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Wei C, Kesner B, Yin H, Lee JT. Imprinted X chromosome inactivation at the gamete-to-embryo transition. Mol Cell 2024; 84:1442-1459.e7. [PMID: 38458200 PMCID: PMC11031340 DOI: 10.1016/j.molcel.2024.02.013] [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: 07/22/2023] [Revised: 12/23/2023] [Accepted: 02/13/2024] [Indexed: 03/10/2024]
Abstract
In mammals, dosage compensation involves two parallel processes: (1) X inactivation, which equalizes X chromosome dosage between males and females, and (2) X hyperactivation, which upregulates the active X for X-autosome balance. The field currently favors models whereby dosage compensation initiates "de novo" during mouse development. Here, we develop "So-Smart-seq" to revisit the question and interrogate a comprehensive transcriptome including noncoding genes and repeats in mice. Intriguingly, de novo silencing pertains only to a subset of Xp genes. Evolutionarily older genes and repetitive elements demonstrate constitutive Xp silencing, adopt distinct signatures, and do not require Xist to initiate silencing. We trace Xp silencing backward in developmental time to meiotic sex chromosome inactivation in the male germ line and observe that Xm hyperactivation is timed to Xp silencing on a gene-by-gene basis. Thus, during the gamete-to-embryo transition, older Xp genes are transmitted in a "pre-inactivated" state. These findings have implications for the evolution of imprinting.
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Affiliation(s)
- Chunyao Wei
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Barry Kesner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Hao Yin
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA.
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2
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Casanova M, Moscatelli M, Chauvière LÉ, Huret C, Samson J, Liyakat Ali TM, Rosspopoff O, Rougeulle C. A primate-specific retroviral enhancer wires the XACT lncRNA into the core pluripotency network in humans. Nat Commun 2019; 10:5652. [PMID: 31827084 PMCID: PMC6906429 DOI: 10.1038/s41467-019-13551-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/05/2019] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) have been proposed to play an important role in driving the expansion of gene regulatory networks during mammalian evolution, notably by contributing to the evolution and function of long non-coding RNAs (lncRNAs). XACT is a primate-specific TE-derived lncRNA that coats active X chromosomes in pluripotent cells and may contribute to species-specific regulation of X-chromosome inactivation. Here we explore how different families of TEs have contributed to shaping the XACT locus and coupling its expression to pluripotency. Through a combination of sequence analysis across primates, transcriptional interference, and genome editing, we identify a critical enhancer for the regulation of the XACT locus that evolved from an ancestral group of mammalian endogenous retroviruses (ERVs), prior to the emergence of XACT. This ERV was hijacked by younger hominoid-specific ERVs that gave rise to the promoter of XACT, thus wiring its expression to the pluripotency network. This work illustrates how retroviral-derived sequences may intervene in species-specific regulatory pathways.
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Affiliation(s)
- Miguel Casanova
- Université de Paris, Epigenetics and Cell Fate, CNRS, F-75013, Paris, France.
| | | | | | - Christophe Huret
- Université de Paris, Epigenetics and Cell Fate, CNRS, F-75013, Paris, France
| | - Julia Samson
- Université de Paris, Epigenetics and Cell Fate, CNRS, F-75013, Paris, France
| | | | - Olga Rosspopoff
- Université de Paris, Epigenetics and Cell Fate, CNRS, F-75013, Paris, France
| | - Claire Rougeulle
- Université de Paris, Epigenetics and Cell Fate, CNRS, F-75013, Paris, France.
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3
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Karner H, Webb CH, Carmona S, Liu Y, Lin B, Erhard M, Chan D, Baldi P, Spitale RC, Sun S. Functional Conservation of LncRNA JPX Despite Sequence and Structural Divergence. J Mol Biol 2019; 432:283-300. [PMID: 31518612 DOI: 10.1016/j.jmb.2019.09.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/29/2019] [Accepted: 09/02/2019] [Indexed: 02/02/2023]
Abstract
Long noncoding RNAs (lncRNAs) have been identified in all eukaryotes and are most abundant in the human genome. However, the functional importance and mechanisms of action for human lncRNAs are largely unknown. Using comparative sequence, structural, and functional analyses, we characterize the evolution and molecular function of human lncRNA JPX. We find that human JPX and its mouse homolog, lncRNA Jpx, have deep divergence in their nucleotide sequences and RNA secondary structures. Despite such differences, both lncRNAs demonstrate robust binding to CTCF, a protein that is central to Jpx's role in X chromosome inactivation. In addition, our functional rescue experiment using Jpx-deletion mutant cells shows that human JPX can functionally complement the loss of Jpx in mouse embryonic stem cells. Our findings support a model for functional conservation of lncRNAs independent from sequence and structural divergence. This study provides mechanistic insight into the evolution of lncRNA function.
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Affiliation(s)
- Heather Karner
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
| | - Chiu-Ho Webb
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
| | - Sarah Carmona
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
| | - Yu Liu
- Department of Computer Science, Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, CA 92697, USA
| | - Benjamin Lin
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
| | - Micaela Erhard
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
| | - Dalen Chan
- Department of Pharmaceutical Sciences, College of Health Sciences, University of California Irvine, Irvine, CA 92697, USA
| | - Pierre Baldi
- Department of Computer Science, Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, CA 92697, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, College of Health Sciences, University of California Irvine, Irvine, CA 92697, USA
| | - Sha Sun
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA.
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4
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Santiwatana S, Mahachoklertwattana P, Limwongse C, Khlairit P, Pongratanakul S, Roothumnong E, Prangphan K, Choubtum L, Songdej D, Poomthavorn P. Skewed X chromosome inactivation in girls and female adolescents with autoimmune thyroid disease. Clin Endocrinol (Oxf) 2018; 89:863-869. [PMID: 30229980 DOI: 10.1111/cen.13857] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/11/2018] [Accepted: 09/14/2018] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Skewed X chromosome inactivation (XCI) was associated with female predominance in adult autoimmune thyroid disease (ATD). In normal females, skewed XCI is increased with age. Whether early-onset skewed XCI is associated with childhood ATD remains unknown. This study aimed to determine XCI skewing in paediatric ATD. DESIGN, PATIENTS AND MEASUREMENTS Ninety-one female ATD patients, aged 3-20 years and 57 age-matched, female controls were enrolled. XCI was analysed by enzymatic digestion of DNA with methylation-sensitive enzymes followed by PCR of the polymorphic CAG repeat in the androgen receptor gene. Skewed XCI was defined as having 80% or greater of the cells preferentially inactivated on the same X chromosome. XCI pattern of the enrolled patients and parental origin of the skewed XCI were determined. RESULTS After exclusion of samples with homozygous CAG repeats, skewed XCI was analysed in 83 patients (57 Graves' disease and 26 Hashimoto thyroiditis) and 52 controls. There was an increased frequency of skewed XCI in ATD patients as compared with the controls (23% vs 8%, P = 0.022). Patients with Hashimoto thyroiditis had greater frequency of skewed XCI than patients with Graves' disease (38% vs 16%, P = 0.023). There were no differences in clinical parameters between patients with skewed and random XCI. Analysis of 7 patients with skewed XCI showed a preferential inactivation of paternal X chromosome in 6 patients (86%). CONCLUSIONS Frequency of skewed XCI was increased in childhood ATD. This observation suggests a possible association of skewed XCI in the development of paediatric ATD.
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Affiliation(s)
- Suttikarn Santiwatana
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pat Mahachoklertwattana
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Chanin Limwongse
- Department of Internal Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Patcharin Khlairit
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sarunyu Pongratanakul
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Ekkapong Roothumnong
- Department of Internal Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Kanjana Prangphan
- Division of Medical Genetics Research and Laboratory, Siriraj Medical Research Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Lulin Choubtum
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Duantida Songdej
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Preamrudee Poomthavorn
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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Migeon BR, Beer MA, Bjornsson HT. Embryonic loss of human females with partial trisomy 19 identifies region critical for the single active X. PLoS One 2017; 12:e0170403. [PMID: 28403217 PMCID: PMC5389809 DOI: 10.1371/journal.pone.0170403] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 01/04/2017] [Indexed: 11/18/2022] Open
Abstract
To compensate for the sex difference in the number of X chromosomes, human females, like human males have only one active X. The other X chromosomes in cells of both sexes are silenced in utero by XIST, the Inactive X Specific Transcript gene, that is present on all X chromosomes. To investigate the means by which the human active X is protected from silencing by XIST, we updated the search for a key dosage sensitive XIST repressor using new cytogenetic data with more precise resolution. Here, based on a previously unknown sex bias in copy number variations, we identify a unique region in our genome, and propose candidate genes that lie within, as they could inactivate XIST. Unlike males, the females who duplicate this region of chromosome 19 (partial 19 trisomy) do not survive embryogenesis; this preimplantation loss of females may be one reason that more human males are born than females.
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Affiliation(s)
- Barbara R. Migeon
- McKusick Nathans Institute of Genetic Medicine, Baltimore, MD, United States of America
- Department of Pediatrics, Johns Hopkins University, School of Medicine, Baltimore, MD, United States of America
- * E-mail:
| | - Michael A. Beer
- McKusick Nathans Institute of Genetic Medicine, Baltimore, MD, United States of America
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Hans T. Bjornsson
- McKusick Nathans Institute of Genetic Medicine, Baltimore, MD, United States of America
- Department of Pediatrics, Johns Hopkins University, School of Medicine, Baltimore, MD, United States of America
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6
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Cerase A. X chromosome inactivation: The importance of being inactive. Semin Cell Dev Biol 2016; 56:1-2. [PMID: 27431781 DOI: 10.1016/j.semcdb.2016.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Andrea Cerase
- EMBL-Monterotondo, Via Ramarini 32, Monterotondo, Italy.
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7
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Vallot C, Ouimette JF, Rougeulle C. Establishment of X chromosome inactivation and epigenomic features of the inactive X depend on cellular contexts. Bioessays 2016; 38:869-80. [PMID: 27389958 DOI: 10.1002/bies.201600121] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
X chromosome inactivation (XCI) is an essential epigenetic process that ensures X-linked gene dosage equilibrium between sexes in mammals. XCI is dynamically regulated during development in a manner that is intimately linked to differentiation. Numerous studies, which we review here, have explored the dynamics of X inactivation and reactivation in the context of development, differentiation and diseases, and the phenotypic and molecular link between the inactive status, and the cellular context. Here, we also assess whether XCI is a uniform mechanism in mammals by analyzing epigenetic signatures of the inactive X (Xi) in different species and cellular contexts. It appears that the timing of XCI and the epigenetic signature of the inactive X greatly vary between species. Surprisingly, even within a given species, various Xi configurations are found across cellular states. We discuss possible mechanisms underlying these variations, and how they might influence the fate of the Xi.
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Affiliation(s)
- Céline Vallot
- Sorbonne Paris Cité, Epigenetics and Cell Fate, Université Paris Diderot, Paris, France
| | | | - Claire Rougeulle
- Sorbonne Paris Cité, Epigenetics and Cell Fate, Université Paris Diderot, Paris, France
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