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Lu Y, Li M, Cao H, Zhou J, Li F, Yu D, Yu M. Ten-eleven translocation 1 mediating DNA demethylation regulates the proliferation of chicken primordial germ cells through the activation of Wnt4/β-catenin signaling pathway. Anim Biosci 2024; 37:471-480. [PMID: 38271970 PMCID: PMC10915191 DOI: 10.5713/ab.23.0310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/22/2023] [Accepted: 11/28/2023] [Indexed: 01/27/2024] Open
Abstract
OBJECTIVE The objective of this study was to investigate the regulation relationship of Teneleven translocation 1 (Tet1) in DNA demethylation and the proliferation of primordial germ cells (PGCs) in chickens. METHODS siRNA targeting Tet1 was used to transiently knockdown the expression of Tet1 in chicken PGCs, and the genomic DNA methylation status was measured. The proliferation of chicken PGCs was detected by flow cytometry analysis and cell counting kit-8 assay when activation or inhibition of Wnt4/β-catenin signaling pathway. And the level of DNA methylation and hisotne methylation was also tested. RESULTS Results revealed that knockdown of Tet1 inhibited the proliferation of chicken PGCs and downregulated the mRNA expression of Cyclin D1 and cyclin-dependent kinase 6 (CDK6), as well as pluripotency-associated genes (Nanog, PouV, and Sox2). Flow cytometry analysis confirmed that the population of PGCs in Tet1 knockdown group displayed a significant decrease in the proportion of S and G2 phase cells, which meant that there were less PGCs entered the mitosis process than that of control. Furthermore, Tet1 knockdown delayed the entrance to G1/S phase and this inhibition was rescued by treated with BIO. Consistent with these findings, Wnt/β-catenin signaling was inactivated in Tet1 knockdown PGCs, leading to aberrant proliferation. Further analysis showed that the methylation of the whole genome increased significantly after Tet1 downregulation, while hydroxymethylation obviously declined. Meanwhile, the level of H3K27me3 was upregulated and H3K9me2 was downregulated in Tet1 knockdown PGCs, which was achieved by regulating Wnt/β-catenin signaling pathway. CONCLUSION These results suggested that the self-renewal of chicken PGCs and the maintenance of their characteristics were regulated by Tet1 mediating DNA demethylation through the activation of Wnt4/β-catenin signaling pathway.
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Affiliation(s)
- Yinglin Lu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095,
China
| | - Ming Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095,
China
| | - Heng Cao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095,
China
| | - Jing Zhou
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095,
China
| | - Fan Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095,
China
| | - Debing Yu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095,
China
| | - Minli Yu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095,
China
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2
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Zhang G, Mao Y, Zhang Y, Huang H, Pan J. Assisted reproductive technology and imprinting errors: analyzing underlying mechanisms from epigenetic regulation. HUM FERTIL 2023; 26:864-878. [PMID: 37929309 DOI: 10.1080/14647273.2023.2261628] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 08/11/2023] [Indexed: 11/07/2023]
Abstract
With the increasing maturity and widespread application of assisted reproductive technology (ART), more attention has been paid to the health outcomes of offspring following ART. It is well established that children born from ART treatment are at an increased risk of imprinting errors and imprinting disorders. The disturbances of genetic imprinting are attributed to the overlap of ART procedures and important epigenetic reprogramming events during the development of gametes and early embryos, but the detailed mechanisms are hitherto obscure. In this review, we summarized the DNA methylation-dependent and independent mechanisms that control the dynamic epigenetic regulation of imprinted genes throughout the life cycle of a mammal, including erasure, establishment, and maintenance. In addition, we systematically described the dysregulation of imprinted genes in embryos conceived through ART and discussed the corresponding underlying mechanisms according to findings in animal models. This work is conducive to evaluating and improving the safety of ART.
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Affiliation(s)
- Gaochen Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences (No. 2019RU056), Shanghai, China
| | - Yiting Mao
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Yu Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Hefeng Huang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences (No. 2019RU056), Shanghai, China
- Key Laboratory of Reproductive Genetics (Ministry of Education), Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiexue Pan
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences (No. 2019RU056), Shanghai, China
- Key Laboratory of Reproductive Genetics (Ministry of Education), Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
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3
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Ramakrishna NB, Battistoni G, Surani MA, Hannon GJ, Miska EA. Mouse primordial germ-cell-like cells lack piRNAs. Dev Cell 2022; 57:2661-2668.e5. [PMID: 36473462 DOI: 10.1016/j.devcel.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 08/03/2022] [Accepted: 11/03/2022] [Indexed: 12/12/2022]
Abstract
PIWI-interacting RNAs (piRNAs) are small RNAs bound by PIWI-clade Argonaute proteins that function to silence transposable elements (TEs). Following mouse primordial germ cell (mPGC) specification around E6.25, fetal piRNAs emerge in male gonocytes from E13.5 onward. The in vitro differentiation of mPGC-like cells (mPGCLCs) has raised the possibility of studying the fetal piRNA pathway in greater depth. However, using single-cell RNA-seq and RT-qPCR along mPGCLC differentiation, we find that piRNA pathway factors are not fully expressed in Day 6 mPGCLCs. Moreover, we do not detect piRNAs across a panel of Day 6 mPGCLC lines using small RNA-seq. Our combined efforts highlight that in vitro differentiated Day 6 mPGCLCs do not yet resemble E13.5 or later mouse gonocytes where the piRNA pathway is active. This Matters Arising paper is in response to von Meyenn et al. (2016), published in Developmental Cell. See also the correction by von Meyenn et al. published in this issue.
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Affiliation(s)
- Navin B Ramakrishna
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EL, UK
| | - Giorgia Battistoni
- CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - M Azim Surani
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EL, UK; Wellcome/MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK.
| | - Gregory J Hannon
- CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK.
| | - Eric A Miska
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.
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4
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Tan K, Wilkinson MF. Regulation of both transcription and RNA turnover contribute to germline specification. Nucleic Acids Res 2022; 50:7310-7325. [PMID: 35776114 PMCID: PMC9303369 DOI: 10.1093/nar/gkac542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/29/2022] [Accepted: 06/29/2022] [Indexed: 12/25/2022] Open
Abstract
The nuanced mechanisms driving primordial germ cells (PGC) specification remain incompletely understood since genome-wide transcriptional regulation in developing PGCs has previously only been defined indirectly. Here, using SLAMseq analysis, we determined genome-wide transcription rates during the differentiation of embryonic stem cells (ESCs) to form epiblast-like (EpiLC) cells and ultimately PGC-like cells (PGCLCs). This revealed thousands of genes undergoing bursts of transcriptional induction and rapid shut-off not detectable by RNAseq analysis. Our SLAMseq datasets also allowed us to infer RNA turnover rates, which revealed thousands of mRNAs stabilized and destabilized during PGCLC specification. mRNAs tend to be unstable in ESCs and then are progressively stabilized as they differentiate. For some classes of genes, mRNA turnover regulation collaborates with transcriptional regulation, but these processes oppose each other in a surprisingly high frequency of genes. To test whether regulated mRNA turnover has a physiological role in PGC development, we examined three genes that we found were regulated by RNA turnover: Sox2, Klf2 and Ccne1. Circumvention of their regulated RNA turnover severely impaired the ESC-to-EpiLC and EpiLC-to-PGCLC transitions. Our study demonstrates the functional importance of regulated RNA stability in germline development and provides a roadmap of transcriptional and post-transcriptional regulation during germline specification.
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Affiliation(s)
- Kun Tan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Miles F Wilkinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Institute of Genomic Medicine (IGM), University of California San Diego, La Jolla, CA 92093, USA
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5
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Kobayashi M, Kobayashi M, Odajima J, Shioda K, Hwang YS, Sasaki K, Chatterjee P, Kramme C, Kohman RE, Church GM, Loehr AR, Weiss RS, Jüppner H, Gell JJ, Lau CC, Shioda T. Expanding homogeneous culture of human primordial germ cell-like cells maintaining germline features without serum or feeder layers. Stem Cell Reports 2022; 17:507-521. [PMID: 35148847 PMCID: PMC9039862 DOI: 10.1016/j.stemcr.2022.01.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 01/02/2023] Open
Abstract
In vitro expansion of human primordial germ cell-like cells (hPGCLCs), a pluripotent stem cell-derived PGC model, has proved challenging due to rapid loss of primordial germ cell (PGC)-like identity and limited cell survival/proliferation. Here, we describe long-term culture hPGCLCs (LTC-hPGCLCs), which actively proliferate in a serum-free, feeder-free condition without apparent limit as highly homogeneous diploid cell populations maintaining transcriptomic and epigenomic characteristics of hPGCLCs. Histone proteomics confirmed reduced H3K9me2 and increased H3K27me3 marks in LTC-hPGCLCs compared with induced pluripotent stem cells (iPSCs). LTC-hPGCLCs established from multiple human iPSC clones of both sexes were telomerase positive, senescence-free cells readily passaged with minimal cell death or deviation from the PGC-like identity. LTC-hPGCLCs are capable of differentiating to DAZL-positive M-spermatogonia-like cells in the xenogeneic reconstituted testis (xrTestis) organ culture milieu as well as efficiently producing fully pluripotent embryonic germ cell-like cells in the presence of stem cell factor and fibroblast growth factor 2. Thus, LTC-hPGCLCs provide convenient access to unlimited amounts of high-quality and homogeneous hPGCLCs.
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Affiliation(s)
- Mutsumi Kobayashi
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA.
| | - Misato Kobayashi
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Junko Odajima
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Keiko Shioda
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Young Sun Hwang
- Institute for Regenerative Medicine, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Kotaro Sasaki
- Institute for Regenerative Medicine, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Pranam Chatterjee
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Christian Kramme
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Richie E Kohman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Amanda R Loehr
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Robert S Weiss
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Harald Jüppner
- Endocrine Unit and Pediatric Nephrology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Joanna J Gell
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Connecticut Children's Medical Center, Hartford, CT 06106, USA; University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Ching C Lau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Connecticut Children's Medical Center, Hartford, CT 06106, USA; University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Toshi Shioda
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; Connecticut Children's Medical Center, Hartford, CT 06106, USA.
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6
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Abstract
Primordial germ cells (PGCs) form early in embryo development and are crucial precursors to functioning gamete cells. Considerable research has focussed on identifying the transcriptional characteristics and signalling pathway requirements that confer PGC specification and development, enabling the derivation of PGC-like cells (PGCLCs) in vitro using specific signalling cocktails. However, full maturation to germ cells still relies on co-culture with supporting cell types, implicating an additional requirement for cellular- and tissue-level regulation. Here, we discuss the experimental evidence that highlights the nature of intercellular interactions between PGCs and neighbouring cell populations during mouse PGC development. We posit that the role that tissue interactions play on PGCs is not limited solely to signalling-based induction but extends to coordination of development by robust regulation of the proportions and position of the cells and tissues within the embryo, which is crucial for functional germ cell maturation. Such tissue co-development provides a dynamic, contextual niche for PGC development. We argue that there is evidence for a clear role for inter-tissue dependence of mouse PGCs, with potential implications for generating mammalian PGCLCs in vitro.
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Affiliation(s)
- Christopher B Cooke
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK.,Abcam Plc, Discovery Drive, Cambridge Biomedical Campus, Cambridge, CB2 0AX, UK.,The Francis Crick Institute, 1 Midland Road, Somers Town, London, NW1 1AT, UK
| | - Naomi Moris
- The Francis Crick Institute, 1 Midland Road, Somers Town, London, NW1 1AT, UK
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7
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Generation of developmentally competent oocytes and fertile mice from parthenogenetic embryonic stem cells. Protein Cell 2021; 12:947-964. [PMID: 34845589 PMCID: PMC8674391 DOI: 10.1007/s13238-021-00865-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 06/20/2021] [Indexed: 12/11/2022] Open
Abstract
Parthenogenetic embryos, created by activation and diploidization of oocytes, arrest at mid-gestation for defective paternal imprints, which impair placental development. Also, viable offspring has not been obtained without genetic manipulation from parthenogenetic embryonic stem cells (pESCs) derived from parthenogenetic embryos, presumably attributable to their aberrant imprinting. We show that an unlimited number of oocytes can be derived from pESCs and produce healthy offspring. Moreover, normal expression of imprinted genes is found in the germ cells and the mice. pESCs exhibited imprinting consistent with exclusively maternal lineage, and higher X-chromosome activation compared to female ESCs derived from the same mouse genetic background. pESCs differentiated into primordial germ cell-like cells (PGCLCs) and formed oocytes following in vivo transplantation into kidney capsule that produced fertile pups and reconstituted ovarian endocrine function. The transcriptome and methylation of imprinted and X-linked genes in pESC-PGCLCs closely resembled those of in vivo produced PGCs, consistent with efficient reprogramming of methylation and genomic imprinting. These results demonstrate that amplification of germ cells through parthenogenesis faithfully maintains maternal imprinting, offering a promising route for deriving functional oocytes and having potential in rebuilding ovarian endocrine function.
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8
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Bend family proteins mark chromatin boundaries and synergistically promote early germ cell differentiation. Protein Cell 2021; 13:721-741. [PMID: 34731408 PMCID: PMC9233729 DOI: 10.1007/s13238-021-00884-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/19/2021] [Indexed: 12/30/2022] Open
Abstract
Understanding the regulatory networks for germ cell fate specification is necessary to developing strategies for improving the efficiency of germ cell production in vitro. In this study, we developed a coupled screening strategy that took advantage of an arrayed bi-molecular fluorescence complementation (BiFC) platform for protein-protein interaction screens and epiblast-like cell (EpiLC)-induction assays using reporter mouse embryonic stem cells (mESCs). Investigation of candidate interaction partners of core human pluripotent factors OCT4, NANOG, KLF4 and SOX2 in EpiLC differentiation assays identified novel primordial germ cell (PGC)-inducing factors including BEN-domain (BEND/Bend) family members. Through RNA-seq, ChIP-seq, and ATAC-seq analyses, we showed that Bend5 worked together with Bend4 and helped mark chromatin boundaries to promote EpiLC induction in vitro. Our findings suggest that BEND/Bend proteins represent a new family of transcriptional modulators and chromatin boundary factors that participate in gene expression regulation during early germline development.
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9
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Keyhan S, Burke E, Schrott R, Huang Z, Grenier C, Price T, Raburn D, Corcoran DL, Soubry A, Hoyo C, Murphy SK. Male obesity impacts DNA methylation reprogramming in sperm. Clin Epigenetics 2021; 13:17. [PMID: 33494820 PMCID: PMC7831195 DOI: 10.1186/s13148-020-00997-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Male obesity has profound effects on morbidity and mortality, but relatively little is known about the impact of obesity on gametes and the potential for adverse effects of male obesity to be passed to the next generation. DNA methylation contributes to gene regulation and is erased and re-established during gametogenesis. Throughout post-pubertal spermatogenesis, there are continual needs to both maintain established methylation and complete DNA methylation programming, even during epididymal maturation. This dynamic epigenetic landscape may confer increased vulnerability to environmental influences, including the obesogenic environment, that could disrupt reprogramming fidelity. Here we conducted an exploratory analysis that showed that overweight/obesity (n = 20) is associated with differences in mature spermatozoa DNA methylation profiles relative to controls with normal BMI (n = 47). RESULTS We identified 3264 CpG sites in human sperm that are significantly associated with BMI (p < 0.05) using Infinium HumanMethylation450 BeadChips. These CpG sites were significantly overrepresented among genes involved in transcriptional regulation and misregulation in cancer, nervous system development, and stem cell pluripotency. Analysis of individual sperm using bisulfite sequencing of cloned alleles revealed that the methylation differences are present in a subset of sperm rather than being randomly distributed across all sperm. CONCLUSIONS Male obesity is associated with altered sperm DNA methylation profiles that appear to affect reprogramming fidelity in a subset of sperm, suggestive of an influence on the spermatogonia. Further work is required to determine the potential heritability of these DNA methylation alterations. If heritable, these changes have the potential to impede normal development.
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Affiliation(s)
- Sanaz Keyhan
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, 27713, USA
| | - Emily Burke
- Department of Biostatistics, Duke University, Durham, 27710, USA
| | - Rose Schrott
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Duke University Medical Center, 501 W. Main Street, Suite 510, The Chestefield Building, PO Box 90534, Durham, NC, 27701, USA.,Duke University Integrated Toxicology and Environmental Health Program, The Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA
| | - Zhiqing Huang
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Duke University Medical Center, 501 W. Main Street, Suite 510, The Chestefield Building, PO Box 90534, Durham, NC, 27701, USA
| | - Carole Grenier
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Duke University Medical Center, 501 W. Main Street, Suite 510, The Chestefield Building, PO Box 90534, Durham, NC, 27701, USA
| | - Thomas Price
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, 27713, USA
| | - Doug Raburn
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, 27713, USA
| | - David L Corcoran
- Center for Genomics and Computational Biology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Adelheid Soubry
- Epidemiology Research Group, Department of Public Health and Primary Care, Faculty of Medicine, KU Leuven University, 2000, Leuven, Belgium
| | - Catherine Hoyo
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27633, USA
| | - Susan K Murphy
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Duke University Medical Center, 501 W. Main Street, Suite 510, The Chestefield Building, PO Box 90534, Durham, NC, 27701, USA. .,Duke University Integrated Toxicology and Environmental Health Program, The Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA.
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10
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Wang LJ, Li XX, Hou J, Song XH, Xie WH, Shen L. Integrated Analyses of Mouse Stem Cell Transcriptomes Provide Clues for Stem Cell Maintenance and Transdifferentiation. Front Genet 2020; 11:563798. [PMID: 33101382 PMCID: PMC7500244 DOI: 10.3389/fgene.2020.563798] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/17/2020] [Indexed: 01/05/2023] Open
Abstract
In vivo cell fate reprogramming has emerged as a new method for understanding cell plasticity and as potential treatment for tissue regeneration. Highly efficient and precise reprogramming requires fully understanding of the transcriptomes which function within different cell types. Here, we adopt weighted gene co-expression network analysis (WGCNA) to explore the molecular mechanisms of self-renewal in several well-known stem cell types, including embryonic stem cells (ESC), primordial germ cells (PGC), spermatogonia stem cells (SSC), neural stem cells (NSC), mesenchymal stem cells (MSC), and hematopoietic stem cells (HSC). We identified 37 core genes that were up-regulated in all of the stem cell types examined, as well as stem cell correlated gene co-expression networks. The validation of the co-expression genes revealed a continued protein-protein interaction network that included 823 nodes and 3113 edges. Based on the topology, we identified six densely connected regions within the continued protein-protein interaction network. The SSC specific genes Itgam, Cxcr6, and Agtr2 bridged four densely connected regions that consisted primarily of HSC-, NSC-, and MSC-correlated genes. The expression levels of identified stem cell related transcription factors were confirmed consistent with bioinformatics prediction in ESCs and NSCs by qPCR. Exploring the mechanisms underlying adult stem cell self-renewal will aid in the understanding of stem cell pool maintenance and will promote more accurate and efficient strategies for tissue regeneration and repair.
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Affiliation(s)
- Li-Juan Wang
- Zibo Key Laboratory of New Drug Development of Neurodegenerative Diseases, Shandong Provincial Research Center for Bioinformatics Engineering and Technique, Institute of Biomedical Research, Shandong University of Technology, Zibo, China.,School of Life Sciences, Shandong University of Technology, Zibo, China
| | - Xiao-Xiao Li
- Zibo Key Laboratory of New Drug Development of Neurodegenerative Diseases, Shandong Provincial Research Center for Bioinformatics Engineering and Technique, Institute of Biomedical Research, Shandong University of Technology, Zibo, China.,School of Life Sciences, Shandong University of Technology, Zibo, China
| | - Jie Hou
- School of Life Sciences, Shandong University of Technology, Zibo, China
| | - Xin-Hua Song
- School of Life Sciences, Shandong University of Technology, Zibo, China
| | - Wen-Hai Xie
- Zibo Key Laboratory of New Drug Development of Neurodegenerative Diseases, Shandong Provincial Research Center for Bioinformatics Engineering and Technique, Institute of Biomedical Research, Shandong University of Technology, Zibo, China.,School of Life Sciences, Shandong University of Technology, Zibo, China
| | - Liang Shen
- Zibo Key Laboratory of New Drug Development of Neurodegenerative Diseases, Shandong Provincial Research Center for Bioinformatics Engineering and Technique, Institute of Biomedical Research, Shandong University of Technology, Zibo, China.,School of Life Sciences, Shandong University of Technology, Zibo, China
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11
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Van der Mude A. Structure encoding in DNA. J Theor Biol 2020; 492:110205. [PMID: 32070719 DOI: 10.1016/j.jtbi.2020.110205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 12/29/2019] [Accepted: 02/14/2020] [Indexed: 12/21/2022]
Abstract
It is proposed that transposons and related long non-coding RNA define the fine structure of body parts. Although morphogens have long been known to direct the formation of many gross structures in early embryonic development, they do not have the necessary precision to define a structure down to the individual cellular level. Using the distinction between procedural and declarative knowledge in information processing as an analogy, it is hypothesized that DNA encodes fine structure in a manner that is different from the genetic code for proteins. The hypothesis states that repeated or near-repeated sequences that are in transposons and non-coding RNA define body part structures. As the cells in a body part go through the epigenetic process of differentiation, the action of methylation serves to inactivate all but the relevant structure definitions and some associated cell type genes. The transposons left active will then physically modify the DNA sequence in the heterochromatin to establish the local context in the three-dimensional body part structure. This brings the encoded definition of the cell type to the histone. The histone code for that cell type starts the regulatory cascade that turns on the genes associated with that particular type of cell, transforming it from a multipotent cell to a fully differentiated cell. This mechanism creates structures in the musculoskeletal system, the organs of the body, the major parts of the brain, and other systems.
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12
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Angers B, Perez M, Menicucci T, Leung C. Sources of epigenetic variation and their applications in natural populations. Evol Appl 2020; 13:1262-1278. [PMID: 32684958 PMCID: PMC7359850 DOI: 10.1111/eva.12946] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 12/13/2022] Open
Abstract
Epigenetic processes manage gene expression and products in a real‐time manner, allowing a single genome to display different phenotypes. In this paper, we discussed the relevance of assessing the different sources of epigenetic variation in natural populations. For a given genotype, the epigenetic variation could be environmentally induced or occur randomly. Strategies developed by organisms to face environmental fluctuations such as phenotypic plasticity and diversified bet‐hedging rely, respectively, on these different sources. Random variation can also represent a proxy of developmental stability and can be used to assess how organisms deal with stressful environmental conditions. We then proposed the microbiome as an extension of the epigenotype of the host to assess the factors determining the establishment of the community of microorganisms. Finally, we discussed these perspectives in the applied context of conservation.
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Affiliation(s)
- Bernard Angers
- Department of biological sciences Université de Montréal Montreal Quebec Canada
| | - Maëva Perez
- Department of biological sciences Université de Montréal Montreal Quebec Canada
| | - Tatiana Menicucci
- Department of biological sciences Université de Montréal Montreal Quebec Canada
| | - Christelle Leung
- CEFE CNRS Université de Montpellier Université Paul Valéry Montpellier 3 EPHE Montpellier France
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Seo BJ, Jang HS, Song H, Park C, Hong K, Lee JW, Do JT. Generation of Mouse Parthenogenetic Epiblast Stem Cells and Their Imprinting Patterns. Int J Mol Sci 2019; 20:ijms20215428. [PMID: 31683583 PMCID: PMC6862121 DOI: 10.3390/ijms20215428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 12/21/2022] Open
Abstract
Pluripotent stem cells can be established from parthenogenetic embryos, which only possess maternal alleles with maternal-specific imprinting patterns. Previously, we and others showed that parthenogenetic embryonic stem cells (pESCs) and parthenogenetic induced pluripotent stem cells (piPSCs) progressively lose the bimaternal imprinting patterns. As ESCs and iPSCs are naïve pluripotent stem cells, parthenogenetic primed pluripotent stem cells have not yet been established, and thus, their imprinting patterns have not been studied. Here, we first established parthenogenetic epiblast stem cells (pEpiSCs) from 7.5 dpc parthenogenetic implantation embryos and compared the expression patterns and DNA methylation status of the representative imprinted genes with biparental EpiSCs. We found that there were no striking differences between pEpiSCs and biparental EpiSCs with respect to morphology, pluripotency gene expression, and differentiation potential, but there were differences in the expression and DNA methylation status of imprinted genes (H19, Igf2, Peg1, and Peg3). Moreover, pEpiSCs displayed a different DNA methylation pattern compared with that of parthenogenetic neural stem cells (pNSCs), which showed a typical bimaternal imprinting pattern. These results suggest that both naïve pluripotent stem cells and primed pluripotent stem cells have an unstable imprinting status.
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Affiliation(s)
- Bong Jong Seo
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea.
| | - Hyun Sik Jang
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea.
| | - Hyuk Song
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea.
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea.
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea.
| | - Jeong Woong Lee
- Research Center of Integrative Cellulomics, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea.
| | - Jeong Tae Do
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea.
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El Khoury D, Fayjaloun S, Nassar M, Sahakian J, Aad PY. Updates on the Effect of Mycotoxins on Male Reproductive Efficiency in Mammals. Toxins (Basel) 2019; 11:E515. [PMID: 31484408 PMCID: PMC6784030 DOI: 10.3390/toxins11090515] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 08/19/2019] [Accepted: 08/30/2019] [Indexed: 12/15/2022] Open
Abstract
Mycotoxins are ubiquitous and unavoidable harmful fungal products with the ability to cause disease in both animals and humans, and are found in almost all types of foods, with a greater prevalence in hot humid environments. These mycotoxins vary greatly in structure and biochemical effects; therefore, by better understanding the toxicological and pathological aspects of mycotoxins, we can be better equipped to fight the diseases, as well as the biological and economic devastations, they induce. Multiple studies point to the association between a recent increase in male infertility and the increased occurrence of these mycotoxins in the environment. Furthermore, understanding how mycotoxins may induce an accumulation of epimutations during parental lifetimes can shed light on their implications with respect to fertility and reproductive efficiency. By acknowledging the diversity of mycotoxin molecular function and mode of action, this review aims to address the current limited knowledge on the effects of these chemicals on spermatogenesis and the various endocrine and epigenetics patterns associated with their disruptions.
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Affiliation(s)
- Diala El Khoury
- Department of Sciences, Faculty of Natural and Applied Sciences, Notre Dame University-Louaize, Zouk Mosbeh 2207, Lebanon
| | - Salma Fayjaloun
- Department of Sciences, Faculty of Natural and Applied Sciences, Notre Dame University-Louaize, Zouk Mosbeh 2207, Lebanon
| | - Marc Nassar
- Department of Sciences, Faculty of Natural and Applied Sciences, Notre Dame University-Louaize, Zouk Mosbeh 2207, Lebanon
| | - Joseph Sahakian
- Department of Sciences, Faculty of Natural and Applied Sciences, Notre Dame University-Louaize, Zouk Mosbeh 2207, Lebanon
| | - Pauline Y Aad
- Department of Sciences, Faculty of Natural and Applied Sciences, Notre Dame University-Louaize, Zouk Mosbeh 2207, Lebanon.
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15
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Genome imprinting in stem cells: A mini-review. Gene Expr Patterns 2019; 34:119063. [PMID: 31279979 DOI: 10.1016/j.gep.2019.119063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/21/2019] [Accepted: 06/30/2019] [Indexed: 12/19/2022]
Abstract
Genomic imprinting is an epigenetic process result in silencing of one of the two alleles (maternal or paternal) based on the parent of origin. Dysregulation of imprinted genes results in detectable developmental and differential abnormalities. Epigenetics erasure is required for resetting the cell identity to a ground state during the production of induced pluripotent stem (iPS) cells from somatic cells. There are some contradictory reports regarding the status of the imprinting marks in the genome of iPS cells. Additionally, many studies highlighted the existence of subtle differences in the imprinting loci between different types of iPS cells and embryonic stem (ES) cells. These observations could ultimately undermine the use of patient-derived iPS cells for regenerative medicine.
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Bloom JC, Loehr AR, Schimenti JC, Weiss RS. Germline genome protection: implications for gamete quality and germ cell tumorigenesis. Andrology 2019; 7:516-526. [PMID: 31119900 DOI: 10.1111/andr.12651] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND Germ cells have a unique and critical role as the conduit for hereditary information and therefore employ multiple strategies to protect genomic integrity and avoid mutations. Unlike somatic cells, which often respond to DNA damage by arresting the cell cycle and conducting DNA repair, germ cells as well as long-lived pluripotent stem cells typically avoid the use of error-prone repair mechanisms and favor apoptosis, reducing the risk of genetic alterations. Testicular germ cell tumors, the most common cancers of young men, arise from pre-natal germ cells. OBJECTIVES To summarize the current understanding of DNA damage response mechanisms in pre-meiotic germ cells and to discuss how they impact both the origins of testicular germ cell tumors and their remarkable responsiveness to genotoxic chemotherapy. MATERIALS AND METHODS We conducted a review of literature gathered from PubMed regarding the DNA damage response properties of testicular germ cell tumors and the germ cells from which they arise, as well as the influence of these mechanisms on therapeutic responses by testicular germ cell tumors. RESULTS AND DISCUSSION This review provides a comprehensive evaluation of how the developmental origins of male germ cells and their inherent germ cell-like DNA damage response directly impact the development and therapeutic sensitivity of testicular germ cell tumors. CONCLUSIONS The DNA damage response of germ cells directly impacts the development and therapeutic sensitivity of testicular germ cell tumors. Recent advances in the study of primordial germ cells, post-natal mitotically dividing germ cells, and pluripotent stem cells will allow for new investigations into the initiation, progression, and treatment of testicular germ cell tumors.
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Affiliation(s)
- J C Bloom
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - A R Loehr
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - J C Schimenti
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - R S Weiss
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
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17
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Abstract
Germ cells undergo epigenome reprogramming for proper development of the next generation. The achievement of in vitro germ cell derivation from human and mouse pluripotent stem cells and further differentiation in a plane culture and in aggregation with gonadal somatic cells offers unprecedented opportunities for investigation of the germ cell development. Moreover, advances in low-input/single-cell genomics have enabled detailed investigation of epigenome dynamics during germ cell development. These technologies have advanced our knowledge of epigenome reprogramming during the specification and development of primordial germ cells, their sex differentiation, and gametogenesis. Key findings include details of chromatin remodeling and transcriptional regulation, progressive and comprehensive DNA demethylation, and tight links between DNA demethylation and histone marks during the development of primordial germ cells, acquisition of unique totipotent epigenome during oogenesis (e.g., broad H3K4me3 domains and low-level three-dimensional genomic organization), and unexpected organization of the sperm genome. Moreover, these studies suggest the importance of epigenome analyses for in-depth evaluations of in vitro gametogenesis.
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Affiliation(s)
- Kazuki Kurimoto
- Department of Embryology, Nara Medical University, Nara, Japan.
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan; Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
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18
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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: 591] [Impact Index Per Article: 98.5] [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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19
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Zhao S, Xu J, Liu S, Cui K, Li Z, Liu N. Dppa3 in pluripotency maintenance of ES cells and early embryogenesis. J Cell Biochem 2018; 120:4794-4799. [PMID: 30417435 DOI: 10.1002/jcb.28063] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/22/2018] [Indexed: 01/11/2023]
Abstract
Embryonic development is precisely regulated by a network of signal pathways and specific genes. Dppa3 (also known as Pgc7 or Stella) plays an important role in early embryonic development during the cleavage stage as a maternal effect gene. Dppa3 expresses in many species, and its homologous gene in human and rat genomes is located at the same chromosomal regions and have the same exon-intron structure. However, unlike mouse embryonic stem (ES) cells, in which the Dppa3 promoter maintains hypomethylation that allows a high transcription level, the DPPA3 promoter region in human ES cells is methylated, much like that of mouse epiblast stem cell. Dppa3 is essential for early embryogenesis and pluripotency maintenance; however, the precise mechanism and downstream passage remains unknown. In this review, we will summarize some important functions of Dppa3 in early embryogenesis and pluripotency maintenance of mouse ES cells.
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Affiliation(s)
- Shuang Zhao
- School of Medicine, Nankai University, Tianjin, China.,Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Jia Xu
- School of Medicine, Nankai University, Tianjin, China
| | - Siying Liu
- School of Medicine, Nankai University, Tianjin, China
| | - Kaige Cui
- School of Medicine, Nankai University, Tianjin, China
| | - Zongjin Li
- School of Medicine, Nankai University, Tianjin, China.,Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Na Liu
- School of Medicine, Nankai University, Tianjin, China.,Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
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20
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Kurimoto K, Saitou M. Epigenome regulation during germ cell specification and development from pluripotent stem cells. Curr Opin Genet Dev 2018; 52:57-64. [PMID: 29908427 DOI: 10.1016/j.gde.2018.06.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/30/2018] [Accepted: 06/04/2018] [Indexed: 01/04/2023]
Abstract
Germ cells undergo epigenome reprogramming for proper development of the next generation. The realization of germ cell derivation from human and mouse pluripotent stem cells offers unprecedented opportunity for investigation of germline development. Primordial germ cells reconstituted in vitro (PGC-like cells [PGCLCs]) show progressive dilution of genomic DNA methylation, tightly linked with chromatin remodeling, during their specification. PGCLCs can be further expanded by plane culture, allowing maintenance of the gene-expression profiles of early PGCs and continuance of the DNA methylation erasure, thereby establishing an epigenetic `blank slate'. PGCLCs undergo further epigenome regulation to acquire the male or female fates. These findings will provide a foundation for basic germ cell biology and for in-depth evaluations of in vitro gametogenesis.
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Affiliation(s)
- Kazuki Kurimoto
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan; JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Mitinori Saitou
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan; JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan; Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan; Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan.
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21
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Identification of rare de novo epigenetic variations in congenital disorders. Nat Commun 2018; 9:2064. [PMID: 29802345 PMCID: PMC5970273 DOI: 10.1038/s41467-018-04540-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 05/08/2018] [Indexed: 01/05/2023] Open
Abstract
Certain human traits such as neurodevelopmental disorders (NDs) and congenital anomalies (CAs) are believed to be primarily genetic in origin. However, even after whole-genome sequencing (WGS), a substantial fraction of such disorders remain unexplained. We hypothesize that some cases of ND-CA are caused by aberrant DNA methylation leading to dysregulated genome function. Comparing DNA methylation profiles from 489 individuals with ND-CAs against 1534 controls, we identify epivariations as a frequent occurrence in the human genome. De novo epivariations are significantly enriched in cases, while RNAseq analysis shows that epivariations often have an impact on gene expression comparable to loss-of-function mutations. Additionally, we detect and replicate an enrichment of rare sequence mutations overlapping CTCF binding sites close to epivariations, providing a rationale for interpreting non-coding variation. We propose that epivariations contribute to the pathogenesis of some patients with unexplained ND-CAs, and as such likely have diagnostic relevance.
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22
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Mitsunaga S, Shioda T. Evolutionarily diverse mechanisms of germline specification among mammals: what about us? Stem Cell Investig 2018; 5:12. [PMID: 29782583 PMCID: PMC5945857 DOI: 10.21037/sci.2018.04.03] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 03/31/2018] [Indexed: 01/03/2023]
Affiliation(s)
- Shino Mitsunaga
- Massachusetts General Hospital Center for Cancer Research, Charlestown, MA, USA
| | - Toshi Shioda
- Massachusetts General Hospital Center for Cancer Research, Charlestown, MA, USA
- Harvard Medical School, Boston, MA, USA
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23
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Ben Maamar M, Sadler-Riggleman I, Beck D, McBirney M, Nilsson E, Klukovich R, Xie Y, Tang C, Yan W, Skinner MK. Alterations in sperm DNA methylation, non-coding RNA expression, and histone retention mediate vinclozolin-induced epigenetic transgenerational inheritance of disease. ENVIRONMENTAL EPIGENETICS 2018; 4:dvy010. [PMID: 29732173 PMCID: PMC5920293 DOI: 10.1093/eep/dvy010] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/20/2018] [Accepted: 03/22/2018] [Indexed: 05/24/2023]
Abstract
Epigenetic transgenerational inheritance of disease and phenotypic variation can be induced by several toxicants, such as vinclozolin. This phenomenon can involve DNA methylation, non-coding RNA (ncRNA) and histone retention, and/or modification in the germline (e.g. sperm). These different epigenetic marks are called epimutations and can transmit in part the transgenerational phenotypes. This study was designed to investigate the vinclozolin-induced concurrent alterations of a number of different epigenetic factors, including DNA methylation, ncRNA, and histone retention in rat sperm. Gestating females (F0 generation) were exposed transiently to vinclozolin during fetal gonadal development. The directly exposed F1 generation fetus, the directly exposed germline within the fetus that will generate the F2 generation, and the transgenerational F3 generation sperm were studied. DNA methylation and ncRNA were altered in each generation rat sperm with the direct exposure F1 and F2 generations being distinct from the F3 generation epimutations. Interestingly, an increased number of differential histone retention sites were found in the F3 generation vinclozolin sperm, but not in the F1 or F2 generations. All three different epimutation types were affected in the vinclozolin lineage transgenerational sperm (F3 generation). The direct exposure generations (F1 and F2) epigenetic alterations were distinct from the transgenerational sperm epimutations. The genomic features and gene pathways associated with the epimutations were investigated to help elucidate the integration of these different epigenetic processes. Our results show that the three different types of epimutations are involved and integrated in the mediation of the epigenetic transgenerational inheritance phenomenon.
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Affiliation(s)
- Millissia Ben Maamar
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Ingrid Sadler-Riggleman
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Margaux McBirney
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Rachel Klukovich
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, 1664 North Virginia Street, MS557, Reno, NV 89557, USA
| | - Yeming Xie
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, 1664 North Virginia Street, MS557, Reno, NV 89557, USA
| | - Chong Tang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, 1664 North Virginia Street, MS557, Reno, NV 89557, USA
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, 1664 North Virginia Street, MS557, Reno, NV 89557, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
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24
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The POU5F1 gene expression in colorectal cancer: a novel prognostic marker. Surg Today 2018; 48:709-715. [DOI: 10.1007/s00595-018-1644-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 02/06/2018] [Indexed: 12/19/2022]
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25
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Skinner MK, Ben Maamar M, Sadler-Riggleman I, Beck D, Nilsson E, McBirney M, Klukovich R, Xie Y, Tang C, Yan W. Alterations in sperm DNA methylation, non-coding RNA and histone retention associate with DDT-induced epigenetic transgenerational inheritance of disease. Epigenetics Chromatin 2018; 11:8. [PMID: 29482626 PMCID: PMC5827984 DOI: 10.1186/s13072-018-0178-0] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/16/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Environmental toxicants such as DDT have been shown to induce the epigenetic transgenerational inheritance of disease (e.g., obesity) through the germline. The current study was designed to investigate the DDT-induced concurrent alterations of a number of different epigenetic processes including DNA methylation, non-coding RNA (ncRNA) and histone retention in sperm. METHODS Gestating females were exposed transiently to DDT during fetal gonadal development, and then, the directly exposed F1 generation, the directly exposed germline F2 generation and the transgenerational F3 generation sperm were investigated. RESULTS DNA methylation and ncRNA were altered in each generation sperm with the direct exposure F1 and F2 generations being predominantly distinct from the F3 generation epimutations. The piRNA and small tRNA were the most predominant classes of ncRNA altered. A highly conserved set of histone retention sites were found in the control lineage generations which was not significantly altered between generations, but a large number of new histone retention sites were found only in the transgenerational generation DDT lineage sperm. CONCLUSIONS Therefore, all three different epigenetic processes were concurrently altered as DDT induced the epigenetic transgenerational inheritance of sperm epimutations. The direct exposure generations sperm epigenetic alterations were distinct from the transgenerational sperm epimutations. The genomic features and gene associations with the epimutations were investigated to help elucidate the integration of these different epigenetic processes. Observations demonstrate all three epigenetic processes are involved in transgenerational inheritance. The different epigenetic processes appear to be integrated in mediating the epigenetic transgenerational inheritance phenomenon.
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Affiliation(s)
- Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA.
| | - Millissia Ben Maamar
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Ingrid Sadler-Riggleman
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Margaux McBirney
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Rachel Klukovich
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - Yeming Xie
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - Chong Tang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
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Taylor JA, Shioda K, Mitsunaga S, Yawata S, Angle BM, Nagel SC, vom Saal FS, Shioda T. Prenatal Exposure to Bisphenol A Disrupts Naturally Occurring Bimodal DNA Methylation at Proximal Promoter of fggy, an Obesity-Relevant Gene Encoding a Carbohydrate Kinase, in Gonadal White Adipose Tissues of CD-1 Mice. Endocrinology 2018; 159:779-794. [PMID: 29220483 PMCID: PMC5774244 DOI: 10.1210/en.2017-00711] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 12/01/2017] [Indexed: 12/13/2022]
Abstract
Exposure of mammalian fetuses to endocrine disruptors can increase the risk of adult-onset diseases. We previously showed that exposure of mouse fetuses to bisphenol A (BPA) caused adult-onset obesity. To examine roles of epigenetic changes in this delayed toxicity, we determined the effects of fetal mouse exposure to BPA on genome-wide DNA methylation and messenger RNA (mRNA) expression in gonadal white adipose tissues (WATs) by deep sequencing, bisulfite pyrosequencing, and real-time quantitative polymerase chain reaction. Pregnant CD-1 mice (F0) were dosed daily with 0, 5, or 500 μg/kg/d BPA during gestational days 9 to 18, and the weaned F1 animals were fed ad libitum with standard chow until they were euthanized at 19 weeks old. In the vehicle-exposed F1 animals, fggy promoter showed a clear bimodal pattern of very strong (55% to 95%) or very weak (5% to 30%) DNA methylation occurring at nearly equal incidence with no intermediate strength. Promoter hypermethylation completely suppressed mRNA expression. BPA exposure eliminated this naturally occurring dichotomy, shifting fggy promoter toward the hypomethylation state to release transcriptional suppression. The strength of Fggy mRNA expression significantly correlated with increased whole body weight and gonadal fat weight of males but not females. Bioinformatics studies showed that expression of Fggy mRNA is stronger in mouse WATs than in brown adipose tissues and enhanced in gonadal fat by diet-induced obesity. These observations suggest that prenatal exposure to BPA may disrupt the physiological bimodal nature of epigenetic regulation of fggy in mouse WATs, possibly contributing to the adult-onset obesity phenotype.
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Affiliation(s)
- Julia A. Taylor
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
| | - Keiko Shioda
- Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02114
| | - Shino Mitsunaga
- Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02114
| | - Shiomi Yawata
- Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02114
| | - Brittany M. Angle
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
| | - Susan C. Nagel
- Department of Obstetrics, Gynecology and Women’s Health, University of Missouri, Columbia, Missouri 65211
| | | | - Toshi Shioda
- Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02114
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115
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Khan MFJ, Little J, Mossey PA, Steegers-Theunissen RPM, Autelitano L, Lombardo I, Andreasi RB, Rubini M. Evaluating LINE-1 methylation in cleft lip tissues and its association with early pregnancy exposures. Epigenomics 2018; 10:105-113. [DOI: 10.2217/epi-2017-0081] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Aim: To pilot investigation of methylation of long interspersed nucleotide element-1 in lip tissues from infants with nonsyndromic cleft lip, and its association with maternal periconceptional exposures. Methods: The lateral and medial sides of the cleft lips of 23 affected infants were analyzed for long interspersed nucleotide element-1 methylation by bisulfite conversion and pyrosequencing. Results: The medial side showed 1.8% higher methylation compared with the lateral side; p = 0.031, particularly in male infants (2.7% difference; p = 0.011) or when the mothers did not take folic acid during periconceptional period (2.4% difference; p = 0.011). These results were not statistically significant when Bonferroni adjustment was used. Conclusion: The observed differences in DNA methylation, although nonsignificant after correction for multiple comparisons, suggest that differential regulation of the two sides may impact lip fusion and warrant larger-scale replication.
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Affiliation(s)
- Mohammad Faisal J Khan
- Department of Biomedical & Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology & Genetics, University of Ferrara, Ferrara, Italy
| | - Julian Little
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Peter A Mossey
- Craniofacial Development at the WHO-collaborating Centre for Oral & Craniofacial Research, Dental Hospital & School, University of Dundee, Dundee, Scotland
| | - Régine PM Steegers-Theunissen
- Department of Obstetrics & Gynaecology, Department of Pediatrics, Division Neonatology Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Luca Autelitano
- Department of Cranio-Maxillo-Facial Surgery, Regional Centre for Orofacial Clefts & Craniofacial Anomalies, San Paolo Hospital, University of Milan, Milan, Italy
| | - Ilenia Lombardo
- Department of Biomedical & Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology & Genetics, University of Ferrara, Ferrara, Italy
| | - Rita Bassi Andreasi
- Department of Biomedical & Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology & Genetics, University of Ferrara, Ferrara, Italy
| | - Michele Rubini
- Department of Biomedical & Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology & Genetics, University of Ferrara, Ferrara, Italy
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Relevance of iPSC-derived human PGC-like cells at the surface of embryoid bodies to prechemotaxis migrating PGCs. Proc Natl Acad Sci U S A 2017; 114:E9913-E9922. [PMID: 29087313 PMCID: PMC5699045 DOI: 10.1073/pnas.1707779114] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Human primordial germ cell-like cells (hPGCLCs) generated from pluripotent stem cells in vitro hold promise, with broad applications for studies of human germline cells. We show that hPGCLCs generated using several distinct protocols are transcriptomally comparable and that primed pluripotency human iPSCs gain competence to generate hPGCLCs after only 72 hours of reprogramming toward ERK-independent state-naïve pluripotency. hPGCLCs were localized in the outermost surface layer of embryoid bodies and strongly expressed CXCR4. Live cell imaging showed active migratory activity of hPGCLCs, and their exposure to the CXCR4 ligand CXCL12/SDF-1 induced enriched expression of promigratory genes and antiapoptotic genes. These results support the resemblance of hPGCLCs to prechemotaxis human embryonic primordial germ cells migrating in the midline region of embryos. Pluripotent stem cell-derived human primordial germ cell-like cells (hPGCLCs) provide important opportunities to study primordial germ cells (PGCs). We robustly produced CD38+ hPGCLCs [∼43% of FACS-sorted embryoid body (EB) cells] from primed-state induced pluripotent stem cells (iPSCs) after a 72-hour transient incubation in the four chemical inhibitors (4i)-naïve reprogramming medium and showed transcriptional consistency of our hPGCLCs with hPGCLCs generated in previous studies using various and distinct protocols. Both CD38+ hPGCLCs and CD38− EB cells significantly expressed PRDM1 and TFAP2C, although PRDM1 mRNA in CD38− cells lacked the 3′-UTR harboring miRNA binding sites regulating mRNA stability. Genes up-regulated in hPGCLCs were enriched for cell migration genes, and their promoters were enriched for the binding motifs of TFAP2 (which was identified in promoters of T, NANOS3, and SOX17) and the RREB-1 cell adhesion regulator. In EBs, hPGCLCs were identified exclusively in the outermost surface monolayer as dispersed cells or cell aggregates with strong and specific expression of POU5F1/OCT4 protein. Time-lapse live cell imaging revealed active migration of hPGCLCs on Matrigel. Whereas all hPGCLCs strongly expressed the CXCR4 chemotaxis receptor, its ligand CXCL12/SDF1 was not significantly expressed in the whole EBs. Exposure of hPGCLCs to CXCL12/SDF1 induced cell migration genes and antiapoptosis genes. Thus, our study shows that transcriptionally consistent hPGCLCs can be readily produced from hiPSCs after transition of their pluripotency from the primed state using various methods and that hPGCLCs resemble the early-stage PGCs randomly migrating in the midline region of human embryos before initiation of the CXCL12/SDF1-guided chemotaxis.
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Krejcova L, Richtera L, Hynek D, Labuda J, Adam V. Current trends in electrochemical sensing and biosensing of DNA methylation. Biosens Bioelectron 2017. [PMID: 28641203 DOI: 10.1016/j.bios.2017.06.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA methylation plays an important role in physiological and pathological processes. Several genetic diseases and most malignancies tend to be associated with aberrant DNA methylation. Among other analytical methods, electrochemical approaches have been successfully employed for characterisation of DNA methylation patterns that are essential for the diagnosis and treatment of particular diseases. This article discusses current trends in the electrochemical sensing and biosensing of DNA methylation. Particularly, it provides an overview of applied electrode materials, electrode modifications and biorecognition elements applications with an emphasis on strategies that form the core DNA methylation detection approaches. The three main strategies as (i) bisulfite treatment, (ii) cleavage by restriction endonucleases, and (iii) immuno/affinity reaction were described in greater detail. Additionally, the availability of the reviewed platforms for early cancer diagnosis and the approval of methylation inhibitors for anticancer therapy were discussed.
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Affiliation(s)
- Ludmila Krejcova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic; Department of Inorganic Chemistry, University of Chemistry and Technology Prague, Technicka 5, CZ-166 28 Prague, Czech Republic
| | - Lukas Richtera
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - David Hynek
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Jan Labuda
- Institute of Analytical Chemistry, Slovak University of Technology in Bratislava, Radlinskeho 9, SK-812 37 Bratislava, Slovakia
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic.
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Vogt G. Facilitation of environmental adaptation and evolution by epigenetic phenotype variation: insights from clonal, invasive, polyploid, and domesticated animals. ENVIRONMENTAL EPIGENETICS 2017; 3:dvx002. [PMID: 29492304 PMCID: PMC5804542 DOI: 10.1093/eep/dvx002] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 01/28/2017] [Accepted: 02/02/2017] [Indexed: 05/13/2023]
Abstract
There is increasing evidence, particularly from plants, that epigenetic mechanisms can contribute to environmental adaptation and evolution. The present article provides an overview on this topic for animals and highlights the special suitability of clonal, invasive, hybrid, polyploid, and domesticated species for environmental and evolutionary epigenetics. Laboratory and field studies with asexually reproducing animals have shown that epigenetically diverse phenotypes can be produced from the same genome either by developmental stochasticity or environmental induction. The analysis of invasions revealed that epigenetic phenotype variation may help to overcome genetic barriers typically associated with invasions such as bottlenecks and inbreeding. Research with hybrids and polyploids established that epigenetic mechanisms are involved in consolidation of speciation by contributing to reproductive isolation and restructuring of the genome in the neo-species. Epigenetic mechanisms may even have the potential to trigger speciation but evidence is still meager. The comparison of domesticated animals and their wild ancestors demonstrated heritability and selectability of phenotype modulating DNA methylation patterns. Hypotheses, model predictions, and empirical results are presented to explain how epigenetic phenotype variation could facilitate adaptation and speciation. Clonal laboratory lineages, monoclonal invaders, and adaptive radiations of different evolutionary age seem particularly suitable to empirically test the proposed ideas. A respective research agenda is presented.
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Affiliation(s)
- Günter Vogt
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
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