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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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52
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Zhao Y, Gao N, Li X, El-Ashram S, Wang Z, Zhu L, Jiang W, Peng X, Zhang C, Chen Y, Li Z. Identifying candidate genes associated with sperm morphology abnormalities using weighted single-step GWAS in a Duroc boar population. Theriogenology 2019; 141:9-15. [PMID: 31479777 DOI: 10.1016/j.theriogenology.2019.08.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/23/2019] [Accepted: 08/25/2019] [Indexed: 12/31/2022]
Abstract
Artificial insemination (AI) has been used as a routine technology globally in the pig production industry since 1930. One of the preferable advantages of AI technology is that the semen of elite boars can be disseminated to the commercial sow population rapidly. Understanding the genetic background of semen traits may help in developing genetic improvement programs of boars by including these traits into the selection index. In this study, we utilized weighted single-step genome-wide association study (wssGWAS) to identify genetic regions and further candidate genes associated with sperm morphology abnormalities (proximal droplet, distal droplet, bent tail, coiled tail, and distal midpiece reflex) in a Duroc boar population. Several genomic regions explained 2.76%-9.22% of the genetic variances for sperm morphology abnormalities were identified. The first three detected QTL regions together explained about 7.65%-25.10% of the total genetic variances of the studied traits. Several genes were detected and considered as candidate genes for each of the traits under study: coiled tail, HOOK1, ARSA, SYCE3, SOD3, GMNN, RBPJ, STIL, and FGF1; bent tail, FGF1, ADIPOR1, ARPC5, FGFR3, PANX1, IZUMO1R, ANKRD49, and GAL; proximal droplet, NSF, WNT3, WNT9B, LYZL6, FGFR1OP, RNASET2, FYN, LRRC6, EPC1, DICER1, FNDC3A, and PFN1; distal droplet, ARSA, SYCE3, MOV10L1, CBR1, KDM6B, TP53, PTBP2, UBR7, KIF18A, ADAM15, FAAH, TEKT3, and SRD5A1; and distal midpiece reflex, OMA1, PFN1, PELP1, BMP2, GPR18, TM9SF2, and SPIN1. GO and KEGG enrichment analysis revealed the potential function of the identified candidate genes in spermatogenesis, testis functioning, and boar spermatozoa plasma membrane activating and maintenance. In conclusion, we detected candidate genes associated with the coiled tail, bent tail, proximal droplet, distal droplet, and distal midpiece reflex in a Duroc boar population using wssGWAS. Overall, these novel results reflect the polygenic genetic architecture of the studied sperm morphology abnormality traits, which may provide knowledge for conducting genomic selection on these traits. The detected genetic regions can be used in developing trait-specific marker assisted selection models by assigning higher genetic variances to these regions.
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Affiliation(s)
- Yunxiang Zhao
- College of Life Science and Engineering, Foshan University, 18 Jiangwan Street, Foshan, 528231, Guangdong Province, China; Guangxi Yangxiang Agriculture and Husbandry Co.,LTD, Guigang, 537100, China
| | - Ning Gao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, North Third Road, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Saeed El-Ashram
- College of Life Science and Engineering, Foshan University, 18 Jiangwan Street, Foshan, 528231, Guangdong Province, China
| | - Zhiquan Wang
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Lin Zhu
- Guangxi Yangxiang Agriculture and Husbandry Co.,LTD, Guigang, 537100, China
| | - Wei Jiang
- Guangxi Yangxiang Agriculture and Husbandry Co.,LTD, Guigang, 537100, China
| | - Xing Peng
- Guangxi Yangxiang Agriculture and Husbandry Co.,LTD, Guigang, 537100, China
| | - Conglin Zhang
- Guangxi Yangxiang Agriculture and Husbandry Co.,LTD, Guigang, 537100, China
| | - Yilong Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhili Li
- College of Life Science and Engineering, Foshan University, 18 Jiangwan Street, Foshan, 528231, Guangdong Province, China.
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53
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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: 87] [Impact Index Per Article: 17.4] [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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54
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Hill RJ, Crossan GP. DNA cross-link repair safeguards genomic stability during premeiotic germ cell development. Nat Genet 2019; 51:1283-1294. [PMID: 31367016 PMCID: PMC6675612 DOI: 10.1038/s41588-019-0471-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 06/24/2019] [Indexed: 11/09/2022]
Abstract
Germline de novo mutations are the basis of evolutionary diversity but also of genetic disease. However, the molecular origin, mechanisms and timing of germline mutagenesis are not fully understood. Here, we define a fundamental role for DNA interstrand cross-link repair in the germline. This repair process is essential for primordial germ cell (PGC) maturation during embryonic development. Inactivation of cross-link repair leads to genetic instability that is restricted to PGCs within the genital ridge during a narrow temporal window. Having successfully activated the PGC transcriptional program, a potent quality control mechanism detects and drives damaged PGCs into apoptosis. Therefore, these findings define a source of DNA damage and the nature of the subsequent DNA repair response in germ cells, which ensures faithful transmission of the genome between generations.
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Affiliation(s)
- Ross J Hill
- MRC Laboratory of Molecular Biology, Cambridge, UK
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55
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Kawano K, Doucet AJ, Ueno M, Kariya R, An W, Marzetta F, Kuroki M, Turelli P, Sukegawa S, Okada S, Strebel K, Trono D, Ariumi Y. HIV-1 Vpr and p21 restrict LINE-1 mobility. Nucleic Acids Res 2019; 46:8454-8470. [PMID: 30085096 PMCID: PMC6144823 DOI: 10.1093/nar/gky688] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 07/18/2018] [Indexed: 01/12/2023] Open
Abstract
Long interspersed element-1 (LINE-1, L1) composes ∼17% of the human genome. However, genetic interactions between L1 and human immunodeficiency virus type 1 (HIV-1) remain poorly understood. In this study, we found that HIV-1 suppresses L1 retrotransposition. Notably, HIV-1 Vpr strongly inhibited retrotransposition without inhibiting L1 promoter activity. Since Vpr is known to regulate host cell cycle, we examined the possibility whether Vpr suppresses L1 retrotransposition in a cell cycle dependent manner. We showed that the inhibitory effect of a mutant Vpr (H71R), which is unable to arrest the cell cycle, was significantly relieved compared with that of wild-type Vpr, suggesting that Vpr suppresses L1 mobility in a cell cycle dependent manner. Furthermore, a host cell cycle regulator p21Waf1 strongly suppressed L1 retrotransposition. The N-terminal kinase inhibitory domain (KID) of p21 was required for this inhibitory effect. Another KID-containing host cell cycle regulator p27Kip1 also strongly suppressed L1 retrotransposition. We showed that Vpr and p21 coimmunoprecipitated with L1 ORF2p and they suppressed the L1 reverse transcriptase activity in LEAP assay, suggesting that Vpr and p21 inhibit ORF2p-mediated reverse transcription. Altogether, our results suggest that viral and host cell cycle regulatory machinery limit L1 mobility in cultured cells.
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Affiliation(s)
- Koudai Kawano
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
| | - Aurélien J Doucet
- Institute for Research on Cancer and Aging, Nice (IRCAN), INSERM U1081, CNRS UMR 7284, Université de Nice-Sophia-Antipolis, Faculté de Médecine, 06107 Nice Cedex 2, France
| | - Mikinori Ueno
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
| | - Ryusho Kariya
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
| | - Wenfeng An
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007, USA
| | - Flavia Marzetta
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Misao Kuroki
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
| | - Priscilla Turelli
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Sayaka Sukegawa
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-0460, USA.,Clinical Research Center, Nagoya Medical Center, Nagoya 460-0001, Japan
| | - Seiji Okada
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
| | - Klaus Strebel
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-0460, USA
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Yasuo Ariumi
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
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56
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Pértille F, Da Silva VH, Johansson AM, Lindström T, Wright D, Coutinho LL, Jensen P, Guerrero-Bosagna C. Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification. Epigenetics 2019; 14:685-707. [PMID: 31070073 PMCID: PMC6557589 DOI: 10.1080/15592294.2019.1609868] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
DNA methylation in CpGs dinucleotides is associated with high mutability and disappearance of CpG sites during evolution. Although the high mutability of CpGs is thought to be relevant for vertebrate evolution, very little is known on the role of CpG-related mutations in the genomic diversification of vertebrates. Our study analysed genetic differences in chickens, between Red Junglefowl (RJF; the living closest relative to the ancestor of domesticated chickens) and domesticated breeds, to identify genomic dynamics that have occurred during the process of their domestication, focusing particularly on CpG-related mutations. Single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) between RJF and these domesticated breeds were assessed in a reduced fraction of their genome. Additionally, DNA methylation in the same fraction of the genome was measured in the sperm of RJF individuals to identify possible correlations with the mutations found between RJF and the domesticated breeds. Our study shows that although the vast majority of CpG-related mutations found relate to CNVs, CpGs disproportionally associate to SNPs in comparison to CNVs, where they are indeed substantially under-represented. Moreover, CpGs seem to be hotspots of mutations related to speciation. We suggest that, on the one hand, CpG-related mutations in CNV regions would promote genomic ‘flexibility’ in evolution, i.e., the ability of the genome to expand its functional possibilities; on the other hand, CpG-related mutations in SNPs would relate to genomic ‘specificity’ in evolution, thus, representing mutations that would associate with phenotypic traits relevant for speciation.
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Affiliation(s)
- Fábio Pértille
- a Avian Behavioral Genomics and Physiology Group, IFM Biology , Linköping University , Linköping , Sweden.,b Animal Biotechnology Laboratory, Animal Science Department , University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ) , Piracicaba , São Paulo , Brazil
| | - Vinicius H Da Silva
- c Animal Breeding and Genomics Centre , Wageningen University & Research , Wageningen , The Netherlands.,d Department of Animal Ecology (AnE) , Netherlands Institute of Ecology (NIOO-KNAW) , Wageningen , The Netherlands.,e Department of Animal Breeding and Genetics , Swedish University of Agricultural Sciences , Uppsala , Sweden
| | - Anna M Johansson
- e Department of Animal Breeding and Genetics , Swedish University of Agricultural Sciences , Uppsala , Sweden
| | - Tom Lindström
- f Division of Theoretical Biology, IFM , Linköping University , Linköping , Sweden
| | - Dominic Wright
- a Avian Behavioral Genomics and Physiology Group, IFM Biology , Linköping University , Linköping , Sweden
| | - Luiz L Coutinho
- b Animal Biotechnology Laboratory, Animal Science Department , University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ) , Piracicaba , São Paulo , Brazil
| | - Per Jensen
- a Avian Behavioral Genomics and Physiology Group, IFM Biology , Linköping University , Linköping , Sweden
| | - Carlos Guerrero-Bosagna
- a Avian Behavioral Genomics and Physiology Group, IFM Biology , Linköping University , Linköping , Sweden
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57
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Wang Z, McSwiggin H, Newkirk SJ, Wang Y, Oliver D, Tang C, Lee S, Wang S, Yuan S, Zheng H, Ye P, An W, Yan W. Insertion of a chimeric retrotransposon sequence in mouse Axin1 locus causes metastable kinky tail phenotype. Mob DNA 2019; 10:17. [PMID: 31073336 PMCID: PMC6500023 DOI: 10.1186/s13100-019-0162-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 04/21/2019] [Indexed: 12/12/2022] Open
Abstract
Background Transposable elements (TEs) make up > 50% of the human genome, and the majority of retrotransposon insertions are truncated and many are located in introns. However, the effects of retrotransposition on the host genes remain incompletely known. Results We report here that insertion of a chimeric L1 (cL1), but not IAP solo LTR, into intron 6 of Axin1 using CRIPSR/Cas9 induced the kinky tail phenotype with ~ 80% penetrance in heterozygous Axin cL1 mice. Both penetrant (with kinky tails) and silent (without kinky tails) Axin cL1 mice, regardless of sex, could transmit the phenotype to subsequent generations with similar penetrance (~ 80%). Further analyses revealed that a longer Axin1 transcript isoform containing partial cL1-targeted intron was present in penetrant, but absent in silent and wild type mice, and the production of this unique Axin1 transcript appeared to correlate with altered levels of an activating histone modification, H3K9ac. Conclusions The mechanism for Axin cL1 mice is different from those previously identified in mice with spontaneous retrotransposition of IAP, e.g., Axin Fu and A vy , both of which have been associated with DNA methylation changes. Our data suggest that Axin1 locus is sensitive to genetic and epigenetic alteration by retrotransposons and thus, ideally suited for studying the effects of new retrotransposition events on target gene function in mice.
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Affiliation(s)
- Zhuqing Wang
- 1Department of Physiology and Cell Biology, University of Nevada School of Medicine Center for Molecular Medicine, Room 207B 1664 North Virginia Street MS/0575, Reno, NV 89557 USA
| | - Hayden McSwiggin
- 1Department of Physiology and Cell Biology, University of Nevada School of Medicine Center for Molecular Medicine, Room 207B 1664 North Virginia Street MS/0575, Reno, NV 89557 USA
| | - Simon J Newkirk
- 3Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007 USA
| | - Yue Wang
- 1Department of Physiology and Cell Biology, University of Nevada School of Medicine Center for Molecular Medicine, Room 207B 1664 North Virginia Street MS/0575, Reno, NV 89557 USA
| | - Daniel Oliver
- 1Department of Physiology and Cell Biology, University of Nevada School of Medicine Center for Molecular Medicine, Room 207B 1664 North Virginia Street MS/0575, Reno, NV 89557 USA
| | - Chong Tang
- 1Department of Physiology and Cell Biology, University of Nevada School of Medicine Center for Molecular Medicine, Room 207B 1664 North Virginia Street MS/0575, Reno, NV 89557 USA
| | - Sandy Lee
- 1Department of Physiology and Cell Biology, University of Nevada School of Medicine Center for Molecular Medicine, Room 207B 1664 North Virginia Street MS/0575, Reno, NV 89557 USA
| | - Shawn Wang
- 1Department of Physiology and Cell Biology, University of Nevada School of Medicine Center for Molecular Medicine, Room 207B 1664 North Virginia Street MS/0575, Reno, NV 89557 USA
| | - Shuiqiao Yuan
- 1Department of Physiology and Cell Biology, University of Nevada School of Medicine Center for Molecular Medicine, Room 207B 1664 North Virginia Street MS/0575, Reno, NV 89557 USA
| | - Huili Zheng
- 1Department of Physiology and Cell Biology, University of Nevada School of Medicine Center for Molecular Medicine, Room 207B 1664 North Virginia Street MS/0575, Reno, NV 89557 USA
| | - Ping Ye
- 2Avera McKennan Hospital and University Health Center, Sioux Falls, SD 57108 USA.,3Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007 USA
| | - Wenfeng An
- 3Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007 USA
| | - Wei Yan
- 1Department of Physiology and Cell Biology, University of Nevada School of Medicine Center for Molecular Medicine, Room 207B 1664 North Virginia Street MS/0575, Reno, NV 89557 USA.,4Department of Obstetrics and Gynecology, University of Nevada, Reno School of Medicine, Reno, NV 89557 USA.,5Department of Biology, University of Nevada, Reno, Reno, NV 89557 USA
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58
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Bodea GO, McKelvey EGZ, Faulkner GJ. Retrotransposon-induced mosaicism in the neural genome. Open Biol 2019; 8:rsob.180074. [PMID: 30021882 PMCID: PMC6070720 DOI: 10.1098/rsob.180074] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/21/2018] [Indexed: 12/18/2022] Open
Abstract
Over the past decade, major discoveries in retrotransposon biology have depicted the neural genome as a dynamic structure during life. In particular, the retrotransposon LINE-1 (L1) has been shown to be transcribed and mobilized in the brain. Retrotransposition in the developing brain, as well as during adult neurogenesis, provides a milieu in which neural diversity can arise. Dysregulation of retrotransposon activity may also contribute to neurological disease. Here, we review recent reports of retrotransposon activity in the brain, and discuss the temporal nature of retrotransposition and its regulation in neural cells in response to stimuli. We also put forward hypotheses regarding the significance of retrotransposons for brain development and neurological function, and consider the potential implications of this phenomenon for neuropsychiatric and neurodegenerative conditions.
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Affiliation(s)
- Gabriela O Bodea
- Mater Research Institute-University of Queensland, TRI Building, Brisbane, Queensland 4102, Australia .,Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Eleanor G Z McKelvey
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute-University of Queensland, TRI Building, Brisbane, Queensland 4102, Australia .,Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia
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59
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Reznik B, Cincotta SA, Jaszczak RG, Mateo LJ, Shen J, Cao M, Baskin L, Ye P, An W, Laird DJ. Heterogeneity of transposon expression and activation of the repressive network in human fetal germ cells. Development 2019; 146:dev.171157. [PMID: 30658985 DOI: 10.1242/dev.171157] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/07/2019] [Indexed: 12/16/2022]
Abstract
Epigenetic resetting in germ cells during development de-represses transposable elements (TEs). piRNAs protect fetal germ cells by targeted mRNA destruction and deposition of repressive epigenetic marks. Here, we provide the first evidence for an active piRNA pathway and TE repression in germ cells of human fetal testis. We identify pre-pachytene piRNAs with features of secondary amplification that map most abundantly to the long interspersed element type 1 (L1) family of TEs. L1-ORF1p expression is heterogeneous in fetal germ cells, peaks at mid-gestation and declines concomitantly with increases in piRNAs, nuclear localization of HIWI2 and an increase in H3K9me3. Surprisingly, the same cells with accumulation of L1-ORF1p display highest levels of HIWI2 and H3K9me3. Conversely, the earliest germ cells with high levels of L1-ORF1p express low levels of the chaperone HSP90α. We propose that a subset of germ cells resists L1 expression, whereas L1-expressing germ cells activate the repression pathway that leads to epigenetic silencing of L1 via H3K9me3.
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Affiliation(s)
- Boris Reznik
- Department of Obstetrics, Gynecology and Reproductive Science; Center for Reproductive Sciences; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Steven A Cincotta
- Department of Obstetrics, Gynecology and Reproductive Science; Center for Reproductive Sciences; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Rebecca G Jaszczak
- Department of Obstetrics, Gynecology and Reproductive Science; Center for Reproductive Sciences; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Leslie J Mateo
- Department of Obstetrics, Gynecology and Reproductive Science; Center for Reproductive Sciences; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joel Shen
- Department of Urology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mei Cao
- Department of Urology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Laurence Baskin
- Department of Urology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ping Ye
- Avera McKennan Hospital and University Health Center, Sioux Falls, SD 57105, USA.,Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007, USA
| | - Wenfeng An
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007, USA
| | - Diana J Laird
- Department of Obstetrics, Gynecology and Reproductive Science; Center for Reproductive Sciences; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
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60
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Tangsuwansri C, Saeliw T, Thongkorn S, Chonchaiya W, Suphapeetiporn K, Mutirangura A, Tencomnao T, Hu VW, Sarachana T. Investigation of epigenetic regulatory networks associated with autism spectrum disorder (ASD) by integrated global LINE-1 methylation and gene expression profiling analyses. PLoS One 2018; 13:e0201071. [PMID: 30036398 PMCID: PMC6056057 DOI: 10.1371/journal.pone.0201071] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 07/06/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The exact cause and mechanisms underlying the pathobiology of autism spectrum disorder (ASD) remain unclear. Dysregulation of long interspersed element-1 (LINE-1) has been reported in the brains of ASD-like mutant mice and ASD brain tissues. However, the role and methylation of LINE-1 in individuals with ASD remain unclear. In this study, we aimed to investigate whether LINE-1 insertion is associated with differentially expressed genes (DEGs) and to assess LINE-1 methylation in ASD. METHODS To identify DEGs associated with LINE-1 in ASD, we reanalyzed previously published transcriptome profiles and overlapped them with the list of LINE-1-containing genes from the TranspoGene database. An Ingenuity Pathway Analysis (IPA) of DEGs associated with LINE-1 insertion was conducted. DNA methylation of LINE-1 was assessed via combined bisulfite restriction analysis (COBRA) of lymphoblastoid cell lines from ASD individuals and unaffected individuals, and the methylation levels were correlated with the expression levels of LINE-1 and two LINE-1-inserted DEGs, C1orf27 and ARMC8. RESULTS We found that LINE-1 insertion was significantly associated with DEGs in ASD. The IPA showed that LINE-1-inserted DEGs were associated with ASD-related mechanisms, including sex hormone receptor signaling and axon guidance signaling. Moreover, we observed that the LINE-1 methylation level was significantly reduced in lymphoblastoid cell lines from ASD individuals with severe language impairment and was inversely correlated with the transcript level. The methylation level of LINE-1 was also correlated with the expression of the LINE-1-inserted DEG C1orf27 but not ARMC8. CONCLUSIONS In ASD individuals with severe language impairment, LINE-1 methylation was reduced and correlated with the expression levels of LINE-1 and the LINE-1-inserted DEG C1orf27. Our findings highlight the association of LINE-1 with DEGs in ASD blood samples and warrant further investigation. The molecular mechanisms of LINE-1 and the effects of its methylation in ASD pathobiology deserve further study.
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Affiliation(s)
- Chayanin Tangsuwansri
- M.Sc. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Thanit Saeliw
- M.Sc. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Surangrat Thongkorn
- M.Sc. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Weerasak Chonchaiya
- Division of Growth and Development and Maximizing Thai Children’s Developmental Potential Research Unit, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Apiwat Mutirangura
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Tewin Tencomnao
- Age-related Inflammation and Degeneration Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Valerie Wailin Hu
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States of America
| | - Tewarit Sarachana
- Age-related Inflammation and Degeneration Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
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61
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Percharde M, Lin CJ, Yin Y, Guan J, Peixoto GA, Bulut-Karslioglu A, Biechele S, Huang B, Shen X, Ramalho-Santos M. A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity. Cell 2018; 174:391-405.e19. [PMID: 29937225 PMCID: PMC6046266 DOI: 10.1016/j.cell.2018.05.043] [Citation(s) in RCA: 313] [Impact Index Per Article: 52.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 03/20/2018] [Accepted: 05/17/2018] [Indexed: 01/07/2023]
Abstract
Transposable elements represent nearly half of mammalian genomes and are generally described as parasites, or "junk DNA." The LINE1 retrotransposon is the most abundant class and is thought to be deleterious for cells, yet it is paradoxically highly expressed during early development. Here, we report that LINE1 plays essential roles in mouse embryonic stem cells (ESCs) and pre-implantation embryos. In ESCs, LINE1 acts as a nuclear RNA scaffold that recruits Nucleolin and Kap1/Trim28 to repress Dux, the master activator of a transcriptional program specific to the 2-cell embryo. In parallel, LINE1 RNA mediates binding of Nucleolin and Kap1 to rDNA, promoting rRNA synthesis and ESC self-renewal. In embryos, LINE1 RNA is required for Dux silencing, synthesis of rRNA, and exit from the 2-cell stage. The results reveal an essential partnership between LINE1 RNA, Nucleolin, Kap1, and peri-nucleolar chromatin in the regulation of transcription, developmental potency, and ESC self-renewal.
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Affiliation(s)
- Michelle Percharde
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chih-Jen Lin
- The University of Edinburgh, MRC Centre for Reproductive Health, Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, Scotland, UK
| | - Yafei Yin
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Juan Guan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Gabriel A Peixoto
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Aydan Bulut-Karslioglu
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Steffen Biechele
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Xiaohua Shen
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Miguel Ramalho-Santos
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA.
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62
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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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63
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Griswold MD. 50 years of spermatogenesis: Sertoli cells and their interactions with germ cells. Biol Reprod 2018; 99:87-100. [PMID: 29462262 PMCID: PMC7328471 DOI: 10.1093/biolre/ioy027] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/22/2018] [Accepted: 02/02/2018] [Indexed: 01/15/2023] Open
Abstract
The complex morphology of the Sertoli cells and their interactions with germ cells has been a focus of investigators since they were first described by Enrico Sertoli. In the past 50 years, information on Sertoli cells has transcended morphology alone to become increasingly more focused on molecular questions. The goal of investigators has been to understand the role of the Sertoli cells in spermatogenesis and to apply that information to problems relating to male fertility. Sertoli cells are unique in that they are a nondividing cell population that is active for the reproductive lifetime of the animal and cyclically change morphology and gene expression. The numerous and distinctive junctional complexes and membrane specializations made by Sertoli cells provide a scaffold and environment for germ cell development. The increased focus of investigators on the molecular components and putative functions of testicular cells has resulted primarily from procedures that isolate specific cell types from the testicular milieu. Products of Sertoli cells that influence germ cell development and vice versa have been characterized from cultured cells and from the application of transgenic technologies. Germ cell transplantation has shown that the Sertoli cells respond to cues from germ cells with regard to developmental timing and has furthered a focus on spermatogenic stem cells and the stem cell niche. Very basic and universal features of spermatogenesis such as the cycle of the seminiferous epithelium and the spermatogenic wave are initiated by Sertoli cells and maintained by Sertoli-germ cell cooperation.
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Affiliation(s)
- Michael D Griswold
- Center for Reproductive Biology, Washington State University, Pullman, Washington, USA
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64
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Blaudin de Thé FX, Rekaik H, Peze-Heidsieck E, Massiani-Beaudoin O, Joshi RL, Fuchs J, Prochiantz A. Engrailed homeoprotein blocks degeneration in adult dopaminergic neurons through LINE-1 repression. EMBO J 2018; 37:embj.201797374. [PMID: 29941661 DOI: 10.15252/embj.201797374] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 05/07/2018] [Accepted: 05/28/2018] [Indexed: 12/21/2022] Open
Abstract
LINE-1 mobile genetic elements have shaped the mammalian genome during evolution. A minority of them have escaped fossilization which, when activated, can threaten genome integrity. We report that LINE-1 are expressed in substantia nigra ventral midbrain dopaminergic neurons, a class of neurons that degenerate in Parkinson's disease. In Engrailed-1 heterozygotes, these neurons show a progressive degeneration that starts at 6 weeks of age, coinciding with an increase in LINE-1 expression. Similarly, DNA damage and cell death, induced by an acute oxidative stress applied to embryonic midbrain neurons in culture or to adult midbrain dopaminergic neurons in vivo, are accompanied by enhanced LINE-1 expression. Reduction of LINE-1 activity through (i) direct transcriptional repression by Engrailed, (ii) a siRNA directed against LINE-1, (iii) the nucleoside analogue reverse transcriptase inhibitor stavudine, and (iv) viral Piwil1 expression, protects against oxidative stress in vitro and in vivo We thus propose that LINE-1 overexpression triggers oxidative stress-induced DNA strand breaks and that an Engrailed adult function is to protect mesencephalic dopaminergic neurons through the repression of LINE-1 expression.
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Affiliation(s)
- François-Xavier Blaudin de Thé
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241/INSERM U1050, PSL Research University, Paris Cedex 05, France
| | - Hocine Rekaik
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241/INSERM U1050, PSL Research University, Paris Cedex 05, France
| | - Eugenie Peze-Heidsieck
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241/INSERM U1050, PSL Research University, Paris Cedex 05, France
| | - Olivia Massiani-Beaudoin
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241/INSERM U1050, PSL Research University, Paris Cedex 05, France
| | - Rajiv L Joshi
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241/INSERM U1050, PSL Research University, Paris Cedex 05, France
| | - Julia Fuchs
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241/INSERM U1050, PSL Research University, Paris Cedex 05, France
| | - Alain Prochiantz
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241/INSERM U1050, PSL Research University, Paris Cedex 05, France
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65
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Richardson SR, Faulkner GJ. Heritable L1 Retrotransposition Events During Development: Understanding Their Origins: Examination of heritable, endogenous L1 retrotransposition in mice opens up exciting new questions and research directions. Bioessays 2018; 40:e1700189. [PMID: 29709066 PMCID: PMC6681178 DOI: 10.1002/bies.201700189] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 03/04/2018] [Indexed: 01/08/2023]
Abstract
The retrotransposon Long Interspersed Element 1 (LINE-1 or L1) has played a major role in shaping the sequence composition of the mammalian genome. In our recent publication, "Heritable L1 retrotransposition in the mouse primordial germline and early embryo," we systematically assessed the rate and developmental timing of de novo, heritable endogenous L1 insertions in mice. Such heritable retrotransposition events allow L1 to exert an ongoing influence upon genome evolution. Here, we place our findings in the context of earlier studies, and highlight how our results corroborate, and depart from, previous research based on human patient samples and transgenic mouse models harboring engineered L1 reporter genes. In parallel, we outline outstanding questions regarding the stage-specificity, regulation, and functional impact of embryonic and germline L1 retrotransposition, and propose avenues for future research in this field.
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Affiliation(s)
- Sandra R. Richardson
- Mater Research Institute–University of QueenslandWoolloongabbaQueensland 4102Australia
| | - Geoffrey J. Faulkner
- Mater Research Institute–University of QueenslandWoolloongabbaQueensland 4102Australia
- Queensland Brain InstituteUniversity of QueenslandBrisbaneQueensland 4072Australia
- School of Biomedical SciencesUniversity of QueenslandBrisbaneQueensland 4072Australia
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66
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Suarez NA, Macia A, Muotri AR. LINE-1 retrotransposons in healthy and diseased human brain. Dev Neurobiol 2017; 78:434-455. [PMID: 29239145 DOI: 10.1002/dneu.22567] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 12/12/2022]
Abstract
Long interspersed element-1 (LINE-1 or L1) is a transposable element with the ability to self-mobilize throughout the human genome. The L1 elements found in the human brain is hypothesized to date back 56 million years ago and has survived evolution, currently accounting for 17% of the human genome. L1 retrotransposition has been theorized to contribute to somatic mosaicism. This review focuses on the presence of L1 in the healthy and diseased human brain, such as in autism spectrum disorders. Throughout this exploration, we will discuss the impact L1 has on neurological disorders that can occur throughout the human lifetime. With this, we hope to better understand the complex role of L1 in the human brain development and its implications to human cognition. © 2017 Wiley Periodicals, Inc. Develop Neurobiol 78: 434-455, 2018.
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Affiliation(s)
- Nicole A Suarez
- Department of Pediatrics/Rady Children's Hospital San Diego, University of California San Diego, La Jolla, California, 92093
| | - Angela Macia
- Department of Pediatrics/Rady Children's Hospital San Diego, University of California San Diego, La Jolla, California, 92093
| | - Alysson R Muotri
- Department of Pediatrics/Rady Children's Hospital San Diego, University of California San Diego, La Jolla, California, 92093
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67
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Chen C. A novel reporter mouse to monitor in vivo retrotransposition in the germline. Biol Reprod 2017; 97:335-336. [PMID: 29024952 DOI: 10.1093/biolre/iox111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 08/29/2017] [Indexed: 01/16/2023] Open
Affiliation(s)
- Chen Chen
- Department of Animal Science, Michigan State University, East Lansing, Michigan, USA.,Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan, USA.,Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, Grand Rapids, Michigan, USA
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68
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L1 Mosaicism in Mammals: Extent, Effects, and Evolution. Trends Genet 2017; 33:802-816. [PMID: 28797643 DOI: 10.1016/j.tig.2017.07.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 06/30/2017] [Accepted: 07/14/2017] [Indexed: 10/19/2022]
Abstract
The retrotransposon LINE-1 (long interspersed element 1, L1) is a transposable element that has extensively colonized the mammalian germline. L1 retrotransposition can also occur in somatic cells, causing genomic mosaicism, as well as in cancer. However, the extent of L1-driven mosaicism arising during ontogenesis is unclear. We discuss here recent experimental data which, at a minimum, fully substantiate L1 mosaicism in early embryonic development and neural cells, including post-mitotic neurons. We also consider the possible biological impact of somatic L1 insertions in neurons, the existence of donor L1s that are highly active ('hot') in specific spatiotemporal niches, and the evolutionary selection of donor L1s driving neuronal mosaicism.
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