51
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Faulkner GJ, Billon V. L1 retrotransposition in the soma: a field jumping ahead. Mob DNA 2018; 9:22. [PMID: 30002735 PMCID: PMC6035798 DOI: 10.1186/s13100-018-0128-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 06/27/2018] [Indexed: 12/13/2022] Open
Abstract
Retrotransposons are transposable elements (TEs) capable of "jumping" in germ, embryonic and tumor cells and, as is now clearly established, in the neuronal lineage. Mosaic TE insertions form part of a broader landscape of somatic genome variation and hold significant potential to generate phenotypic diversity, in the brain and elsewhere. At present, the LINE-1 (L1) retrotransposon family appears to be the most active autonomous TE in most mammals, based on experimental data obtained from disease-causing L1 mutations, engineered L1 reporter systems tested in cultured cells and transgenic rodents, and single-cell genomic analyses. However, the biological consequences of almost all somatic L1 insertions identified thus far remain unknown. In this review, we briefly summarize the current state-of-the-art in the field, including estimates of L1 retrotransposition rate in neurons. We bring forward the hypothesis that an extensive subset of retrotransposition-competent L1s may be de-repressed and mobile in the soma but largely inactive in the germline. We discuss recent reports of non-canonical L1-associated sequence variants in the brain and propose that the elevated L1 DNA content reported in several neurological disorders may predominantly comprise accumulated, unintegrated L1 nucleic acids, rather than somatic L1 insertions. Finally, we consider the main objectives and obstacles going forward in elucidating the biological impact of somatic retrotransposition.
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Affiliation(s)
- Geoffrey J. Faulkner
- Mater Research Institute – University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia
- School of Biomedical Sciences, University of Queensland, Brisbane, QLD 4072 Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072 Australia
| | - Victor Billon
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072 Australia
- Biology Department, École Normale Supérieure Paris-Saclay, 61 Avenue du Président Wilson, 94230 Cachan, France
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52
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Transcription factor profiling reveals molecular choreography and key regulators of human retrotransposon expression. Proc Natl Acad Sci U S A 2018; 115:E5526-E5535. [PMID: 29802231 PMCID: PMC6004460 DOI: 10.1073/pnas.1722565115] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transposable elements (TEs) represent a substantial fraction of many eukaryotic genomes, and transcriptional regulation of these factors is important to determine TE activities in human cells. However, due to the repetitive nature of TEs, identifying transcription factor (TF)-binding sites from ChIP-sequencing (ChIP-seq) datasets is challenging. Current algorithms are focused on subtle differences between TE copies and thus bias the analysis to relatively old and inactive TEs. Here we describe an approach termed "MapRRCon" (mapping repeat reads to a consensus) which allows us to identify proteins binding to TE DNA sequences by mapping ChIP-seq reads to the TE consensus sequence after whole-genome alignment. Although this method does not assign binding sites to individual insertions in the genome, it provides a landscape of interacting TFs by capturing factors that bind to TEs under various conditions. We applied this method to screen TFs' interaction with L1 in human cells/tissues using ENCODE ChIP-seq datasets and identified 178 of the 512 TFs tested as bound to L1 in at least one biological condition with most of them (138) localized to the promoter. Among these L1-binding factors, we focused on Myc and CTCF, as they play important roles in cancer progression and 3D chromatin structure formation. Furthermore, we explored the transcriptomes of The Cancer Genome Atlas breast and ovarian tumor samples in which a consistent anti-/correlation between L1 and Myc/CTCF expression was observed, suggesting that these two factors may play roles in regulating L1 transcription during the development of such tumors.
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53
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Coluccio A, Ecco G, Duc J, Offner S, Turelli P, Trono D. Individual retrotransposon integrants are differentially controlled by KZFP/KAP1-dependent histone methylation, DNA methylation and TET-mediated hydroxymethylation in naïve embryonic stem cells. Epigenetics Chromatin 2018; 11:7. [PMID: 29482634 PMCID: PMC6389204 DOI: 10.1186/s13072-018-0177-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 02/16/2018] [Indexed: 01/18/2023] Open
Abstract
Background The KZFP/KAP1 (KRAB zinc finger proteins/KRAB-associated protein 1) system plays a central role in repressing transposable elements (TEs) and maintaining parent-of-origin DNA methylation at imprinting control regions (ICRs) during the wave of genome-wide reprogramming that precedes implantation. In naïve murine embryonic stem cells (mESCs), the genome is maintained highly hypomethylated by a combination of TET-mediated active demethylation and lack of de novo methylation, yet KAP1 is tethered by sequence-specific KZFPs to ICRs and TEs where it recruits histone and DNA methyltransferases to impose heterochromatin formation and DNA methylation. Results Here, upon removing either KAP1 or the cognate KZFP, we observed rapid TET2-dependent accumulation of 5hmC at both ICRs and TEs. In the absence of the KZFP/KAP1 complex, ICRs lost heterochromatic histone marks and underwent both active and passive DNA demethylation. For KAP1-bound TEs, 5mC hydroxylation correlated with transcriptional reactivation. Using RNA-seq, we further compared the expression profiles of TEs upon Kap1 removal in wild-type, Dnmt and Tet triple knockout mESCs. While we found that KAP1 represents the main effector of TEs repression in all three settings, we could additionally identify specific groups of TEs further controlled by DNA methylation. Furthermore, we observed that in the absence of TET proteins, activation upon Kap1 depletion was blunted for some TE integrants and increased for others. Conclusions Our results indicate that the KZFP/KAP1 complex maintains heterochromatin and DNA methylation at ICRs and TEs in naïve embryonic stem cells partly by protecting these loci from TET-mediated demethylation. Our study further unveils an unsuspected level of complexity in the transcriptional control of the endovirome by demonstrating often integrant-specific differential influences of histone-based heterochromatin modifications, DNA methylation and 5mC oxidation in regulating TEs expression. Electronic supplementary material The online version of this article (10.1186/s13072-018-0177-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrea Coluccio
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland
| | - Gabriela Ecco
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland
| | - Sandra Offner
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland
| | - Priscilla Turelli
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland.
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54
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Guallar D, Bi X, Pardavila JA, Huang X, Saenz C, Shi X, Zhou H, Faiola F, Ding J, Haruehanroengra P, Yang F, Li D, Sanchez-Priego C, Saunders A, Pan F, Valdes VJ, Kelley K, Blanco MG, Chen L, Wang H, Sheng J, Xu M, Fidalgo M, Shen X, Wang J. RNA-dependent chromatin targeting of TET2 for endogenous retrovirus control in pluripotent stem cells. Nat Genet 2018; 50:443-451. [PMID: 29483655 PMCID: PMC5862756 DOI: 10.1038/s41588-018-0060-9] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 01/16/2018] [Indexed: 12/13/2022]
Abstract
Ten-eleven translocation (TET) proteins play key roles in the regulation of DNA-methylation status by oxidizing 5-methylcytosine (5mC) to generate 5-hydroxymethylcytosine (5hmC), which can both serve as a stable epigenetic mark and participate in active demethylation. Unlike the other members of the TET family, TET2 does not contain a DNA-binding domain, and it remains unclear how it is recruited to chromatin. Here we show that TET2 is recruited by the RNA-binding protein Paraspeckle component 1 (PSPC1) through transcriptionally active loci, including endogenous retroviruses (ERVs) whose long terminal repeats (LTRs) have been co-opted by mammalian genomes as stage- and tissue-specific transcriptional regulatory modules. We found that PSPC1 and TET2 contribute to ERVL and ERVL-associated gene regulation by both transcriptional repression via histone deacetylases and post-transcriptional destabilization of RNAs through 5hmC modification. Our findings provide evidence for a functional role of transcriptionally active ERVs as specific docking sites for RNA epigenetic modulation and gene regulation.
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Affiliation(s)
- Diana Guallar
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,CiMUS, Universidade de Santiago de Compostela-Health Research Institute (IDIS), Santiago de Compostela, Coruña, Spain
| | - Xianju Bi
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Jose Angel Pardavila
- CiMUS, Universidade de Santiago de Compostela-Health Research Institute (IDIS), Santiago de Compostela, Coruña, Spain
| | - Xin Huang
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carmen Saenz
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xianle Shi
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China
| | - Hongwei Zhou
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesco Faiola
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Junjun Ding
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Phensinee Haruehanroengra
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Fan Yang
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Animal Biotechnology, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Dan Li
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlos Sanchez-Priego
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arven Saunders
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Feng Pan
- Sylvester Comprehensive Cancer Center, Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, USA
| | - Victor Julian Valdes
- Department of Cell Biology and Development, Instituto de Fisiologia Celular, UNAM, Mexico City, Mexico
| | - Kevin Kelley
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miguel G Blanco
- CiMUS, Universidade de Santiago de Compostela-Health Research Institute (IDIS), Santiago de Compostela, Coruña, Spain
| | - Lingyi Chen
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China
| | - Huayan Wang
- Department of Animal Biotechnology, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Jia Sheng
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Mingjiang Xu
- Sylvester Comprehensive Cancer Center, Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, USA
| | - Miguel Fidalgo
- CiMUS, Universidade de Santiago de Compostela-Health Research Institute (IDIS), Santiago de Compostela, Coruña, Spain
| | - Xiaohua Shen
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Jianlong Wang
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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55
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Zhang J, Cao H, Xie J, Fan C, Xie Y, He X, Liao M, Zhang S, Wang H. The oncogene Etv5 promotes MET in somatic reprogramming and orchestrates epiblast/primitive endoderm specification during mESCs differentiation. Cell Death Dis 2018; 9:224. [PMID: 29445086 PMCID: PMC5833841 DOI: 10.1038/s41419-018-0335-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/10/2018] [Accepted: 01/18/2018] [Indexed: 01/10/2023]
Abstract
Unipotent spermatogonial stem cells (SSCs) can be efficiently reprogrammed into pluripotent stem cells only by manipulating the culture condition, without introducing exogenous reprogramming factors. This phenotype raises the hypothesis that the endogenous transcription factors (TFs) in SSCs may facilitate reprogramming to acquire pluripotency. In this study, we screened a pool of SSCs TFs (Bcl6b, Lhx1, Foxo1, Plzf, Id4, Taf4b, and Etv5), and found that oncogene Etv5 could dramatically increase the efficiency of induced pluripotent stem cells (iPSCs) generation when combined with Yamanaka factors. We also demonstrated that Etv5 could promote mesenchymal-epithelial transition (MET) at the early stage of reprogramming by regulating Tet2-miR200s-Zeb1 axis. In addition, Etv5 knockdown in mouse embryonic stem cells (mESCs) could decrease the genomic 5hmC level by downregulating Tet2. Furthermore, the embryoid body assay revealed that Etv5 could positively regulate primitive endoderm specification through regulating Gata6 and negatively regulate epiblast specification by inhibiting Fgf5 expression. In summary, our findings provide insights into understanding the regulation mechanisms of Etv5 under the context of somatic reprogramming, mESCs maintenance, and differentiation.
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Affiliation(s)
- Jinglong Zhang
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hongxia Cao
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jing Xie
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chen Fan
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Youlong Xie
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xin He
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mingzhi Liao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shiqiang Zhang
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Huayan Wang
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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56
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Deniz Ö, de la Rica L, Cheng KCL, Spensberger D, Branco MR. SETDB1 prevents TET2-dependent activation of IAP retroelements in naïve embryonic stem cells. Genome Biol 2018; 19:6. [PMID: 29351814 PMCID: PMC5775534 DOI: 10.1186/s13059-017-1376-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/07/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Endogenous retroviruses (ERVs), which are responsible for 10% of spontaneous mouse mutations, are kept under control via several epigenetic mechanisms. The H3K9 histone methyltransferase SETDB1 is essential for ERV repression in embryonic stem cells (ESCs), with DNA methylation also playing an important role. It has been suggested that SETDB1 protects ERVs from TET-dependent DNA demethylation, but the relevance of this mechanism for ERV expression remains unclear. Moreover, previous studies have been performed in primed ESCs, which are not epigenetically or transcriptionally representative of preimplantation embryos. RESULTS We use naïve ESCs to investigate the role of SETDB1 in ERV regulation and its relationship with TET-mediated DNA demethylation. Naïve ESCs show an increased dependency on SETDB1 for ERV silencing when compared to primed ESCs, including at the highly mutagenic intracisternal A particles (IAPs). We find that in the absence of SETDB1, TET2 activates IAP elements in a catalytic-dependent manner. Surprisingly, TET2 does not drive changes in DNA methylation levels at IAPs, suggesting that it regulates these retrotransposons indirectly. Instead, SETDB1 depletion leads to a TET2-dependent loss of H4R3me2s, which is indispensable for IAP silencing during epigenetic reprogramming. CONCLUSIONS Our results demonstrate a novel and unexpected role for SETDB1 in protecting IAPs from TET2-dependent histone arginine demethylation.
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Affiliation(s)
- Özgen Deniz
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London, E1 2AT, UK
| | - Lorenzo de la Rica
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London, E1 2AT, UK.,Present address: The Royal Society, 6-9 Carlton House Terrace, London, SW1Y 5AG, UK
| | - Kevin C L Cheng
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London, E1 2AT, UK
| | - Dominik Spensberger
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.,Present address: Gene Targeting Facility, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Miguel R Branco
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London, E1 2AT, UK.
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57
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Dai Q, Shen Y, Wang Y, Wang X, Francisco JC, Luo Z, Lin C. Striking a balance: regulation of transposable elements by Zfp281 and Mll2 in mouse embryonic stem cells. Nucleic Acids Res 2017; 45:12301-12310. [PMID: 29036642 PMCID: PMC5716208 DOI: 10.1093/nar/gkx841] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 09/12/2017] [Indexed: 01/22/2023] Open
Abstract
Transposable elements (TEs) compose about 40% of the murine genome. Retrotransposition of active TEs such as LINE-1 (L1) tremendously impacts genetic diversification and genome stability. Therefore, transcription and transposition activities of retrotransposons are tightly controlled. Here, we show that the Krüppel-like zinc finger protein Zfp281 directly binds and suppresses a subset of retrotransposons, including the active young L1 repeat elements, in mouse embryonic stem (ES) cells. In addition, we find that Zfp281-regulated L1s are highly enriched for 5-hydroxymethylcytosine (5hmC) and H3K4me3. The COMPASS-like H3K4 methyltransferase Mll2 is the major H3K4me3 methylase at the Zfp281-regulated L1s and required for their proper expression. Our studies also reveal that Zfp281 functions partially through recruiting the L1 regulators DNA hydroxymethylase Tet1 and Sin3A, and restricting Mll2 at these active L1s, leading to their balanced expression. In summary, our data indicate an instrumental role of Zfp281 in suppressing the young active L1s in mouse ES cells.
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Affiliation(s)
- Qian Dai
- Institute of Life Sciences, the Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Yang Shen
- Bioinformatics Group, A*STAR Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Yan Wang
- Institute of Life Sciences, the Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Xin Wang
- Institute of Life Sciences, the Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Joel Celio Francisco
- Transcriptional Control in Development and Disease Laboratory, A*STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore
| | - Zhuojuan Luo
- Institute of Life Sciences, the Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Chengqi Lin
- Institute of Life Sciences, the Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China.,Transcriptional Control in Development and Disease Laboratory, A*STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore
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58
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MacLennan M, García-Cañadas M, Reichmann J, Khazina E, Wagner G, Playfoot CJ, Salvador-Palomeque C, Mann AR, Peressini P, Sanchez L, Dobie K, Read D, Hung CC, Eskeland R, Meehan RR, Weichenrieder O, García-Pérez JL, Adams IR. Mobilization of LINE-1 retrotransposons is restricted by Tex19.1 in mouse embryonic stem cells. eLife 2017; 6:e26152. [PMID: 28806172 PMCID: PMC5570191 DOI: 10.7554/elife.26152] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 07/11/2017] [Indexed: 12/21/2022] Open
Abstract
Mobilization of retrotransposons to new genomic locations is a significant driver of mammalian genome evolution, but these mutagenic events can also cause genetic disorders. In humans, retrotransposon mobilization is mediated primarily by proteins encoded by LINE-1 (L1) retrotransposons, which mobilize in pluripotent cells early in development. Here we show that TEX19.1, which is induced by developmentally programmed DNA hypomethylation, can directly interact with the L1-encoded protein L1-ORF1p, stimulate its polyubiquitylation and degradation, and restrict L1 mobilization. We also show that TEX19.1 likely acts, at least in part, through promoting the activity of the E3 ubiquitin ligase UBR2 towards L1-ORF1p. Moreover, loss of Tex19.1 increases L1-ORF1p levels and L1 mobilization in pluripotent mouse embryonic stem cells, implying that Tex19.1 prevents de novo retrotransposition in the pluripotent phase of the germline cycle. These data show that post-translational regulation of L1 retrotransposons plays a key role in maintaining trans-generational genome stability in mammals.
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Affiliation(s)
- Marie MacLennan
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| | - Marta García-Cañadas
- Centro de Genómica e
Investigación Oncológica (GENYO), Pfizer-Universidad de
Granada-Junta de Andalucía, PTS Granada, Granada,
Spain
| | - Judith Reichmann
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| | - Elena Khazina
- Department of
Biochemistry, Max Planck Institute for Developmental
Biology, Tübingen, Germany
| | - Gabriele Wagner
- Department of
Biochemistry, Max Planck Institute for Developmental
Biology, Tübingen, Germany
| | - Christopher J Playfoot
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| | - Carmen Salvador-Palomeque
- Centro de Genómica e
Investigación Oncológica (GENYO), Pfizer-Universidad de
Granada-Junta de Andalucía, PTS Granada, Granada,
Spain
| | - Abigail R Mann
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| | - Paula Peressini
- Centro de Genómica e
Investigación Oncológica (GENYO), Pfizer-Universidad de
Granada-Junta de Andalucía, PTS Granada, Granada,
Spain
| | - Laura Sanchez
- Centro de Genómica e
Investigación Oncológica (GENYO), Pfizer-Universidad de
Granada-Junta de Andalucía, PTS Granada, Granada,
Spain
| | - Karen Dobie
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| | - David Read
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| | - Chao-Chun Hung
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| | - Ragnhild Eskeland
- Department of
Biosciences, University of Oslo,
Oslo,
Norway
- Norwegian Center for
Stem Cell Research, Department of Immunology, Oslo
University Hospital, Oslo, Norway
| | - Richard R Meehan
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
| | - Oliver Weichenrieder
- Department of
Biochemistry, Max Planck Institute for Developmental
Biology, Tübingen, Germany
| | - Jose Luis García-Pérez
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
- Centro de Genómica e
Investigación Oncológica (GENYO), Pfizer-Universidad de
Granada-Junta de Andalucía, PTS Granada, Granada,
Spain
| | - Ian R Adams
- MRC Human Genetics Unit,
MRC Institute of Genetics and Molecular Medicine,
University of Edinburgh, Edinburgh, United
Kingdom
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59
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Tie CHC, Rowe HM. Epigenetic control of retrotransposons in adult tissues: implications for immune regulation. Curr Opin Virol 2017; 25:28-33. [DOI: 10.1016/j.coviro.2017.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/26/2017] [Accepted: 06/19/2017] [Indexed: 12/29/2022]
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60
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Gerdes P, Richardson SR, Faulkner GJ. TET enzymes: double agents in the transposable element-host genome conflict. Genome Biol 2016; 17:259. [PMID: 27993162 PMCID: PMC5170891 DOI: 10.1186/s13059-016-1124-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The mouse genome is replete with retrotransposon sequences, from evolutionarily young elements with mutagenic potential that must be controlled, to inactive molecular fossils whose sequences can be domesticated over evolutionary time to benefit the host genome. In an exciting new study, de la Rica and colleagues have uncovered a complex relationship between ten-eleven translocation (TET) proteins and retrotransposons in mouse embryonic stem cells (ESCs), implicating TETs as enhancers in the exaptation and function of retroelement sequences. Furthermore, they have demonstrated that active demethylation of retrotransposons does not correlate with their increased expression in ESCs, calling into question long-held assumptions regarding the importance of DNA demethylation for retrotransposon expression, and revealing novel epigenetic players in retrotransposon control. Please see related Research article: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1096-8
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Affiliation(s)
- Patricia Gerdes
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Sandra R Richardson
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia. .,School of Biomedical Sciences, University of Queensland, Brisbane, QLD 4072, Australia. .,Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia.
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