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Kohlrausch FB, Wang F, McKerrow W, Grivainis M, Fenyo D, Keefe DL. Mapping of long interspersed element-1 (L1) insertions by TIPseq provides information about sub chromosomal genetic variation in human embryos. J Assist Reprod Genet 2024:10.1007/s10815-024-03176-9. [PMID: 38951360 DOI: 10.1007/s10815-024-03176-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 06/12/2024] [Indexed: 07/03/2024] Open
Abstract
PURPOSE Retrotransposons play important roles during early development when they are transiently de-repressed during epigenetic reprogramming. Long interspersed element-1 (L1), the only autonomous retrotransposon in humans, comprises 17% of the human genome. We applied the Single Cell Transposon Insertion Profiling by Sequencing (scTIPseq) to characterize and map L1 insertions in human embryos. METHODS Sixteen cryopreserved, genetically tested, human blastocysts, were accessed from consenting couples undergoing IVF at NYU Langone Fertility Center. Additionally, four trios (father, mother, and embryos) were also evaluated. scTIPseq was applied to map L1 insertions in all samples, using L1 locations reported in the 1000 Genomes as controls. RESULTS Twenty-nine unknown and unique insertions were observed in the sixteen embryos. Most were intergenic; no insertions were located in exons or immediately upstream of genes. The location or number of unknown insertions did not differ between euploid and aneuploid embryos, suggesting they are not merely markers of aneuploidy. Rather, scTIPseq provides novel information about sub-chromosomal structural variation in human embryos. Trio analyses showed a parental origin of all L1 insertions in embryos. CONCLUSION Several studies have measured L1 expression at different stages of development in mice, but this study for the first time reports unknown insertions in human embryos that were inherited from one parent, confirming no de novo L1 insertions occurred in parental germline or during embryogenesis. Since one-third of euploid embryo transfers fail, future studies would be useful for understanding whether these sub-chromosomal genetic variants or de novo L1 insertions affect embryo developmental potential.
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Affiliation(s)
- Fabiana B Kohlrausch
- Departamento de Biologia Geral, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, 24210-201, Brazil.
- Department of Obstetrics and Gynecology, New York University, New York, NY, 10016, USA.
| | - Fang Wang
- Department of Obstetrics and Gynecology, New York University, New York, NY, 10016, USA
| | - Wilson McKerrow
- Institute for Systems Genetics, New York University, New York, NY, 10016, USA
| | - Mark Grivainis
- Institute for Systems Genetics, New York University, New York, NY, 10016, USA
| | - David Fenyo
- Institute for Systems Genetics, New York University, New York, NY, 10016, USA
| | - David L Keefe
- Department of Obstetrics and Gynecology, New York University, New York, NY, 10016, USA
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Bayramov AV, Ermakova GV, Kuchryavyy AV, Zaraisky AG. Genome Duplications as the Basis of Vertebrates’ Evolutionary Success. Russ J Dev Biol 2021. [DOI: 10.1134/s1062360421030024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Kohlrausch FB, Berteli TS, Wang F, Navarro PA, Keefe DL. Control of LINE-1 Expression Maintains Genome Integrity in Germline and Early Embryo Development. Reprod Sci 2021; 29:328-340. [PMID: 33481218 DOI: 10.1007/s43032-021-00461-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/06/2021] [Indexed: 11/28/2022]
Abstract
Maintenance of genome integrity in the germline and in preimplantation embryos is crucial for mammalian development. Epigenetic remodeling during primordial germ cell (PGC) and preimplantation embryo development may contribute to genomic instability in these cells, since DNA methylation is an important mechanism to silence retrotransposons. Long interspersed elements 1 (LINE-1 or L1) are the most common autonomous retrotransposons in mammals, corresponding to approximately 17% of the human genome. Retrotransposition events are more frequent in germ cells and in early stages of embryo development compared with somatic cells. It has been shown that L1 activation and expression occurs in germline and is essential for preimplantation development. In this review, we focus on the role of L1 retrotransposon in mouse and human germline and early embryo development and discuss the possible relationship between L1 expression and genomic instability during these stages. Although several studies have addressed L1 expression at different stages of development, the developmental consequences of this expression remain poorly understood. Future research is still needed to highlight the relationship between L1 retrotransposition events and genomic instability during germline and early embryo development.
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Affiliation(s)
- Fabiana B Kohlrausch
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA.,Departamento de Biologia Geral, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Thalita S Berteli
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA.,Departamento de Ginecologia e Obstetrícia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Fang Wang
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA
| | - Paula A Navarro
- Departamento de Ginecologia e Obstetrícia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - David L Keefe
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA.
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York JR, McCauley DW. Functional genetic analysis in a jawless vertebrate, the sea lamprey: insights into the developmental evolution of early vertebrates. J Exp Biol 2020; 223:223/Suppl_1/jeb206433. [DOI: 10.1242/jeb.206433] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
ABSTRACT
Lampreys and hagfishes are the only surviving relicts of an ancient but ecologically dominant group of jawless fishes that evolved in the seas of the Cambrian era over half a billion years ago. Because of their phylogenetic position as the sister group to all other vertebrates (jawed vertebrates), comparisons of embryonic development between jawless and jawed vertebrates offers researchers in the field of evolutionary developmental biology the unique opportunity to address fundamental questions related to the nature of our earliest vertebrate ancestors. Here, we describe how genetic analysis of embryogenesis in the sea lamprey (Petromyzon marinus) has provided insight into the origin and evolution of developmental-genetic programs in vertebrates. We focus on recent work involving CRISPR/Cas9-mediated genome editing to study gene regulatory mechanisms involved in the development and evolution of neural crest cells and new cell types in the vertebrate nervous system, and transient transgenic assays that have been instrumental in dissecting the evolution of cis-regulatory control of gene expression in vertebrates. Finally, we discuss the broad potential for these functional genomic tools to address previously unanswerable questions related to the evolution of genomic regulatory mechanisms as well as issues related to invasive sea lamprey population control.
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Affiliation(s)
- Joshua R. York
- Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
| | - David W. McCauley
- Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
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Liu J, Hu H, Panserat S, Marandel L. Evolutionary history of DNA methylation related genes in chordates: new insights from multiple whole genome duplications. Sci Rep 2020; 10:970. [PMID: 31969623 PMCID: PMC6976628 DOI: 10.1038/s41598-020-57753-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 12/20/2019] [Indexed: 01/11/2023] Open
Abstract
DNA methylation is an important epigenetic mechanism involved in many biological processes, i.e. gametogenesis and embryonic development. However, increased copy numbers of DNA methylation related genes (dnmt, tet and tdg) have been found during chordate evolution due to successive whole genome duplication (WGD) events. Their evolutionary history and phylogenetic relationships remain unclear. The present study is the first to clarify the evolutionary history of DNA methylation genes in chordates. In particular, our results highlight the fixation of several dnmt3-related genes following successive WGD throughout evolution. The rainbow trout genome offered a unique opportunity to study the early evolutionary fates of duplicated genes due to a recent round of WGD at the radiation of salmonids. Differences highlighted in transcriptional patterns of these genes during gametogenesis and ontogenesis in trout indicated that they might be subjected to sub- or neo-functionalisation after WDG. The fixation of multiple dnmt3 genes in genomes after WGD could contribute to the diversification and plastic adaptation of the teleost.
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Affiliation(s)
- Jingwei Liu
- INRAE, Univ Pau & Pays de l'Adour, E2S-UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, F-64310, Saint-Pée-sur-Nivelle, France
| | - Huihua Hu
- INRAE, Univ Pau & Pays de l'Adour, E2S-UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, F-64310, Saint-Pée-sur-Nivelle, France.,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Stéphane Panserat
- INRAE, Univ Pau & Pays de l'Adour, E2S-UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, F-64310, Saint-Pée-sur-Nivelle, France
| | - Lucie Marandel
- INRAE, Univ Pau & Pays de l'Adour, E2S-UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, F-64310, Saint-Pée-sur-Nivelle, France.
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Zhao E, Tang C, Jiang X, Weng X, Zhong X, Zhang D, Hou J, Wang F, Huang M, Cui H. Inhibition of cell proliferation and induction of autophagy by KDM2B/FBXL10 knockdown in gastric cancer cells. Cell Signal 2017; 36:222-229. [PMID: 28506929 DOI: 10.1016/j.cellsig.2017.05.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 04/28/2017] [Accepted: 05/11/2017] [Indexed: 12/22/2022]
Abstract
Gastric cancer is difficult to cure due to its clinical heterogeneity and the complexity of its molecular mechanisms. KDM2B, a member of the JHDM family, functions as a histone lysine demethylase. However, the role and mechanisms of KDM2B in gastric cancer have not been elucidated. Here, we showed that KDM2B is commonly expressed in gastric cancer cells. The downregulation of KDM2B immediately induces autophagy, followed by the inhibition of proliferation. The compound 3-methyladenine (3-MA), an inhibitor of autophagy, largely rescues autophagy and the inhibition of cell proliferation induced by KDM2B knockdown. In this process, we observed a downregulation of the phosphorylation of Akt and its downstream effectors mTOR and p70S6K and an upregulation of Erk phosphorylation after KDM2B knockdown. In a xenograft model, the downregulation of KDM2B can inhibit tumour growth. The conversion of LC3-I to LC3-II also decreased concomitantly in vivo, which is a hallmark of autophagy. Taken together, our study was the first to demonstrate a novel regulatory role of KDM2B in autophagy and cell growth in gastric cancer cells. Our findings suggest that KDM2B may serve as a novel therapeutic target for gastric cancer therapy.
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Affiliation(s)
- Erhu Zhao
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Chunling Tang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Xiaolan Jiang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Xiong Weng
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Xiaoxia Zhong
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Dunke Zhang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Jianbing Hou
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Feng Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Mengying Huang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China.
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