1
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Shahu L, Chowdhury SR, Lu HP. Single-Molecule Human Nucleosome Spontaneously Ruptures under the Stress of Compressive Force: A New Perspective on Gene Stability and Epigenetic Pathways. J Phys Chem B 2023; 127:37-44. [PMID: 36537668 DOI: 10.1021/acs.jpcb.2c04449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Force manipulation on the biological entities from living cells to protein molecules has revealed many mechanical details of cell biology from resolving folding and unfolding pathways to finding molecular interaction forces. A nucleosome is the basic repeating unit of chromatin where the histone octamer is wrapped by DNA, important for gene stability and regulation. How the inner side of the DNA gets accessed by other DNA binding molecules has been a puzzle that has been intensively studied and debated, important to epigenetics, gene stability, and regulations. Here we report our observation of spontaneous ruptures of human nucleosomes under pico-Newton (pN) compressive force. The amplitude of the compressive force, a squeezing rather than pulling force, involved in our experiment is tens of pN, which can be thermally available by biological force fluctuation at room temperature and under physiological conditions. This kind of structural rupture can loosen up the DNA around the histone, which in turn makes the DNA accessible to transcription and epigenetic modifications.
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Affiliation(s)
- Lalita Shahu
- Department of Chemistry, Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - S Roy Chowdhury
- Department of Chemistry, Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - H Peter Lu
- Department of Chemistry, Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
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2
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Tamura Y, Ohhata T, Niida H, Sakai S, Uchida C, Masumoto K, Katou F, Wutz A, Kitagawa M. Homologous recombination is reduced in female embryonic stem cells by two active X chromosomes. EMBO Rep 2021; 22:e52190. [PMID: 34309165 DOI: 10.15252/embr.202052190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 12/16/2022] Open
Abstract
The reactivation of X-linked genes is observed in some primary breast tumors. Two active X chromosomes are also observed in female embryonic stem cells (ESCs), but whether double doses of X-linked genes affect DNA repair efficiency remains unclear. Here, we establish isogenic female/male ESCs and show that the female ESCs are more sensitive to camptothecin and have lower gene targeting efficiency than male ESCs, suggesting that homologous recombination (HR) efficiency is reduced in female ESCs. We also generate Xist-inducible female ESCs and show that the lower HR efficiency is restored when X chromosome inactivation is induced. Finally, we assess the X-linked genes with a role in DNA repair and find that Brcc3 is one of the genes involved in a network promoting proper HR. Our findings link the double doses of X-linked genes with lower DNA repair activity, and this may have relevance for common diseases in female patients, such as breast cancer.
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Affiliation(s)
- Yuka Tamura
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Japan.,Department of Oral and Maxillofacial Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tatsuya Ohhata
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hiroyuki Niida
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Satoshi Sakai
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Chiharu Uchida
- Advanced Research Facilities & Services, Preeminent Medical Photonics Education & Research Center, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kazuma Masumoto
- Department of Oral and Maxillofacial Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Fuminori Katou
- Department of Oral and Maxillofacial Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Anton Wutz
- Institute of Molecular Health Sciences, ETH Zürich, Zurich, Switzerland
| | - Masatoshi Kitagawa
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Japan
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3
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Haramoto Y, Sakata M, Kobayashi S. Visualization of X chromosome reactivation in mouse primordial germ cells in vivo. Biol Open 2021; 10:261692. [PMID: 33913476 PMCID: PMC8096617 DOI: 10.1242/bio.058602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/30/2021] [Indexed: 02/01/2023] Open
Abstract
X chromosome inactivation (XCI), determined during development, remains stable after embryonic cell divisions. However, primordial germ cells (PGCs) are exceptions in that XCI is reprogrammed and inactivated X chromosomes are reactivated. Although interactions between PGCs and somatic cells are thought to be important for PGC development, little is known about them. Here, we performed imaging of X chromosome reactivation (XCR) using the ‘Momiji’ mouse system, which can monitor the X chromosome's inactive and active states using two color fluorescence reporter genes, and investigated whether interactions would affect XCR in PGCs. Based on their expression levels, we found that XCR of the Pgk1 locus began at embryonic day (E)10.5 and was almost complete by E13.5. During this period, PGCs became distributed uniformly in the genital ridge, proliferated, and formed clusters; XCR progressed accordingly. In addition, XCR of the Pgk1 locus preceded that of the Hprt locus, indicating that the timing of epigenetic memory erasure varied according to the locus of each of these X-linked genes. Our results indicate that XCR proceeds along with the proliferation of PGCs clustered within the genital ridge. This article has an associated First Person interview with the first author of the paper. Summary: Imaging of mouse X chromosome activities reveals that they undergo reprogramming and reactivation while the primordial germ cells form clusters and proliferate in the genital ridge.
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Affiliation(s)
- Yoshikazu Haramoto
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Mino Sakata
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Shin Kobayashi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koutou-ku, Tokyo 135-0064, Japan.,Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
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4
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Kundu P, Pant I, Jain R, Rao SG, Kondaiah P. Genome-wide DNA methylation changes in oral submucous fibrosis. Oral Dis 2021; 28:1094-1103. [PMID: 33615634 DOI: 10.1111/odi.13811] [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: 11/06/2020] [Revised: 01/08/2021] [Accepted: 02/15/2021] [Indexed: 12/23/2022]
Abstract
OBJECTIVE Oral submucous fibrosis (OSF) is a debilitating potentially malignant condition of the buccal cavity characterized by extensive extracellular matrix deposition resulting in stiffness and trismus. As OSF is a progressive disease, we hypothesized that there would be extensive epigenetic changes in OSF tissues. MATERIALS AND METHODS Using the Infinium HumanMethylation450 BeadChip Array, we analyzed gross DNA methylation changes in seven OSF tissues compared to five controls. Comparison with transcriptomic data and pathway analyses was conducted to find commonly regulated genes. RESULTS A total of 3,294 differentially methylated regions mapping to 857 genes were identified. Comparison with transcriptome data revealed 38 downregulated-hypermethylated genes and 55 hypomethylated-upregulated genes. Using methylation-specific and qRT-PCR, aberrant hypomethylation and increased expression of FGF13, RPS6KA3, and ACSL4 genes were confirmed. Pathways involved in insulin signaling, ubiquitin-mediated proteolysis, nicotine addiction, and RAS/MAPK pathways were dysregulated, among others. Intriguingly, numerous genes located on the X chromosome were dysregulated in OSF tissues as the transcript for XIST gene was downregulated due to hypermethylation of the XIST promoter. CONCLUSIONS This study highlights global epigenetic dysregulation of tissues of the oral cavity in OSF patients and hints at possible X chromosomal dysregulation, previously not implicated in the pathogenesis of OSF.
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Affiliation(s)
- Paramita Kundu
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Ila Pant
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Ruchi Jain
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Somanahalli Girish Rao
- Department of Oral and Maxillofacial Surgery, D.A Pandu Memorial RV Dental College, Bangalore, India
| | - Paturu Kondaiah
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
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Advance in the Role of Epigenetic Reprogramming in Somatic Cell Nuclear Transfer-Mediated Embryonic Development. Stem Cells Int 2021; 2021:6681337. [PMID: 33628270 PMCID: PMC7880704 DOI: 10.1155/2021/6681337] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/06/2021] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
Somatic cell nuclear transfer (SCNT) enables terminally differentiated somatic cells to gain totipotency. Many species are successfully cloned up to date, including nonhuman primate. With this technology, not only the protection of endangered animals but also human therapeutics is going to be a reality. However, the low efficiency of the SCNT-mediated reprogramming and the defects of extraembryonic tissues as well as abnormalities of cloned individuals limit the application of reproductive cloning on animals. Also, due to the scarcity of human oocytes, low efficiency of blastocyst development and embryonic stem cell line derivation from nuclear transfer embryo (ntESCs), it is far away from the application of this technology on human therapeutics to date. In recent years, multiple epigenetic barriers are reported, which gives us clues to improve reprogramming efficiency. Here, we reviewed the reprogramming process and reprogramming defects of several important epigenetic marks and highlighted epigenetic barriers that may lead to the aberrant reprogramming. Finally, we give our insights into improving the efficiency and quality of SCNT-mediated reprogramming.
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6
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Panda A, Zylicz JJ, Pasque V. New Insights into X-Chromosome Reactivation during Reprogramming to Pluripotency. Cells 2020; 9:E2706. [PMID: 33348832 PMCID: PMC7766869 DOI: 10.3390/cells9122706] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Dosage compensation between the sexes results in one X chromosome being inactivated during female mammalian development. Chromosome-wide transcriptional silencing from the inactive X chromosome (Xi) in mammalian cells is erased in a process termed X-chromosome reactivation (XCR), which has emerged as a paradigm for studying the reversal of chromatin silencing. XCR is linked with germline development and induction of naive pluripotency in the epiblast, and also takes place upon reprogramming somatic cells to induced pluripotency. XCR depends on silencing of the long non-coding RNA (lncRNA) X inactive specific transcript (Xist) and is linked with the erasure of chromatin silencing. Over the past years, the advent of transcriptomics and epigenomics has provided new insights into the transcriptional and chromatin dynamics with which XCR takes place. However, multiple questions remain unanswered about how chromatin and transcription related processes enable XCR. Here, we review recent work on establishing the transcriptional and chromatin kinetics of XCR, as well as discuss a model by which transcription factors mediate XCR not only via Xist repression, but also by direct targeting of X-linked genes.
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Affiliation(s)
- Amitesh Panda
- Laboratory of Cellular Reprogramming and Epigenetic Regulation, Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven-University of Leuven, 3000 Leuven, Belgium;
| | - Jan J. Zylicz
- The Novo Nordisk Foundation Center for Stem Cell Biology, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - Vincent Pasque
- Laboratory of Cellular Reprogramming and Epigenetic Regulation, Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven-University of Leuven, 3000 Leuven, Belgium;
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7
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Kanwal S, Guo X, Ward C, Volpe G, Qin B, Esteban MA, Bao X. Role of Long Non-coding RNAs in Reprogramming to Induced Pluripotency. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:16-25. [PMID: 32445708 PMCID: PMC7393543 DOI: 10.1016/j.gpb.2019.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 05/25/2019] [Accepted: 06/26/2019] [Indexed: 12/13/2022]
Abstract
The generation of induced pluripotent stem cells through somatic cell reprogramming requires a global reorganization of cellular functions. This reorganization occurs in a multi-phased manner and involves a gradual revision of both the epigenome and transcriptome. Recent studies have shown that the large-scale transcriptional changes observed during reprogramming also apply to long non-coding RNAs (lncRNAs), a type of traditionally neglected RNA species that are increasingly viewed as critical regulators of cellular function. Deeper understanding of lncRNAs in reprogramming may not only help to improve this process but also have implications for studying cell plasticity in other contexts, such as development, aging, and cancer. In this review, we summarize the current progress made in profiling and analyzing the role of lncRNAs in various phases of somatic cell reprogramming, with emphasis on the re-establishment of the pluripotency gene network and X chromosome reactivation.
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Affiliation(s)
- Shahzina Kanwal
- (1)Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Guangzhou 511436, China; (2)Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (3)Laboratory of RNA, Chromatin, and Human Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (4)Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou 510005, China
| | - Xiangpeng Guo
- (1)Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Guangzhou 511436, China; (2)Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (3)Laboratory of RNA, Chromatin, and Human Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (4)Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou 510005, China
| | - Carl Ward
- (1)Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Guangzhou 511436, China; (2)Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (3)Laboratory of RNA, Chromatin, and Human Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (4)Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou 510005, China
| | - Giacomo Volpe
- (1)Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Guangzhou 511436, China; (2)Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (3)Laboratory of RNA, Chromatin, and Human Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (4)Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou 510005, China
| | - Baoming Qin
- (1)Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Guangzhou 511436, China; (2)Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (3)Laboratory of RNA, Chromatin, and Human Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (5)Laboratory of Metabolism and Cell Fate, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Miguel A Esteban
- (1)Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Guangzhou 511436, China; (2)Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (3)Laboratory of RNA, Chromatin, and Human Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (4)Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou 510005, China; (6)Institute for Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xichen Bao
- (1)Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Guangzhou 511436, China; (2)Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (4)Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou 510005, China; (7)Laboratory of RNA Molecular Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
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8
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Mendonça ADS, Silveira MM, Rios ÁFL, Mangiavacchi PM, Caetano AR, Dode MAN, Franco MM. DNA methylation and functional characterization of the XIST gene during in vitro early embryo development in cattle. Epigenetics 2019; 14:568-588. [PMID: 30925851 DOI: 10.1080/15592294.2019.1600828] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
XIST, in association with the shorter ncRNA RepA, are essential for the initiation of X chromosome inactivation (XCI) in mice. The molecular mechanisms controlling XIST and RepA expression are well characterized in that specie. However, little is known in livestock. We aimed to characterize the DNA methylation status along the 5' portion of XIST and to characterize its transcriptional profile during early development in cattle. Three genomic regions of XIST named here as promoter, RepA and DMR1 had their DNA methylation status characterized in gametes and embryos. Expression profile of XIST was evaluated, including sense and antisense transcription. Oocytes showed higher levels of methylation than spermatozoa that was demethylated. DMR1 was hypermethylated throughout oogenesis. At the 8-16-cell embryo stage DMR1 was completed demethylated. Interestingly, RepA gain methylation during oocyte maturation and was demethylated at the blastocyst stage, later than DMR1. These results suggest that DMR1 and RepA are transient differentially methylated regions in cattle. XIST RNA was detected in matured oocytes and in single cells from the 2-cell to the morula stage, confirming the presence of maternal and embryonic transcripts. Sense and antisense transcripts were detected along the XIST in blastocyst. In silico analysis identified 63 novel transcript candidates at bovine XIST locus from both the plus and minus strands. Taking together these results improve our understanding of the molecular mechanisms involved in XCI initiation in cattle. This information may be useful for the improvement of assisted reproductive technologies in livestock considering that in vitro conditions may impair epigenetic reprogramming.
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Affiliation(s)
- Anelise Dos Santos Mendonça
- a Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology , Parque Estação Biológica , Brasília , Brazil.,b Institute of Genetics and Biochemistry , Federal University of Uberlândia , Umuarama , Brazil.,c Federal Institute of Education, Science and Technology of Piauí , Uruçuí Campus , Portal dos Cerrados , Brazil
| | - Márcia Marques Silveira
- a Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology , Parque Estação Biológica , Brasília , Brazil.,b Institute of Genetics and Biochemistry , Federal University of Uberlândia , Umuarama , Brazil
| | - Álvaro Fabrício Lopes Rios
- d Biotechnology Laboratory, Center of Biosciences and Biotechnology , North Fluminense State University , Campos dos Goytacazes , Brazil
| | - Paula Magnelli Mangiavacchi
- e Laboratory of Reproduction and Animal Genetic Improvement, Center for Agricultural Sciences and Technologies , North Fluminense State University , Campos dos Goytacazes , Brazil
| | - Alexandre Rodrigues Caetano
- f Embrapa Genetic Resources and Biotechnology , Parque Estação Biológica , Brasília , Brazil.,g School of Agriculture and Veterinary Medicine , University of Brasília, Darcy Ribeiro Campus , Brasília , Brazil
| | - Margot Alves Nunes Dode
- a Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology , Parque Estação Biológica , Brasília , Brazil.,g School of Agriculture and Veterinary Medicine , University of Brasília, Darcy Ribeiro Campus , Brasília , Brazil
| | - Maurício Machaim Franco
- a Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology , Parque Estação Biológica , Brasília , Brazil.,b Institute of Genetics and Biochemistry , Federal University of Uberlândia , Umuarama , Brazil.,h Faculty of Veterinary Medicine , Federal University of Uberlândia , Umuarama , Brazil
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9
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Cheng S, Pei Y, He L, Peng G, Reinius B, Tam PP, Jing N, Deng Q. Single-Cell RNA-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X Chromosome Dynamics during Early Mouse Development. Cell Rep 2019; 26:2593-2607.e3. [DOI: 10.1016/j.celrep.2019.02.031] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/29/2018] [Accepted: 02/08/2019] [Indexed: 01/13/2023] Open
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10
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Abstract
Mammalian sex chromosomes evolved from an ordinary pair of autosomes. The X chromosome is highly conserved, whereas the Y chromosome varies among species in size, structure, and gene content. Unlike autosomes that contain randomly mixed collections of genes, the sex chromosomes are enriched in testis-biased genes related to sexual development and reproduction, particularly in spermatogenesis and male fertility. This review focuses on how sex chromosome dosage compensation takes place and why meiotic sex chromosome inactivation occurs during spermatogenesis. Furthermore, the review also emphasizes how testis-biased genes are enriched on the sex chromosomes and their functions in male fertility. It is concluded that sex chromosomes are critical to sexual development and male fertility; however, our understanding of how sex chromosome genes direct sexual development and fertility has been hampered by the structural complexities of the sex chromosomes and by the multicopy nature of the testis gene families that also play a role in immunity, cancer development, and brain function.
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Affiliation(s)
- Wan-Sheng Liu
- Department of Animal Science, Center for Reproductive Biology and Health, College of Agricultural Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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11
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Lobo J, Gillis AJM, Jerónimo C, Henrique R, Looijenga LHJ. Human Germ Cell Tumors are Developmental Cancers: Impact of Epigenetics on Pathobiology and Clinic. Int J Mol Sci 2019; 20:E258. [PMID: 30634670 PMCID: PMC6359418 DOI: 10.3390/ijms20020258] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 12/25/2018] [Accepted: 01/07/2019] [Indexed: 02/03/2023] Open
Abstract
Current (high throughput omics-based) data support the model that human (malignant) germ cell tumors are not initiated by somatic mutations, but, instead through a defined locked epigenetic status, representative of their cell of origin. This elegantly explains the role of both genetic susceptibility as well as environmental factors in the pathogenesis, referred to as 'genvironment'. Moreover, it could also explain various epidemiological findings, including the rising incidence of this type of cancer in Western societies. In addition, it allows for identification of clinically relevant and informative biomarkers both for diagnosis and follow-up of individual patients. The current status of these findings will be discussed, including the use of high throughput DNA methylation profiling for determination of differentially methylated regions (DMRs) as well as chromosomal copy number variation (CNV). Finally, the potential value of methylation-specific tumor DNA fragments (i.e., XIST promotor) as well as embryonic microRNAs as molecular biomarkers for cancer detection in liquid biopsies will be presented.
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Affiliation(s)
- João Lobo
- Cancer Biology and Epigenetics Group, Research Center of Portuguese Oncology Institute of Porto (GEBC CI-IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal;.
| | - Ad J M Gillis
- Laboratory of Experimental Patho-Oncology (LEPO), Josephine Nefkens Building, Erasmus MC, Department of Pathology, University Medical Center, Cancer Institute, Be-432A, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands.
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center of Portuguese Oncology Institute of Porto (GEBC CI-IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal;.
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center of Portuguese Oncology Institute of Porto (GEBC CI-IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal;.
| | - Leendert H J Looijenga
- Laboratory of Experimental Patho-Oncology (LEPO), Josephine Nefkens Building, Erasmus MC, Department of Pathology, University Medical Center, Cancer Institute, Be-432A, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands.
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12
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Duan JE, Shi W, Jue NK, Jiang Z, Kuo L, O'Neill R, Wolf E, Dong H, Zheng X, Chen J, Tian XC. Dosage Compensation of the X Chromosomes in Bovine Germline, Early Embryos, and Somatic Tissues. Genome Biol Evol 2019; 11:242-252. [PMID: 30566637 PMCID: PMC6354180 DOI: 10.1093/gbe/evy270] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2018] [Indexed: 12/15/2022] Open
Abstract
Dosage compensation of the mammalian X chromosome (X) was proposed by Susumu Ohno as a mechanism wherein the inactivation of one X in females would lead to doubling the expression of the other. This would resolve the dosage imbalance between eutherian females (XX) versus male (XY) and between a single active X versus autosome pairs (A). Expression ratio of X- and A-linked genes has been relatively well studied in humans and mice, despite controversial results over the existence of upregulation of X-linked genes. Here we report the first comprehensive test of Ohno’s hypothesis in bovine preattachment embryos, germline, and somatic tissues. Overall an incomplete dosage compensation (0.5 < X:A < 1) of expressed genes and an excess X dosage compensation (X:A > 1) of ubiquitously expressed “dosage-sensitive” genes were seen. No significant differences in X:A ratios were observed between bovine female and male somatic tissues, further supporting Ohno’s hypothesis. Interestingly, preimplantation embryos manifested a unique pattern of X dosage compensation dynamics. Specifically, X dosage decreased after fertilization, indicating that the sperm brings in an inactive X to the matured oocyte. Subsequently, the activation of the bovine embryonic genome enhanced expression of X-linked genes and increased the X dosage. As a result, an excess compensation was exhibited from the 8-cell stage to the compact morula stage. The X dosage peaked at the 16-cell stage and stabilized after the blastocyst stage. Together, our findings confirm Ohno’s hypothesis of X dosage compensation in the bovine and extend it by showing incomplete and over-compensation for expressed and “dosage-sensitive” genes, respectively.
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Affiliation(s)
| | - Wei Shi
- Department of Statistics, University of Connecticut, Storrs, CT
| | - Nathaniel K Jue
- School of Natural Sciences, California State University, Monterey Bay, CA
| | - Zongliang Jiang
- School of Animal Science, Louisiana State University, Agricultural Center, Baton Rouge, LA
| | - Lynn Kuo
- Department of Statistics, University of Connecticut, Storrs, CT
| | - Rachel O'Neill
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT
| | - Eckhard Wolf
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität Muünchen, Germany
| | - Hong Dong
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, P.R. China
| | - Xinbao Zheng
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, P.R. China
| | - Jingbo Chen
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, P.R. China
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13
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Galupa R, Heard E. X-Chromosome Inactivation: A Crossroads Between Chromosome Architecture and Gene Regulation. Annu Rev Genet 2018; 52:535-566. [PMID: 30256677 DOI: 10.1146/annurev-genet-120116-024611] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In somatic nuclei of female therian mammals, the two X chromosomes display very different chromatin states: One X is typically euchromatic and transcriptionally active, and the other is mostly silent and forms a cytologically detectable heterochromatic structure termed the Barr body. These differences, which arise during female development as a result of X-chromosome inactivation (XCI), have been the focus of research for many decades. Initial approaches to define the structure of the inactive X chromosome (Xi) and its relationship to gene expression mainly involved microscopy-based approaches. More recently, with the advent of genomic techniques such as chromosome conformation capture, molecular details of the structure and expression of the Xi have been revealed. Here, we review our current knowledge of the 3D organization of the mammalian X-chromosome chromatin and discuss its relationship with gene activity in light of the initiation, spreading, and maintenance of XCI, as well as escape from gene silencing.
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Affiliation(s)
- Rafael Galupa
- Genetics and Developmental Biology Unit and Mammalian Developmental Epigenetics Group, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, 75248 Paris, France; .,Current affiliation: Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Edith Heard
- Genetics and Developmental Biology Unit and Mammalian Developmental Epigenetics Group, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, 75248 Paris, France; .,Collège de France, 75231 Paris, France
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14
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Live-Cell Imaging and Functional Dissection of Xist RNA Reveal Mechanisms of X Chromosome Inactivation and Reactivation. iScience 2018; 8:1-14. [PMID: 30266032 PMCID: PMC6159346 DOI: 10.1016/j.isci.2018.09.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 09/04/2018] [Accepted: 09/07/2018] [Indexed: 11/24/2022] Open
Abstract
We double-tagged Xist (inactivated X chromosome-specific transcript), a prototype long non-coding RNA pivotal for X chromosome inactivation (XCI), using the programmable RNA sequence binding domain of Pumilio protein, one tag for live-cell imaging and the other replacing A-repeat (a critical domain of Xist) to generate “ΔA mutant” and to tether effector proteins for dissecting Xist functionality. Based on the observation in live cells that the induced XCI in undifferentiated embryonic stem (ES) cells is counteracted by the intrinsic X chromosome reactivation (XCR), we identified Kat8 and Msl2, homologs of Drosophila dosage compensation proteins, as players involved in mammalian XCR. Furthermore, live-cell imaging revealed the obviously undersized ΔA Xist cloud signals, clarifying an issue regarding the previous RNA fluorescence in situ hybridization results. Tethering candidate proteins onto the ΔA mutant reveals the significant roles of Ythdc1, Ezh2, and SPOC (Spen) in Xist-mediated gene silencing and the significant role of Ezh2 in Xist RNA spreading. A Pumilio-based system allows efficient double-tagging of Xist RNA in live cells Induced XCI in undifferentiated ES cells reveals the roles of Kat8 and Msl2 in XCR Live-cell imaging reveals the undersized “ΔA mutant” Xist signals Tethering proteins onto “ΔA mutant” reveals their role in Xist-mediated silencing
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15
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Cantone I, Fisher AG. Human X chromosome inactivation and reactivation: implications for cell reprogramming and disease. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0358. [PMID: 28947657 DOI: 10.1098/rstb.2016.0358] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2017] [Indexed: 11/12/2022] Open
Abstract
X-chromosome inactivation (XCI) is an exemplar of epigenetic regulation that is set up as pluripotent cells differentiate. Once established, XCI is stably propagated, but can be reversed in vivo or by pluripotent reprogramming in vitro Although reprogramming provides a useful model for inactive X (Xi) reactivation in mouse, the relative instability and heterogeneity of human embryonic stem (ES) cells and induced pluripotent stem cells hampers comparable progress in human. Here we review studies aimed at reactivating the human Xi using different reprogramming strategies. We outline our recent results using mouse ES cells to reprogramme female human fibroblasts by cell-cell fusion. We show that pluripotent reprogramming induces widespread and rapid chromatin remodelling in which the human Xi loses XIST and H3K27m3 enrichment and selected Xi genes become reactivated, ahead of mitotic division. Using RNA sequencing to map the extent of human Xi reactivation, and chromatin-modifying drugs to potentiate reactivation, we outline how this approach could be used to better design strategies to re-express human X-linked loci. As cell fusion induces the expression of human pluripotency genes that represent both the 'primed' and 'naive' states, this approach may also offer a fresh opportunity to segregate human pluripotent states with distinct Xi expression profiles, using single-cell-based approaches.This article is part of the themed issue 'X-chromosome inactivation: a tribute to Mary Lyon'.
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Affiliation(s)
- Irene Cantone
- Lymphocyte Development, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK
| | - Amanda G Fisher
- Lymphocyte Development, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK .,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
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16
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Takahashi S, Kobayashi S, Hiratani I. Epigenetic differences between naïve and primed pluripotent stem cells. Cell Mol Life Sci 2018; 75:1191-1203. [PMID: 29134247 PMCID: PMC5843680 DOI: 10.1007/s00018-017-2703-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/22/2017] [Accepted: 10/30/2017] [Indexed: 02/07/2023]
Abstract
It has been 8 years since the concept of naïve and primed pluripotent stem cell states was first proposed. Both are states of pluripotency, but exhibit slightly different properties. The naïve state represents the cellular state of the preimplantation mouse blastocyst inner cell mass, while the primed state is representative of the post-implantation epiblast cells. These two cell types exhibit clearly distinct developmental potential, as evidenced by the fact that naïve cells are able to contribute to blastocyst chimeras, while primed cells cannot. However, the epigenetic differences that underlie the distinct developmental potential of these cell types remain unclear, which is rather surprising given the large amount of active investigation over the years. Elucidating such epigenetic differences should lead to a better understanding of the fundamental properties of these states of pluripotency and the means by which the naïve-to-primed transition occurs, which may provide insights into the essence of stem cell commitment.
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Affiliation(s)
- Saori Takahashi
- Laboratory for Developmental Epigenetics, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Shin Kobayashi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koutou-ku, Tokyo, 135-0064, Japan.
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
| | - Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
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17
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Tao C, Li J, Zhang X, Chen B, Chi D, Zeng Y, Niu Y, Wang C, Cheng W, Wu W, Pan Z, Lian J, Liu H, Miao YL. Dynamic Reorganization of Nucleosome Positioning in Somatic Cells after Transfer into Porcine Enucleated Oocytes. Stem Cell Reports 2017; 9:642-653. [PMID: 28689997 PMCID: PMC5549837 DOI: 10.1016/j.stemcr.2017.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 06/06/2017] [Accepted: 06/06/2017] [Indexed: 11/30/2022] Open
Abstract
The nucleosome, the fundamental structural unit of chromatin, is a critical regulator of gene expression. The mechanisms governing changes to nucleosome occupancy and positioning during somatic cell reprogramming remain poorly understood. We established a method for generating genome-wide nucleosome maps of porcine embryonic fibroblasts (PEF), reconstructed 1-cell embryos generated by somatic cell nuclear transfer (SCNT), and fertilized zygotes (FZ) using MNase sequencing with only 1,000 cells. We found that donor PEF chromatin, especially X chromosome, became more open after transfer into porcine oocytes and nucleosome occupancy decreased in promoters but increased in the genic regions. Nucleosome arrangements around transcriptional start sites of genes with different expression levels in somatic cells tended to become transcriptionally silent in SCNT; however, some pluripotency genes adopted transcriptionally active nucleosome arrangements. FZ and SCNT had similar characteristics, unlike PEF. This study reveals the dynamics and importance of nucleosome positioning and chromatin organization early after reprogramming.
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Affiliation(s)
- Chenyu Tao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Juan Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xia Zhang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Baobao Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Daming Chi
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yaqiong Zeng
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yingjie Niu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Chengfei Wang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Wei Cheng
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Wangjun Wu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zengxiang Pan
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | | | - Honglin Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China.
| | - Yi-Liang Miao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China.
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18
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Abstract
The epigenetic phenomenon called X chromosome inactivation plays critical roles in female development in eutherian mammals, and has attracted attention in the fields of developmental biology and regenerative biology in efforts to understand the pluripotency of stem cells. X chromosome inactivation is routinely studied after cell fixation, but live imaging is increasingly being required to improve our understanding of the dynamics and kinetics of X chromosome inactivation and reactivation processes. Here, we describe our live imaging method to monitor the epigenetic status of X chromosomes using a gene knock-in mouse strain named "Momiji" and give an overview of the application of this strain as a resource for biological and stem cell research.
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Affiliation(s)
- Shin Kobayashi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koutou-ku, Tokyo, 135-0064, Japan.,Department of Epigenetics, Medical Research Institute, Tokyo Medical & Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
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19
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Lyu C, Shen J, Zhang J, Xue F, Liu X, Liu W, Fu R, Zhang L, Li H, Zhang D, Zhang X, Cheng T, Yang R, Zhang L. The State of Skewed X Chromosome Inactivation is Retained in the Induced Pluripotent Stem Cells from a Female with Hemophilia B. Stem Cells Dev 2017; 26:1003-1011. [PMID: 28401797 DOI: 10.1089/scd.2016.0323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Skewed X chromosome inactivation (XCI) is a rare reason for hemophilia B in females. It is indefinite whether X chromosome reactivation (XCR) would occur when cells of hemophilia B patients with skewed XCI were reprogrammed into induced pluripotent stem cells (iPSCs). In this study, we investigated a female hemophilia B patient with a known F9 gene mutation: c.676C>T, p.Arg226Trp. We demonstrated that skewed XCI was the pathogenesis of the patient, and we successfully generated numerous iPSC colonies of the patient from peripheral blood mononuclear cells (PBMNCs), which was the first time for generating hemophilia-specific iPSCs from PBMNCs. Then we detected the XCI state of these iPSCs. Ninety-two iPSC lines were picked for XCI analysis. All of them retained an inactive X chromosome, which could be proved by amplification of the androgen receptor gene and XIST (X inactivation-specific transcript), expression of H3K27me3, and existence of XIST clouds in XIST RNA fluorescence in situ hybridization (FISH) analysis. We attempted to obtain iPSC lines with the wild-type F9 gene on the active X chromosome for further disease treatment. But it turned out that the patient's iPSCs were still skewed such as the somatic cells with 92 iPSC lines having mutant F9 on the active X chromosome. In conclusion, skewed XCI is one reason for hemophilia in females. PBMNCs are excellent somatic cell resources for hemophilia patients to do reprogramming. More attentions should be paid to generate naive iPSCs with two active X chromosomes for further clinical disease treatment. The state of skewed XCI is retained in the iPSCs from a female with hemophilia B.
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Affiliation(s)
- Cuicui Lyu
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China .,2 Department of Hematology, The First Central Hospital of Tianjin , Tianjin, China
| | - Jun Shen
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Jianping Zhang
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Feng Xue
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Xiaofan Liu
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Wei Liu
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Rongfeng Fu
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Liyan Zhang
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Huiyuan Li
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Donglei Zhang
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Xiaobing Zhang
- 3 Division of Regenerative Medicine MC1528B, Department of Medicine, Loma Linda University , Loma Linda, California
| | - Tao Cheng
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Renchi Yang
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Lei Zhang
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
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20
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Cantone I, Dharmalingam G, Chan YW, Kohler AC, Lenhard B, Merkenschlager M, Fisher AG. Allele-specific analysis of cell fusion-mediated pluripotent reprograming reveals distinct and predictive susceptibilities of human X-linked genes to reactivation. Genome Biol 2017; 18:2. [PMID: 28118853 PMCID: PMC5264468 DOI: 10.1186/s13059-016-1136-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/14/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Inactivation of one X chromosome is established early in female mammalian development and can be reversed in vivo and in vitro when pluripotency factors are re-expressed. The extent of reactivation along the inactive X chromosome (Xi) and the determinants of locus susceptibility are, however, poorly understood. Here we use cell fusion-mediated pluripotent reprograming to study human Xi reactivation and allele-specific single nucleotide polymorphisms (SNPs) to identify reactivated loci. RESULTS We show that a subset of human Xi genes is rapidly reactivated upon re-expression of the pluripotency network. These genes lie within the most evolutionary recent segments of the human X chromosome that are depleted of LINE1 and enriched for SINE elements, predicted to impair XIST spreading. Interestingly, this cadre of genes displays stochastic Xi expression in human fibroblasts ahead of reprograming. This stochastic variability is evident between clones, by RNA-sequencing, and at the single-cell level, by RNA-FISH, and is not attributable to differences in repressive histone H3K9me3 or H3K27me3 levels. Treatment with the DNA demethylating agent 5-deoxy-azacytidine does not increase Xi expression ahead of reprograming, but instead reveals a second cadre of genes that only become susceptible to reactivation upon induction of pluripotency. CONCLUSIONS Collectively, these data not only underscore the multiple pathways that contribute to maintaining silencing along the human Xi chromosome but also suggest that transcriptional stochasticity among human cells could be useful for predicting and engineering epigenetic strategies to achieve locus-specific or domain-specific human Xi gene reactivation.
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Affiliation(s)
- Irene Cantone
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Hammersmith Campus, Imperial College London, Du Cane Road, London, W12 0NN, UK.
| | - Gopuraja Dharmalingam
- Bioinformatics and Computing facility, MRC London Institute of Medical Sciences, Imperial College, London, UK
| | - Yi-Wah Chan
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Hammersmith Campus, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Anne-Celine Kohler
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Hammersmith Campus, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Boris Lenhard
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Imperial College, London, UK
| | - Matthias Merkenschlager
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Hammersmith Campus, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Amanda G Fisher
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Hammersmith Campus, Imperial College London, Du Cane Road, London, W12 0NN, UK.
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21
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Abstract
X-chromosome inactivation, which was discovered by Mary Lyon in 1961 results in random silencing of one X chromosome in female mammals. This review is dedicated to Mary Lyon, who passed away last year. She predicted many of the features of X inactivation, for e.g., the existence of an X inactivation center, the role of L1 elements in spreading of silencing and the existence of genes that escape X inactivation. Starting from her published work here we summarize advances in the field.
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22
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Muñoz-López A, Romero-Moya D, Prieto C, Ramos-Mejía V, Agraz-Doblas A, Varela I, Buschbeck M, Palau A, Carvajal-Vergara X, Giorgetti A, Ford A, Lako M, Granada I, Ruiz-Xivillé N, Rodríguez-Perales S, Torres-Ruíz R, Stam RW, Fuster JL, Fraga MF, Nakanishi M, Cazzaniga G, Bardini M, Cobo I, Bayon GF, Fernandez AF, Bueno C, Menendez P. Development Refractoriness of MLL-Rearranged Human B Cell Acute Leukemias to Reprogramming into Pluripotency. Stem Cell Reports 2016; 7:602-618. [PMID: 27666791 PMCID: PMC5063541 DOI: 10.1016/j.stemcr.2016.08.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 01/09/2023] Open
Abstract
Induced pluripotent stem cells (iPSCs) are a powerful tool for disease modeling. They are routinely generated from healthy donors and patients from multiple cell types at different developmental stages. However, reprogramming leukemias is an extremely inefficient process. Few studies generated iPSCs from primary chronic myeloid leukemias, but iPSC generation from acute myeloid or lymphoid leukemias (ALL) has not been achieved. We attempted to generate iPSCs from different subtypes of B-ALL to address the developmental impact of leukemic fusion genes. OKSM(L)-expressing mono/polycistronic-, retroviral/lentiviral/episomal-, and Sendai virus vector-based reprogramming strategies failed to render iPSCs in vitro and in vivo. Addition of transcriptomic-epigenetic reprogramming “boosters” also failed to generate iPSCs from B cell blasts and B-ALL lines, and when iPSCs emerged they lacked leukemic fusion genes, demonstrating non-leukemic myeloid origin. Conversely, MLL-AF4-overexpressing hematopoietic stem cells/B progenitors were successfully reprogrammed, indicating that B cell origin and leukemic fusion gene were not reprogramming barriers. Global transcriptome/DNA methylome profiling suggested a developmental/differentiation refractoriness of MLL-rearranged B-ALL to reprogramming into pluripotency. Neither primary B-ALL blasts nor leukemic B cell lines can be reprogrammed to iPSCs Global transcriptome and DNA methylome suggest a developmental refractoriness
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Affiliation(s)
- Alvaro Muñoz-López
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain; Department of Biomedicine, School of Medicine, University of Barcelona, 08036 Barcelona, Spain
| | - Damià Romero-Moya
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain; Department of Biomedicine, School of Medicine, University of Barcelona, 08036 Barcelona, Spain
| | - Cristina Prieto
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain; Department of Biomedicine, School of Medicine, University of Barcelona, 08036 Barcelona, Spain
| | - Verónica Ramos-Mejía
- Genomic Oncology Department, Centre for Genomics and Oncology GENyO, 18016 Granada, Spain
| | - Antonio Agraz-Doblas
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain; Department of Biomedicine, School of Medicine, University of Barcelona, 08036 Barcelona, Spain; IBBTEC, CSIC-University of Cantabria, 39011 Santander, Spain
| | - Ignacio Varela
- IBBTEC, CSIC-University of Cantabria, 39011 Santander, Spain
| | - Marcus Buschbeck
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain
| | - Anna Palau
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain
| | - Xonia Carvajal-Vergara
- Cell Therapy Department, Centro de Investigación Médica Aplicada (CIMA), 31008 Pamplona, Spain
| | - Alessandra Giorgetti
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain
| | - Anthony Ford
- Centre for Evolution and Cancer, Institute of Cancer Research, London SW7 3RP, UK
| | - Majlinda Lako
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 7RU, UK
| | - Isabel Granada
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain; Hematology Department, Hospital Germans Trias i Pujol, Institut Català d'Oncología, 08916 Badalona, Spain
| | - Neus Ruiz-Xivillé
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain; Hematology Department, Hospital Germans Trias i Pujol, Institut Català d'Oncología, 08916 Badalona, Spain
| | | | - Raul Torres-Ruíz
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain; Cytogenetics Group, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029 Madrid, Spain
| | - Ronald W Stam
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center, Erasmus University, 3015 CN Rotterdam, the Netherlands
| | - Jose Luis Fuster
- Department of Pediatric Oncohematology, Clinical University Hospital Virgen de la Arrixaca, 30120 Murcia, Spain
| | - Mario F Fraga
- Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA-HUCA), Universidad de Oviedo, 33003 Oviedo, Spain
| | - Mahito Nakanishi
- Research Center for Stem Cell Engineering, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraka 305-0046, Japan
| | - Gianni Cazzaniga
- University di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, 20052 Monza MB, Italy
| | - Michela Bardini
- University di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, 20052 Monza MB, Italy
| | - Isabel Cobo
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain; Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA-HUCA), Universidad de Oviedo, 33003 Oviedo, Spain
| | - Gustavo F Bayon
- Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA-HUCA), Universidad de Oviedo, 33003 Oviedo, Spain
| | - Agustin F Fernandez
- Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA-HUCA), Universidad de Oviedo, 33003 Oviedo, Spain
| | - Clara Bueno
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain; Department of Biomedicine, School of Medicine, University of Barcelona, 08036 Barcelona, Spain.
| | - Pablo Menendez
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain; Department of Biomedicine, School of Medicine, University of Barcelona, 08036 Barcelona, Spain; Instituciò Catalana de Recerca i Estudis Avançats (ICREA), 08036 Barcelona, Spain.
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23
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Petropoulos S, Panula SP, Schell JP, Lanner F. Single-cell RNA sequencing: revealing human pre-implantation development, pluripotency and germline development. J Intern Med 2016; 280:252-64. [PMID: 27046137 DOI: 10.1111/joim.12493] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Early human development is a dynamic, heterogeneous, complex and multidimensional process. During the first week, the single-cell zygote undergoes eight to nine rounds of cell division generating the multicellular blastocyst, which consists of hundreds of cells forming spatially organized embryonic and extra-embryonic tissues. At the level of transcription, degradation of maternal RNA commences at around the two-cell stage, coinciding with embryonic genome activation. Although numerous efforts have recently focused on delineating this process in humans, many questions still remain as thorough investigation has been limited by ethical issues, scarce availability of human embryos and the presence of minute amounts of DNA and RNA. In vitro cultures of embryonic stem cells provide some insight into early human development, but such studies have been confounded by analysis on a population level failing to appreciate cellular heterogeneity. Recent technical developments in single-cell RNA sequencing have provided a novel and powerful tool to explore the early human embryo in a systematic manner. In this review, we will discuss the advantages and disadvantages of the techniques utilized to specifically investigate human development and consider how the technology has yielded new insights into pre-implantation development, embryonic stem cells and the establishment of the germ line.
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Affiliation(s)
- S Petropoulos
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet and, Division of Obstetrics and Gynecology, Karolinska University Hospital, Stockholm, Sweden.,Ludwig Institute for Cancer Research, Stockholm, Sweden
| | - S P Panula
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet and, Division of Obstetrics and Gynecology, Karolinska University Hospital, Stockholm, Sweden
| | - J P Schell
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet and, Division of Obstetrics and Gynecology, Karolinska University Hospital, Stockholm, Sweden
| | - F Lanner
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet and, Division of Obstetrics and Gynecology, Karolinska University Hospital, Stockholm, Sweden
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24
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Ordered chromatin changes and human X chromosome reactivation by cell fusion-mediated pluripotent reprogramming. Nat Commun 2016; 7:12354. [PMID: 27507283 PMCID: PMC4987517 DOI: 10.1038/ncomms12354] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 06/24/2016] [Indexed: 12/17/2022] Open
Abstract
Erasure of epigenetic memory is required to convert somatic cells towards pluripotency. Reactivation of the inactive X chromosome (Xi) has been used to model epigenetic reprogramming in mouse, but human studies are hampered by Xi epigenetic instability and difficulties in tracking partially reprogrammed iPSCs. Here we use cell fusion to examine the earliest events in the reprogramming-induced Xi reactivation of human female fibroblasts. We show that a rapid and widespread loss of Xi-associated H3K27me3 and XIST occurs in fused cells and precedes the bi-allelic expression of selected Xi-genes by many heterokaryons (30–50%). After cell division, RNA-FISH and RNA-seq analyses confirm that Xi reactivation remains partial and that induction of human pluripotency-specific XACT transcripts is rare (1%). These data effectively separate pre- and post-mitotic events in reprogramming-induced Xi reactivation and reveal a complex hierarchy of epigenetic changes that are required to reactivate the genes on the human Xi chromosome. Reactivation of the inactive X chromosome (Xi) has modelled epigenetic reprogramming in mouse. Here, by using cell fusion between human female fibroblasts and mouse embryonic stem cells, the authors show a complex hierarchy of epigenetic changes that are required to reactivate the genes on the human Xi chromosome.
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25
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Kobayashi S, Hosoi Y, Shiura H, Yamagata K, Takahashi S, Fujihara Y, Kohda T, Okabe M, Ishino F. Live imaging of X chromosome reactivation dynamics in early mouse development can discriminate naïve from primed pluripotent stem cells. Development 2016; 143:2958-64. [PMID: 27471261 DOI: 10.1242/dev.136739] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 07/08/2016] [Indexed: 02/04/2023]
Abstract
Pluripotent stem cells can be classified into two distinct states, naïve and primed, which show different degrees of potency. One difficulty in stem cell research is the inability to distinguish these states in live cells. Studies on female mice have shown that reactivation of inactive X chromosomes occurs in the naïve state, while one of the X chromosomes is inactivated in the primed state. Therefore, we aimed to distinguish the two states by monitoring X chromosome reactivation. Thus far, X chromosome reactivation has been analysed using fixed cells; here, we inserted different fluorescent reporter gene cassettes (mCherry and eGFP) into each X chromosome. Using these knock-in 'Momiji' mice, we detected X chromosome reactivation accurately in live embryos, and confirmed that the pluripotent states of embryos were stable ex vivo, as represented by embryonic and epiblast stem cells in terms of X chromosome reactivation. Thus, Momiji mice provide a simple and accurate method for identifying stem cell status based on X chromosome reactivation.
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Affiliation(s)
- Shin Kobayashi
- Department of Epigenetics, Medical Research Institute, Tokyo Medical & Dental University, 1-5-45 Yushima Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yusuke Hosoi
- Department of Epigenetics, Medical Research Institute, Tokyo Medical & Dental University, 1-5-45 Yushima Bunkyo-ku, Tokyo 113-8510, Japan
| | - Hirosuke Shiura
- Department of Epigenetics, Medical Research Institute, Tokyo Medical & Dental University, 1-5-45 Yushima Bunkyo-ku, Tokyo 113-8510, Japan
| | - Kazuo Yamagata
- Research Institute for Microbial Diseases, Osaka University, Yamadaoka 3-1, Suita, Osaka 565-0871, Japan
| | - Saori Takahashi
- Department of Epigenetics, Medical Research Institute, Tokyo Medical & Dental University, 1-5-45 Yushima Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yoshitaka Fujihara
- Research Institute for Microbial Diseases, Osaka University, Yamadaoka 3-1, Suita, Osaka 565-0871, Japan
| | - Takashi Kohda
- Department of Epigenetics, Medical Research Institute, Tokyo Medical & Dental University, 1-5-45 Yushima Bunkyo-ku, Tokyo 113-8510, Japan
| | - Masaru Okabe
- Research Institute for Microbial Diseases, Osaka University, Yamadaoka 3-1, Suita, Osaka 565-0871, Japan
| | - Fumitoshi Ishino
- Department of Epigenetics, Medical Research Institute, Tokyo Medical & Dental University, 1-5-45 Yushima Bunkyo-ku, Tokyo 113-8510, Japan
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26
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Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture. Proc Natl Acad Sci U S A 2016; 113:E4504-12. [PMID: 27432957 DOI: 10.1073/pnas.1609643113] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
During interphase, the inactive X chromosome (Xi) is largely transcriptionally silent and adopts an unusual 3D configuration known as the "Barr body." Despite the importance of X chromosome inactivation, little is known about this 3D conformation. We recently showed that in humans the Xi chromosome exhibits three structural features, two of which are not shared by other chromosomes. First, like the chromosomes of many species, Xi forms compartments. Second, Xi is partitioned into two huge intervals, called "superdomains," such that pairs of loci in the same superdomain tend to colocalize. The boundary between the superdomains lies near DXZ4, a macrosatellite repeat whose Xi allele extensively binds the protein CCCTC-binding factor. Third, Xi exhibits extremely large loops, up to 77 megabases long, called "superloops." DXZ4 lies at the anchor of several superloops. Here, we combine 3D mapping, microscopy, and genome editing to study the structure of Xi, focusing on the role of DXZ4 We show that superloops and superdomains are conserved across eutherian mammals. By analyzing ligation events involving three or more loci, we demonstrate that DXZ4 and other superloop anchors tend to colocate simultaneously. Finally, we show that deleting DXZ4 on Xi leads to the disappearance of superdomains and superloops, changes in compartmentalization patterns, and changes in the distribution of chromatin marks. Thus, DXZ4 is essential for proper Xi packaging.
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27
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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: 21] [Impact Index Per Article: 2.6] [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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28
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Abstract
X chromosome inactivation (XCI) is the dosage compensation mechanism that evolved in female mammals to correct the genetic imbalance of X-linked genes between sexes. X chromosome inactivation occurs in early development when one of the two X chromosomes of females is nearly-completely silenced. Differentiating Embryonic Stem cells (ESC) are regarded as a useful tool to study XCI, since they recapitulate many events occurring during early development. In this review we aim to summarise the advances in the field and to discuss the close connection between cell differentiation and X chromosome inactivation, with a particular focus on mouse ESCs.
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Affiliation(s)
- Greta Pintacuda
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
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29
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Vacca M, Della Ragione F, Scalabrì F, D'Esposito M. X inactivation and reactivation in X-linked diseases. Semin Cell Dev Biol 2016; 56:78-87. [PMID: 26994527 DOI: 10.1016/j.semcdb.2016.03.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/10/2016] [Accepted: 03/11/2016] [Indexed: 12/22/2022]
Abstract
X chromosome inactivation (XCI) is the phenomenon by which mammals compensate for dosage of X-linked genes in females (XX) versus males (XY). XCI patterns can be random or show extreme skewing, and can modify the mode of inheritance of X-driven phenotypes, which contributes to the variability of human pathologies. Recent findings have shown reversibility of the XCI process, which has opened new avenues in the approaches used for the treatment of X-linked diseases.
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Affiliation(s)
- Marcella Vacca
- Institute of Genetics and Biophysics "A. Buzzati Traverso", CNR, via Pietro Castellino, 111, 80131, Naples, Italy.
| | - Floriana Della Ragione
- Institute of Genetics and Biophysics "A. Buzzati Traverso", CNR, via Pietro Castellino, 111, 80131, Naples, Italy; IRCCS Neuromed, Pozzilli, Isernia, Italy
| | | | - Maurizio D'Esposito
- Institute of Genetics and Biophysics "A. Buzzati Traverso", CNR, via Pietro Castellino, 111, 80131, Naples, Italy; IRCCS Neuromed, Pozzilli, Isernia, Italy
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30
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KIT D816V–mutated bone marrow mesenchymal stem cells in indolent systemic mastocytosis are associated with disease progression. Blood 2016; 127:761-8. [DOI: 10.1182/blood-2015-07-655100] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 11/19/2015] [Indexed: 02/06/2023] Open
Abstract
Key Points
Acquisition of the KIT D816V mutation in an early pluripotent progenitor cell confers ISM cases a greater risk for disease progression. Despite the early acquisition of the KIT mutation, onset of clinical symptoms of ISM is often delayed to middle adulthood.
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31
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Abstract
Differentiated sex chromosomes in mammals and other vertebrates evolved independently but in strikingly similar ways. Vertebrates with differentiated sex chromosomes share the problems of the unequal expression of the genes borne on sex chromosomes, both between the sexes and with respect to autosomes. Dosage compensation of genes on sex chromosomes is surprisingly variable - and can even be absent - in different vertebrate groups. Systems that compensate for different gene dosages include a wide range of global, regional and gene-by-gene processes that differ in their extent and their molecular mechanisms. However, many elements of these control systems are similar across distant phylogenetic divisions and show parallels to other gene silencing systems. These dosage systems cannot be identical by descent but were probably constructed from elements of ancient silencing mechanisms that are ubiquitous among vertebrates and shared throughout eukaryotes.
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32
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Hwang JY, Choi KH, Lee DK, Kim SH, Kim EB, Hyun SH, Lee CK. Overexpression of OCT4A ortholog elevates endogenous XIST in porcine parthenogenic blastocysts. J Reprod Dev 2015; 61:533-40. [PMID: 26255835 PMCID: PMC4685219 DOI: 10.1262/jrd.2015-017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
X-chromosome inactivation (XCI) is an epigenetic process that equalizes expression of X-borne genes between
male and female eutherians. This process is observed in early eutherian embryo development in a
species-specific manner. Until recently, various pluripotent factors have been suggested to regulate the
process of XCI by repressing XIST expression, which is the master inducer for XCI. Recent
insights into the process and its regulation have been restricted in mouse species despite the evolutionary
diversity of the process and molecular mechanism among the species. OCT4A is one of the
represented pluripotent factors, the gate-keeper for maintaining pluripotency, and an XIST
repressor. Therefore, in here, we examined the relation between OCT4A and X-linked genes in
porcine preimplantation embryos. Three X-linked genes, XIST,
LOC102165544, and RLIM, were selected in present study because their
orthologues have been known to regulate XCI in mice. Expression levels of OCT4A were
positively correlated with XIST and LOC102165544 in female blastocysts.
Furthermore, overexpression of exogenous human OCT4A in cleaved parthenotes generated
blastocysts with increased XIST expression levels. However, increased XIST
expression was not observed when exogenous OCT4A was obtained from early blastocysts. These
results suggest the possibility that OCT4A would be directly or indirectly involved in
XIST expression in earlier stage porcine embryos rather than blastocysts.
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Affiliation(s)
- Jae Yeon Hwang
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
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33
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D'Amico F, Skarmoutsou E, Mazzarino MC. The sex bias in systemic sclerosis: on the possible mechanisms underlying the female disease preponderance. Clin Rev Allergy Immunol 2015; 47:334-43. [PMID: 24126759 DOI: 10.1007/s12016-013-8392-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Systemic sclerosis is a multifactorial and heterogeneous disease. Genetic and environmental factors are known to interplay in the onset and progression of systemic sclerosis. Sex plays an important and determinant role in the development of such a disorder. Systemic sclerosis shows a significant female preponderance. However, the reason for this female preponderance is incompletely understood. Hormonal status, genetic and epigenetic differences, and lifestyle have been considered in order to explain female preponderance in systemic sclerosis. Sex chromosomes play a determinant role in contributing to systemic sclerosis onset and progression, as well as in its sex-biased prevalence. It is known, in fact, that X chromosome contains many sex- and immuno-related genes, thus contributing to immuno tolerance and sex hormone status. This review focuses mainly on the recent progress on epigenetic mechanisms--exclusively linked to the X chromosome--which would contribute to the development of systemic sclerosis. Furthermore, we report also some hypotheses (dealing with skewed X chromosome inactivation, X gene reactivation, acquired monosomy) that have been proposed in order to justify the female preponderance in autoimmune diseases. However, despite the intensive efforts in elucidating the mechanisms involved in the pathogenesis of systemic sclerosis, many questions remain still unanswered.
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Affiliation(s)
- Fabio D'Amico
- Department of Bio-medical Sciences, University of Catania, via Androne 83, 95124, Catania, Italy,
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34
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Baird A, Barsby T, Guest DJ. Derivation of Canine Induced Pluripotent Stem Cells. Reprod Domest Anim 2015; 50:669-76. [PMID: 26074059 DOI: 10.1111/rda.12562] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 05/23/2015] [Indexed: 12/31/2022]
Abstract
Dogs and humans have many inherited genetic diseases in common and conditions that are increasingly prevalent in humans also occur naturally in dogs. The use of dogs for the experimental and clinical testing of stem cell and regenerative medicine products would benefit canine health and welfare and provide relevant animal models for the translation of therapies to the human field. Induced pluripotent stem cells (iPSCs) have the capacity to turn into all cells of the body and therefore have the potential to provide cells for therapeutic use and for disease modelling. The objective of this study was to derive and characterize iPSCs from karyotypically abnormal adult canine cells. Aneuploid adipose-derived mesenchymal stromal cells (AdMSCs) from an adult female Weimeraner were re-programmed into iPSCs via overexpression of four human pluripotency factors (Oct 4, Sox2, Klf4 and c-myc) using retroviral vectors. The iPSCs showed similarity to human ESCs with regard to morphology, pluripotency marker expression and the ability to differentiate into derivatives of all three germ layers in vitro (endoderm, ectoderm and mesoderm). The iPSCs also demonstrated silencing of the viral transgenes and re-activation of the silent X chromosome, suggesting full reprogramming had occurred. The levels of aneuploidy observed in the AdMSCs were maintained in the iPSCs. This finding demonstrates the potential for generating canine induced pluripotent stem cells for use as disease models in addition to regenerative medicine and pharmaceutical testing.
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Affiliation(s)
- Aeg Baird
- Animal Health Trust, Kentford, Newmarket, Suffolk, UK
| | - T Barsby
- Animal Health Trust, Kentford, Newmarket, Suffolk, UK
| | - D J Guest
- Animal Health Trust, Kentford, Newmarket, Suffolk, UK
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35
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Chen Q, Gao S, He W, Kou X, Zhao Y, Wang H, Gao S. Xist repression shows time-dependent effects on the reprogramming of female somatic cells to induced pluripotent stem cells. Stem Cells 2015; 32:2642-56. [PMID: 24965076 DOI: 10.1002/stem.1775] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 05/17/2014] [Accepted: 05/23/2014] [Indexed: 11/10/2022]
Abstract
Although the reactivation of silenced X chromosomes has been observed as part of the process of reprogramming female somatic cells into induced pluripotent stem cells (iPSCs), it remains unknown whether repression of the X-inactive specific transcript (Xist) can greatly enhance female iPSC induction similar to that observed in somatic cell nuclear transfer studies. In this study, we discovered that the repression of Xist plays opposite roles in the early and late phases of female iPSCs induction. Our results demonstrate that the downregulation of Xist by an isopropyl β-d-1-thiogalactopyranoside (IPTG)-inducible short hairpin RNA (shRNA) system can greatly impair the mesenchymal-to-epithelial transition (MET) in the early phase of iPSC induction but can significantly promote the transition of pre-iPSCs to iPSCs in the late phase. Furthermore, we demonstrate that although the knockdown of Xist did not affect the H3K27me3 modification on the X chromosome, macroH2A was released from the inactivated X chromosome (Xi). This enables the X chromosome silencing to be a reversible event. Moreover, we demonstrate that the supplementation of vitamin C (Vc) can augment and stabilize the reversible X chromosome by preventing the relocalization of macroH2A to the Xi. Therefore, our study reveals an opposite role of Xist repression in the early and late stages of reprogramming female somatic cells to pluripotency and demonstrates that the release of macroH2A by Xist repression enables the transition from pre-iPSCs to iPSCs.
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Affiliation(s)
- Qi Chen
- School of Life Sciences, Beijing Normal University, Beijing, China; National Institute of Biological Sciences (NIBS), Beijing, China
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36
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Rijlaarsdam MA, Tax DMJ, Gillis AJM, Dorssers LCJ, Koestler DC, de Ridder J, Looijenga LHJ. Genome wide DNA methylation profiles provide clues to the origin and pathogenesis of germ cell tumors. PLoS One 2015; 10:e0122146. [PMID: 25859847 PMCID: PMC4479500 DOI: 10.1371/journal.pone.0122146] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 02/07/2015] [Indexed: 12/18/2022] Open
Abstract
The cell of origin of the five subtypes (I-V) of germ cell tumors (GCTs) are assumed to be germ cells from different maturation stages. This is (potentially) reflected in their methylation status as fetal maturing primordial germ cells are globally demethylated during migration from the yolk sac to the gonad. Imprinted regions are erased in the gonad and later become uniparentally imprinted according to fetal sex. Here, 91 GCTs (type I-IV) and four cell lines were profiled (Illumina’s HumanMethylation450BeadChip). Data was pre-processed controlling for cross hybridization, SNPs, detection rate, probe-type bias and batch effects. The annotation was extended, covering snRNAs/microRNAs, repeat elements and imprinted regions. A Hidden Markov Model-based genome segmentation was devised to identify differentially methylated genomic regions. Methylation profiles allowed for separation of clusters of non-seminomas (type II), seminomas/dysgerminomas (type II), spermatocytic seminomas (type III) and teratomas/dermoid cysts (type I/IV). The seminomas, dysgerminomas and spermatocytic seminomas were globally hypomethylated, in line with previous reports and their demethylated precursor. Differential methylation and imprinting status between subtypes reflected their presumed cell of origin. Ovarian type I teratomas and dermoid cysts showed (partial) sex specific uniparental maternal imprinting. The spermatocytic seminomas showed uniparental paternal imprinting while testicular teratomas exhibited partial imprinting erasure. Somatic imprinting in type II GCTs might indicate a cell of origin after global demethylation but before imprinting erasure. This is earlier than previously described, but agrees with the totipotent/embryonic stem cell like potential of type II GCTs and their rare extra-gonadal localization. The results support the common origin of the type I teratomas and show strong similarity between ovarian type I teratomas and dermoid cysts. In conclusion, we identified specific and global methylation differences between GCT subtypes, providing insight into their developmental timing and underlying developmental biology. Data and extended annotation are deposited at GEO (GSE58538 and GPL18809).
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Affiliation(s)
- Martin A. Rijlaarsdam
- Department of Pathology, Erasmus MC Cancer Institute—University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - David M. J. Tax
- Faculty of Electrical Engineering, Mathematics and Computer Science Intelligent Systems—Delft Bioinformatics Lab, Technical University of Delft, Delft, The Netherlands
| | - Ad J. M. Gillis
- Department of Pathology, Erasmus MC Cancer Institute—University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Lambert C. J. Dorssers
- Department of Pathology, Erasmus MC Cancer Institute—University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Devin C. Koestler
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Jeroen de Ridder
- Faculty of Electrical Engineering, Mathematics and Computer Science Intelligent Systems—Delft Bioinformatics Lab, Technical University of Delft, Delft, The Netherlands
| | - Leendert H. J. Looijenga
- Department of Pathology, Erasmus MC Cancer Institute—University Medical Center Rotterdam, Rotterdam, The Netherlands
- * E-mail:
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37
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Di KQ, Gao S, Cui LF, Chang G, Wu FJ, Ren LK, An L, Miao K, Tan K, Tao L, Chen H, Wang ZL, Wang SM, Wu ZH, Gao S, Li XY, Tian JH. Generation of fully pluripotent female murine-induced pluripotent stem cells. Biol Reprod 2015; 92:123. [PMID: 25788660 DOI: 10.1095/biolreprod.114.124958] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 03/03/2015] [Indexed: 02/05/2023] Open
Abstract
The high quality of induced pluripotent stem cells (iPSCs) has been determined to be high-grade chimeras that are competent for germline transmission, and viable mice can be generated through tetraploid complementation. Most of the high-quality iPSCs described to date have been male. Female iPSCs, especially fully pluripotent female iPSCs, are also essential for clinical applications and scientific research. Here, we show, for the first time, that a gender-mixed induction strategy could lead to a skewed sex ratio of iPSCs. After reprogramming, 50%, 70%, and 90% female initiating mouse embryonic fibroblasts at different male ratios resulted in 14.1 ± 6.8% (P < 0.05), 31.8 ± 5.4% (P < 0.05), and 80.1 ± 2.8% (P < 0.05) female iPSCs, respectively. Furthermore, these female iPSCs had pluripotent properties typical of embryonic stem cells. Importantly, these fully pluripotent female iPSCs could generate viable mice by tetraploid complementation. These findings indicate that high-quality female iPSCs could be derived effectively, and suggest that clinical application of female iPSCs is feasible.
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Affiliation(s)
- Ke-Qian Di
- Department of Animal Reproduction, College of Animal Science and Technology, Agricultural University of Hebei, Baoding, Hebei, People's Republic of China Health Science Center, Hebei University, Baoding, Hebei, People's Republic of China
| | - Shuai Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China National Institute of Biological Sciences, Beijing, People's Republic of China
| | - Li-Fang Cui
- Department of Animal Reproduction, College of Animal Science and Technology, Agricultural University of Hebei, Baoding, Hebei, People's Republic of China Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
| | - Gang Chang
- National Institute of Biological Sciences, Beijing, People's Republic of China
| | - Fu-Jia Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
| | - Li-Kun Ren
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
| | - Lei An
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
| | - Kai Miao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
| | - Kun Tan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
| | - Li Tao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
| | - Hui Chen
- Department of Animal Reproduction, College of Animal Science and Technology, Agricultural University of Hebei, Baoding, Hebei, People's Republic of China
| | - Zhi-Long Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
| | - Shu-Min Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
| | - Zhong-Hong Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
| | - Shaorong Gao
- National Institute of Biological Sciences, Beijing, People's Republic of China The School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Xiang-Yun Li
- Department of Animal Reproduction, College of Animal Science and Technology, Agricultural University of Hebei, Baoding, Hebei, People's Republic of China
| | - Jian-Hui Tian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
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The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation. Genome Biol 2015; 16:52. [PMID: 25887447 PMCID: PMC4391730 DOI: 10.1186/s13059-015-0618-0] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 02/23/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In mammals, X chromosome genes are present in one copy in males and two in females. To balance the dosage of X-linked gene expression between the sexes, one of the X chromosomes in females is silenced. X inactivation is initiated by upregulation of the lncRNA (long non-coding RNA) Xist and recruitment of specific chromatin modifiers. The inactivated X chromosome becomes heterochromatic and visits a specific nuclear compartment adjacent to the nucleolus. RESULTS Here, we show a novel role for the lncRNA Firre in anchoring the inactive mouse X chromosome and preserving one of its main epigenetic features, H3K27me3. Similar to Dxz4, Firre is X-linked and expressed from a macrosatellite repeat locus associated with a cluster of CTCF and cohesin binding sites, and is preferentially located adjacent to the nucleolus. CTCF binding present initially in both male and female mouse embryonic stem cells is lost from the active X during development. Knockdown of Firre disrupts perinucleolar targeting and H3K27me3 levels in mouse fibroblasts, demonstrating a role in maintenance of an important epigenetic feature of the inactive X chromosome. No X-linked gene reactivation is seen after Firre knockdown; however, a compensatory increase in the expression of chromatin modifier genes implicated in X silencing is observed. Further experiments in female embryonic stem cells suggest that Firre does not play a role in X inactivation onset. CONCLUSIONS The X-linked lncRNA Firre helps to position the inactive X chromosome near the nucleolus and to preserve one of its main epigenetic features.
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Brooks WH, Renaudineau Y. Epigenetics and autoimmune diseases: the X chromosome-nucleolus nexus. Front Genet 2015; 6:22. [PMID: 25763008 PMCID: PMC4329817 DOI: 10.3389/fgene.2015.00022] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 01/16/2015] [Indexed: 12/18/2022] Open
Abstract
Autoimmune diseases occur more often in females, suggesting a key role for the X chromosome. X chromosome inactivation, a major epigenetic feature in female cells that provides dosage compensation of X-linked genes to avoid overexpression, presents special vulnerabilities that can contribute to the disease process. Disruption of X inactivation can result in loss of dosage compensation with expression from previously sequestered genes, imbalance of gene products, and altered endogenous material out of normal epigenetic context. In addition, the human X has significant differences compared to other species and these differences can contribute to the frequency and intensity of the autoimmune disease in humans as well as the types of autoantigens encountered. Here a link is demonstrated between autoimmune diseases, such as systemic lupus erythematosus, and the X chromosome by discussing cases in which typically non-autoimmune disorders complicated with X chromosome abnormalities also present lupus-like symptoms. The discussion is then extended to the reported spatial and temporal associations of the inactive X chromosome with the nucleolus. When frequent episodes of cellular stress occur, the inactive X chromosome may be disrupted and inadvertently become involved in the nucleolar stress response. Development of autoantigens, many of which are at least transiently components of the nucleolus, is then described. Polyamines, which aid in nucleoprotein complex assembly in the nucleolus, increase further during cell stress, and appear to have an important role in the autoimmune disease process. Autoantigenic endogenous material can potentially be stabilized by polyamines. This presents a new paradigm for autoimmune diseases: that many are antigen-driven and the autoantigens originate from altered endogenous material due to episodes of cellular stress that disrupt epigenetic control. This suggests that epigenetics and the X chromosome are important aspects of autoimmune diseases.
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Affiliation(s)
- Wesley H Brooks
- Department of Chemistry, University of South Florida Tampa, FL, USA
| | - Yves Renaudineau
- Research Unit INSERM ERI29/EA2216, SFR ScinBios, Labex Igo "Immunotherapy Graft, Oncology", Réseau Épigénétique et Réseau Canaux Ioniques du Cancéropole Grand Ouest, European University of Brittany Brest, France ; Laboratory of Immunology and Immunotherapy, Hôpital Morvan Brest, France
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Richard JLC, Ogawa Y. Understanding the Complex Circuitry of lncRNAs at the X-inactivation Center and Its Implications in Disease Conditions. Curr Top Microbiol Immunol 2015; 394:1-27. [PMID: 25982976 DOI: 10.1007/82_2015_443] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Balanced gene expression is a high priority in order to maintain optimal functioning since alterations and variations could result in acute consequences. X chromosome inactivation (X-inactivation) is one such strategy utilized by mammalian species to silence the extra X chromosome in females to uphold a similar level of expression between the two sexes. A functionally versatile class of molecules called long noncoding RNA (lncRNA) has emerged as key regulators of gene expression and plays important roles during development. An lncRNA that is indispensable for X-inactivation is X-inactive specific transcript (Xist), which induces a repressive epigenetic landscape and creates the inactive X chromosome (Xi). With recent advents in the field of X-inactivation, novel positive and negative lncRNA regulators of Xist such as Jpx and Tsix, respectively, have broadened the regulatory network of X-inactivation. Xist expression failure or dysregulation has been implicated in producing developmental anomalies and disease states. Subsequently, reactivation of the Xi at a later stage of development has also been associated with certain tumors. With the recent influx of information about lncRNA biology and advancements in methods to probe lncRNA, we can now attempt to understand this complex network of Xist regulation in development and disease. It has become clear that the presence of an extra set of genes could be fatal for the organism. Only by understanding the precise ways in which lncRNAs function can treatments be developed to bring aberrations under control. This chapter summarizes our current understanding and knowledge with regard to how lncRNAs are orchestrated at the X-inactivation center (Xic), with a special focus on how genetic diseases come about as a consequence of lncRNA dysregulation.
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Affiliation(s)
- John Lalith Charles Richard
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center; Department of Pediatrics, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - Yuya Ogawa
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center; Department of Pediatrics, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.
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Briggs SF, Reijo Pera RA. X chromosome inactivation: recent advances and a look forward. Curr Opin Genet Dev 2014; 28:78-82. [PMID: 25461454 PMCID: PMC4339055 DOI: 10.1016/j.gde.2014.09.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 08/28/2014] [Accepted: 09/16/2014] [Indexed: 12/21/2022]
Abstract
X chromosome inactivation, the transcriptional inactivation of one X chromosome in somatic cells of female mammals, has revealed important advances in our understanding of development, epigenetic control, and RNA biology. Most of this knowledge comes from extensive studies in the mouse; however, there are some significant differences when compared to human biology. This is especially true in pluripotent cell types and, over the past few years, a significant amount of work has been dedicated to understanding these differences. This review focuses specifically on recent advances in the mechanism of Xist spreading, the role of Xist in cancer, the effects of reprogramming on X chromosome inactivation in human induced pluripotent stem cells, and new tools for studying X chromosome inactivation.
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Affiliation(s)
- Sharon F Briggs
- Department of Genetics, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, CA, USA
| | - Renee A Reijo Pera
- Department of Cell Biology and Neurosciences, Montana State University, 207 Montana Hall, Bozeman, MT 59711-2460, USA; Department of Chemistry and Biochemistry, Montana State University, 207 Montana Hall, Bozeman, MT 59711-2460, USA.
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42
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Payer B, Lee JT. Coupling of X-chromosome reactivation with the pluripotent stem cell state. RNA Biol 2014; 11:798-807. [PMID: 25137047 DOI: 10.4161/rna.29779] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
X-chromosome inactivation (XCI) in female mammals is a dramatic example of epigenetic gene regulation, which entails the silencing of an entire chromosome through a wide range of mechanisms involving noncoding RNAs, chromatin-modifications, and DNA-methylation. While XCI is associated with the differentiated cell state, it is reversed by X-chromosome reactivation (XCR) ex vivo in pluripotent stem cells and in vivo in the early mouse embryo and the germline. Critical in the regulation of XCI vs. XCR is the X-inactivation center, a multigene locus on the X-chromosome harboring several long noncoding RNA genes including, most prominently, Xist and Tsix. These genes, which sit at the top of the XCI hierarchy, are by themselves controlled by pluripotency factors, coupling XCR with the naïve pluripotent stem cell state. In this point-of-view article we review the latest findings regarding this intricate relationship between cell differentiation state and epigenetic control of the X-chromosome. In particular, we discuss the emerging picture of complex multifactorial regulatory mechanisms, ensuring both a fine-tuned and robust X-reactivation process.
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Affiliation(s)
- Bernhard Payer
- Howard Hughes Medical Institute; Department of Molecular Biology; Massachusetts General Hospital; Department of Genetics; Harvard Medical School; Boston, MA USA
| | - Jeannie T Lee
- Howard Hughes Medical Institute; Department of Molecular Biology; Massachusetts General Hospital; Department of Genetics; Harvard Medical School; Boston, MA USA
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43
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Rijlaarsdam MA, Looijenga LHJ. An oncofetal and developmental perspective on testicular germ cell cancer. Semin Cancer Biol 2014; 29:59-74. [PMID: 25066859 DOI: 10.1016/j.semcancer.2014.07.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 07/17/2014] [Indexed: 12/19/2022]
Abstract
Germ cell tumors (GCTs) represent a diverse group of tumors presumably originating from (early fetal) developing germ cells. Most frequent are the testicular germ cell cancers (TGCC). Overall, TGCC is the most frequent malignancy in Caucasian males (20-40 years) and remains an important cause of (treatment related) mortality in these young men. The strong association between the phenotype of TGCC stem cell components and their totipotent ancestor (fetal primordial germ cell or gonocyte) makes these tumors highly relevant from an onco-fetal point of view. This review subsequently discusses the evidence for the early embryonic origin of TGCCs, followed by an overview of the crucial association between TGCC pathogenesis, genetics, environmental exposure and the (fetal) testicular micro-environment (genvironment). This culminates in an evaluation of three genvironmentally modulated hallmarks of TGCC directly related to the oncofetal pathogenesis of TGCC: (1) maintenance of pluripotency, (2) cell cycle control/cisplatin sensitivity and (3) regulation of proliferation/migration/apoptosis by KIT-KITL mediated receptor tyrosine kinase signaling. Briefly, TGCC exhibit identifiable stem cell components (seminoma and embryonal carcinoma) and progenitors that show large and consistent similarities to primordial/embryonic germ cells, their presumed totipotent cells of origin. TGCC pathogenesis depends crucially on a complex interaction of genetic and (micro-)environmental, i.e. genvironmental risk factors that have only been partly elucidated despite significant effort. TGCC stem cell components also show a high degree of similarity with embryonic stem/germ cells (ES) in the regulation of pluripotency and cell cycle control, directly related to their exquisite sensitivity to DNA damaging agents (e.g. cisplatin). Of note, (ES specific) micro-RNAs play a pivotal role in the crossover between cell cycle control, pluripotency and chemosensitivity. Moreover, multiple consistent observations reported TGCC to be associated with KIT-KITL mediated receptor tyrosine kinase signaling, a pathway crucially implicated in proliferation, migration and survival during embryogenesis including germ cell development. In conclusion, TGCCs are a fascinating model for onco-fetal developmental processes especially with regard to studying cell cycle control, pluripotency maintenance and KIT-KITL signaling. The knowledge presented here contributes to better understanding of the molecular characteristics of TGCC pathogenesis, translating to identification of at risk individuals and enhanced quality of care for TGCC patients (diagnosis, treatment and follow-up).
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Affiliation(s)
- Martin A Rijlaarsdam
- Department of Pathology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Leendert H J Looijenga
- Department of Pathology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands.
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44
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Abstract
In mammals, the process of X-chromosome inactivation ensures equivalent levels of X-linked gene expression between males and females through the silencing of one of the two X chromosomes in female cells. The process is established early in development and is initiated by a unique locus, which produces a long noncoding RNA, Xist. The Xist transcript triggers gene silencing in cis by coating the future inactive X chromosome. It also induces a cascade of chromatin changes, including posttranslational histone modifications and DNA methylation, and leads to the stable repression of all X-linked genes throughout development and adult life. We review here recent progress in our understanding of the molecular mechanisms involved in the initiation of Xist expression, the propagation of the Xist RNA along the chromosome, and the cis-elements and trans-acting factors involved in the maintenance of the repressed state. We also describe the diverse strategies used by nonplacental mammals for X-chromosome dosage compensation and highlight the common features and differences between eutherians and metatherians, in particular regarding the involvement of long noncoding RNAs.
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Affiliation(s)
- Anne-Valerie Gendrel
- Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, 75248 Paris, France;
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45
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Chaligné R, Heard E. X-chromosome inactivation in development and cancer. FEBS Lett 2014; 588:2514-22. [PMID: 24937141 DOI: 10.1016/j.febslet.2014.06.023] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 06/06/2014] [Indexed: 12/21/2022]
Abstract
X-chromosome inactivation represents an epigenetics paradigm and a powerful model system of facultative heterochromatin formation triggered by a non-coding RNA, Xist, during development. Once established, the inactive state of the Xi is highly stable in somatic cells, thanks to a combination of chromatin associated proteins, DNA methylation and nuclear organization. However, sporadic reactivation of X-linked genes has been reported during ageing and in transformed cells and disappearance of the Barr body is frequently observed in cancer cells. In this review we summarise current knowledge on the epigenetic changes that accompany X inactivation and discuss the extent to which the inactive X chromosome may be epigenetically or genetically perturbed in breast cancer.
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Affiliation(s)
- Ronan Chaligné
- Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, CNRS UMR3215, INSERM U934, 75248 Paris, France
| | - Edith Heard
- Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, CNRS UMR3215, INSERM U934, 75248 Paris, France.
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46
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Deng X, Berletch JB, Nguyen DK, Disteche CM. X chromosome regulation: diverse patterns in development, tissues and disease. Nat Rev Genet 2014; 15:367-78. [PMID: 24733023 PMCID: PMC4117651 DOI: 10.1038/nrg3687] [Citation(s) in RCA: 216] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Genes on the mammalian X chromosome are present in one copy in males and two copies in females. The complex mechanisms that regulate the X chromosome lead to evolutionary and physiological variability in gene expression between species, the sexes, individuals, developmental stages, tissues and cell types. In early development, delayed and incomplete X chromosome inactivation (XCI) in some species causes variability in gene expression. Additional diversity stems from escape from XCI and from mosaicism or XCI skewing in females. This causes sex-specific differences that manifest as differential gene expression and associated phenotypes. Furthermore, the complexity and diversity of X dosage regulation affect the severity of diseases caused by X-linked mutations.
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Affiliation(s)
- Xinxian Deng
- Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA
| | - Joel B Berletch
- Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA
| | - Di K Nguyen
- Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA
| | - Christine M Disteche
- 1] Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA. [2] Department of Medicine, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA
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47
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Abstract
Genes on the mammalian X chromosome are present in one copy in males and two copies in females. The complex mechanisms that regulate the X chromosome lead to evolutionary and physiological variability in gene expression between species, the sexes, individuals, developmental stages, tissues and cell types. In early development, delayed and incomplete X chromosome inactivation (XCI) in some species causes variability in gene expression. Additional diversity stems from escape from XCI and from mosaicism or XCI skewing in females. This causes sex-specific differences that manifest as differential gene expression and associated phenotypes. Furthermore, the complexity and diversity of X dosage regulation affect the severity of diseases caused by X-linked mutations.
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48
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Deng X, Berletch JB, Nguyen DK, Disteche CM. X chromosome regulation: diverse patterns in development, tissues and disease. Nat Rev Genet 2014. [PMID: 24733023 DOI: 10.1038/nrg3687,+10.1038/nrn3745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genes on the mammalian X chromosome are present in one copy in males and two copies in females. The complex mechanisms that regulate the X chromosome lead to evolutionary and physiological variability in gene expression between species, the sexes, individuals, developmental stages, tissues and cell types. In early development, delayed and incomplete X chromosome inactivation (XCI) in some species causes variability in gene expression. Additional diversity stems from escape from XCI and from mosaicism or XCI skewing in females. This causes sex-specific differences that manifest as differential gene expression and associated phenotypes. Furthermore, the complexity and diversity of X dosage regulation affect the severity of diseases caused by X-linked mutations.
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Affiliation(s)
- Xinxian Deng
- Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA
| | - Joel B Berletch
- Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA
| | - Di K Nguyen
- Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA
| | - Christine M Disteche
- 1] Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA. [2] Department of Medicine, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA
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Pessia E, Engelstädter J, Marais GAB. The evolution of X chromosome inactivation in mammals: the demise of Ohno's hypothesis? Cell Mol Life Sci 2014; 71:1383-94. [PMID: 24173285 PMCID: PMC11113734 DOI: 10.1007/s00018-013-1499-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/11/2013] [Accepted: 10/14/2013] [Indexed: 12/24/2022]
Abstract
Ohno's hypothesis states that dosage compensation in mammals evolved in two steps: a twofold hyperactivation of the X chromosome in both sexes to compensate for gene losses on the Y chromosome, and silencing of one X (X-chromosome inactivation, XCI) in females to restore optimal dosage. Recent tests of this hypothesis have returned contradictory results. In this review, we explain this ongoing controversy and argue that a novel view on dosage compensation evolution in mammals is starting to emerge. Ohno's hypothesis may be true for a few, dosage-sensitive genes only. If so few genes are compensated, then why has XCI evolved as a chromosome-wide mechanism? This and several other questions raised by the new data in mammals are discussed, and future research directions are proposed.
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Affiliation(s)
- Eugénie Pessia
- Laboratoire de Biométrie et Biologie Évolutive, Centre National de la Recherche Scientifique, Université Lyon 1, Bat. Gregor Mendel, 16 rue Raphaël Dubois, 69622, Villeurbanne Cedex, France,
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50
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Kim JS, Choi HW, Araúzo-Bravo MJ, Schöler HR, Do JT. Reactivation of inactive X chromosome and post-transcriptional reprogramming of Xist in induced pluripotent stem cells. J Cell Sci 2014; 128:81-7. [DOI: 10.1242/jcs.154294] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Direct reprogramming of somatic cells to pluripotent stem cells entails the obliteration of somatic cell memory and the reestablishment of epigenetic events. Induced pluripotent stem (iPS) cells have been created by reprogramming somatic cells through the transduction of reprogramming factors. During cell reprogramming, female somatic cells must overcome at least one more barrier than male somatic cells in order to enter a pluripotent state, as they must reactivate an inactive X chromosome (Xi). In this study, we investigated whether the sex of somatic cells affects reprogramming efficiency, differentiation potential, and the post-transcriptional processing of Xist RNA after reprogramming. There were no differences between male and female iPS cells with respect to reprogramming efficiency or their differentiation potential in vivo. However, reactivating Xi took longer than reactivating pluripotency-related genes. We also found that direct reprogramming leads to gender appropriate posttranscriptional reprogramming: like male embryonic stem (ES) cells, male iPS cells expressed only the long Xist isoform, whereas female iPS cells, like female ES cells, expressed both the long and short isoforms.
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