1
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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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2
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Janiszewski A, Talon I, Chappell J, Collombet S, Song J, De Geest N, To SK, Bervoets G, Marin-Bejar O, Provenzano C, Vanheer L, Marine JC, Rambow F, Pasque V. Dynamic reversal of random X-Chromosome inactivation during iPSC reprogramming. Genome Res 2019; 29:1659-1672. [PMID: 31515287 PMCID: PMC6771397 DOI: 10.1101/gr.249706.119] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 08/07/2019] [Indexed: 12/13/2022]
Abstract
Induction and reversal of chromatin silencing is critical for successful development, tissue homeostasis, and the derivation of induced pluripotent stem cells (iPSCs). X-Chromosome inactivation (XCI) and reactivation (XCR) in female cells represent chromosome-wide transitions between active and inactive chromatin states. Although XCI has long been studied, providing important insights into gene regulation, the dynamics and mechanisms underlying the reversal of stable chromatin silencing of X-linked genes are much less understood. Here, we use allele-specific transcriptomics to study XCR during mouse iPSC reprogramming in order to elucidate the timing and mechanisms of chromosome-wide reversal of gene silencing. We show that XCR is hierarchical, with subsets of genes reactivating early, late, and very late during reprogramming. Early genes are activated before the onset of late pluripotency genes activation. Early genes are located genomically closer to genes that escape XCI, unlike genes reactivating late. Early genes also show increased pluripotency transcription factor (TF) binding. We also reveal that histone deacetylases (HDACs) restrict XCR in reprogramming intermediates and that the severe hypoacetylation state of the inactive X Chromosome (Xi) persists until late reprogramming stages. Altogether, these results reveal the timing of transcriptional activation of monoallelically repressed genes during iPSC reprogramming, and suggest that allelic activation involves the combined action of chromatin topology, pluripotency TFs, and chromatin regulators. These findings are important for our understanding of gene silencing, maintenance of cell identity, reprogramming, and disease.
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Affiliation(s)
- Adrian Janiszewski
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
| | - Irene Talon
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
| | - Joel Chappell
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
| | - Samuel Collombet
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Juan Song
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
| | - Natalie De Geest
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
| | - San Kit To
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
| | - Greet Bervoets
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, 3000 Leuven, Belgium.,Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Oskar Marin-Bejar
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, 3000 Leuven, Belgium.,Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Caterina Provenzano
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
| | - Lotte Vanheer
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, 3000 Leuven, Belgium.,Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Florian Rambow
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, 3000 Leuven, Belgium.,Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Vincent Pasque
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
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3
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Talon I, Janiszewski A, Chappell J, Vanheer L, Pasque V. Recent Advances in Understanding the Reversal of Gene Silencing During X Chromosome Reactivation. Front Cell Dev Biol 2019; 7:169. [PMID: 31552244 PMCID: PMC6733891 DOI: 10.3389/fcell.2019.00169] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/07/2019] [Indexed: 12/24/2022] Open
Abstract
Dosage compensation between XX female and XY male cells is achieved by a process known as X chromosome inactivation (XCI) in mammals. XCI is initiated early during development in female cells and is subsequently stably maintained in most somatic cells. Despite its stability, the robust transcriptional silencing of XCI is reversible, in the embryo and also in a number of reprogramming settings. Although XCI has been intensively studied, the dynamics, factors, and mechanisms of X chromosome reactivation (XCR) remain largely unknown. In this review, we discuss how new sequencing technologies and reprogramming approaches have enabled recent advances that revealed the timing of transcriptional activation during XCR. We also discuss the factors and chromatin features that might be important to understand the dynamics and mechanisms of the erasure of transcriptional gene silencing on the inactive X chromosome (Xi).
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Affiliation(s)
| | | | | | | | - Vincent Pasque
- Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven, Leuven, Belgium
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4
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Shu X, Shu S, Cheng H. A novel lncRNA-mediated trans-regulatory mechanism in the development of cleft palate in mouse. Mol Genet Genomic Med 2019; 7:e00522. [PMID: 30548829 PMCID: PMC6393661 DOI: 10.1002/mgg3.522] [Citation(s) in RCA: 9] [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: 08/14/2018] [Revised: 09/24/2018] [Accepted: 11/03/2018] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Increasing evidence indicates that long non-coding RNAs (lncRNAs) play crucial regulatory roles in epithelial-mesenchymal transition (EMT). However, the regulatory mechanisms during EMT of the medial edge epithelium (MEE) remain elusive. The aim of this work is to reveal a novel lncRNA-regulated dysfunction of EMT involved in the development of cleft palate (CP). METHODS C57BL/6 J mice at embryonic gestation day 14.5 (n = 6, 3 case samples vs. 3 control samples) were used to establish the CP model for lncRNA-mRNA co-expression profile analysis after high-throughput sequencing. Functional predictions for the differentially expressed lncRNA-mRNA co-expression with transcription factor (TF)-target gene relationship Gene Ontology/Kyoto Encyclopedia of Genes and Genomes pathway (GO/KEGG) analyses identified the regulatory "lncRNA-TF-target gene" trans model. RESULTS A total of 583 differentially expressed lncRNAs and 703 differentially expressed mRNAs were identified. The results of trans analysis revealed that some TFs (LEF1, SMAD4, and FOXD3) regulate lncRNAs and gene expression. Finally, we identified the NONMMUT034790.2-LEF1-SMAD7 co-expression trans-regulatory network that might be associated with CP. CONCLUSIONS Our results revealed that NONMMUT034790.2 might be a novel epigenetic biomarker in CP. The integration of lncRNA modulators into trans-regulatory networks will further enhance our understanding of lncRNA functions and regulatory mechanisms during palatal fusion in ATRA-induced mouse CP.
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Affiliation(s)
- Xuan Shu
- The Cleft Lip and Palate Treatment CenterSecond Affiliated Hospital of Shantou University Medical CollegeShantouChina
| | - Shenyou Shu
- The Cleft Lip and Palate Treatment CenterSecond Affiliated Hospital of Shantou University Medical CollegeShantouChina
| | - Hongqiu Cheng
- Department of Infectious DiseasesSecond Affiliated Hospital of Shantou University Medical CollegeShantouChina
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5
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Chang JY, Yu WH, Juan HF, Huang HC. Dynamics of alternative polyadenylation in human preimplantation embryos. Biochem Biophys Res Commun 2018; 504:727-733. [PMID: 30217451 DOI: 10.1016/j.bbrc.2018.09.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 09/06/2018] [Indexed: 01/22/2023]
Abstract
Alternative polyadenylation (APA) affects the length of the 3' untranslated region (3'-UTR) and the regulation of microRNAs. Previous studies have shown that cancer cells tend to have shorter 3'-UTRs than normal cells. A plausible explanation for this is that it enables cancer cells to escape the regulation of microRNAs. Here, we extend this concept to an opposing context: changes in 3'-UTR length in the development of the human preimplantation embryo. Unlike cancer cells, during early development 3'-UTRs tended to become longer, and gene expression was negatively correlated with 3'-UTR length. Moreover, our functional enrichment results showed that length changes are part of the development mechanism. We also investigated the analogy of 3'-UTR length variation with respect to lncRNAs and found that, similarly, lncRNA length tended to increase during embryo development.
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Affiliation(s)
- Jen-Yun Chang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Wen-Hsuan Yu
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Hsueh-Fen Juan
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan; Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan; Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan.
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6
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Tang Y, Zhou T, Yu X, Xue Z, Shen N. The role of long non-coding RNAs in rheumatic diseases. Nat Rev Rheumatol 2017; 13:657-669. [PMID: 28978995 DOI: 10.1038/nrrheum.2017.162] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Long non-coding RNAs (lncRNAs) have emerged as key epigenetic regulators that govern gene expression and influence multiple biological processes. Accumulating evidence demonstrates that lncRNAs have critical roles in immune cell development and function. In this Review, the molecular mechanisms of gene expression regulation by lncRNAs are described and current knowledge of the role of lncRNAs in immune regulation and inflammation are presented, highlighting strategies for defining the roles of lncRNAs in the pathogenesis of multiple rheumatic diseases. Finally, research progress in understanding the role of lncRNAs in rheumatic diseases is discussed.
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Affiliation(s)
- Yuanjia Tang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 145 Shan Dong Road (c), Shanghai 200001, China.,Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences (SIBS), University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai, China
| | - Tian Zhou
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 145 Shan Dong Road (c), Shanghai 200001, China
| | - Xiang Yu
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 145 Shan Dong Road (c), Shanghai 200001, China
| | - Zhixin Xue
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 145 Shan Dong Road (c), Shanghai 200001, China
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 145 Shan Dong Road (c), Shanghai 200001, China.,Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences (SIBS), University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, 2200 Lane 25 Xietu Road, Shanghai, China.,Collaborative Innovation Centre for Translational Medicine, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai, China.,Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, Ohio, USA
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7
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Dang Y, Cheng J, Sun X, Zhou Z, Liu Y. Antisense transcription licenses nascent transcripts to mediate transcriptional gene silencing. Genes Dev 2016; 30:2417-2432. [PMID: 27856616 PMCID: PMC5131781 DOI: 10.1101/gad.285791.116] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/21/2016] [Indexed: 12/21/2022]
Abstract
In this study, Dang et al. use Neurospora to demonstrate a critical role for transcription kinetics in long noncoding RNA-mediated epigenetic modifications and identify ERI-1 as an important regulator of cotranscriptional gene silencing and post-transcriptional RNA metabolism. In eukaryotes, antisense transcription can regulate sense transcription by induction of epigenetic modifications. We showed previously that antisense transcription triggers Dicer-independent siRNA (disiRNA) production and disiRNA locus DNA methylation (DLDM) in Neurospora crassa. Here we show that the conserved exonuclease ERI-1 (enhanced RNAi-1) is a critical component in this process. Antisense transcription and ERI-1 binding to target RNAs are necessary and sufficient to trigger DLDM. Convergent transcription causes stalling of RNA polymerase II during transcription, which permits ERI-1 to bind nascent RNAs in the nucleus and recruit a histone methyltransferase complex that catalyzes chromatin modifications. Furthermore, we show that, in the cytoplasm, ERI-1 targets hundreds of transcripts from loci without antisense transcription to regulate RNA stability. Together, our results demonstrate a critical role for transcription kinetics in long noncoding RNA-mediated epigenetic modifications and identify ERI-1 as an important regulator of cotranscriptional gene silencing and post-transcriptional RNA metabolism.
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Affiliation(s)
- Yunkun Dang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xianyun Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, ZhongGuanCun, Beijing 100080, China
| | - Zhipeng Zhou
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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8
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Goodrich L, Panning B, Leung KN. Activators and repressors: A balancing act for X-inactivation. Semin Cell Dev Biol 2016; 56:3-8. [DOI: 10.1016/j.semcdb.2016.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 05/06/2016] [Accepted: 05/06/2016] [Indexed: 10/21/2022]
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9
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Gao L, Liu Y, Wen Y, Wu W. LncRNA H19-mediated mouse cleft palate induced by all-trans retinoic acid. Hum Exp Toxicol 2016; 36:395-401. [DOI: 10.1177/0960327116651121] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Long noncoding RNAs (lncRNAs) are the new class of transcripts and pervasively transcribed in the genome, which have been found to play important functional roles in many tissues and organs. LncRNAs can interact with target gene to exert their functions. However, the function and mechanism of lncRNA in cleft palate (CP) development remain elusive. Here, we investigated the role of lncRNA H19 and its target gene insulin-like growth factor 2 (IGF2) in CP of mice. All-trans retinoic acid (atRA) is a well-known teratogenic effecter of CP. After establishment of the CP mouse model using atRA in vivo, we found that the rate of CP in mice was 100%. The tail lengths of fetuses in atRA-treated mice were shorter than those of control mice from embryonic day (E)12 to E17. The expression of lncRNA H19 and IGF2 were embryo age-related differences between atRNA-treated and control mice. In addition, the the relationship between lncRNA H19 and IGF2 were negative correlation in the critical period of developmental palate. These findings suggest that lncRNA H19 mediate atRA-induced CP in mice.
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Affiliation(s)
- L Gao
- School of Public Health, Xinxiang Medical College, Xinxiang, Henan, People’s Republic of China
- College of Public Health, Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Y Liu
- School of Pharmacy, Xinxiang Medical College, Xinxiang, Henan, People’s Republic of China
| | - Y Wen
- School of Public Health, Xinxiang Medical College, Xinxiang, Henan, People’s Republic of China
| | - W Wu
- School of Public Health, Xinxiang Medical College, Xinxiang, Henan, People’s Republic of China
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10
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Prudhomme J, Morey C. Epigenesis and plasticity of mouse trophoblast stem cells. Cell Mol Life Sci 2016; 73:757-74. [PMID: 26542801 PMCID: PMC11108370 DOI: 10.1007/s00018-015-2086-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 10/27/2015] [Indexed: 12/28/2022]
Abstract
The critical role of the placenta in supporting a healthy pregnancy is mostly ensured by the extraembryonic trophoblast lineage that acts as the interface between the maternal and the foetal compartments. The diverse trophoblast cell subtypes that form the placenta originate from a single layer of stem cells that emerge from the embryo when the earliest cell fate decisions are occurring. Recent studies show that these trophoblast stem cells exhibit extensive plasticity as they are capable of differentiating down multiple pathways and are easily converted into embryonic stem cells in vitro. In this review, we discuss current knowledge of the mechanisms and control of the epigenesis of mouse trophoblast stem cells through a comparison with the corresponding mechanisms in pluripotent embryonic stem cells. To illustrate some of the more striking manifestations of the epigenetic plasticity of mouse trophoblast stem cells, we discuss them within the context of two paradigms of epigenetic regulation of gene expression: the imprinted gene expression of specific loci and the process of X-chromosome inactivation.
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Affiliation(s)
- Julie Prudhomme
- Laboratoire de Génétique Moléculaire Murine, Institut Pasteur, 75015, Paris, France
| | - Céline Morey
- CNRS, UMR7216 Epigenetics and Cell Fate, 75013, Paris, France.
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11
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An overview of X inactivation based on species differences. Semin Cell Dev Biol 2016; 56:111-116. [PMID: 26805440 DOI: 10.1016/j.semcdb.2016.01.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 01/14/2016] [Accepted: 01/19/2016] [Indexed: 12/29/2022]
Abstract
X inactivation, a developmental process that takes place in early stages of mammalian embryogenesis, balances the sex difference in dosage of X-linked genes. Although all mammals use this form of dosage compensation, the details differ from one species to another because of variations in the staging of embryogenesis and evolutionary tinkering with the DNA blueprint for development. Such differences provide a broader view of the process than that afforded by a single species. My overview of X inactivation is based on these species variations.
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12
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Prudhomme J, Dubois A, Navarro P, Arnaud D, Avner P, Morey C. A rapid passage through a two-active-X-chromosome state accompanies the switch of imprinted X-inactivation patterns in mouse trophoblast stem cells. Epigenetics Chromatin 2015; 8:52. [PMID: 26628922 PMCID: PMC4665903 DOI: 10.1186/s13072-015-0044-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/16/2015] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND In female mice, while the presence of two-active X-chromosomes characterises pluripotency, it is not tolerated in most other cellular contexts. In particular, in the trophoblastic lineage, impairment of paternal X (X(P)) inactivation results in placental defects. RESULTS Here, we show that Trophoblast Stem (TS) cells can undergo a complete reversal of imprinted X-inactivation without detectable change in cell-type identity. This reversal occurs through a reactivation of the X(P) leading to TS clones showing two active Xs. Intriguingly, within such clones, all the cells rapidly and homogeneously either re-inactivate the X(P) or inactivate, de novo, the X(M). CONCLUSION This secondary non-random inactivation suggests that the two-active-X states in TS and in pluripotent contexts are epigenetically distinct. These observations also reveal a pronounced plasticity of the TS epigenome allowing TS cells to dramatically and accurately reprogram gene expression profiles. This plasticity may serve as a back-up system when X-linked mono-allelic gene expression is perturbed.
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Affiliation(s)
- Julie Prudhomme
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France
| | - Agnès Dubois
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France ; Epigenetics of Stem Cells Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France
| | - Pablo Navarro
- Epigenetics of Stem Cells Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France
| | - Danielle Arnaud
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France
| | - Philip Avner
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France ; Dynamics of Epigenetic Regulation, EMBL Monterotondo, Adriano Buzzati-Traverso Campus, Via Ramarini 32, 00015 Monterotondo, Italy
| | - Céline Morey
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France ; CNRS, UMR7216 Epigenetics and Cell Fate, 35 rue Hélène Brion, 75013 Paris, France
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13
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Abstract
Epigenetic mechanisms play an essential role in the germline and imprinting cycle. Germ cells show extensive epigenetic programming in preparation for the generation of the totipotent state, which in turn leads to the establishment of pluripotent cells in blastocysts. The latter are the cells from which pluripotent embryonic stem cells are derived and maintained in culture. Following blastocyst implantation, postimplantation epiblast cells develop, which give rise to all somatic cells as well as primordial germ cells, the precursors of sperm and eggs. Pluripotent stem cells in culture can be induced to undergo differentiation into somatic cells and germ cells in culture. Understanding the natural cycles of epigenetic reprogramming that occur in the germline will allow the generation of better and more versatile stem cells for both therapeutic and research purposes.
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Affiliation(s)
- Wolf Reik
- The Babraham Institute, Babraham Research Campus, Cambridge CB2 3EG, United Kingdom Wellcome Trust Cancer Research UK Gurdon Institute & Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - M Azim Surani
- Wellcome Trust Cancer Research UK Gurdon Institute & Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
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14
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Sun T, Plutynski A, Ward S, Rubin JB. An integrative view on sex differences in brain tumors. Cell Mol Life Sci 2015; 72:3323-42. [PMID: 25985759 PMCID: PMC4531141 DOI: 10.1007/s00018-015-1930-2] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 04/27/2015] [Accepted: 05/11/2015] [Indexed: 02/07/2023]
Abstract
Sex differences in human health and disease can range from undetectable to profound. Differences in brain tumor rates and outcome are evident in males and females throughout the world and regardless of age. These observations indicate that fundamental aspects of sex determination can impact the biology of brain tumors. It is likely that optimal personalized approaches to the treatment of male and female brain tumor patients will require recognizing and understanding the ways in which the biology of their tumors can differ. It is our view that sex-specific approaches to brain tumor screening and care will be enhanced by rigorously documenting differences in brain tumor rates and outcomes in males and females, and understanding the developmental and evolutionary origins of sex differences. Here we offer such an integrative perspective on brain tumors. It is our intent to encourage the consideration of sex differences in clinical and basic scientific investigations.
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Affiliation(s)
- Tao Sun
- />Department of Pediatrics, Washington University School of Medicine, St Louis, USA
| | - Anya Plutynski
- />Department of Philosophy, Washington University in St Louis, St Louis, USA
| | - Stacey Ward
- />Department of Pediatrics, Washington University School of Medicine, St Louis, USA
| | - Joshua B. Rubin
- />Department of Pediatrics, Washington University School of Medicine, St Louis, USA
- />Department of Anatomy and Neurobiology, Washington University School of Medicine, 660 South Euclid Ave, St Louis, MO 63110 USA
- />Campus Box 8208, 660 South Euclid Ave, St Louis, MO 63110 USA
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15
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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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16
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Abstract
RNAs not encoding proteins have gained prominence over the last couple of decades as fundamental regulators of cellular function. Not surprisingly, their dysregulation is increasingly being linked to pathology. Here, we review recent reports investigating the pathophysiological relevance of this species of RNA for the cardiovascular system, concentrating mainly on recent findings on long noncoding RNAs and microRNAs in cardiac hypertrophy and failure.
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Affiliation(s)
- Thomas Thum
- From the Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Integrated Research and Treatment Center Transplantation, and REBIRTH Excellence Cluster, Hannover Medical School, Hannover, Germany (T.T.); National Heart and Lung Institute, Imperial College London, London, United Kingdom (T.T.); Humanitas Clinical and Research Center, Rozzano, Milan, Italy (G.C.); Institute of Genetics and Biomedical Research, National Research Country of Italy, Milan, Italy (G.C.); University of
| | - Gianluigi Condorelli
- From the Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Integrated Research and Treatment Center Transplantation, and REBIRTH Excellence Cluster, Hannover Medical School, Hannover, Germany (T.T.); National Heart and Lung Institute, Imperial College London, London, United Kingdom (T.T.); Humanitas Clinical and Research Center, Rozzano, Milan, Italy (G.C.); Institute of Genetics and Biomedical Research, National Research Country of Italy, Milan, Italy (G.C.); University of
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17
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Kota SK, Roy Chowdhury D, Rao LK, Padmalatha V, Singh L, Bhadra U. Uncoupling of X-linked gene silencing from XIST binding by DICER1 and chromatin modulation on human inactive X chromosome. Chromosoma 2014; 124:249-62. [PMID: 25428210 DOI: 10.1007/s00412-014-0495-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 10/24/2014] [Accepted: 11/07/2014] [Indexed: 12/18/2022]
Abstract
In mammals, X-inactivation process is achieved by the cis-spreading of long noncoding Xist RNA over one of the female X chromosomes. The Xist binding accumulates histones H3 methylation and H4 hypoacetylation required for X inactivation that leads to proper dosage compensation of the X-linked genes. Co-transcription of Tsix, an antisense copy of Xist, blocks the Xist coating on the Xi. In mice ES cells, an RNase III enzyme Dicer1 disrupts Xist binding and methylated H3K27me3 accumulation on the Xi. Later, multiple reports opposed these findings raising a question regarding the possible role of Dicer1 in murine X silencing. Here, we show that reduction of DICER1 in human female cells increases XIST transcripts without compromising the binding of the XIST and histone tail modifications on the Xi. Moreover, DICER1-depleted cells show differential upregulation of many human X-linked genes by binding different amounts of acetylated histone predominantly on their active promoter sites. Therefore, X-linked gene silencing, which is thought to be coupled with the accumulation of XIST and heterochromatin markers on Xi can be disrupted in DICER1 depleted human cells. These results suggest that DICER1 has no apparent effect on the recruitment of heterochromatic markers on the Xi but is required for inactivation of differentially regulated genes for the maintenance of proper dosage compensation in differentiated cells.
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Affiliation(s)
- Satya Keerthi Kota
- Functional Genomics and Gene Silencing Group, Centre For Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India
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18
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Xue Z, Ye Q, Anson SR, Yang J, Xiao G, Kowbel D, Glass NL, Crosthwaite SK, Liu Y. Transcriptional interference by antisense RNA is required for circadian clock function. Nature 2014; 514:650-3. [PMID: 25132551 PMCID: PMC4214883 DOI: 10.1038/nature13671] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 07/10/2014] [Indexed: 01/24/2023]
Abstract
Eukaryotic circadian oscillators consist of negative feedback loops that generate endogenous rhythmicities1. Natural antisense RNAs are found in a wide range of eukaryotic organisms2-5. Nevertheless, the physiological importance and mode of action of most antisense RNAs is not clear6-9. frequency (frq) encodes a component of the Neurospora core circadian negative feedback loop which was thought to generate sustained rhythmicity10. Transcription of qrf, the long non-coding frq antisense RNA, is light induced, and its level oscillates in antiphase to frq sense RNA3. Here we show that qrf transcription is regulated by both light-dependent and -independent mechanisms. Light-dependent qrf transcription represses frq expression and regulates clock resetting. qrf expression in the dark, on the other hand, is required for circadian rhythmicity. frq transcription also inhibits qrf expression and surprisingly, drives the antiphasic rhythm of qrf transcripts. The mutual inhibition of frq and qrf transcription thus forms a double negative feedback loop that is interlocked with the core feedback loop. Genetic and mathematical modeling analyses indicate that such an arrangement is required for robust and sustained circadian rhythmicity. Moreover, our results suggest that antisense transcription inhibits sense expression by mediating chromatin modifications and premature transcription termination. Together, our results established antisense transcription as an essential feature in a circadian system and shed light on the importance and mechanism of antisense action.
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Affiliation(s)
- Zhihong Xue
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Qiaohong Ye
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Simon R Anson
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Jichen Yang
- Department of Clinical Sciences, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Guanghua Xiao
- Department of Clinical Sciences, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - David Kowbel
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - N Louise Glass
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | | | - Yi Liu
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
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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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20
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Chelmicki T, Dündar F, Turley MJ, Khanam T, Aktas T, Ramírez F, Gendrel AV, Wright PR, Videm P, Backofen R, Heard E, Manke T, Akhtar A. MOF-associated complexes ensure stem cell identity and Xist repression. eLife 2014; 3:e02024. [PMID: 24842875 PMCID: PMC4059889 DOI: 10.7554/elife.02024] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Histone acetyl transferases (HATs) play distinct roles in many cellular processes and are frequently misregulated in cancers. Here, we study the regulatory potential of MYST1-(MOF)-containing MSL and NSL complexes in mouse embryonic stem cells (ESCs) and neuronal progenitors. We find that both complexes influence transcription by targeting promoters and TSS-distal enhancers. In contrast to flies, the MSL complex is not exclusively enriched on the X chromosome, yet it is crucial for mammalian X chromosome regulation as it specifically regulates Tsix, the major repressor of Xist lncRNA. MSL depletion leads to decreased Tsix expression, reduced REX1 recruitment, and consequently, enhanced accumulation of Xist and variable numbers of inactivated X chromosomes during early differentiation. The NSL complex provides additional, Tsix-independent repression of Xist by maintaining pluripotency. MSL and NSL complexes therefore act synergistically by using distinct pathways to ensure a fail-safe mechanism for the repression of X inactivation in ESCs. DOI:http://dx.doi.org/10.7554/eLife.02024.001 Gene expression is controlled by a complicated network of mechanisms involving a wide range of enzymes and protein complexes. Many of these mechanisms are identical in males and females, but some are not. Female mammals, for example, carry two X chromosomes, whereas males have one X and one Y chromosome. Since the two X chromosomes in females contain essentially the same set of genes, one of them undergoes silencing to prevent the overproduction of certain proteins. This process, which is called X-inactivation, occurs during different stages of development and it must be tightly controlled. An enzyme called MOF was originally found in flies in two distinct complexes—the male-specific lethal (MSL) complex, which forms only in males, and the non-specific lethal (NSL) complex, which is ubiquitous in both males and females. These complexes are evolutionary conserved and are also found in mammals. While mammalian MOF is reasonably well understood, the MSL and NSL complexes are not, so Chelmicki, Dündar et al. have used various sequencing techniques, in combination with biochemical experiments, to investigate their roles in embryonic stem cells and neuronal progenitor cells in mice. These experiments show that MSL and NSL complexes engage in the regulation of thousands of genes. Although the two complexes often show different gene preferences, they often regulate the same cellular processes. The MSL/NSL-dependent regulation of X chromosome inactivation is a prime example of this phenomenon. The MSL complex reduces the production of an RNA molecule called Xist, which is responsible for the inactivation of one of the two X chromosomes in females. The NSL complex, meanwhile, ensures the production of multiple proteins that are crucial for the development of embryonic stem cells, and are also involved in the repression of X inactivation. This analysis sheds light on how different complexes can cooperate and complement each other in order to reach the same goal in the cell. The knowledge gained from this study will pave the way towards better understanding of complex processes such as embryonic development, organogenesis and the pathogenesis of disorders like cancer. DOI:http://dx.doi.org/10.7554/eLife.02024.002
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Affiliation(s)
- Tomasz Chelmicki
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Friederike Dündar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany Faculty of Biology, University of Freiburg, Freiburg, Germany Bioinformatics Department, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Matthew James Turley
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Tasneem Khanam
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Tugce Aktas
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Fidel Ramírez
- Bioinformatics Department, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Patrick Rudolf Wright
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Pavankumar Videm
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany BIOSS Center for Biological Signalling Studies, University of Freiburg, Freiburg, Germany Center for Biological Systems Analysis, University of Freiburg, Freiburg, Germany Center for Non-Coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark
| | - Edith Heard
- Mammalian Developmental Epigenetics Group, Institute Curie, Paris, France
| | - Thomas Manke
- Bioinformatics Department, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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21
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Kim KY, Hysolli E, Tanaka Y, Wang B, Jung YW, Pan X, Weissman SM, Park IH. X Chromosome of female cells shows dynamic changes in status during human somatic cell reprogramming. Stem Cell Reports 2014; 2:896-909. [PMID: 24936474 PMCID: PMC4050354 DOI: 10.1016/j.stemcr.2014.04.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 04/05/2014] [Accepted: 04/07/2014] [Indexed: 12/17/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) acquire embryonic stem cell (ESC)-like epigenetic states, including the X chromosome. Previous studies reported that human iPSCs retain the inactive X chromosome of parental cells, or acquire two active X chromosomes through reprogramming. Most studies investigated the X chromosome states in established human iPSC clones after completion of reprogramming. Thus, it is still not fully understood when and how the X chromosome reactivation occurs during reprogramming. Here, we report a dynamic change in the X chromosome state throughout reprogramming, with an initial robust reactivation of the inactive X chromosome followed by an inactivation upon generation of nascent iPSC clones. iPSCs with two active X chromosomes or an eroded X chromosome arise in passaging iPSCs. These data provide important insights into the plasticity of the X chromosome of human female iPSCs and will be crucial for the future application of such cells in cell therapy and X-linked disease modeling. The X chromosome state changes dynamically during human somatic cell reprogramming Ectopic reprogramming factors transiently activate the inactive X chromosome Nascent iPSC colonies carry an inactive X chromosome Class I and class III iPSCs arise from nascent iPSCs
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Affiliation(s)
- Kun-Yong Kim
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
| | - Eriona Hysolli
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
| | - Yoshiaki Tanaka
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
| | - Brandon Wang
- Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA
| | - Yong-Wook Jung
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA ; Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul 135-080, Republic of Korea
| | - Xinghua Pan
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
| | - Sherman Morton Weissman
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
| | - In-Hyun Park
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
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22
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Papait R, Kunderfranco P, Stirparo GG, Latronico MVG, Condorelli G. Long noncoding RNA: a new player of heart failure? J Cardiovasc Transl Res 2013; 6:876-83. [PMID: 23835777 PMCID: PMC3838575 DOI: 10.1007/s12265-013-9488-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 06/14/2013] [Indexed: 01/10/2023]
Abstract
One the most important discoveries of the post-genomic era is that a large fraction of the genome transcribes a heterogeneous population of noncoding RNAs (ncRNA). ncRNAs shorter than 200 nucleotides are usually identified as short/small ncRNAs--examples include PIWI-interacting RNAs, small interfering RNAs, and microRNAs (miRNAs)--whereas those longer than 200 nucleotides are classified as long ncRNAs (lncRNAs). These molecules are emerging as important regulators of cellular process, such as development, differentiation, and metabolism. Not surprisingly, ncRNAs are involved also in human diseases, such as cancer and metabolic and neuronal disorders. Although the role of miRNAs is being largely investigated in cardiovascular biology, little is known about other classes of ncRNA in this field. However, recent reports have started to reveal the importance of lncRNA in heart development and suggest also an involvement in heart failure. Here, we will discuss these reports and the therapeutic potential of lncRNA for heart failure.
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Affiliation(s)
- Roberto Papait
- Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano, MI 20098 Italy
- Institute of Genetics and Biomedical Research, National Research Council of Italy (CNR), Rozzano, MI 20098 Italy
| | - Paolo Kunderfranco
- Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano, MI 20098 Italy
| | - Giuliano Giuseppe Stirparo
- Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano, MI 20098 Italy
- University of Milan, Milan, 20100 Italy
| | | | - Gianluigi Condorelli
- Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano, MI 20098 Italy
- University of Milan, Milan, 20100 Italy
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23
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Portha B, Fournier A, Kioon MDA, Mezger V, Movassat J. Early environmental factors, alteration of epigenetic marks and metabolic disease susceptibility. Biochimie 2013; 97:1-15. [PMID: 24139903 DOI: 10.1016/j.biochi.2013.10.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 10/07/2013] [Indexed: 12/11/2022]
Abstract
The environmental conditions that are experienced in early life can profoundly influence human biology and long-term health. Early-life nutrition and stress are among the best documented examples of such conditions because they influence the adult risk of developing metabolic diseases, such as type 2 diabetes mellitus (T2D) and cardiovascular diseases. It is now becoming increasingly accepted that environmental compounds including nutrients can produce changes in the genome activity that in spite of not altering DNA sequence can produce important, stable and transgenerational alterations in the phenotype. Epigenetic changes, in particular DNA methylation and histone acetylation/methylation, provide a 'memory' of developmental plastic responses to early environment and are central to the generation of phenotypes and their stability throughout the life course. Their effects may only become manifest later in life, e.g. in terms of altered responses to environmental challenges.
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Affiliation(s)
- B Portha
- Université Paris-Diderot, Sorbonne-Paris-Cité, Laboratoire B2PE (Biologie et Pathologie du Pancréas Endocrine), Unité BFA (Biologie Fonctionnelle et Adaptive), CNRS EAC 4413, Bâtiment BUFFON, 5ème étage, 4 Rue Lagroua Weill Hallé, Case 7126, F-75205 Paris Cedex 13, France.
| | - A Fournier
- Univ ParisDiderot, Sorbonne-Paris-Cité, Unité EDC (Epigénétique et Destin Cellulaire), CNRS UMR7216, F-75205 Paris Cedex 13, Paris, France
| | - M D Ah Kioon
- Université Paris-Diderot, Sorbonne-Paris-Cité, Laboratoire B2PE (Biologie et Pathologie du Pancréas Endocrine), Unité BFA (Biologie Fonctionnelle et Adaptive), CNRS EAC 4413, Bâtiment BUFFON, 5ème étage, 4 Rue Lagroua Weill Hallé, Case 7126, F-75205 Paris Cedex 13, France
| | - V Mezger
- Univ ParisDiderot, Sorbonne-Paris-Cité, Unité EDC (Epigénétique et Destin Cellulaire), CNRS UMR7216, F-75205 Paris Cedex 13, Paris, France
| | - J Movassat
- Université Paris-Diderot, Sorbonne-Paris-Cité, Laboratoire B2PE (Biologie et Pathologie du Pancréas Endocrine), Unité BFA (Biologie Fonctionnelle et Adaptive), CNRS EAC 4413, Bâtiment BUFFON, 5ème étage, 4 Rue Lagroua Weill Hallé, Case 7126, F-75205 Paris Cedex 13, France
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24
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Abstract
Long noncoding RNAs (lncRNAs) have gained widespread attention in recent years as a potentially new and crucial layer of biological regulation. lncRNAs of all kinds have been implicated in a range of developmental processes and diseases, but knowledge of the mechanisms by which they act is still surprisingly limited, and claims that almost the entirety of the mammalian genome is transcribed into functional noncoding transcripts remain controversial. At the same time, a small number of well-studied lncRNAs have given us important clues about the biology of these molecules, and a few key functional and mechanistic themes have begun to emerge, although the robustness of these models and classification schemes remains to be seen. Here, we review the current state of knowledge of the lncRNA field, discussing what is known about the genomic contexts, biological functions, and mechanisms of action of lncRNAs. We also reflect on how the recent interest in lncRNAs is deeply rooted in biology's longstanding concern with the evolution and function of genomes.
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Affiliation(s)
- Johnny T Y Kung
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02114, USA
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25
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Demarcation of stable subpopulations within the pluripotent hESC compartment. PLoS One 2013; 8:e57276. [PMID: 23437358 PMCID: PMC3578859 DOI: 10.1371/journal.pone.0057276] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 01/20/2013] [Indexed: 11/19/2022] Open
Abstract
Heterogeneity is a feature of stem cell populations, resulting from innate cellular hierarchies that govern differentiation capability. How heterogeneity impacts human pluripotent stem cell populations is directly relevant to their efficacious use in regenerative medicine applications. The control of pluripotency is asserted by a core transcription factor network, of which Oct4 is a necessary member. In mouse embryonic stem cells (ESCs), the zinc finger transcription factor Rex1 (Zfp42) closely tracks the undifferentiated state and is capable of segregating Oct4 positive mESCs into metastable populations expressing or lacking Rex1 that are inter-convertible. However, little is currently understood about the extent or function of heterogeneous populations in the human pluripotent compartment. Human ESCs express REX1 transcripts but the distribution and properties of REX1 expressing cells have yet to be described. To address these questions, we used gene targeting in human ESCs to insert the fluorescent protein Venus and an antibiotic selection marker under the control of the endogenous REX1 transcription regulatory elements, generating a sensitive, selectable reporter of pluripotency. REX1 is co-expressed in OCT4 and TRA-1-60 positive hESCs and rapidly lost upon differentiation. Importantly, REX1 expression reveals significant heterogeneity within seemingly homogenous populations of OCT4 and TRA-1-60 hESCs. REX1 expression is extinguished before OCT4 during differentiation, but, in contrast to the mouse, loss of REX1 expression demarcates a stable, OCT4 positive lineage-primed state in pluripotent hESCs that does not revert back to REX1 positivity under normal conditions. We show that loss of REX1 expression correlates with altered patterns of DNA methylation at the REX1 locus, implying that epigenetic mechanisms may interfere with the metastable phenotype commonly found in murine pluripotency.
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26
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Ooi J, Liu P. Pluripotency and its layers of complexity. CELL REGENERATION 2012; 1:7. [PMID: 25408870 PMCID: PMC4230502 DOI: 10.1186/2045-9769-1-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 08/02/2012] [Indexed: 12/15/2022]
Abstract
Pluripotency is depicted by a self-renewing state that can competently differentiate to form the three germ layers. Different stages of early murine development can be captured on a petri dish, delineating a spectrum of pluripotent states, ranging from embryonic stem cells, embryonic germ cells to epiblast stem cells. Anomalous cell populations displaying signs of pluripotency have also been uncovered, from the isolation of embryonic carcinoma cells to the derivation of induced pluripotent stem cells. Gaining insight into the molecular circuitry within these cell types enlightens us about the significance and contribution of each stage, hence deepening our understanding of vertebrate development. In this review, we aim to describe experimental milestones that led to the understanding of embryonic development and the conception of pluripotency. We also discuss attempts at exploring the realm of pluripotency with the identification of pluripotent stem cells within mouse teratocarcinomas and embryos, and the generation of pluripotent cells through nuclear reprogramming. In conclusion, we illustrate pluripotent cells derived from other organisms, including human derivatives, and describe current paradigms in the comprehension of human pluripotency.
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Affiliation(s)
- Jolene Ooi
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA UK ; Technology and Research, Agency for Science, 1 Fusionopolis Way, #20-10, Connexis North Tower, Kragujevac, 138632 Singapore
| | - Pentao Liu
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA UK
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Mugford JW, Yee D, Magnuson T. Failure of extra-embryonic progenitor maintenance in the absence of dosage compensation. Development 2012; 139:2130-8. [PMID: 22573614 DOI: 10.1242/dev.076497] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Proper regulation of X-linked gene expression, termed dosage compensation, is required for the normal development of mammalian embryos. Through the process of X chromosome inactivation (XCI), somatic cells of mammalian females inactivate one of their two X chromosomes in order to balance X-linked gene dosage with their male counterparts. The process of XCI is dependent upon the long non-coding RNA Xist, which is expressed from and coats the inactivated X chromosome (Xi) in cis. During mouse embryogenesis, imprinted XCI inactivates the paternally inherited X chromosome (Xp) within the extra-embryonic lineages. Consequently, females harboring a paternally derived Xist mutation (X/X(Xist-)) die owing to failure of imprinted XCI and, presumably, poor trophoblast development. Here, we investigate the consequence of two active X chromosomes in the extra-embryonic ectoderm (ExE) of X/X(Xist-) female embryos. At embryonic day (E) 6.5, we find that the X/X(Xist-) ExE lacks the transcriptional regulator CDX2, a factor required to maintain the ExE in a progenitor state. In addition, spongiotrophoblast progenitors are not maintained. Surprisingly, we observe evidence of an Xi in a subpopulation of X/X(Xist-) ExE cells. We demonstrate further that trophectodermal stem cells derived from X/X(Xist-) embryos completely reverse normal imprinted XCI patterns. Taken together, our data suggest that, much like in the cells of the epiblast, the initial imprint that establishes imprinted XCI is probably erased in ExE cells. Conversely, unlike the epiblast, in which XCI is not required for progenitor cell maintenance, we demonstrate that dosage compensation is indispensable for the maintenance of trophoblast progenitors.
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Affiliation(s)
- Joshua W Mugford
- The University of North Carolina at Chapel Hill, Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599-7264, USA
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Whitworth DJ, Ovchinnikov DA, Wolvetang EJ. Generation and characterization of LIF-dependent canine induced pluripotent stem cells from adult dermal fibroblasts. Stem Cells Dev 2012; 21:2288-97. [PMID: 22221227 DOI: 10.1089/scd.2011.0608] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Dogs provide a more clinically relevant model of human disease than rodents, particularly with respect to hereditary diseases. Thus, the availability of canine stem cells will greatly facilitate the use of the dog in the development of stem cell-based gene therapies and regenerative medicine. In this study we describe the production of canine induced pluripotent stem cells (ciPSCs) from adult dermal fibroblasts. These cells have a morphology resembling previously described canine embryonic stem cells, a normal karyotype, and express pluripotency markers including alkaline phosphatase, Nanog, Oct4, Telomerase, SSEA1, SSEA4, TRA1-60, TRA1-81, and Rex1. Furthermore, the inactive X chromosome is reactivated indicating a ground-state pluripotency. In culture they readily form embryoid bodies, which in turn give rise to cell types from all 3 embryonic germ layers, as indicated by expression of the definitive endoderm markers Cxcr4 and α-fetoprotein, mesoderm markers Collagen IIA and Gata2, and ectoderm markers βIII-tubulin, Enolase, and Nestin. Of particular significance is the observation that these ciPSCs are dependent only on leukemia inhibitory factor (LIF), making them similar to mouse and canine embryonic stem cells, but strikingly unlike the ciPSCs recently described in two other studies, which were dependent on both basic fibroblast growth factor and LIF in order to maintain their pluripotency. Thus, our ciPSCs closely resemble mouse ESCs derived from the inner cell mass of preimplantation embryos, while the previously described ciPSCs appear to be more representative of cells from the epiblast of mouse postimplantation embryos.
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Affiliation(s)
- Deanne J Whitworth
- School of Veterinary Science, University of Queensland, Gatton, Queensland, Australia.
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Pasque V, Halley-Stott RP, Gillich A, Garrett N, Gurdon JB. Epigenetic stability of repressed states involving the histone variant macroH2A revealed by nuclear transfer to Xenopus oocytes. Nucleus 2011; 2:533-9. [PMID: 22064467 PMCID: PMC3324342 DOI: 10.4161/nucl.2.6.17799] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
How various epigenetic mechanisms restrict chromatin plasticity to determine the stability of repressed genes is poorly understood. Nuclear transfer to Xenopus oocytes induces the transcriptional reactivation of previously silenced genes. Recent work suggests that it can be used to analyze the epigenetic stability of repressed states. The notion that the epigenetic state of genes is an important determinant of the efficiency of nuclear reprogramming is supported by the differential reprogramming of given genes from different starting epigenetic configurations. After nuclear transfer, transcription from the inactive X chromosome of post-implantation-derived epiblast stem cells is reactivated. However, the same chromosome is resistant to reactivation when embryonic fibroblasts are used. Here, we discuss different kinds of evidence that link the histone variant macroH2A to the increased stability of repressed states. We focus on developmentally regulated X chromosome inactivation and repression of autosomal pluripotency genes, where macroH2A may help maintain the long-term stability of the differentiated state of somatic cells.
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Affiliation(s)
- Vincent Pasque
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK.
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