repressing one of its X chromosomes through a process called X chromosome inactivation (XCI), exemplifying the control of gene expression by epigenetic mechanisms. A critical player in this mechanism is Xist, a long, non-coding RNA upregulated from a single X chromosome during early embryonic development in female cells. Over the past few decades, many factors involved at different levels in the regulation of Xist have been discovered. In this review, we hierarchically describe and analyze the different layers of Xist regulation operating concurrently and intricately interacting with each other to achieve asymmetric and monoallelic upregulation of Xist in murine female cells. We categorize these into five different classes: DNA elements, transcription factors, other regulatory proteins, long non-coding RNAs, and the chromatin and topological landscape surrounding Xist.
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Affiliation(s)
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Hegias Mira-Bontenbal
- Department of Developmental Biology, Erasmus MC, University Medical Center, 3015 GD Rotterdam, The Netherlands
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Malzl D, Peycheva M, Rahjouei A, Gnan S, Klein KN, Nazarova M, Schoeberl UE, Gilbert DM, Buonomo SCB, Di Virgilio M, Neumann T, Pavri R. RIF1 regulates early replication timing in murine B cells. Nat Commun 2023; 14:8049. [PMID: 38081811 PMCID: PMC10713614 DOI: 10.1038/s41467-023-43778-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
The mammalian DNA replication timing (RT) program is crucial for the proper functioning and integrity of the genome. The best-known mechanism for controlling RT is the suppression of late origins of replication in heterochromatin by RIF1. Here, we report that in antigen-activated, hypermutating murine B lymphocytes, RIF1 binds predominantly to early-replicating active chromatin and promotes early replication, but plays a minor role in regulating replication origin activity, gene expression and genome organization in B cells. Furthermore, we find that RIF1 functions in a complementary and non-epistatic manner with minichromosome maintenance (MCM) proteins to establish early RT signatures genome-wide and, specifically, to ensure the early replication of highly transcribed genes. These findings reveal additional layers of regulation within the B cell RT program, driven by the coordinated activity of RIF1 and MCM proteins.
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Affiliation(s)
- Daniel Malzl
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Lazarettgasse 14, Vienna, Austria
| | - Mihaela Peycheva
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Lazarettgasse 14, Vienna, Austria
| | - Ali Rahjouei
- Max-Delbruck Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Stefano Gnan
- School of Biological Sciences, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Kyle N Klein
- San Diego Biomedical Research Institute, San Diego, CA, 92121, USA
| | - Mariia Nazarova
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria
| | - Ursula E Schoeberl
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria
| | - David M Gilbert
- San Diego Biomedical Research Institute, San Diego, CA, 92121, USA
| | - Sara C B Buonomo
- School of Biological Sciences, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Michela Di Virgilio
- Max-Delbruck Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria.
- Quantro Therapeutics, Vienna Biocenter, 1030, Vienna, Austria.
| | - Rushad Pavri
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria.
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Schwämmle T, Schulz EG. Regulatory principles and mechanisms governing the onset of random X-chromosome inactivation. Curr Opin Genet Dev 2023; 81:102063. [PMID: 37356341 PMCID: PMC10465972 DOI: 10.1016/j.gde.2023.102063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/27/2023]
Abstract
X-chromosome inactivation (XCI) has evolved in mammals to compensate for the difference in X-chromosomal dosage between the sexes. In placental mammals, XCI is initiated during early embryonic development through upregulation of the long noncoding RNA Xist from one randomly chosen X chromosome in each female cell. The Xist locus must thus integrate both X-linked and developmental trans-regulatory factors in a dosage-dependent manner. Furthermore, the two alleles must coordinate to ensure inactivation of exactly one X chromosome per cell. In this review, we summarize the regulatory principles that govern the onset of XCI. We go on to provide an overview over the factors that have been implicated in Xist regulation and discuss recent advances in our understanding of how Xist's cis-regulatory landscape integrates information in a precise fashion.
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Affiliation(s)
- Till Schwämmle
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany. https://twitter.com/@TSchwammle
| | - Edda G Schulz
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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Abstract
Early in development, placental and marsupial mammals harbouring at least two X chromosomes per nucleus are faced with a choice that affects the rest of their lives: which of those X chromosomes to transcriptionally inactivate. This choice underlies phenotypical diversity in the composition of tissues and organs and in their response to the environment, and can determine whether an individual will be healthy or affected by an X-linked disease. Here, we review our current understanding of the process of choice during X-chromosome inactivation and its implications, focusing on the strategies evolved by different mammalian lineages and on the known and unknown molecular mechanisms and players involved.
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Gjaltema RAF, Schwämmle T, Kautz P, Robson M, Schöpflin R, Ravid Lustig L, Brandenburg L, Dunkel I, Vechiatto C, Ntini E, Mutzel V, Schmiedel V, Marsico A, Mundlos S, Schulz EG. Distal and proximal cis-regulatory elements sense X chromosome dosage and developmental state at the Xist locus. Mol Cell 2022; 82:190-208.e17. [PMID: 34932975 DOI: 10.1016/j.molcel.2021.11.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/15/2022]
Abstract
Developmental genes such as Xist, which initiates X chromosome inactivation, are controlled by complex cis-regulatory landscapes, which decode multiple signals to establish specific spatiotemporal expression patterns. Xist integrates information on X chromosome dosage and developmental stage to trigger X inactivation in the epiblast specifically in female embryos. Through a pooled CRISPR screen in differentiating mouse embryonic stem cells, we identify functional enhancer elements of Xist at the onset of random X inactivation. Chromatin profiling reveals that X-dosage controls the promoter-proximal region, while differentiation cues activate several distal enhancers. The strongest distal element lies in an enhancer cluster associated with a previously unannotated Xist-enhancing regulatory transcript, which we named Xert. Developmental cues and X-dosage are thus decoded by distinct regulatory regions, which cooperate to ensure female-specific Xist upregulation at the correct developmental time. With this study, we start to disentangle how multiple, functionally distinct regulatory elements interact to generate complex expression patterns in mammals.
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Affiliation(s)
- Rutger A F Gjaltema
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Till Schwämmle
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Pauline Kautz
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Michael Robson
- Development and Disease Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh EH4 2XU, Edinburgh, UK
| | - Robert Schöpflin
- Development and Disease Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Liat Ravid Lustig
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Lennart Brandenburg
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Ilona Dunkel
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Carolina Vechiatto
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Evgenia Ntini
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Verena Mutzel
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Vera Schmiedel
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Annalisa Marsico
- Computational Health Center, Helmholtz Center München, 85764 Neuherberg, Germany
| | - Stefan Mundlos
- Development and Disease Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Edda G Schulz
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
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