101
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Tharp ME, Malki S, Bortvin A. Maximizing the ovarian reserve in mice by evading LINE-1 genotoxicity. Nat Commun 2020; 11:330. [PMID: 31949138 PMCID: PMC6965193 DOI: 10.1038/s41467-019-14055-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 12/06/2019] [Indexed: 11/21/2022] Open
Abstract
Female reproductive success critically depends on the size and quality of a finite ovarian reserve. Paradoxically, mammals eliminate up to 80% of the initial oocyte pool through the enigmatic process of fetal oocyte attrition (FOA). Here, we interrogate the striking correlation of FOA with retrotransposon LINE-1 (L1) expression in mice to understand how L1 activity influences FOA and its biological relevance. We report that L1 activity triggers FOA through DNA damage-driven apoptosis and the complement system of immunity. We demonstrate this by combined inhibition of L1 reverse transcriptase activity and the Chk2-dependent DNA damage checkpoint to prevent FOA. Remarkably, reverse transcriptase inhibitor AZT-treated Chk2 mutant oocytes that evade FOA initially accumulate, but subsequently resolve, L1-instigated genotoxic threats independent of piRNAs and differentiate, resulting in an increased functional ovarian reserve. We conclude that FOA serves as quality control for oocyte genome integrity, and is not obligatory for oogenesis nor fertility.
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Affiliation(s)
- Marla E Tharp
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Safia Malki
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA
| | - Alex Bortvin
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA.
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102
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Zhang W, Chen F, Chen R, Xie D, Yang J, Zhao X, Guo R, Zhang Y, Shen Y, Göke J, Liu L, Lu X. Zscan4c activates endogenous retrovirus MERVL and cleavage embryo genes. Nucleic Acids Res 2019; 47:8485-8501. [PMID: 31304534 PMCID: PMC7145578 DOI: 10.1093/nar/gkz594] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/24/2019] [Accepted: 06/28/2019] [Indexed: 01/09/2023] Open
Abstract
Endogenous retroviruses (ERVs) contribute to ∼10 percent of the mouse genome. They are often silenced in differentiated somatic cells but differentially expressed at various embryonic developmental stages. A minority of mouse embryonic stem cells (ESCs), like 2-cell cleavage embryos, highly express ERV MERVL. However, the role of ERVs and mechanism of their activation in these cells are still poorly understood. In this study, we investigated the regulation and function of the stage-specific expressed ERVs, with a particular focus on the totipotency marker MT2/MERVL. We show that the transcription factor Zscan4c functions as an activator of MT2/MERVL and 2-cell/4-cell embryo genes. Zinc finger domains of Zscan4c play an important role in this process. In addition, Zscan4c interacts with MT2 and regulates MT2-nearby 2-cell/4-cell genes through promoting enhancer activity of MT2. Furthermore, MT2 activation is accompanied by enhanced H3K4me1, H3K27ac, and H3K14ac deposition on MT2. Zscan4c also interacts with GBAF chromatin remodelling complex through SCAN domain to further activate MT2 enhancer activity. Taken together, we delineate a previously unrecognized regulatory axis that Zscan4c interacts with and activates MT2/MERVL loci and their nearby genes through epigenetic regulation.
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Affiliation(s)
- Weiyu Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Fuquan Chen
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Ruiqing Chen
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Dan Xie
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Jiao Yang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Life Sciences, Nankai University, Tianjin 300071, People's Republic of China
| | - Xin Zhao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Renpeng Guo
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Life Sciences, Nankai University, Tianjin 300071, People's Republic of China
| | - Yongwang Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Yang Shen
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Jonathan Göke
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Life Sciences, Nankai University, Tianjin 300071, People's Republic of China
| | - Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
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103
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Ni Z, Zhou XY, Aslam S, Niu DK. Characterization of Human Dosage-Sensitive Transcription Factor Genes. Front Genet 2019; 10:1208. [PMID: 31867040 PMCID: PMC6904359 DOI: 10.3389/fgene.2019.01208] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 11/01/2019] [Indexed: 11/13/2022] Open
Abstract
Copy number changes in protein-coding genes are detrimental if the consequent changes in protein concentrations disrupt essential cellular functions. The dosage sensitivity of transcription factor (TF) genes is particularly interesting because their products are essential in regulating the expression of genetic information. From four recently curated data sets of dosage-sensitive genes (genes with conserved copy numbers across mammals, ohnologs, and two data sets of haploinsufficient genes), we compiled a data set of the most reliable dosage-sensitive (MRDS) genes and a data set of the most reliable dosage-insensitive (MRDIS) genes. The MRDS genes were those present in all four data sets, while the MRDIS genes were those absent from any one of the four data sets and with the probability of being loss of function-intolerant (pLI) values < 0.5 in both of the haploinsufficient gene data sets. Enrichment analysis of TF genes among the MRDS and MRDIS gene data sets showed that TF genes are more likely to be dosage-sensitive than other genes in the human genome. The nuclear receptor family was the most enriched TF family among the dosage-sensitive genes. TF families with very few members were also deemed more likely to be dosage-sensitive than TF families with more members. In addition, we found a certain number of dosage-insensitive TFs. The most typical were the Krüppel-associated box domain-containing zinc-finger proteins (KZFPs). Gene ontology (GO) enrichment analysis showed that the MRDS TFs were enriched for many more terms than the MRDIS TFs; however, the proteins interacting with these two groups of TFs did not show such sharp differences. Furthermore, we found that the MRDIS KZFPs were not significantly enriched for any GO terms, whereas their interacting proteins were significantly enriched for thousands of GO terms. Further characterizations revealed significant differences between MRDS TFs and MRDIS TFs in the lengths and nucleotide compositions of DNA-binding sites as well as in expression level, protein size, and selective force.
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Affiliation(s)
- Zhihua Ni
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
- College of Life Sciences, Hebei University, Baoding, China
| | - Xiao-Yu Zhou
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Sidra Aslam
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Deng-Ke Niu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
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104
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Abstract
Transposable elements (TEs) are mobile DNA sequences that colonize genomes and threaten genome integrity. As a result, several mechanisms appear to have emerged during eukaryotic evolution to suppress TE activity. However, TEs are ubiquitous and account for a prominent fraction of most eukaryotic genomes. We argue that the evolutionary success of TEs cannot be explained solely by evasion from host control mechanisms. Rather, some TEs have evolved commensal and even mutualistic strategies that mitigate the cost of their propagation. These coevolutionary processes promote the emergence of complex cellular activities, which in turn pave the way for cooption of TE sequences for organismal function.
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Affiliation(s)
- Rachel L Cosby
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Ni-Chen Chang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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105
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Rohrmoser M, Kluge M, Yahia Y, Gruber-Eber A, Maqbool MA, Forné I, Krebs S, Blum H, Greifenberg AK, Geyer M, Descostes N, Imhof A, Andrau JC, Friedel CC, Eick D. MIR sequences recruit zinc finger protein ZNF768 to expressed genes. Nucleic Acids Res 2019; 47:700-715. [PMID: 30476274 PMCID: PMC6344866 DOI: 10.1093/nar/gky1148] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/29/2018] [Indexed: 12/16/2022] Open
Abstract
Mammalian-wide interspersed repeats (MIRs) are retrotransposed elements of mammalian genomes. Here, we report the specific binding of zinc finger protein ZNF768 to the sequence motif GCTGTGTG (N20) CCTCTCTG in the core region of MIRs. ZNF768 binding is preferentially associated with euchromatin and promoter regions of genes. Binding was observed for genes expressed in a cell type-specific manner in human B cell line Raji and osteosarcoma U2OS cells. Mass spectrometric analysis revealed binding of ZNF768 to Elongator components Elp1, Elp2 and Elp3 and other nuclear factors. The N-terminus of ZNF768 contains a heptad repeat array structurally related to the C-terminal domain (CTD) of RNA polymerase II. This array evolved in placental animals but not marsupials and monotreme species, displays species-specific length variations, and possibly fulfills CTD related functions in gene regulation. We propose that the evolution of MIRs and ZNF768 has extended the repertoire of gene regulatory mechanisms in mammals and that ZNF768 binding is associated with cell type-specific gene expression.
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Affiliation(s)
- Michaela Rohrmoser
- Department of Molecular Epigenetics, Helmholtz Center Munich and Center for Integrated Protein Science Munich (CIPSM), Marchioninistrasse 25, 81377 Munich, Germany
| | - Michael Kluge
- Institute for Informatics, Ludwig-Maximilians-Universität München, Amalienstrasse 17, 80333 Munich, Germany
| | - Yousra Yahia
- Institut de Génétique Moléculaire de Montpellier (IGMM), Univ Montpellier, CNRS-UMR5535, Montpellier, France
| | - Anita Gruber-Eber
- Department of Molecular Epigenetics, Helmholtz Center Munich and Center for Integrated Protein Science Munich (CIPSM), Marchioninistrasse 25, 81377 Munich, Germany
| | - Muhammad Ahmad Maqbool
- Institut de Génétique Moléculaire de Montpellier (IGMM), Univ Montpellier, CNRS-UMR5535, Montpellier, France
| | - Ignasi Forné
- Biomedical Center Munich, ZFP, Großhadener Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA) at the Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA) at the Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Ann Katrin Greifenberg
- Institute of Structural Biology, University of Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
| | - Nicolas Descostes
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA.,Howard Hughes Medical Institute, New York University Langone School of Medicine, New York, NY 10016, USA
| | - Axel Imhof
- Biomedical Center Munich, ZFP, Großhadener Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Jean-Christophe Andrau
- Institut de Génétique Moléculaire de Montpellier (IGMM), Univ Montpellier, CNRS-UMR5535, Montpellier, France
| | - Caroline C Friedel
- Institute for Informatics, Ludwig-Maximilians-Universität München, Amalienstrasse 17, 80333 Munich, Germany
| | - Dirk Eick
- Department of Molecular Epigenetics, Helmholtz Center Munich and Center for Integrated Protein Science Munich (CIPSM), Marchioninistrasse 25, 81377 Munich, Germany
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106
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Saleh A, Macia A, Muotri AR. Transposable Elements, Inflammation, and Neurological Disease. Front Neurol 2019; 10:894. [PMID: 31481926 PMCID: PMC6710400 DOI: 10.3389/fneur.2019.00894] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 08/02/2019] [Indexed: 12/13/2022] Open
Abstract
Transposable Elements (TE) are mobile DNA elements that can replicate and insert themselves into different locations within the host genome. Their propensity to self-propagate has a myriad of consequences and yet their biological significance is not well-understood. Indeed, retrotransposons have evaded evolutionary attempts at repression and may contribute to somatic mosaicism. Retrotransposons are emerging as potent regulatory elements within the human genome. In the diseased state, there is mounting evidence that endogenous retroelements play a role in etiopathogenesis of inflammatory diseases, with a disposition for both autoimmune and neurological disorders. We postulate that active mobile genetic elements contribute more to human disease pathogenesis than previously thought.
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Affiliation(s)
- Aurian Saleh
- Department of Pediatrics, Rady Children's Hospital San Diego, University of California, San Diego, San Diego, CA, United States
| | - Angela Macia
- Department of Pediatrics, Rady Children's Hospital San Diego, University of California, San Diego, San Diego, CA, United States
| | - Alysson R Muotri
- Department of Pediatrics, Rady Children's Hospital San Diego, University of California, San Diego, San Diego, CA, United States
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107
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Batki J, Schnabl J, Wang J, Handler D, Andreev VI, Stieger CE, Novatchkova M, Lampersberger L, Kauneckaite K, Xie W, Mechtler K, Patel DJ, Brennecke J. The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation. Nat Struct Mol Biol 2019; 26:720-731. [PMID: 31384064 PMCID: PMC6828549 DOI: 10.1038/s41594-019-0270-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/17/2019] [Indexed: 12/21/2022]
Abstract
The PIWI-interacting RNA (piRNA) pathway protects genome integrity in part through establishing repressive heterochromatin at transposon loci. Silencing requires piRNA-guided targeting of nuclear PIWI proteins to nascent transposon transcripts, yet the subsequent molecular events are not understood. Here, we identify SFiNX (silencing factor interacting nuclear export variant), an interdependent protein complex required for Piwi-mediated cotranscriptional silencing in Drosophila. SFiNX consists of Nxf2-Nxt1, a gonad-specific variant of the heterodimeric messenger RNA export receptor Nxf1-Nxt1 and the Piwi-associated protein Panoramix. SFiNX mutant flies are sterile and exhibit transposon derepression because piRNA-loaded Piwi is unable to establish heterochromatin. Within SFiNX, Panoramix recruits heterochromatin effectors, while the RNA binding protein Nxf2 licenses cotranscriptional silencing. Our data reveal how Nxf2 might have evolved from an RNA transport receptor into a cotranscriptional silencing factor. Thus, NXF variants, which are abundant in metazoans, can have diverse molecular functions and might have been coopted for host genome defense more broadly.
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Affiliation(s)
- Julia Batki
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Vienna, Austria
| | - Jakob Schnabl
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Vienna, Austria
| | - Juncheng Wang
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dominik Handler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Vienna, Austria
| | - Veselin I Andreev
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Vienna, Austria
| | - Christian E Stieger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Vienna, Austria
- Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Vienna, Austria
- Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
| | - Lisa Lampersberger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Vienna, Austria
| | - Kotryna Kauneckaite
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Vienna, Austria
| | - Wei Xie
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karl Mechtler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Vienna, Austria
- Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Vienna, Austria.
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108
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Weilguny L, Kofler R. DeviaTE: Assembly-free analysis and visualization of mobile genetic element composition. Mol Ecol Resour 2019; 19:1346-1354. [PMID: 31056858 PMCID: PMC6791034 DOI: 10.1111/1755-0998.13030] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 04/19/2019] [Accepted: 04/22/2019] [Indexed: 11/28/2022]
Abstract
Transposable elements (TEs) are selfish DNA sequences that multiply within host genomes. They are present in most species investigated so far at varying degrees of abundance and sequence diversity. The TE composition may not only vary between but also within species and could have important biological implications. Variation in prevalence among populations may for example indicate a recent TE invasion, whereas sequence variation could indicate the presence of hyperactive or inactive forms. Gaining unbiased estimates of TE composition is thus vital for understanding the evolutionary dynamics of transposons. To this end, we developed DeviaTE, a tool to analyse and visualize TE abundance using Illumina or Sanger sequencing reads. Our tool requires sequencing reads of one or more samples (tissue, individual or population) and consensus sequences of TEs. It generates a table and a visual representation of TE composition. This allows for an intuitive assessment of coverage, sequence divergence, segregating SNPs and indels, as well as the presence of internal and terminal deletions. By contrasting the coverage between TEs and single copy genes, DeviaTE derives unbiased estimates of TE abundance. We show that naive approaches, which do not consider regions spanned by internal deletions, may substantially underestimate TE abundance. Using published data we demonstrate that DeviaTE can be used to study the TE composition within samples, identify clinal variation in TEs, compare TE diversity among species, and monitor TE invasions. Finally we present careful validations with publicly available and simulated data. DeviaTE is implemented in Python and distributed under the GPLv3 (https://github.com/W-L/deviaTE).
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Affiliation(s)
- Lukas Weilguny
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
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109
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Bhullar S, Denby Wilkes C, Arnaiz O, Nowacki M, Sperling L, Meyer E. A mating-type mutagenesis screen identifies a zinc-finger protein required for specific DNA excision events in Paramecium. Nucleic Acids Res 2019; 46:9550-9562. [PMID: 30165457 PMCID: PMC6182129 DOI: 10.1093/nar/gky772] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/24/2018] [Indexed: 12/16/2022] Open
Abstract
In the ciliate Paramecium tetraurelia, functional genes are reconstituted during development of the somatic macronucleus through the precise excision of ∼45 000 single-copy Internal Eliminated Sequences (IESs), thought to be the degenerate remnants of ancient transposon insertions. Like introns, IESs are marked only by a weak consensus at their ends. How such a diverse set of sequences is faithfully recognized and precisely excised remains unclear: specialized small RNAs have been implicated, but in their absence up to ∼60% of IESs are still correctly excised. To get further insight, we designed a mutagenesis screen based on the hypersensitivity of a specific excision event in the mtA gene, which determines mating types. Unlike most IES-containing genes, the active form of mtA is the unexcised one, allowing the recovery of hypomorphic alleles of essential IES recognition/excision factors. Such is the case of one mutation recovered in the Piwi gene PTIWI09, a key player in small RNA-mediated IES recognition. Another mutation identified a novel protein with a C2H2 zinc finger, mtGa, which is required for excision of a small subset of IESs characterized by enrichment in a 5-bp motif. The unexpected implication of a sequence-specific factor establishes a new paradigm for IES recognition and/or excision.
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Affiliation(s)
- Simran Bhullar
- IBENS, Ecole Normale Supérieure, CNRS, Inserm, PSL University, F-75005 Paris, France.,Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
| | - Cyril Denby Wilkes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Olivier Arnaiz
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
| | - Linda Sperling
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Eric Meyer
- IBENS, Ecole Normale Supérieure, CNRS, Inserm, PSL University, F-75005 Paris, France
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110
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Sanchez-Luque FJ, Kempen MJHC, Gerdes P, Vargas-Landin DB, Richardson SR, Troskie RL, Jesuadian JS, Cheetham SW, Carreira PE, Salvador-Palomeque C, García-Cañadas M, Muñoz-Lopez M, Sanchez L, Lundberg M, Macia A, Heras SR, Brennan PM, Lister R, Garcia-Perez JL, Ewing AD, Faulkner GJ. LINE-1 Evasion of Epigenetic Repression in Humans. Mol Cell 2019; 75:590-604.e12. [PMID: 31230816 DOI: 10.1016/j.molcel.2019.05.024] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 04/08/2019] [Accepted: 05/15/2019] [Indexed: 02/07/2023]
Abstract
Epigenetic silencing defends against LINE-1 (L1) retrotransposition in mammalian cells. However, the mechanisms that repress young L1 families and how L1 escapes to cause somatic genome mosaicism in the brain remain unclear. Here we report that a conserved Yin Yang 1 (YY1) transcription factor binding site mediates L1 promoter DNA methylation in pluripotent and differentiated cells. By analyzing 24 hippocampal neurons with three distinct single-cell genomic approaches, we characterized and validated a somatic L1 insertion bearing a 3' transduction. The source (donor) L1 for this insertion was slightly 5' truncated, lacked the YY1 binding site, and was highly mobile when tested in vitro. Locus-specific bisulfite sequencing revealed that the donor L1 and other young L1s with mutated YY1 binding sites were hypomethylated in embryonic stem cells, during neurodifferentiation, and in liver and brain tissue. These results explain how L1 can evade repression and retrotranspose in the human body.
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Affiliation(s)
- Francisco J Sanchez-Luque
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; GENYO Centre for Genomics and Oncological Research, Pfizer University of Granada, Andalusian Regional Government, Avda Ilustración, 114, PTS Granada 18016, Spain.
| | - Marie-Jeanne H C Kempen
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Patricia Gerdes
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Dulce B Vargas-Landin
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, the University of Western Australia, Perth, WA 6009, Australia; Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Sandra R Richardson
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Robin-Lee Troskie
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - J Samuel Jesuadian
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Seth W Cheetham
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Patricia E Carreira
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Carmen Salvador-Palomeque
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Marta García-Cañadas
- GENYO Centre for Genomics and Oncological Research, Pfizer University of Granada, Andalusian Regional Government, Avda Ilustración, 114, PTS Granada 18016, Spain
| | - Martin Muñoz-Lopez
- GENYO Centre for Genomics and Oncological Research, Pfizer University of Granada, Andalusian Regional Government, Avda Ilustración, 114, PTS Granada 18016, Spain
| | - Laura Sanchez
- GENYO Centre for Genomics and Oncological Research, Pfizer University of Granada, Andalusian Regional Government, Avda Ilustración, 114, PTS Granada 18016, Spain
| | - Mischa Lundberg
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Angela Macia
- Department of Pediatrics/Rady Children's Hospital San Diego, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Sara R Heras
- GENYO Centre for Genomics and Oncological Research, Pfizer University of Granada, Andalusian Regional Government, Avda Ilustración, 114, PTS Granada 18016, Spain; Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, 18071 Granada, Spain
| | - Paul M Brennan
- Edinburgh Cancer Research Centre, Western General Hospital, Edinburgh, EH4 2XR, UK
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, the University of Western Australia, Perth, WA 6009, Australia; Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Jose L Garcia-Perez
- GENYO Centre for Genomics and Oncological Research, Pfizer University of Granada, Andalusian Regional Government, Avda Ilustración, 114, PTS Granada 18016, Spain; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Adam D Ewing
- 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; Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia.
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111
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Li Y, Zhang Z, Yang L, Li X, Zhou J, Li D, Luo S. Colla corii asini might upregulate ZNF471 and THOC5 by KRAB domain-containing zinc-finger protein pathway and THO complex subunit 5 pathway to improve anemia of pregnant women with β-thalassemia. Ann Hematol 2019; 98:1813-1826. [PMID: 31098739 DOI: 10.1007/s00277-019-03710-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/05/2019] [Indexed: 12/25/2022]
Abstract
Pregnant patients with β-thalassemia are more likely to have progressive anemia which expose them to risk of adverse pregnancy outcomes, blood transfusion, and iron overload. Results from our previous study indicated that Colla corii asini (CCA, E'jiao), a natural ingredient of traditional Chinese medicine, could significantly increase hemoglobin level of pregnant women with β- thalassemia, but the underlying molecular mechanism was unclear. Thus, we applied high-throughput transcriptome sequencing to study the transcriptomic change before and after the CCA treatment. Twenty eligible pregnant women were recruited and randomized to either the CCA treatment group or the blank control group in a 3:1 ratio. Patients in the treatment group orally received daily 15 g CCA powder for 4 weeks. We analyzed the therapeutic effect indexes and the transcriptomic change in subjects' peripheral blood before and after treatment. We found that β CD 41-42(-TTCT)/βA was the main genotype of the subjects. The regulatory impact of CCA treatment became more evident among the subjects of genotype β CD 41-42(-TTCT)/βA. Gene ontogenesis analysis revealed that the top five molecular functions of differentially expressed genes were involved in membrane functionality and cellular structure. We further identified two consistent upregulated genes ZNF471 and THOC5 in the effective treatment group, which were engaged in Kruppel-associated box (KRAB) domain-containing zinc-finger protein pathway and THOC5 pathway, respectively. Based on our current findings, we hypothesize that the anti-anemia effect of CCA on pregnant women with β-thalassemia might be related to translation regulation of spectrin synthesis, membrane stability, and eventually prolonged the life span of erythrocytes.
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Affiliation(s)
- Yanfang Li
- Department of Obstetrics, the First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhanfeng Zhang
- Department of Clinical Laboratory, the First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lilin Yang
- Department of Gynecology, the First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiangyi Li
- Department of Obstetrics, the First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jingwen Zhou
- Department of Obstetrics, the First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Daocheng Li
- Department of Obstetrics, the First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Songping Luo
- First School of Clinical Medicine, Guangzhou University of Chinese Medicine, No.12 Jichang Road, Guangzhou, 510405, Guangdong, China.
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112
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Pontis J, Planet E, Offner S, Turelli P, Duc J, Coudray A, Theunissen TW, Jaenisch R, Trono D. Hominoid-Specific Transposable Elements and KZFPs Facilitate Human Embryonic Genome Activation and Control Transcription in Naive Human ESCs. Cell Stem Cell 2019; 24:724-735.e5. [PMID: 31006620 PMCID: PMC6509360 DOI: 10.1016/j.stem.2019.03.012] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/04/2019] [Accepted: 03/12/2019] [Indexed: 11/17/2022]
Abstract
Expansion of transposable elements (TEs) coincides with evolutionary shifts in gene expression. TEs frequently harbor binding sites for transcriptional regulators, thus enabling coordinated genome-wide activation of species- and context-specific gene expression programs, but such regulation must be balanced against their genotoxic potential. Here, we show that Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFPs) control the timely and pleiotropic activation of TE-derived transcriptional cis regulators during early embryogenesis. Evolutionarily recent SVA, HERVK, and HERVH TE subgroups contribute significantly to chromatin opening during human embryonic genome activation and are KLF-stimulated enhancers in naive human embryonic stem cells (hESCs). KZFPs of corresponding evolutionary ages are simultaneously induced and repress the transcriptional activity of these TEs. Finally, the same KZFP-controlled TE-based enhancers later serve as developmental and tissue-specific enhancers. Thus, by controlling the transcriptional impact of TEs during embryogenesis, KZFPs facilitate their genome-wide incorporation into transcriptional networks, thereby contributing to human genome regulation. KLFs foster EGA by activating enhancers embedded in young TEs (TEENhancers) TEENhancers confer a degree of species specificity to early genome activation TEENhancers stimulate the expression of KZFPs responsible for their repression These KZFPs in turn facilitate TEENhancers’ exaptation as tissue-specific regulators
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Affiliation(s)
- Julien Pontis
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Evarist Planet
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Sandra Offner
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Priscilla Turelli
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Alexandre Coudray
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Thorold W Theunissen
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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113
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Chen W, Schwalie PC, Pankevich EV, Gubelmann C, Raghav SK, Dainese R, Cassano M, Imbeault M, Jang SM, Russeil J, Delessa T, Duc J, Trono D, Wolfrum C, Deplancke B. ZFP30 promotes adipogenesis through the KAP1-mediated activation of a retrotransposon-derived Pparg2 enhancer. Nat Commun 2019; 10:1809. [PMID: 31000713 PMCID: PMC6472429 DOI: 10.1038/s41467-019-09803-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 03/29/2019] [Indexed: 12/15/2022] Open
Abstract
Krüppel-associated box zinc finger proteins (KZFPs) constitute the largest family of mammalian transcription factors, but most remain completely uncharacterized. While initially proposed to primarily repress transposable elements, recent reports have revealed that KFZPs contribute to a wide variety of other biological processes. Using murine and human in vitro and in vivo models, we demonstrate here that one poorly studied KZFP, ZFP30, promotes adipogenesis by directly targeting and activating a retrotransposon-derived Pparg2 enhancer. Through mechanistic studies, we further show that ZFP30 recruits the co-regulator KRAB-associated protein 1 (KAP1), which, surprisingly, acts as a ZFP30 co-activator in this adipogenic context. Our findings provide an understanding of both adipogenic and KZFP-KAP1 complex-mediated gene regulation, showing that the KZFP-KAP1 axis can also function in a non-repressive manner.
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Affiliation(s)
- Wanze Chen
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), CH-1015, Lausanne, Switzerland
| | - Petra C Schwalie
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), CH-1015, Lausanne, Switzerland
| | - Eugenia V Pankevich
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234, Moscow, Russian Federation
| | - Carine Gubelmann
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), CH-1015, Lausanne, Switzerland
| | - Sunil K Raghav
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- Immunogenomics & Systems Biology group, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
| | - Riccardo Dainese
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), CH-1015, Lausanne, Switzerland
| | - Marco Cassano
- Laboratory of Virology and Genetics, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Michael Imbeault
- Laboratory of Virology and Genetics, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Suk Min Jang
- Laboratory of Virology and Genetics, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Julie Russeil
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), CH-1015, Lausanne, Switzerland
| | - Tenagne Delessa
- Institute of Food Nutrition and Health, Eidgenössische Technische Hochschule Zürich (ETHZ), CH-8603, Schwerzenbach, Switzerland
| | - Julien Duc
- Laboratory of Virology and Genetics, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Didier Trono
- Laboratory of Virology and Genetics, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Christian Wolfrum
- Institute of Food Nutrition and Health, Eidgenössische Technische Hochschule Zürich (ETHZ), CH-8603, Schwerzenbach, Switzerland
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics (SIB), CH-1015, Lausanne, Switzerland.
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114
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Su Y, Cockerill I, Wang Y, Qin YX, Chang L, Zheng Y, Zhu D. Zinc-Based Biomaterials for Regeneration and Therapy. Trends Biotechnol 2019; 37:428-441. [PMID: 30470548 PMCID: PMC6421092 DOI: 10.1016/j.tibtech.2018.10.009] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 09/20/2018] [Accepted: 10/22/2018] [Indexed: 12/14/2022]
Abstract
Zinc has been described as the 'calcium of the twenty-first century'. Zinc-based degradable biomaterials have recently emerged thanks to their intrinsic physiological relevance, biocompatibility, biodegradability, and pro-regeneration properties. Zinc-based biomaterials mainly include: metallic zinc alloys, zinc ceramic nanomaterials, and zinc metal-organic frameworks (MOFs). Metallic zinc implants degrade at a desirable rate, matching the healing pace of local tissues, and stimulating remodeling and formation of new tissues. Zinc ceramic nanomaterials are also beneficial for tissue engineering and therapy thanks to their nanostructures and antibacterial properties. MOFs have large surface areas and are easily functionalized, making them ideal for drug delivery and cancer therapy. This review highlights recent developments in zinc-based biomaterials, discusses obstacles to overcome, and pinpoints directions for future research.
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Affiliation(s)
- Yingchao Su
- Department of Biomedical Engineering, University of North Texas, Denton, TX, USA
| | - Irsalan Cockerill
- Department of Biomedical Engineering, University of North Texas, Denton, TX, USA
| | - Yadong Wang
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Yi-Xian Qin
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA
| | - Lingqian Chang
- Department of Biomedical Engineering, University of North Texas, Denton, TX, USA.
| | - Yufeng Zheng
- Department of Materials Science and Engineering, College of Engineering, Peking University, Beijing, China.
| | - Donghui Zhu
- Department of Biomedical Engineering, University of North Texas, Denton, TX, USA.
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115
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Epigenetic Components of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Uncover Potential Transposable Element Activation. Clin Ther 2019; 41:675-698. [PMID: 30910331 DOI: 10.1016/j.clinthera.2019.02.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 02/02/2019] [Accepted: 02/13/2019] [Indexed: 12/19/2022]
Abstract
PURPOSE Studies to determine epigenetic changes associated with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) remain scarce; however, current evidence clearly shows that methylation patterns of genomic DNA and noncoding RNA profiles of immune cells differ between patients and healthy subjects, suggesting an active role of these epigenetic mechanisms in the disease. The present study compares and contrasts the available ME/CFS epigenetic data in an effort to evidence overlapping pathways capable of explaining at least some of the dysfunctional immune parameters linked to this disease. METHODS A systematic search of the literature evaluating the ME/CFS epigenome landscape was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses criteria. Differential DNA methylation and noncoding RNA differential expression patterns associated with ME/CFS were used to screen for the presence of transposable elements using the Dfam browser, a search program nurtured with the Repbase repetitive sequence database and the RepeatMasker annotation tool. FINDINGS Unexpectedly, particular associations of transposable elements and ME/CFS epigenetic hallmarks were uncovered. A model for the disease emerged involving transcriptional induction of endogenous dormant transposons and structured cellular RNA interactions, triggering the activation of the innate immune system without a concomitant active infection. IMPLICATIONS Repetitive sequence filters (ie, RepeatMasker) should be avoided when analyzing transcriptomic data to assess the potential participation of repetitive sequences ("junk repetitive DNA"), representing >45% of the human genome, in the onset and evolution of ME/CFS. In addition, transposable element screenings aimed at designing cost-effective, focused empirical assays that can confirm or disprove the suspected involvement of transposon transcriptional activation in this disease, following the pilot strategy presented here, will require databases gathering large ME/CFS epigenetic datasets.
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116
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Baker CL, Walker M, Arat S, Ananda G, Petkova P, Powers NR, Tian H, Spruce C, Ji B, Rausch D, Choi K, Petkov PM, Carter GW, Paigen K. Tissue-Specific Trans Regulation of the Mouse Epigenome. Genetics 2019; 211:831-845. [PMID: 30593494 PMCID: PMC6404261 DOI: 10.1534/genetics.118.301697] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/15/2018] [Indexed: 11/18/2022] Open
Abstract
The epigenetic landscape varies greatly among cell types. Although a variety of writers, readers, and erasers of epigenetic features are known, we have little information about the underlying regulatory systems controlling the establishment and maintenance of these features. Here, we have explored how natural genetic variation affects the epigenome in mice. Studying levels of H3K4me3, a histone modification at sites such as promoters, enhancers, and recombination hotspots, we found tissue-specific trans-regulation of H3K4me3 levels in four highly diverse cell types: male germ cells, embryonic stem cells, hepatocytes, and cardiomyocytes. To identify the genetic loci involved, we measured H3K4me3 levels in male germ cells in a mapping population of 59 BXD recombinant inbred lines. We found extensive trans-regulation of H3K4me3 peaks, including six major histone quantitative trait loci (QTL). These chromatin regulatory loci act dominantly to suppress H3K4me3, which at hotspots reduces the likelihood of subsequent DNA double-strand breaks. QTL locations do not correspond with genes encoding enzymes known to metabolize chromatin features. Instead their locations match clusters of zinc finger genes, making these possible candidates that explain the dominant suppression of H3K4me3. Collectively, these data describe an extensive, set of chromatin regulatory loci that control the epigenetic landscape.
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Affiliation(s)
| | | | - Seda Arat
- The Jackson Laboratory, Bar Harbor, Maine 04609
| | | | | | | | - Hui Tian
- The Jackson Laboratory, Bar Harbor, Maine 04609
| | | | - Bo Ji
- The Jackson Laboratory, Bar Harbor, Maine 04609
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117
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Fu B, Ma H, Liu D. Endogenous Retroviruses Function as Gene Expression Regulatory Elements During Mammalian Pre-implantation Embryo Development. Int J Mol Sci 2019; 20:ijms20030790. [PMID: 30759824 PMCID: PMC6387303 DOI: 10.3390/ijms20030790] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 01/13/2023] Open
Abstract
Pre-implantation embryo development encompasses several key developmental events, especially the activation of zygotic genome activation (ZGA)-related genes. Endogenous retroviruses (ERVs), which are regarded as “deleterious genomic parasites”, were previously considered to be “junk DNA”. However, it is now known that ERVs, with limited conservatism across species, mediate conserved developmental processes (e.g., ZGA). Transcriptional activation of ERVs occurs during the transition from maternal control to zygotic genome control, signifying ZGA. ERVs are versatile participants in rewiring gene expression networks during epigenetic reprogramming. Particularly, a subtle balance exists between ERV activation and ERV repression in host–virus interplay, which leads to stage-specific ERV expression during pre-implantation embryo development. A large portion of somatic cell nuclear transfer (SCNT) embryos display developmental arrest and ZGA failure during pre-implantation embryo development. Furthermore, because of the close relationship between ERV activation and ZGA, exploring the regulatory mechanism underlying ERV activation may also shed more light on the enigma of SCNT embryo development in model animals.
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Affiliation(s)
- Bo Fu
- Institute of Animal Husbandry Research, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China.
- Key Laboratory of Combine of Planting and Feeding, Ministry of Agriculture of the People's Republic of China, Harbin 150086, China.
| | - Hong Ma
- Institute of Animal Husbandry Research, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China.
- Key Laboratory of Combine of Planting and Feeding, Ministry of Agriculture of the People's Republic of China, Harbin 150086, China.
| | - Di Liu
- Institute of Animal Husbandry Research, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China.
- Key Laboratory of Combine of Planting and Feeding, Ministry of Agriculture of the People's Republic of China, Harbin 150086, China.
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118
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Almeida MV, Andrade-Navarro MA, Ketting RF. Function and Evolution of Nematode RNAi Pathways. Noncoding RNA 2019; 5:E8. [PMID: 30650636 PMCID: PMC6468775 DOI: 10.3390/ncrna5010008] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/07/2019] [Accepted: 01/08/2019] [Indexed: 12/11/2022] Open
Abstract
Selfish genetic elements, like transposable elements or viruses, are a threat to genomic stability. A variety of processes, including small RNA-based RNA interference (RNAi)-like pathways, has evolved to counteract these elements. Amongst these, endogenous small interfering RNA and Piwi-interacting RNA (piRNA) pathways were implicated in silencing selfish genetic elements in a variety of organisms. Nematodes have several incredibly specialized, rapidly evolving endogenous RNAi-like pathways serving such purposes. Here, we review recent research regarding the RNAi-like pathways of Caenorhabditis elegans as well as those of other nematodes, to provide an evolutionary perspective. We argue that multiple nematode RNAi-like pathways share piRNA-like properties and together form a broad nematode toolkit that allows for silencing of foreign genetic elements.
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Affiliation(s)
| | - Miguel A Andrade-Navarro
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany.
- Faculty of Biology, Johannes Gutenberg Universität, 55122 Mainz, Germany.
| | - René F Ketting
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany.
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119
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Pirogov SA, Maksimenko OG, Georgiev PG. Transposable Elements in the Evolution of Gene Regulatory Networks. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419010113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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120
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Bourque G, Burns KH, Gehring M, Gorbunova V, Seluanov A, Hammell M, Imbeault M, Izsvák Z, Levin HL, Macfarlan TS, Mager DL, Feschotte C. Ten things you should know about transposable elements. Genome Biol 2018; 19:199. [PMID: 30454069 PMCID: PMC6240941 DOI: 10.1186/s13059-018-1577-z] [Citation(s) in RCA: 639] [Impact Index Per Article: 106.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Transposable elements (TEs) are major components of eukaryotic genomes. However, the extent of their impact on genome evolution, function, and disease remain a matter of intense interrogation. The rise of genomics and large-scale functional assays has shed new light on the multi-faceted activities of TEs and implies that they should no longer be marginalized. Here, we introduce the fundamental properties of TEs and their complex interactions with their cellular environment, which are crucial to understanding their impact and manifold consequences for organismal biology. While we draw examples primarily from mammalian systems, the core concepts outlined here are relevant to a broad range of organisms.
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Affiliation(s)
- Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, Québec, H3A 0G1, Canada.
- Canadian Center for Computational Genomics, McGill University, Montréal, Québec, H3A 0G1, Canada.
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Mary Gehring
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Molly Hammell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Michaël Imbeault
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Henry L Levin
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland, USA
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland, USA
| | - Dixie L Mager
- Terry Fox Laboratory, British Columbia Cancer Agency and Department of Medical Genetics, University of BC, Vancouver, BC, V5Z1L3, Canada
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA.
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121
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Kelleher ES, Jaweria J, Akoma U, Ortega L, Tang W. QTL mapping of natural variation reveals that the developmental regulator bruno reduces tolerance to P-element transposition in the Drosophila female germline. PLoS Biol 2018; 16:e2006040. [PMID: 30376574 PMCID: PMC6207299 DOI: 10.1371/journal.pbio.2006040] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 09/26/2018] [Indexed: 12/15/2022] Open
Abstract
Transposable elements (TEs) are obligate genetic parasites that propagate in host genomes by replicating in germline nuclei, thereby ensuring transmission to offspring. This selfish replication not only produces deleterious mutations—in extreme cases, TE mobilization induces genotoxic stress that prohibits the production of viable gametes. Host genomes could reduce these fitness effects in two ways: resistance and tolerance. Resistance to TE propagation is enacted by germline-specific small-RNA-mediated silencing pathways, such as the Piwi-interacting RNA (piRNA) pathway, and is studied extensively. However, it remains entirely unknown whether host genomes may also evolve tolerance by desensitizing gametogenesis to the harmful effects of TEs. In part, the absence of research on tolerance reflects a lack of opportunity, as small-RNA-mediated silencing evolves rapidly after a new TE invades, thereby masking existing variation in tolerance. We have exploited the recent historical invasion of the Drosophila melanogaster genome by P-element DNA transposons in order to study tolerance of TE activity. In the absence of piRNA-mediated silencing, the genotoxic stress imposed by P-elements disrupts oogenesis and, in extreme cases, leads to atrophied ovaries that completely lack germline cells. By performing quantitative trait locus (QTL) mapping on a panel of recombinant inbred lines (RILs) that lack piRNA-mediated silencing of P-elements, we uncovered multiple QTL that are associated with differences in tolerance of oogenesis to P-element transposition. We localized the most significant QTL to a small 230-kb euchromatic region, with the logarithm of the odds (LOD) peak occurring in the bruno locus, which codes for a critical and well-studied developmental regulator of oogenesis. Genetic, cytological, and expression analyses suggest that bruno dosage modulates germline stem cell (GSC) loss in the presence of P-element activity. Our observations reveal segregating variation in TE tolerance for the first time, and implicate gametogenic regulators as a source of tolerant variants in natural populations. Transposable elements (TEs), or “jumping genes,” are mobile fragments of selfish DNA that leave deleterious mutations and DNA damage in their wake as they spread through host genomes. Their harmful effects are known to select for resistance by the host, in which the propagation of TEs is regulated and reduced. Here, we study for the first time whether host cells might also exhibit tolerance to TEs, by reducing their harmful effects without directly controlling their movement. By taking advantage of a panel of wild-type Drosophila melanogaster that lack resistance to P-element DNA transposons, we identified a small region of the genome that influences tolerance of P-element activity. We further demonstrate that a gene within that region, bruno, strongly influences the negative effects of P-element mobilization on the fly. When bruno dosage is reduced, the fertility of females carrying mobile P-elements is enhanced. The bruno locus encodes a protein with no known role in TE regulation but multiple well-characterized functions in oogenesis. We propose that bruno function reduces tolerance of the developing oocyte to DNA damage that is caused by P-elements.
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Affiliation(s)
- Erin S. Kelleher
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
- * E-mail:
| | - Jaweria Jaweria
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
| | - Uchechukwu Akoma
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lily Ortega
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
| | - Wenpei Tang
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
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Wang L, Dou K, Moon S, Tan FJ, Zhang ZZ. Hijacking Oogenesis Enables Massive Propagation of LINE and Retroviral Transposons. Cell 2018; 174:1082-1094.e12. [PMID: 30057117 DOI: 10.1016/j.cell.2018.06.040] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/08/2018] [Accepted: 06/20/2018] [Indexed: 10/28/2022]
Abstract
Although animals have evolved multiple mechanisms to suppress transposons, "leaky" mobilizations that cause mutations and diseases still occur. This suggests that transposons employ specific tactics to accomplish robust propagation. By directly tracking mobilization, we show that, during a short and specific time window of oogenesis, retrotransposons achieve massive amplification via a cell-type-specific targeting strategy. Retrotransposons rarely mobilize in undifferentiated germline stem cells. However, as oogenesis proceeds, they utilize supporting nurse cells-which are highly polyploid and eventually undergo apoptosis-as factories to massively manufacture invading products. Moreover, retrotransposons rarely integrate into nurse cells themselves but, instead, via microtubule-mediated transport, they preferentially target the DNA of the interconnected oocytes. Blocking microtubule-dependent intercellular transport from nurse cells significantly alleviates damage to the oocyte genome. Our data reveal that parasitic genomic elements can efficiently hijack a host developmental process to propagate robustly, thereby driving evolutionary change and causing disease.
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Affiliation(s)
- Lu Wang
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA
| | - Kun Dou
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA
| | - Sungjin Moon
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA
| | - Frederick J Tan
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA
| | - Zz Zhao Zhang
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA.
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Wang H, Guo R, Du Z, Bai L, Li L, Cui J, Li W, Hoffman AR, Hu JF. Epigenetic Targeting of Granulin in Hepatoma Cells by Synthetic CRISPR dCas9 Epi-suppressors. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 11:23-33. [PMID: 29858058 PMCID: PMC5849805 DOI: 10.1016/j.omtn.2018.01.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 12/31/2017] [Accepted: 01/03/2018] [Indexed: 12/14/2022]
Abstract
The CRISPR-associated Cas9 system can modulate disease-causing alleles both in vivo and ex vivo, raising the possibility of therapeutic genome editing. In addition to gene targeting, epigenetic modulation by the catalytically inactive dCas9 may also be a potential form of cancer therapy. Granulin (GRN), a potent pluripotent mitogen and growth factor that promotes cancer progression by maintaining self-renewal of hepatic stem cancer cells, is upregulated in hepatoma tissues and is associated with decreased tumor survival in patients with hepatoma. We synthesized a group of dCas9 epi-suppressors to target GRN by tethering the C terminus of dCas9 with three epigenetic suppressor genes: DNMT3a (DNA methyltransferase), EZH2 (histone 3 lysine 27 methyltransferase), and KRAB (the Krüppel-associated box transcriptional repression domain). In conjunction with guide RNAs (gRNAs), the dCas9 epi-suppressors caused significant decreases in GRN mRNA abundance in Hep3B hepatoma cells. These dCas9 epi-suppressors initiated de novo CpG DNA methylation in the GRN promoter, and they produced histone codes that favor gene suppression, including decreased H3K4 methylation, increased H3K9 methylation, and enhanced HP1a binding. Epigenetic knockdown of GRN led to the inhibition of cell proliferation, decreased tumor sphere formation, and reduced cell invasion. These changes were achieved at least partially through the MMP/TIMP pathway. This study thus demonstrates the potential utility of using dCas9 epi-suppressors in the development of epigenetic targeting against tumors.
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Affiliation(s)
- Hong Wang
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, China; VA Palo Alto Health Care System and Stanford University Medical School, Palo Alto, CA 94304, USA
| | - Rui Guo
- Clinical Laboratory, First Affiliated Hospital, Jilin University, Changchun, China; VA Palo Alto Health Care System and Stanford University Medical School, Palo Alto, CA 94304, USA
| | - Zhonghua Du
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, China
| | - Ling Bai
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, China
| | - Lingyu Li
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, China
| | - Jiuwei Cui
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, China.
| | - Wei Li
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, China.
| | - Andrew R Hoffman
- VA Palo Alto Health Care System and Stanford University Medical School, Palo Alto, CA 94304, USA.
| | - Ji-Fan Hu
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, China; VA Palo Alto Health Care System and Stanford University Medical School, Palo Alto, CA 94304, USA.
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