1
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Lyu Q, Yang Q, Hao J, Yue Y, Wang X, Tian J, An L. A small proportion of X-linked genes contribute to X chromosome upregulation in early embryos via BRD4-mediated transcriptional activation. Curr Biol 2022; 32:4397-4410.e5. [PMID: 36108637 DOI: 10.1016/j.cub.2022.08.059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/30/2022] [Accepted: 08/19/2022] [Indexed: 02/08/2023]
Abstract
Females have two X chromosomes and males have only one in most mammals. X chromosome inactivation (XCI) occurs in females to equalize X-dosage between sexes. Besides, mammals also balance the dosage between X chromosomes and autosomes via X chromosome upregulation (XCU) to fine-tune X-linked expression and thus maintain genomic homeostasis. Despite some studies highlighting the importance of XCU in somatic cells, little is known about how XCU is achieved and its developmental role during early embryogenesis. Herein, using mouse preimplantation embryos as the model, we reported that XCU initially occurs upon major zygotic genome activation and co-regulates X-linked expression in cooperation with imprinted XCI during preimplantation development. An in-depth analysis further indicated, unexpectedly, only a small proportion of, but not X chromosome-wide, X-linked genes contribute greatly to XCU. Furthermore, we identified that bromodomain containing 4 (BRD4) plays a key role in the transcription activation of XCU during preimplantation development. BRD4 deficiency or inhibition caused an impaired XCU, thus leading to reduced developmental potential and mitochondrial dysfunctions of blastocysts. Our finding was also supported by the tight association of BRD4 dysregulation and XCU disruption in the pathology of cholangiocarcinoma. Thus, our results not only advanced the current knowledge of X-dosage compensation and provided a mechanism for understanding XCU initiation but also presented an important clue for understanding the developmental and pathological role of XCU.
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Affiliation(s)
- Qingji Lyu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Qianying Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Jia Hao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Yuan Yue
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Xiaodong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Jianhui Tian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Lei An
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China.
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2
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Matsuura R, Nakajima T, Ichihara S, Sado T. Ectopic Splicing Disturbs the Function of Xist RNA to Establish the Stable Heterochromatin State. Front Cell Dev Biol 2021; 9:751154. [PMID: 34722536 PMCID: PMC8551810 DOI: 10.3389/fcell.2021.751154] [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] [Received: 07/31/2021] [Accepted: 09/20/2021] [Indexed: 11/29/2022] Open
Abstract
Non-coding Xist RNA plays an essential role in X chromosome inactivation (XCI) in female mammals. It coats the X chromosome in cis and mediates the recruitment of many proteins involved in gene silencing and heterochromatinization. The molecular basis of how Xist RNA initiates chromosomal silencing and what proteins participate in this process has been extensively studied and elucidated. Its involvement in the establishment and maintenance of the X-inactivated state is, however, less understood. The XistIVS allele we previously reported is peculiar in that it can initiate XCI but fails to establish the inactive state that is stably maintained and, therefore, may provide an opportunity to explore how Xist RNA contributes to establish a robust heterochromatin state. Here we demonstrate that ectopic splicing taking place to produce XistIVS RNA disturbs its function to properly establish stable XCI state. This finding warrants the potential of XistIVS RNA to provide further insight into our understanding of how Xist RNA contributes to establish sustainable heterochromatin.
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Affiliation(s)
- Ruka Matsuura
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Japan
| | - Tatsuro Nakajima
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Saya Ichihara
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Japan
| | - Takashi Sado
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Japan.,Agricultural Technology and Innovation Research Institute, Kindai University, Nara, Japan
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3
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Lee DM, Trotman JB, Cherney RE, Inoue K, Schertzer MD, Bischoff SR, Cowley DO, Calabrese JM. RETRACTED: A 5' fragment of Xist can sequester RNA produced from adjacent genes on chromatin. Nucleic Acids Res 2019; 47:7049-7062. [PMID: 31114903 PMCID: PMC6648342 DOI: 10.1093/nar/gkz432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 04/18/2019] [Accepted: 05/09/2019] [Indexed: 12/15/2022] Open
Abstract
Xist requires Repeat-A, a protein-binding module in its first two kilobases (2kb), to repress transcription. We report that when expressed as a standalone transcript in mouse embryonic stem cells (ESCs), the first 2kb of Xist (Xist-2kb) does not induce transcriptional silencing. Instead, Xist-2kb sequesters RNA produced from adjacent genes on chromatin. Sequestration does not spread beyond adjacent genes, requires the same sequence elements in Repeat-A that full-length Xist requires to repress transcription and can be induced by lncRNAs with similar sequence composition to Xist-2kb. We did not detect sequestration by full-length Xist, but we did detect it by mutant forms of Xist with attenuated transcriptional silencing capability. Xist-2kb associated with SPEN, a Repeat-A binding protein required for Xist-induced transcriptional silencing, but SPEN was not necessary for sequestration. Thus, when expressed in mouse ESCs, a 5' fragment of Xist that contains Repeat-A sequesters RNA from adjacent genes on chromatin and associates with the silencing factor SPEN, but it does not induce transcriptional silencing. Instead, Xist-induced transcriptional silencing requires synergy between Repeat-A and additional sequence elements in Xist. We propose that sequestration is mechanistically related to the Repeat-A dependent stabilization and tethering of Xist near actively transcribed regions of chromatin.
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Affiliation(s)
- David M Lee
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jackson B Trotman
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Rachel E Cherney
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kaoru Inoue
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Megan D Schertzer
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Steven R Bischoff
- Animal Models Core, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Dale O Cowley
- Animal Models Core, University of North Carolina, Chapel Hill, NC 27599, USA
| | - J Mauro Calabrese
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
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4
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Kalisch-Smith JI, Steane SE, Simmons DG, Pantaleon M, Anderson ST, Akison LK, Wlodek ME, Moritz KM. Periconceptional alcohol exposure causes female-specific perturbations to trophoblast differentiation and placental formation in the rat. Development 2019; 146:dev172205. [PMID: 31182432 DOI: 10.1242/dev.172205] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 04/18/2019] [Indexed: 12/26/2022]
Abstract
The development of pathologies during pregnancy, including pre-eclampsia, hypertension and fetal growth restriction (FGR), often originates from poor functioning of the placenta. In vivo models of maternal stressors, such as nutrient deficiency, and placental insufficiency often focus on inadequate growth of the fetus and placenta in late gestation. These studies rarely investigate the origins of poor placental formation in early gestation, including those affecting the pre-implantation embryo and/or the uterine environment. The current study characterises the impact on blastocyst, uterine and placental outcomes in a rat model of periconceptional alcohol exposure, in which 12.5% ethanol is administered in a liquid diet from 4 days before until 4 days after conception. We show female-specific effects on trophoblast differentiation, embryo-uterine communication, and formation of the placental vasculature, resulting in markedly reduced placental volume at embryonic day 15. Both sexes exhibited reduced trophectoderm pluripotency and global hypermethylation, suggestive of inappropriate epigenetic reprogramming. Furthermore, evidence of reduced placental nutrient exchange and reduced pre-implantation maternal plasma choline levels offers significant mechanistic insight into the origins of FGR in this model.
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Affiliation(s)
- Jacinta I Kalisch-Smith
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Sarah E Steane
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, St Lucia, QLD 4072, Australia
| | - David G Simmons
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Marie Pantaleon
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Stephen T Anderson
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Lisa K Akison
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, St Lucia, QLD 4072, Australia
- Child Health Research Centre, The University of Queensland, South Brisbane, QLD 4101, Australia
| | - Mary E Wlodek
- Department of Physiology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Karen M Moritz
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, St Lucia, QLD 4072, Australia
- Child Health Research Centre, The University of Queensland, South Brisbane, QLD 4101, Australia
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5
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Sakakibara Y, Nagao K, Blewitt M, Sasaki H, Obuse C, Sado T. Role of SmcHD1 in establishment of epigenetic states required for the maintenance of the X-inactivated state in mice. Development 2018; 145:dev.166462. [PMID: 30126901 DOI: 10.1242/dev.166462] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 08/10/2018] [Indexed: 01/01/2023]
Abstract
X inactivation in mammals is regulated by epigenetic modifications. Functional deficiency of SmcHD1 has been shown to cause de-repression of X-inactivated genes in post-implantation female mouse embryos, suggesting a role of SmcHD1 in the maintenance of X inactivation. Here, we show that de-repression of X-inactivated genes accompanied a local reduction in the enrichment of H3K27me3 in mouse embryonic fibroblasts deficient for SmcHD1. Furthermore, many of these genes overlapped with those having a significantly lower enrichment of H3K27me3 at the blastocyst stage in wild type. Intriguingly, however, depletion of SmcHD1 did not compromise the X-inactivated state in immortalized female mouse embryonic fibroblasts, in which X inactivation had been established and maintained. Taking all these findings together, we suggest that SmcHD1 facilitates the incorporation of H3K27me3 and perhaps other epigenetic modifications at gene loci that are silenced even with the lower enrichment of H3K27me3 at the early stage of X inactivation. The epigenetic state at these loci would, however, remain as it is at the blastocyst stage in the absence of SmcHD1 after implantation, which would eventually compromise the maintenance of the X-inactivated state at later stages.
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Affiliation(s)
- Yuki Sakakibara
- Medical Institute of Bioregulation, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Koji Nagao
- Department of Biological Science, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Marnie Blewitt
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, Parkville 3052 VIC, Australia; The Department of Medical Biology, University of Melbourne, Parkville 3052, VIC, Australia
| | - Hiroyuki Sasaki
- Medical Institute of Bioregulation, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Chikashi Obuse
- Department of Biological Science, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Takashi Sado
- Medical Institute of Bioregulation, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan .,Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, 3327-204, Nakamachi, Nara, 630-8505, Japan
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6
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SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells. Proc Natl Acad Sci U S A 2016; 113:10322-7. [PMID: 27578869 DOI: 10.1073/pnas.1600008113] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The 18-kb Xist long noncoding RNA (lncRNA) is essential for X-chromosome inactivation during female eutherian mammalian development. Global structural architecture, cell-induced conformational changes, and protein-RNA interactions within Xist are poorly understood. We used selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) to examine these features of Xist at single-nucleotide resolution both in living cells and ex vivo. The Xist RNA forms complex well-defined secondary structure domains and the cellular environment strongly modulates the RNA structure, via motifs spanning one-half of all Xist nucleotides. The Xist RNA structure modulates protein interactions in cells via multiple mechanisms. For example, repeat-containing elements adopt accessible and dynamic structures that function as landing pads for protein cofactors. Structured RNA motifs create interaction domains for specific proteins and also sequester other motifs, such that only a subset of potential binding sites forms stable interactions. This work creates a broad quantitative framework for understanding structure-function interrelationships for Xist and other lncRNAs in cells.
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7
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Yang L, Kirby JE, Sunwoo H, Lee JT. Female mice lacking Xist RNA show partial dosage compensation and survive to term. Genes Dev 2016; 30:1747-60. [PMID: 27542829 PMCID: PMC5002979 DOI: 10.1101/gad.281162.116] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 07/22/2016] [Indexed: 11/25/2022]
Abstract
X-chromosome inactivation (XCI) compensates for differences in X-chromosome number between male and female mammals. XCI is orchestrated by Xist RNA, whose expression in early development leads to transcriptional silencing of one X chromosome in the female. Knockout studies have established a requirement for Xist with inviability of female embryos that inherit an Xist deletion from the father. Here, we report that female mice lacking Xist RNA can, surprisingly, develop and survive to term. Xist-null females are born at lower frequency and are smaller at birth, but organogenesis is mostly normal. Transcriptomic analysis indicates significant overexpression of hundreds of X-linked genes across multiple tissues. Therefore, Xist-null mice can develop to term in spite of a deficiency of dosage compensation. However, the degree of X-autosomal dosage imbalance was less than anticipated (1.14-fold to 1.36-fold). Thus, partial dosage compensation can be achieved without Xist, supporting the idea of inherent genome balance. Nevertheless, to date, none of the mutant mice has survived beyond weaning stage. Sudden death is associated with failure of postnatal organ maturation. Our data suggest Xist-independent mechanisms of dosage compensation and demonstrate that small deviations from X-autosomal balance can have profound effects on overall fitness.
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Affiliation(s)
- Lin Yang
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - James E Kirby
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Hongjae Sunwoo
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Jeannie T Lee
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA
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8
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Tan K, Wang Z, Zhang Z, An L, Tian J. IVF affects embryonic development in a sex-biased manner in mice. Reproduction 2016; 151:443-53. [DOI: 10.1530/rep-15-0588] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/28/2016] [Indexed: 11/08/2022]
Abstract
Increasing evidence indicates that IVF (IVF includes in vitro fertilization and culture) embryos and babies are associated with a series of health complications, and some of them show sex-dimorphic patterns. Therefore, we hypothesized that IVF procedures have sex-biased or even sex-specific effects on embryonic and fetal development. Here, we demonstrate that IVF-induced side effects show significant sexual dimorphic patterns from the pre-implantation to the prenatal stage. During the pre-implantation stage, female IVF embryos appear to be more vulnerable to IVF-induced effects, including an increased percentage of apoptosis (7.22±1.94 vs 0.71±0.76, P<0.01), and dysregulated expression of representative sex-dimorphic genes (Xist, Hprt, Pgk1 and Hsp70). During the mid-gestation stage, IVF males had a higher survival rate than IVF females at E13.5 (male:female=1.33:1), accompanied with a female-biased pregnancy loss. In addition, while both IVF males and females had reduced placental vasculogenesis/angiogenesis, the compensatory placental overgrowth was more evident in IVF males. During the late-gestation period, IVF fetuses had a higher sex ratio (male:female=1.48:1) at E19.5, and both male and female IVF placentas showed overgrowth. After birth, IVF males grew faster than their in vivo (IVO) counterparts, while IVF females showed a similar growth pattern with IVO females. The present study provides a new insight into understanding IVF-induced health complications during embryonic and fetal development. By understanding and minimizing these sex-biased effects of the IVF process, the health of IVF-conceived babies may be improved in the future.
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9
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Impaired imprinted X chromosome inactivation is responsible for the skewed sex ratio following in vitro fertilization. Proc Natl Acad Sci U S A 2016; 113:3197-202. [PMID: 26951653 DOI: 10.1073/pnas.1523538113] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dynamic epigenetic reprogramming occurs during normal embryonic development at the preimplantation stage. Erroneous epigenetic modifications due to environmental perturbations such as manipulation and culture of embryos during in vitro fertilization (IVF) are linked to various short- or long-term consequences. Among these, the skewed sex ratio, an indicator of reproductive hazards, was reported in bovine and porcine embryos and even human IVF newborns. However, since the first case of sex skewing reported in 1991, the underlying mechanisms remain unclear. We reported herein that sex ratio is skewed in mouse IVF offspring, and this was a result of female-biased peri-implantation developmental defects that were originated from impaired imprinted X chromosome inactivation (iXCI) through reduced ring finger protein 12 (Rnf12)/X-inactive specific transcript (Xist) expression. Compensation of impaired iXCI by overexpression of Rnf12 to up-regulate Xist significantly rescued female-biased developmental defects and corrected sex ratio in IVF offspring. Moreover, supplementation of an epigenetic modulator retinoic acid in embryo culture medium up-regulated Rnf12/Xist expression, improved iXCI, and successfully redeemed the skewed sex ratio to nearly 50% in mouse IVF offspring. Thus, our data show that iXCI is one of the major epigenetic barriers for the developmental competence of female embryos during preimplantation stage, and targeting erroneous epigenetic modifications may provide a potential approach for preventing IVF-associated complications.
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10
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Prudhomme J, Morey C. Epigenesis and plasticity of mouse trophoblast stem cells. Cell Mol Life Sci 2016; 73:757-74. [PMID: 26542801 PMCID: PMC11108370 DOI: 10.1007/s00018-015-2086-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 10/27/2015] [Indexed: 12/28/2022]
Abstract
The critical role of the placenta in supporting a healthy pregnancy is mostly ensured by the extraembryonic trophoblast lineage that acts as the interface between the maternal and the foetal compartments. The diverse trophoblast cell subtypes that form the placenta originate from a single layer of stem cells that emerge from the embryo when the earliest cell fate decisions are occurring. Recent studies show that these trophoblast stem cells exhibit extensive plasticity as they are capable of differentiating down multiple pathways and are easily converted into embryonic stem cells in vitro. In this review, we discuss current knowledge of the mechanisms and control of the epigenesis of mouse trophoblast stem cells through a comparison with the corresponding mechanisms in pluripotent embryonic stem cells. To illustrate some of the more striking manifestations of the epigenetic plasticity of mouse trophoblast stem cells, we discuss them within the context of two paradigms of epigenetic regulation of gene expression: the imprinted gene expression of specific loci and the process of X-chromosome inactivation.
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Affiliation(s)
- Julie Prudhomme
- Laboratoire de Génétique Moléculaire Murine, Institut Pasteur, 75015, Paris, France
| | - Céline Morey
- CNRS, UMR7216 Epigenetics and Cell Fate, 75013, Paris, France.
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11
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RNA binding proteins implicated in Xist-mediated chromosome silencing. Semin Cell Dev Biol 2016; 56:58-70. [PMID: 26816113 DOI: 10.1016/j.semcdb.2016.01.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 11/20/2022]
Abstract
Chromosome silencing by Xist RNA occurs in two steps; localisation in cis within the nuclear matrix to form a domain that corresponds to the territory of the inactive X chromosome elect, and transduction of silencing signals from Xist RNA to the underlying chromatin. Key factors that mediate these processes have been identified in a series of recent studies that harnessed comprehensive proteomic or genetic screening strategies. In this review we discuss these findings in light of prior knowledge both of Xist-mediated silencing and known functions/properties of the novel factors.
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12
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Prudhomme J, Dubois A, Navarro P, Arnaud D, Avner P, Morey C. A rapid passage through a two-active-X-chromosome state accompanies the switch of imprinted X-inactivation patterns in mouse trophoblast stem cells. Epigenetics Chromatin 2015; 8:52. [PMID: 26628922 PMCID: PMC4665903 DOI: 10.1186/s13072-015-0044-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/16/2015] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND In female mice, while the presence of two-active X-chromosomes characterises pluripotency, it is not tolerated in most other cellular contexts. In particular, in the trophoblastic lineage, impairment of paternal X (X(P)) inactivation results in placental defects. RESULTS Here, we show that Trophoblast Stem (TS) cells can undergo a complete reversal of imprinted X-inactivation without detectable change in cell-type identity. This reversal occurs through a reactivation of the X(P) leading to TS clones showing two active Xs. Intriguingly, within such clones, all the cells rapidly and homogeneously either re-inactivate the X(P) or inactivate, de novo, the X(M). CONCLUSION This secondary non-random inactivation suggests that the two-active-X states in TS and in pluripotent contexts are epigenetically distinct. These observations also reveal a pronounced plasticity of the TS epigenome allowing TS cells to dramatically and accurately reprogram gene expression profiles. This plasticity may serve as a back-up system when X-linked mono-allelic gene expression is perturbed.
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Affiliation(s)
- Julie Prudhomme
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France
| | - Agnès Dubois
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France ; Epigenetics of Stem Cells Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France
| | - Pablo Navarro
- Epigenetics of Stem Cells Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France
| | - Danielle Arnaud
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France
| | - Philip Avner
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France ; Dynamics of Epigenetic Regulation, EMBL Monterotondo, Adriano Buzzati-Traverso Campus, Via Ramarini 32, 00015 Monterotondo, Italy
| | - Céline Morey
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France ; CNRS, UMR7216 Epigenetics and Cell Fate, 35 rue Hélène Brion, 75013 Paris, France
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13
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Sarkar MK, Gayen S, Kumar S, Maclary E, Buttigieg E, Hinten M, Kumari A, Harris C, Sado T, Kalantry S. An Xist-activating antisense RNA required for X-chromosome inactivation. Nat Commun 2015; 6:8564. [PMID: 26477563 PMCID: PMC4616153 DOI: 10.1038/ncomms9564] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/07/2015] [Indexed: 01/06/2023] Open
Abstract
The transcriptional imbalance due to the difference in the number of X chromosomes between male and female mammals is remedied through X-chromosome inactivation, the epigenetic transcriptional silencing of one of the two X chromosomes in females. The X-linked Xist long non-coding RNA functions as an X inactivation master regulator; Xist is selectively upregulated from the prospective inactive X chromosome and is required in cis for X inactivation. Here we discover an Xist antisense long non-coding RNA, XistAR (XistActivating RNA), which is encoded within exon 1 of the mouse Xist gene and is transcribed only from the inactive X chromosome. Selective truncation of XistAR, while sparing the overlapping Xist RNA, leads to a deficiency in Xist RNA expression in cis during the initiation of X inactivation. Thus, the Xist gene carries within its coding sequence an antisense RNA that drives Xist expression. The X-chromosome linked long non-coding RNA, Xist, is a master regulator of the X inactivation. Here, the authors report that XistAR, an Xist anti-sense long non-coding RNA encoded within the mouse Xist gene and transcribed only from the inactive X chromosome, regulates Xist expression.
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Affiliation(s)
- Mrinal K Sarkar
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Srimonta Gayen
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Surinder Kumar
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Emily Maclary
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Emily Buttigieg
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Michael Hinten
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Archana Kumari
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Clair Harris
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Takashi Sado
- Department of Advanced Bioscience, Graduate School of Agriculture, Kinki University, 3327-204 Nakamachi, Nara 631-8505, Japan
| | - Sundeep Kalantry
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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14
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Dubois A, Deuve JL, Navarro P, Merzouk S, Pichard S, Commere PH, Louise A, Arnaud D, Avner P, Morey C. Spontaneous reactivation of clusters of X-linked genes is associated with the plasticity of X-inactivation in mouse trophoblast stem cells. Stem Cells 2014; 32:377-90. [PMID: 24115267 DOI: 10.1002/stem.1557] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 07/29/2013] [Accepted: 08/13/2013] [Indexed: 12/21/2022]
Abstract
Random epigenetic silencing of the X-chromosome in somatic tissues of female mammals equalizes the dosage of X-linked genes between the sexes. Unlike this form of X-inactivation that is essentially irreversible, the imprinted inactivation of the paternal X, which characterizes mouse extra-embryonic tissues, appears highly unstable in the trophoblast giant cells of the placenta. Here, we wished to determine whether such instability is already present in placental progenitor cells prior to differentiation toward lineage-specific cell types. To this end, we analyzed the behavior of a GFP transgene on the paternal X both in vivo and in trophoblast stem (TS) cells derived from the trophectoderm of XX(GFP) blastocysts. Using single-cell studies, we show that not only the GFP transgene but also a large number of endogenous genes on the paternal X are subject to orchestrated cycles of reactivation/de novo inactivation in placental progenitor cells. This reversal of silencing is associated with local losses of histone H3 lysine 27 trimethylation extending over several adjacent genes and with the topological relocation of the hypomethylated loci outside of the nuclear compartment of the inactive X. The "reactivated" state is maintained through several cell divisions. Our study suggests that this type of "metastable epigenetic" states may underlie the plasticity of TS cells and predispose specific genes to relaxed regulation in specific subtypes of placental cells.
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Affiliation(s)
- Agnès Dubois
- Unité de Génétique Moléculaire Murine, Institut Pasteur, Paris Cedex 15, France; Epigenetics of Stem Cells, Institut Pasteur, Paris Cedex 15, France
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15
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Sado T, Brockdorff N. Advances in understanding chromosome silencing by the long non-coding RNA Xist. Philos Trans R Soc Lond B Biol Sci 2013; 368:20110325. [PMID: 23166390 DOI: 10.1098/rstb.2011.0325] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In female mammals, one of the two X chromosomes becomes genetically silenced to compensate for dosage imbalance of X-linked genes between XX females and XY males. X chromosome inactivation (X-inactivation) is a classical model for epigenetic gene regulation in mammals and has been studied for half a century. In the last two decades, efforts have been focused on the X inactive-specific transcript (Xist) locus, discovered to be the master regulator of X-inactivation. The Xist gene produces a non-coding RNA that functions as the primary switch for X-inactivation, coating the X chromosome from which it is transcribed in cis. Significant progress has been made towards understanding how Xist is regulated at the onset of X-inactivation, but our understanding of the molecular basis of silencing mediated by Xist RNA has progressed more slowly. A picture has, however, begun to emerge, and new tools and resources hold out the promise of further advances to come. Here, we provide an overview of the current state of our knowledge, what is known about Xist RNA and how it may trigger chromosome silencing.
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Affiliation(s)
- Takashi Sado
- Division of Epigenomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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16
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Corbel C, Diabangouaya P, Gendrel AV, Chow JC, Heard E. Unusual chromatin status and organization of the inactive X chromosome in murine trophoblast giant cells. Development 2013; 140:861-72. [PMID: 23362347 DOI: 10.1242/dev.087429] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Mammalian X-chromosome inactivation (XCI) enables dosage compensation between XX females and XY males. It is an essential process and its absence in XX individuals results in early lethality due primarily to extra-embryonic defects. This sensitivity to X-linked gene dosage in extra-embryonic tissues is difficult to reconcile with the reported tendency of escape from XCI in these tissues. The precise transcriptional status of the inactive X chromosome in different lineages has mainly been examined using transgenes or in in vitro differentiated stem cells and the degree to which endogenous X-linked genes are silenced in embryonic and extra-embryonic lineages during early postimplantation stages is unclear. Here we investigate the precise temporal and lineage-specific X-inactivation status of several genes in postimplantation mouse embryos. We find stable gene silencing in most lineages, with significant levels of escape from XCI mainly in one extra-embryonic cell type: trophoblast giant cells (TGCs). To investigate the basis of this epigenetic instability, we examined the chromatin structure and organization of the inactive X chromosome in TGCs obtained from ectoplacental cone explants. We find that the Xist RNA-coated X chromosome has a highly unusual chromatin content in TGCs, presenting both heterochromatic marks such as H3K27me3 and euchromatic marks such as histone H4 acetylation and H3K4 methylation. Strikingly, Xist RNA does not form an overt silent nuclear compartment or Cot1 hole in these cells. This unusual combination of silent and active features is likely to reflect, and might underlie, the partial activity of the X chromosome in TGCs.
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Affiliation(s)
- Catherine Corbel
- Unité de Génétique et Biologie du Développement, Institut Curie, CNRS UMR 3215, INSERM U934, 26 rue d'Ulm, 75248 Paris Cedex 05, France.
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17
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Mugford JW, Yee D, Magnuson T. Failure of extra-embryonic progenitor maintenance in the absence of dosage compensation. Development 2012; 139:2130-8. [PMID: 22573614 DOI: 10.1242/dev.076497] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Proper regulation of X-linked gene expression, termed dosage compensation, is required for the normal development of mammalian embryos. Through the process of X chromosome inactivation (XCI), somatic cells of mammalian females inactivate one of their two X chromosomes in order to balance X-linked gene dosage with their male counterparts. The process of XCI is dependent upon the long non-coding RNA Xist, which is expressed from and coats the inactivated X chromosome (Xi) in cis. During mouse embryogenesis, imprinted XCI inactivates the paternally inherited X chromosome (Xp) within the extra-embryonic lineages. Consequently, females harboring a paternally derived Xist mutation (X/X(Xist-)) die owing to failure of imprinted XCI and, presumably, poor trophoblast development. Here, we investigate the consequence of two active X chromosomes in the extra-embryonic ectoderm (ExE) of X/X(Xist-) female embryos. At embryonic day (E) 6.5, we find that the X/X(Xist-) ExE lacks the transcriptional regulator CDX2, a factor required to maintain the ExE in a progenitor state. In addition, spongiotrophoblast progenitors are not maintained. Surprisingly, we observe evidence of an Xi in a subpopulation of X/X(Xist-) ExE cells. We demonstrate further that trophectodermal stem cells derived from X/X(Xist-) embryos completely reverse normal imprinted XCI patterns. Taken together, our data suggest that, much like in the cells of the epiblast, the initial imprint that establishes imprinted XCI is probably erased in ExE cells. Conversely, unlike the epiblast, in which XCI is not required for progenitor cell maintenance, we demonstrate that dosage compensation is indispensable for the maintenance of trophoblast progenitors.
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Affiliation(s)
- Joshua W Mugford
- The University of North Carolina at Chapel Hill, Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599-7264, USA
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18
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Brockdorff N. Chromosome silencing mechanisms in X-chromosome inactivation: unknown unknowns. Development 2012; 138:5057-65. [PMID: 22069184 DOI: 10.1242/dev.065276] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Fifty years ago, Mary Lyon hypothesised that one of the two X chromosomes in female mammalian cells is inactivated at random during early embryogenesis and that the inactive X is then stably maintained through all subsequent cell divisions. Although Lyon's hypothesis is now widely regarded as fact, we should not forget that her conceptual leap met with considerable resistance from the scientific establishment at the time - a common response to new ideas. Taking this point as a theme, I discuss our current understanding of the molecular mechanism of chromosome silencing in X-chromosome inactivation and focus on topics where new findings are challenging the prevailing view.
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Affiliation(s)
- Neil Brockdorff
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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19
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Gene silencing in X-chromosome inactivation: advances in understanding facultative heterochromatin formation. Nat Rev Genet 2011; 12:542-53. [PMID: 21765457 DOI: 10.1038/nrg3035] [Citation(s) in RCA: 263] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In female mammals, one of the two X chromosomes is silenced for dosage compensation between the sexes. X-chromosome inactivation is initiated in early embryogenesis by the Xist RNA that localizes to the inactive X chromosome. During development, the inactive X chromosome is further modified, a specialized form of facultative heterochromatin is formed and gene repression becomes stable and independent of Xist in somatic cells. The recent identification of several factors involved in this process has provided insights into the mechanism of Xist localization and gene silencing. The emerging picture is complex and suggests that chromosome-wide silencing can be partitioned into several steps, the molecular components of which are starting to be defined.
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