1
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Taghehchian N, Maharati A, Akhlaghipour I, Zangouei AS, Moghbeli M. PRC2 mediated KLF2 down regulation: a therapeutic and diagnostic axis during tumor progression. Cancer Cell Int 2023; 23:233. [PMID: 37807067 PMCID: PMC10561470 DOI: 10.1186/s12935-023-03086-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/29/2023] [Indexed: 10/10/2023] Open
Abstract
Surgery and chemo-radiotherapy are used as the common first-line treatment options in many cancers. However, tumor relapse is observed in many cancer patients following such first-line treatments. Therefore, targeted therapy according to the molecular cancer biology can be very important in reducing tumor recurrence. In this regard, a wide range of monoclonal antibodies against the growth factors and their receptors can offer more targeted treatment in cancer patients. However, due to the importance of growth factors in the normal biology of body cells, side effects can also be observed following the application of growth factor inhibitors. Therefore, more specific factors should be introduced as therapeutic targets with less side effects. Krüppel-like factors 2 (KLF2) belongs to the KLF family of transcription factors that are involved in the regulation of many cellular processes. KLF2 deregulations have been also reported during the progression of many tumors. In the present review we discussed the molecular mechanisms of KLF2 during tumor growth and invasion. It has been shown that the KLF2 as a tumor suppressor is mainly inhibited by the non-coding RNAs (ncRNAs) through the polycomb repressive complex 2 (PRC2) recruitment. This review is an effective step towards introducing the KLF2 as a suitable diagnostic and therapeutic target in cancer patients.
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Affiliation(s)
- Negin Taghehchian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhosein Maharati
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Iman Akhlaghipour
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Sadra Zangouei
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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2
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Mattimoe T, Payer B. The compleX balancing act of controlling X-chromosome dosage and how it impacts mammalian germline development. Biochem J 2023; 480:521-537. [PMID: 37096944 DOI: 10.1042/bcj20220450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 04/26/2023]
Abstract
In female mammals, the two X chromosomes are subject to epigenetic gene regulation in order to balance X-linked gene dosage with autosomes and in relation to males, which have one X and one Y chromosome. This is achieved by an intricate interplay of several processes; X-chromosome inactivation and reactivation elicit global epigenetic regulation of expression from one X chromosome in a stage-specific manner, whilst the process of X-chromosome upregulation responds to this by fine-tuning transcription levels of the second X. The germline is unique in its function of transmitting both the genetic and epigenetic information from one generation to the next, and remodelling of the X chromosome is one of the key steps in setting the stage for successful development. Here, we provide an overview of the complex dynamics of X-chromosome dosage control during embryonic and germ cell development, and aim to decipher its potential role for normal germline competency.
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Affiliation(s)
- Tom Mattimoe
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Bernhard Payer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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3
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Bauer M, Payer B, Filion GJ. Causality in transcription and genome folding: Insights from X inactivation. Bioessays 2022; 44:e2200105. [PMID: 36028473 DOI: 10.1002/bies.202200105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/11/2022] [Accepted: 08/14/2022] [Indexed: 11/10/2022]
Abstract
The spatial organization of genomes is becoming increasingly understood. In mammals, where it is most investigated, this organization ties in with transcription, so an important research objective is to understand whether gene activity is a cause or a consequence of genome folding in space. In this regard, the phenomena of X-chromosome inactivation and reactivation open a unique window of investigation because of the singularities of the inactive X chromosome. Here we focus on the cause-consequence nexus between genome conformation and transcription and explain how recent results about the structural changes associated with inactivation and reactivation of the X chromosome shed light on this problem.
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Affiliation(s)
- Moritz Bauer
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bernhard Payer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Guillaume J Filion
- Dept. Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
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4
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Severino J, Bauer M, Mattimoe T, Arecco N, Cozzuto L, Lorden P, Hamada N, Nosaka Y, Nagaoka SI, Audergon P, Tarruell A, Heyn H, Hayashi K, Saitou M, Payer B. Controlled X-chromosome dynamics defines meiotic potential of female mouse in vitro germ cells. EMBO J 2022; 41:e109457. [PMID: 35603814 PMCID: PMC9194795 DOI: 10.15252/embj.2021109457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 04/08/2022] [Accepted: 04/14/2022] [Indexed: 11/23/2022] Open
Abstract
The mammalian germline is characterized by extensive epigenetic reprogramming during its development into functional eggs and sperm. Specifically, the epigenome requires resetting before parental marks can be established and transmitted to the next generation. In the female germline, X‐chromosome inactivation and reactivation are among the most prominent epigenetic reprogramming events, yet very little is known about their kinetics and biological function. Here, we investigate X‐inactivation and reactivation dynamics using a tailor‐made in vitro system of primordial germ cell‐like cell (PGCLC) differentiation from mouse embryonic stem cells. We find that X‐inactivation in PGCLCs in vitro and in germ cell‐competent epiblast cells in vivo is moderate compared to somatic cells, and frequently characterized by escaping genes. X‐inactivation is followed by step‐wise X‐reactivation, which is mostly completed during meiotic prophase I. Furthermore, we find that PGCLCs which fail to undergo X‐inactivation or reactivate too rapidly display impaired meiotic potential. Thus, our data reveal fine‐tuned X‐chromosome remodelling as a critical feature of female germ cell development towards meiosis and oogenesis.
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Affiliation(s)
- Jacqueline Severino
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Moritz Bauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Tom Mattimoe
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Niccolò Arecco
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luca Cozzuto
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Patricia Lorden
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Norio Hamada
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshiaki Nosaka
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - So I Nagaoka
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Pauline Audergon
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Antonio Tarruell
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Katsuhiko Hayashi
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Bernhard Payer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
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5
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Astro V, Alowaysi M, Fiacco E, Saera-Vila A, Cardona-Londoño KJ, Aiese Cigliano R, Adamo A. Pseudoautosomal Region 1 Overdosage Affects the Global Transcriptome in iPSCs From Patients With Klinefelter Syndrome and High-Grade X Chromosome Aneuploidies. Front Cell Dev Biol 2022; 9:801597. [PMID: 35186953 PMCID: PMC8850648 DOI: 10.3389/fcell.2021.801597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/28/2021] [Indexed: 01/19/2023] Open
Abstract
Klinefelter syndrome (KS) is the most prevalent aneuploidy in males and is characterized by a 47,XXY karyotype. Less frequently, higher grade sex chromosome aneuploidies (HGAs) can also occur. Here, using a paradigmatic cohort of KS and HGA induced pluripotent stem cells (iPSCs) carrying 49,XXXXY, 48,XXXY, and 47,XXY karyotypes, we identified the genes within the pseudoautosomal region 1 (PAR1) as the most susceptible to dosage-dependent transcriptional dysregulation and therefore potentially responsible for the progressively worsening phenotype in higher grade X aneuploidies. By contrast, the biallelically expressed non-PAR escape genes displayed high interclonal and interpatient variability in iPSCs and differentiated derivatives, suggesting that these genes could be associated with variable KS traits. By interrogating KS and HGA iPSCs at the single-cell resolution we showed that PAR1 and non-PAR escape genes are not only resilient to the X-inactive specific transcript (XIST)-mediated inactivation but also that their transcriptional regulation is disjointed from the absolute XIST expression level. Finally, we explored the transcriptional effects of X chromosome overdosage on autosomes and identified the nuclear respiratory factor 1 (NRF1) as a key regulator of the zinc finger protein X-linked (ZFX). Our study provides the first evidence of an X-dosage-sensitive autosomal transcription factor regulating an X-linked gene in low- and high-grade X aneuploidies.
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Affiliation(s)
- Veronica Astro
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Maryam Alowaysi
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Elisabetta Fiacco
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | - Kelly J. Cardona-Londoño
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | - Antonio Adamo
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- *Correspondence: Antonio Adamo,
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6
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Chromosome compartments on the inactive X guide TAD formation independently of transcription during X-reactivation. Nat Commun 2021; 12:3499. [PMID: 34108480 PMCID: PMC8190187 DOI: 10.1038/s41467-021-23610-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 05/10/2021] [Indexed: 12/21/2022] Open
Abstract
A hallmark of chromosome organization is the partition into transcriptionally active A and repressed B compartments, and into topologically associating domains (TADs). Both structures were regarded to be absent from the inactive mouse X chromosome, but to be re-established with transcriptional reactivation and chromatin opening during X-reactivation. Here, we combine a tailor-made mouse iPSC reprogramming system and high-resolution Hi-C to produce a time course combining gene reactivation, chromatin opening and chromosome topology during X-reactivation. Contrary to previous observations, we observe A/B-like compartments on the inactive X harbouring multiple subcompartments. While partial X-reactivation initiates within a compartment rich in X-inactivation escapees, it then occurs rapidly along the chromosome, concomitant with downregulation of Xist. Importantly, we find that TAD formation precedes transcription and initiates from Xist-poor compartments. Here, we show that TAD formation and transcriptional reactivation are causally independent during X-reactivation while establishing Xist as a common denominator.
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7
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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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8
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Bar S, Seaton LR, Weissbein U, Eldar-Geva T, Benvenisty N. Global Characterization of X Chromosome Inactivation in Human Pluripotent Stem Cells. Cell Rep 2020; 27:20-29.e3. [PMID: 30943402 DOI: 10.1016/j.celrep.2019.03.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 01/15/2019] [Accepted: 03/05/2019] [Indexed: 02/06/2023] Open
Abstract
Dosage compensation of sex-chromosome gene expression between male and female mammals is achieved via X chromosome inactivation (XCI) by employing epigenetic modifications to randomly silence one X chromosome during early embryogenesis. Human pluripotent stem cells (hPSCs) were reported to present various states of XCI that differ according to the expression of the long non-coding RNA XIST and the degree of X chromosome silencing. To obtain a comprehensive perspective on XCI in female hPSCs, we performed a large-scale analysis characterizing different XCI parameters in more than 700 RNA high-throughput sequencing samples. Our findings suggest differences in XCI status between most published samples of embryonic stem cells (ESCs) and induced PSCs (iPSCs). While the majority of iPSC lines maintain an inactive X chromosome, ESC lines tend to silence the expression of XIST and upregulate distal chromosomal regions. Our study highlights significant epigenetic heterogeneity within hPSCs, which may bear implications for their use in research and regenerative therapy.
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Affiliation(s)
- Shiran Bar
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Lev Roz Seaton
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Uri Weissbein
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Talia Eldar-Geva
- IVF Unit, Division of Obstetrics and Gynecology, Shaare Zedek Medical Center, Jerusalem, Israel; The Hebrew University School of Medicine, Jerusalem, Israel
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel.
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9
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Deegan DF, Engel N. Sexual Dimorphism in the Age of Genomics: How, When, Where. Front Cell Dev Biol 2019; 7:186. [PMID: 31552249 PMCID: PMC6743004 DOI: 10.3389/fcell.2019.00186] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/22/2019] [Indexed: 12/26/2022] Open
Abstract
In mammals, sex chromosomes start to program autosomal gene expression and epigenetic patterns very soon after fertilization. Yet whether the resulting sex differences are perpetuated throughout development and how they connect to the sex-specific expression patterns in adult tissues is not known. There is a dearth of information on the timing and continuity of sex biases during development. It is also unclear whether sex-specific selection operates during embryogenesis. On the other hand, there is mounting evidence that all adult tissues exhibit sex-specific expression patterns, some of which are independent of hormonal influence and due to intrinsic regulatory effects of the sex chromosome constitution. There are many diseases with origins during embryogenesis that also exhibit sex biases. Epigenetics has provided us with viable mechanisms to explain how the genome stores the memory of developmental events. We propose that some of these marks can be traced back to the sex chromosomes, which interact with the autosomes and establish sex-specific epigenetic features soon after fertilization. Sex-biased epigenetic marks that linger after reprograming may reveal themselves at the transcriptional level at later developmental stages and possibly, throughout the lifespan. Detailed molecular information on the ontogeny of sex biases would also elucidate the sex-specific selective pressures operating on embryos and how compensatory mechanisms evolved to resolve sexual conflict.
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Affiliation(s)
| | - Nora Engel
- Fels Institute for Cancer Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
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10
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PRDM14 controls X-chromosomal and global epigenetic reprogramming of H3K27me3 in migrating mouse primordial germ cells. Epigenetics Chromatin 2019; 12:38. [PMID: 31221220 PMCID: PMC6585054 DOI: 10.1186/s13072-019-0284-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 06/12/2019] [Indexed: 01/18/2023] Open
Abstract
Background In order to prepare the genome for gametogenesis, primordial germ cells (PGCs) undergo extensive epigenetic reprogramming during migration toward the gonads in mammalian embryos. This includes changes on a genome-wide scale and additionally in females the remodeling of the inactive X-chromosome to enable X-chromosome reactivation (XCR). However, if global remodeling and X-chromosomal remodeling are related, how they occur in PGCs in vivo in relation to their migration progress and which factors are important are unknown. Results Here we identify the germ cell determinant PR-domain containing protein 14 (PRDM14) as the first known factor that is instrumental for both global reprogramming and X-chromosomal reprogramming in migrating mouse PGCs. We find that global upregulation of the repressive histone H3 lysine 27 trimethylation (H3K27me3) mark is PRDM14 dosage dependent in PGCs of both sexes. When focusing on XCR, we observed that PRDM14 is required for removal of H3K27me3 from the inactive X-chromosome, which, in contrast to global upregulation, takes place progressively along the PGC migration path. Furthermore, we show that global and X-chromosomal reprogramming of H3K27me3 are functionally separable, despite their common regulation by PRDM14. Conclusions In summary, here we provide new insight and spatiotemporal resolution to the progression and regulation of epigenome remodeling along mouse PGC migration in vivo and link epigenetic reprogramming to its developmental context. Electronic supplementary material The online version of this article (10.1186/s13072-019-0284-7) contains supplementary material, which is available to authorized users.
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11
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Bar S, Benvenisty N. Epigenetic aberrations in human pluripotent stem cells. EMBO J 2019; 38:embj.2018101033. [PMID: 31088843 DOI: 10.15252/embj.2018101033] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 03/13/2019] [Accepted: 03/15/2019] [Indexed: 12/14/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) are being increasingly utilized worldwide in investigating human development, and modeling and discovering therapies for a wide range of diseases as well as a source for cellular therapy. Yet, since the first isolation of human embryonic stem cells (hESCs) 20 years ago, followed by the successful reprogramming of human-induced pluripotent stem cells (hiPSCs) 10 years later, various studies shed light on abnormalities that sometimes accumulate in these cells in vitro Whereas genetic aberrations are well documented, epigenetic alterations are not as thoroughly discussed. In this review, we highlight frequent epigenetic aberrations found in hPSCs, including alterations in DNA methylation patterns, parental imprinting, and X chromosome inactivation. We discuss the potential origins of these abnormalities in hESCs and hiPSCs, survey the different methods for detecting them, and elaborate on their potential consequences for the different utilities of hPSCs.
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Affiliation(s)
- Shiran Bar
- Department of Genetics, The Azrieli Center for Stem Cells and Genetic Research, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Nissim Benvenisty
- Department of Genetics, The Azrieli Center for Stem Cells and Genetic Research, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
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12
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Zhu J, Wang Y, Yu W, Xia K, Huang Y, Wang J, Liu B, Tao H, Liang C, Li F. Long Noncoding RNA: Function and Mechanism on Differentiation of Mesenchymal Stem Cells and Embryonic Stem Cells. Curr Stem Cell Res Ther 2019; 14:259-267. [PMID: 30479219 DOI: 10.2174/1574888x14666181127145809] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/20/2018] [Accepted: 11/22/2018] [Indexed: 12/30/2022]
Abstract
Background:Long suspected as transcriptional noise, recently recognized, long non-coding
RNAs (lncRNAs) are emerging as an indicator, biomarker and therapy target in the physiologic and
pathologic process. Mesenchymal stem cells and embryonic stem cells are important source for normal
and therapeutic tissue repair. However, the mechanism of stem cell differentiation is not completely
understood. Research on lncRNAs may provide novel insights into the mechanism of differentiation
process of the stem cell which is important for the application of stem cell therapy. The lncRNAs field
is still very young, new insights into lncRNAs function are emerging to a greater understanding of biological
processes.
Objective:
In this review, we summarize the recent researches studying lncRNAs and illustrate how
they act in the differentiation of the mesenchymal stem cells and embryonic stem cells, and discuss
some future directions in this field.
Results:
Numerous lncRNAs were differentially expressed during differentiation of mesenchymal stem
cells and embryonic stem cells. LncRNAs were able to regulate the differentiation processes through
epigenetic regulation, transcription regulation and post-transcription regulation.
Conclusion:
LncRNAs are involved in the differentiation process of mesenchymal stem cells and embryonic
stem cells, and they could become promising indicator, biomarker and therapeutic targets in the
physiologic and pathologic process. However, the mechanisms of the role of lncRNAs still require further
investigation.
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Affiliation(s)
- Jian Zhu
- Department of Orthopedics, The Second Affiliated Hospital, Zhejiang University School of Medicine, #88 Jie Fang Road, Hangzhou, 310009, Zhejiang, China
| | - Yitian Wang
- Department of Orthopedics, The Second Affiliated Hospital, Zhejiang University School of Medicine, #88 Jie Fang Road, Hangzhou, 310009, Zhejiang, China
| | - Wei Yu
- Department of Orthopedics, The Second Affiliated Hospital, Zhejiang University School of Medicine, #88 Jie Fang Road, Hangzhou, 310009, Zhejiang, China
| | - Kaishun Xia
- Department of Orthopedics, The Second Affiliated Hospital, Zhejiang University School of Medicine, #88 Jie Fang Road, Hangzhou, 310009, Zhejiang, China
| | - Yuluan Huang
- Department of Gynecologic Oncology, Women`s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Junjie Wang
- Department of Orthopedics, The Second Affiliated Hospital, Zhejiang University School of Medicine, #88 Jie Fang Road, Hangzhou, 310009, Zhejiang, China
| | - Bing Liu
- Department of Orthopedics, The Second Affiliated Hospital, Zhejiang University School of Medicine, #88 Jie Fang Road, Hangzhou, 310009, Zhejiang, China
| | - Huimin Tao
- Department of Orthopedics, The Second Affiliated Hospital, Zhejiang University School of Medicine, #88 Jie Fang Road, Hangzhou, 310009, Zhejiang, China
| | - Chengzhen Liang
- Department of Orthopedics, The Second Affiliated Hospital, Zhejiang University School of Medicine, #88 Jie Fang Road, Hangzhou, 310009, Zhejiang, China
| | - Fangcai Li
- Department of Orthopedics, The Second Affiliated Hospital, Zhejiang University School of Medicine, #88 Jie Fang Road, Hangzhou, 310009, Zhejiang, China
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13
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Tran THY, Fukuda A, Aizawa S, Bui PL, Hayashi Y, Nishimura K, Hisatake K. Live cell imaging of X chromosome reactivation during somatic cell reprogramming. Biochem Biophys Rep 2018; 15:86-92. [PMID: 30094351 PMCID: PMC6073053 DOI: 10.1016/j.bbrep.2018.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/12/2018] [Indexed: 12/20/2022] Open
Abstract
Generation of induced pluripotent stem cells (iPSCs) with naive pluripotency is important for their applications in regenerative medicine. In female iPSCs, acquisition of naive pluripotency is coupled to X chromosome reactivation (XCR) during somatic cell reprogramming, and live cell monitoring of XCR is potentially useful for analyzing how iPSCs acquire naive pluripotency. Here we generated female mouse embryonic stem cells (ESCs) that carry the enhanced green fluorescent protein (EGFP) and humanized Kusabira-Orange (hKO) genes inserted into an intergenic site near either the Syap1 or Taf1 gene on both X chromosomes. The ESC clones, which initially expressed both EGFP and hKO, inactivated one of the fluorescent protein genes upon differentiation, indicating that the EGFP and hKO genes are subject to X chromosome inactivation (XCI). When the derived somatic cells carrying the EGFP gene on the inactive X chromosome (Xi) were reprogrammed into iPSCs, the EGFP gene on the Xi was reactivated when pluripotency marker genes were induced. Thus, the fluorescent protein genes inserted into an intergenic locus on both X chromosomes enable live cell monitoring of XCI during ESC differentiation and XCR during reprogramming. This is the first study that succeeded live cell imaging of XCR during reprogramming.
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Affiliation(s)
- Thi Hai Yen Tran
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Aya Fukuda
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Shiho Aizawa
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Phuong Linh Bui
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yohei Hayashi
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan.,iPS Cell Advanced Characterization and Development Team, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Ken Nishimura
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Koji Hisatake
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
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14
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Engel N. Sex Differences in Early Embryogenesis: Inter-Chromosomal Regulation Sets the Stage for Sex-Biased Gene Networks: The dialogue between the sex chromosomes and autosomes imposes sexual identity soon after fertilization. Bioessays 2018; 40:e1800073. [PMID: 29943439 DOI: 10.1002/bies.201800073] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/02/2018] [Indexed: 12/23/2022]
Abstract
Sex-specific transcriptional and epigenomic profiles are detectable in the embryo very soon after fertilization. I propose that in male (XY) and female (XX) pre-implantation embryos sex chromosomes establish sexually dimorphic interactions with the autosomes, before overt differences become apparent and long before gonadogenesis. Lineage determination restricts expression biases between the sexes, but the epigenetic differences are less constrained and can be perpetuated, accounting for dimorphisms that arise later in life. In this way, sexual identity is registered in the epigenome very early in development. As development progresses, sex-specific regulatory modules are harbored within shared transcriptional networks that delineate common traits. In reviewing this field, I propose that analyzing the mechanisms for sexual dimorphisms at the molecular and biochemical level and incorporating developmental and environmental factors will lead to a greater understanding of sex differences in health and disease. Also see the video abstract here: https://youtu.be/9BPlbrHtkHQ.
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Affiliation(s)
- Nora Engel
- Lewis Katz School of Medicine at Temple University - Fels Institute for Cancer Research, 3400 North Broad St., AHB Room 201, Philadelphia, Pennsylvania, 19140, USA
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15
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Zang C, Nie FQ, Wang Q, Sun M, Li W, He J, Zhang M, Lu KH. Long non-coding RNA LINC01133 represses KLF2, P21 and E-cadherin transcription through binding with EZH2, LSD1 in non small cell lung cancer. Oncotarget 2017; 7:11696-707. [PMID: 26840083 PMCID: PMC4905504 DOI: 10.18632/oncotarget.7077] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/20/2016] [Indexed: 12/20/2022] Open
Abstract
Long non-coding RNAs are emerging as crucial regulators and prognostic markers in multiple cancers including non small cell lung cancer (NSCLC). In this study, we screened LINCO1133 as a new candidate lncRNA which promotes NSCLC development and progression, in two independent datasets (GSE18842 and GSE19804) from the Gene Expression Omnibus (GEO). LINC01133 is previously found to be over-expressed in lung squamous cell cancer (LSCC) and knockdown its expression inhibits LSCC cells invasion. However, its' molecular mechanism and downstream targets involving in regulation of cancer cells phenotype is not known. Here, we found that LINC01133 expression is up-regulated in NSCLC tissues, and its' over-expression is associated with patients poor prognosis and short survival time. LINC01133 knockdown decreased NSCLC cells proliferation, migration, invasion and induced cell cycle G1/S phase arrest and cell apoptosis. Mechanistic investigations showed that LINC01133 could interact with EZH2, LSD1 and recruit them to KLF2, P21 or E-cadherin promoter regions to repress their transcription. Furthermore, rescue experiments demonstrated that LINC01133 oncogenic function is partly through regulating KLF2. Lastly, we found that there was negative correlation between LINC01133 and KLF2, P21 or E-cadherin in NSCLC. Overall, our findings illuminate how LINC01133 over-expression confers an oncogenic function in NSCLC that may offer a novel therapy target in this disease.
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Affiliation(s)
- Chongshuang Zang
- Department of Oncology, First Affiliated Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Feng-Qi Nie
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Qian Wang
- Department of Oncology, First Affiliated Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Ming Sun
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, People's Republic of China
| | - Wei Li
- Department of Oncology, First Affiliated Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Jing He
- Department of Oncology, First Affiliated Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Meiling Zhang
- Department of Oncology, First Affiliated Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Kai-Hua Lu
- Department of Oncology, First Affiliated Hospital, Nanjing Medical University, Nanjing, People's Republic of China
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16
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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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17
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He N, Lim SJ, Moreira de Mello JC, Navarro I, Bialecka M, Salvatori DCF, van der Westerlaken LAJ, Pereira LV, Chuva de Sousa Lopes SM. At Term, XmO and XpO Mouse Placentas Show Differences in Glucose Metabolism in the Trophectoderm-Derived Outer Zone. Front Cell Dev Biol 2017; 5:63. [PMID: 28680878 PMCID: PMC5478694 DOI: 10.3389/fcell.2017.00063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/06/2017] [Indexed: 12/21/2022] Open
Abstract
Genetic mouse model (39,XO) for human Turner Syndrome (45,XO) harboring either a single maternally inherited (Xm) or paternally inherited (Xp) chromosome show a pronounced difference in survival rate at term. However, a detailed comparison of XmO and XpO placentas to explain this difference is lacking. We aimed to investigate the morphological and molecular differences between XmO and XpO term mouse placentas. We observed that XpO placentas at term contained a significantly larger area of glycogen cells (GCs) in their outer zone, compared to XmO, XX, and XY placentas. In addition, the outer zone of XpO placentas showed higher expression levels of lactate dehydrogenase (Ldha) than XmO, XX, and XY placentas, suggestive of increased anaerobic glycolysis. In the labyrinth, we detected significantly lower expression level of trophectoderm (TE)-marker keratin 19 (Krt19) in XpO placentas than in XX placentas. The expression of other TE-markers was comparable as well as the area of TE-derived cells between XO and wild-type labyrinths. XpO placentas exhibited specific defects in the amount of GCs and glucose metabolism in the outer zone, suggestive of increased anaerobic glycolysis, as a consequence of having inherited a single Xp chromosome. In conclusion, the XpO genotype results in a more severe placental phenotype at term, with distinct abnormalities regarding glucose metabolism in the outer zone.
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Affiliation(s)
- Nannan He
- Department of Anatomy and Embryology, Leiden University Medical CenterLeiden, Netherlands
| | - Shujing J Lim
- Department of Anatomy and Embryology, Leiden University Medical CenterLeiden, Netherlands
| | | | - Injerreau Navarro
- Department of Anatomy and Embryology, Leiden University Medical CenterLeiden, Netherlands
| | - Monika Bialecka
- Department of Anatomy and Embryology, Leiden University Medical CenterLeiden, Netherlands
| | - Daniela C F Salvatori
- Department of Anatomy and Embryology, Leiden University Medical CenterLeiden, Netherlands.,Central Laboratory Animal Facility, Leiden University Medical CenterLeiden, Netherlands
| | | | - Lygia V Pereira
- Department of Genetics and Evolutionary Biology, University of São PauloSão Paulo, Brazil
| | - Susana M Chuva de Sousa Lopes
- Department of Anatomy and Embryology, Leiden University Medical CenterLeiden, Netherlands.,Department for Reproductive Medicine, Ghent University HospitalGhent, Belgium
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18
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Wang F, Shin J, Shea JM, Yu J, Bošković A, Byron M, Zhu X, Shalek AK, Regev A, Lawrence JB, Torres EM, Zhu LJ, Rando OJ, Bach I. Regulation of X-linked gene expression during early mouse development by Rlim. eLife 2016; 5. [PMID: 27642011 PMCID: PMC5059138 DOI: 10.7554/elife.19127] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 09/15/2016] [Indexed: 01/22/2023] Open
Abstract
Mammalian X-linked gene expression is highly regulated as female cells contain two and male one X chromosome (X). To adjust the X gene dosage between genders, female mouse preimplantation embryos undergo an imprinted form of X chromosome inactivation (iXCI) that requires both Rlim (also known as Rnf12) and the long non-coding RNA Xist. Moreover, it is thought that gene expression from the single active X is upregulated to correct for bi-allelic autosomal (A) gene expression. We have combined mouse genetics with RNA-seq on single mouse embryos to investigate functions of Rlim on the temporal regulation of iXCI and Xist. Our results reveal crucial roles of Rlim for the maintenance of high Xist RNA levels, Xist clouds and X-silencing in female embryos at blastocyst stages, while initial Xist expression appears Rlim-independent. We find further that X/A upregulation is initiated in early male and female preimplantation embryos. DOI:http://dx.doi.org/10.7554/eLife.19127.001
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Affiliation(s)
- Feng Wang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - JongDae Shin
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States.,Department of Cell Biology, College of Medicine, Konyang University, Daejeon, Korea
| | - Jeremy M Shea
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Jun Yu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Ana Bošković
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Meg Byron
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, United States
| | - Xiaochun Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Alex K Shalek
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, United States.,Broad Institute of MIT and Harvard, Cambridge, United States.,Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
| | - Jeanne B Lawrence
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, United States
| | - Eduardo M Torres
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Lihua J Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States.,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Ingolf Bach
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
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19
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Li C, Hong T, Webb CH, Karner H, Sun S, Nie Q. A self-enhanced transport mechanism through long noncoding RNAs for X chromosome inactivation. Sci Rep 2016; 6:31517. [PMID: 27527711 PMCID: PMC4985753 DOI: 10.1038/srep31517] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 07/21/2016] [Indexed: 11/09/2022] Open
Abstract
X-chromosome inactivation (XCI) is the mammalian dosage compensation strategy for balancing sex chromosome content between females and males. While works exist on initiation of symmetric breaking, the underlying allelic choice mechanisms and dynamic regulation responsible for the asymmetric fate determination of XCI remain elusive. Here we combine mathematical modeling and experimental data to examine the mechanism of XCI fate decision by analyzing the signaling regulatory circuit associated with long noncoding RNAs (lncRNAs) involved in XCI. We describe three plausible gene network models that incorporate features of lncRNAs in their localized actions and rapid transcriptional turnovers. In particular, we show experimentally that Jpx (a lncRNA) is transcribed biallelically, escapes XCI, and is asymmetrically dispersed between two X's. Subjecting Jpx to our test of model predictions against previous experimental observations, we identify that a self-enhanced transport feedback mechanism is critical to XCI fate decision. In addition, the analysis indicates that an ultrasensitive response of Jpx signal on CTCF is important in this mechanism. Overall, our combined modeling and experimental data suggest that the self-enhanced transport regulation based on allele-specific nature of lncRNAs and their temporal dynamics provides a robust and novel mechanism for bi-directional fate decisions in critical developmental processes.
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Affiliation(s)
- Chunhe Li
- Department of Mathematics, University of California, Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Tian Hong
- Department of Mathematics, University of California, Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Chiu-Ho Webb
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Heather Karner
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Sha Sun
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
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20
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Payer B. Developmental regulation of X-chromosome inactivation. Semin Cell Dev Biol 2016; 56:88-99. [PMID: 27112543 DOI: 10.1016/j.semcdb.2016.04.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/13/2016] [Accepted: 04/21/2016] [Indexed: 12/01/2022]
Abstract
With the emergence of sex-determination by sex chromosomes, which differ in composition and number between males and females, appeared the need to equalize X-chromosomal gene dosage between the sexes. Mammals have devised the strategy of X-chromosome inactivation (XCI), in which one of the two X-chromosomes is rendered transcriptionally silent in females. In the mouse, the best-studied model organism with respect to XCI, this inactivation process occurs in different forms, imprinted and random, interspersed by periods of X-chromosome reactivation (XCR), which is needed to switch between the different modes of XCI. In this review, I describe the recent advances with respect to the developmental control of XCI and XCR and in particular their link to differentiation and pluripotency. Furthermore, I review the mechanisms, which influence the timing and choice, with which one of the two X-chromosomes is chosen for inactivation during random XCI. This has an impact on how females are mosaics with regard to which X-chromosome is active in different cells, which has implications on the severity of diseases caused by X-linked mutations.
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Affiliation(s)
- Bernhard Payer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology and Universitat Pompeu Fabra (UPF), Dr. Aiguader, 88, Barcelona 08003, Spain.
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21
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Wu T, Donohoe ME. The converging roles of BRD4 and gene transcription in pluripotency and oncogenesis. RNA & DISEASE 2015; 2:e894. [PMID: 26405693 PMCID: PMC4578175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023] Open
Affiliation(s)
- Tao Wu
- Burke Medical Research Institute, White Plains, NY 10605, U.S.A, Department of Neuroscience Brain Mind Research Institute, Department of Cell & Development, Weill Cornell Medical College, New York, NY 10065, U.S.A
| | - Mary E Donohoe
- Burke Medical Research Institute, White Plains, NY 10605, U.S.A, Department of Neuroscience Brain Mind Research Institute, Department of Cell & Development, Weill Cornell Medical College, New York, NY 10065, U.S.A
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22
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Abstract
An analysis of more than 1000 research articles in biology reveals that the name of the species being studied is not mentioned in the title or abstract of many articles. Consequently, such data are not easily accessible in the PubMed database. These omissions can mislead readers about the true nature of developmental processes and delay the acceptance of valid species differences. To improve the accuracy of the scientific record, I suggest that journals should require that authors include the name of the species being studied in the title or abstract of submitted papers.
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Affiliation(s)
- Barbara R Migeon
- Barbara R MigeonMcKusick Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, United States
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