1
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Zhu S, Li J, Wang X, Jin Y, Wang H, An H, Sun H, Han L, Shen B, Wang Q. The chromatin accessibility landscape of mouse oocytes during configuration transition. Cell Prolif 2024:e13733. [PMID: 39245646 DOI: 10.1111/cpr.13733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/15/2024] [Accepted: 07/30/2024] [Indexed: 09/10/2024] Open
Abstract
The transition of chromatin configuration in mammalian oocytes from a non-surrounded nucleolus (NSN) to a surrounded nucleolus (SN) is critical for acquiring the developmental competence. However, the genomic and epigenomic features underlying this process remain poorly understood. In the present study, we first establish the chromatin accessibility landscape of mouse oocytes from NSN to SN stage. Through the integrative analysis of multi-omics, we find that the establishment of DNA methylation in oocytes is independent of the dynamics of chromatin accessibility. In contrast, histone H3K4me3 status is closely associated with the dynamics of accessible regions during configuration transition. Furthermore, by focusing on the actively transcribed genes in NSN and SN oocytes, we discover that chromatin accessibility coupled with histone methylation (H3K4me3 and H3K27me3) participates in the transcriptional control during phase transition. In sum, our data provide a comprehensive resource for probing configuration transition in oocytes, and offer insights into the mechanisms determining chromatin dynamics and oocyte quality.
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Affiliation(s)
- Shuai Zhu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Nanjing, China
| | - Jiashuo Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Nanjing, China
| | - Xiuwan Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Nanjing, China
| | - Yifei Jin
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Nanjing, China
| | - Hengjie Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Nanjing, China
| | - Huiqing An
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Nanjing, China
| | - Hongzheng Sun
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Nanjing, China
| | - Longsen Han
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Nanjing, China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Nanjing, China
| | - Qiang Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Nanjing, China
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
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2
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Kalinderi K, Kalinderis M, Papaliagkas V, Fidani L. The Reproductive Lifespan of Ovarian Follicle. Reprod Sci 2024; 31:2604-2614. [PMID: 38816594 DOI: 10.1007/s43032-024-01606-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 05/27/2024] [Indexed: 06/01/2024]
Abstract
The functional unit within mammalian ovaries is the ovarian follicle. The development of the ovarian follicle is a lengthy process beginning from the time of embryogenesis, passing through multiple different stages of maturation. The purpose of this review is to describe the most basic events in the journey of ovarian follicle development, discussing the importance of ovarian reserve and highlighting the role of several factors that affect oocyte quality and quantity during aging including hormonal, genetic and epigenetic factors. Novel, promising anti-aging strategies are also discussed.
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Affiliation(s)
- Kallirhoe Kalinderi
- Laboratory of Medical Biology-Genetics, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, GR-54124, Greece.
| | - Michail Kalinderis
- Department of Obstetrics and Gynaecology, St George's University Hospital NHS Trust, Blackshaw Road, Tooting, London, SW17 0QT, UK
| | - Vasileios Papaliagkas
- Department of Biomedical Sciences, School of Health Sciences, International Hellenic University, Thessaloniki, 57400, Greece
| | - Liana Fidani
- Laboratory of Medical Biology-Genetics, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, GR-54124, Greece
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3
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Matlosz S, Franzdóttir SR, Pálsson A, Jónsson ZO. DNA methylation reprogramming in teleosts. Evol Dev 2024; 26:e12486. [PMID: 38783650 DOI: 10.1111/ede.12486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 04/29/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
Early embryonic development is crucially important but also remarkably diverse among animal taxa. Axis formation and cell lineage specification occur due to both spatial and temporal control of gene expression. This complex system involves various signaling pathways and developmental genes such as transcription factors as well as other molecular interactants that maintain cellular states, including several types of epigenetic marks. 5mC DNA methylation, the chemical modification of cytosines in eukaryotes, represents one such mark. By influencing the compaction of chromatin (a high-order DNA structure), DNA methylation can either repress or induce transcriptional activity. Mammals exhibit a reprogramming of DNA methylation from the parental genomes in the zygote following fertilization, and later in primordial germ cells (PGCs). Whether these periods of methylation reprogramming are evolutionarily conserved, or an innovation in mammals, is an emerging question. Looking into these processes in other vertebrate lineages is thus important, and teleost fish, with their extensive species richness, phenotypic diversity, and multiple rounds of whole genome duplication, provide the perfect research playground for answering such a question. This review aims to present a concise state of the art of DNA methylation reprogramming in early development in fish by summarizing findings from different research groups investigating methylation reprogramming patterns in teleosts, while keeping in mind the ramifications of the methodology used, then comparing those patterns to reprogramming patterns in mammals.
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Affiliation(s)
- Sébastien Matlosz
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | | | - Arnar Pálsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Zophonías O Jónsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
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4
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Velastegui E, Falconí IB, Garcia VI, Munizaga G, Matias de la Cruz C, Segura Y, Alcivar K, Valencia L, Vera E, Muñoz MS, Vanden Berghe W, Lebeer S, Orellana-Manzano A. Exploring HLA-C methylation patterns and nutritional status in Kichwa mothers and infants from Tena, Ecuador. Front Med (Lausanne) 2024; 11:1356646. [PMID: 39257885 PMCID: PMC11385616 DOI: 10.3389/fmed.2024.1356646] [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: 12/15/2023] [Accepted: 07/26/2024] [Indexed: 09/12/2024] Open
Abstract
Environment and lifestyle can affect the epigenome passed down from generation to generation. A mother's nutrition can impact the methylation levels of her offspring's epigenome, but it's unclear which genes may be affected by malnutrition during gestation or early development. In this study, we examined the levels of methylated GC in the promoter region of HLA-C in mothers and infants from the Kichwa community in Ecuador. To do this, we analyzed saliva samples using bisulfite DNA sequencing. While we did not observe any significant differences in the mean methylation percentages in exon 1 of HLA-C between mothers and their infants after the first two years of lactation and life, respectively, we did find that infants tended to increase their methylation level during the first two years of life, while mothers tended to decrease it after the first two years of breastfeeding. When we compared methylation levels between mothers and infants using an ANOVA/posthoc Tukey test, we found that the average methylation for the entire population was less than 3% at T1 and T2. Although there was a tendency for infants to have higher methylation levels during their first two years of life and for mothers to have lower methylation levels after the first two years of breastfeeding, the mean values were not significantly different. However, we found a significant difference when we contrasted the data using a Kruskal-Wallis test at 0.05 for T1 AND T2 (p-value: 0.0148). Specifically, mothers had an average of X̅ = 2.06% and sons had X̅ = 1.57% at T2 (p-value: 0.7227), while the average for mothers was X̅ = 1.83% and for sons X̅ =1.77%. Finally, we identified three CpG motif nucleotide positions (32-33, 43-44, and 96-97) along the 122 bp analysis of HLA-C exon one, which was found to retain methylation patterns over time and is inherited from mother to offspring. Finally, our small pilot study did not reveal significant correlations between maternal and offspring nutritional status and DNA methylation levels of HLA-C exon one.
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Affiliation(s)
- Erick Velastegui
- Escuela Politécnica Nacional, Departamento de Ciencias de los Alimentos y Biotecnología, Facultad de Ingeniería Química y Agroindustria, Quito, Ecuador
- Escuela Superior Politécnica del Litoral, ESPOL, Laboratorio para investigaciones biomédicas, Facultad de Ciencias de la vida (FCV), ESPOL Polytechnic University, Guayaquil, Ecuador
| | - Isaac B Falconí
- Escuela Superior Politécnica del Litoral, ESPOL, Laboratorio para investigaciones biomédicas, Facultad de Ciencias de la vida (FCV), ESPOL Polytechnic University, Guayaquil, Ecuador
- Epigenetic Signaling Lab (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Valeria I Garcia
- Escuela Superior Politécnica del Litoral, ESPOL, Laboratorio para investigaciones biomédicas, Facultad de Ciencias de la vida (FCV), ESPOL Polytechnic University, Guayaquil, Ecuador
- Epigenetic Signaling Lab (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Gabriela Munizaga
- Escuela Superior Politécnica del Litoral, ESPOL, Laboratorio para investigaciones biomédicas, Facultad de Ciencias de la vida (FCV), ESPOL Polytechnic University, Guayaquil, Ecuador
| | - Carmen Matias de la Cruz
- Escuela Superior Politécnica del Litoral, ESPOL, Laboratorio para investigaciones biomédicas, Facultad de Ciencias de la vida (FCV), ESPOL Polytechnic University, Guayaquil, Ecuador
| | - Yaritza Segura
- Escuela Superior Politécnica del Litoral, ESPOL, Laboratorio para investigaciones biomédicas, Facultad de Ciencias de la vida (FCV), ESPOL Polytechnic University, Guayaquil, Ecuador
| | - Kerly Alcivar
- Escuela Superior Politécnica del Litoral, ESPOL, Laboratorio para investigaciones biomédicas, Facultad de Ciencias de la vida (FCV), ESPOL Polytechnic University, Guayaquil, Ecuador
| | - Luz Valencia
- Escuela Superior Politécnica del Litoral, ESPOL, Laboratorio para investigaciones biomédicas, Facultad de Ciencias de la vida (FCV), ESPOL Polytechnic University, Guayaquil, Ecuador
| | - Edwin Vera
- Escuela Politécnica Nacional, Departamento de Ciencias de los Alimentos y Biotecnología, Facultad de Ingeniería Química y Agroindustria, Quito, Ecuador
| | - Mindy S Muñoz
- Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Wim Vanden Berghe
- Epigenetic Signaling Lab (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Sarah Lebeer
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Andrea Orellana-Manzano
- Escuela Superior Politécnica del Litoral, ESPOL, Laboratorio para investigaciones biomédicas, Facultad de Ciencias de la vida (FCV), ESPOL Polytechnic University, Guayaquil, Ecuador
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5
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Gu LJ, Li L, Li QN, Xu K, Yue W, Qiao JY, Meng TG, Dong MZ, Lei WL, Guo JN, Wang ZB, Sun QY. The transgenerational effects of maternal low-protein diet during lactation on offspring. J Genet Genomics 2024; 51:824-835. [PMID: 38657948 DOI: 10.1016/j.jgg.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 04/26/2024]
Abstract
Environmental factors such as diet and lifestyle can influence the health of both mothers and offspring. However, its transgenerational transmission and underlying mechanisms remain largely unknown. Here, using a maternal lactation-period low-protein diet (LPD) mouse model, we show that maternal LPD during lactation causes decreased survival and stunted growth, significantly reduces ovulation and litter size, and alters the gut microbiome in the female LPD-F1 offspring. The transcriptome of LPD-F1 metaphase II (MII) oocytes shows that differentially expressed genes are enriched in female pregnancy and multiple metabolic processes. Moreover, maternal LPD causes early stunted growth and impairs metabolic health, which is transmitted over two generations. The methylome alteration of LPD-F1 oocytes can be partly transmitted to the F2 oocytes. Together, our results reveal that LPD during lactation transgenerationally affects offspring health, probably via oocyte epigenetic changes.
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Affiliation(s)
- Lin-Jian Gu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Li
- Institute of Laboratory Animal Sciences, CAMS & PUMC, Beijing 100021, China
| | - Qian-Nan Li
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317, China
| | - Ke Xu
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317, China
| | - Wei Yue
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing-Yi Qiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tie-Gang Meng
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317, China
| | - Ming-Zhe Dong
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen-Long Lei
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jia-Ni Guo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen-Bo Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing-Yuan Sun
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317, China.
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6
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Maitin-Shepard M, O'Tierney-Ginn P, Kraneveld AD, Lyall K, Fallin D, Arora M, Fasano A, Mueller NT, Wang X, Caulfield LE, Dickerson AS, Diaz Heijtz R, Tarui T, Blumberg JB, Holingue C, Schmidt RJ, Garssen J, Almendinger K, Lin PID, Mozaffarian D. Food, nutrition, and autism: from soil to fork. Am J Clin Nutr 2024; 120:240-256. [PMID: 38677518 DOI: 10.1016/j.ajcnut.2024.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 04/29/2024] Open
Abstract
Food and nutrition-related factors have the potential to impact development of autism spectrum disorder (ASD) and quality of life for people with ASD, but gaps in evidence exist. On 10 November 2022, Tufts University's Friedman School of Nutrition Science and Policy and Food and Nutrition Innovation Institute hosted a 1-d meeting to explore the evidence and evidence gaps regarding the relationships of food and nutrition with ASD. This meeting report summarizes the presentations and deliberations from the meeting. Topics addressed included prenatal and child dietary intake, the microbiome, obesity, food-related environmental exposures, mechanisms and biological processes linking these factors and ASD, food-related social factors, and data sources for future research. Presentations highlighted evidence for protective associations with prenatal folic acid supplementation and ASD development, increases in risk of ASD with maternal gestational obesity, and the potential for exposure to environmental contaminants in foods and food packaging to influence ASD development. The importance of the maternal and child microbiome in ASD development or ASD-related behaviors in the child was reviewed, as was the role of discrimination in leading to disparities in environmental exposures and psychosocial factors that may influence ASD. The role of child diet and high prevalence of food selectivity in children with ASD and its association with adverse outcomes were also discussed. Priority evidence gaps identified by participants include further clarifying ASD development, including biomarkers and key mechanisms; interactions among psychosocial, social, and biological determinants; interventions addressing diet, supplementation, and the microbiome to prevent and improve quality of life for people with ASD; and mechanisms of action of diet-related factors associated with ASD. Participants developed research proposals to address the priority evidence gaps. The workshop findings serve as a foundation for future prioritization of scientific research to address evidence gaps related to food, nutrition, and ASD.
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Affiliation(s)
| | | | - Aletta D Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, the Netherlands; Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, the Netherlands
| | - Kristen Lyall
- AJ Drexel Autism Institute, Drexel University, Philadelphia, PA, United States
| | - Daniele Fallin
- Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Manish Arora
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Alessio Fasano
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA, United States; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Noel T Mueller
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Xiaobin Wang
- Department of Population, Family and Reproductive Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Laura E Caulfield
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Aisha S Dickerson
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | | | - Tomo Tarui
- Department of Pediatrics, Hasbro Children's Hospital, Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Jeffrey B Blumberg
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, United States
| | - Calliope Holingue
- Center for Autism Services, Science and Innovation, Kennedy Krieger Institute and Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Rebecca J Schmidt
- Department of Public Health Sciences, the MIND Institute, University of California Davis, Davis, CA, United States
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Katherine Almendinger
- Department of Health Policy and Management, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Pi-I Debby Lin
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, United States
| | - Dariush Mozaffarian
- Food is Medicine Institute, Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, United States.
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7
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Fain JS, Wangermez C, Loriot A, Denoue C, De Smet C. DNA Hypomethylation Underlies Epigenetic Swapping between AGO1 and AGO1-V2 Isoforms in Tumors. EPIGENOMES 2024; 8:24. [PMID: 39051182 PMCID: PMC11270204 DOI: 10.3390/epigenomes8030024] [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: 05/08/2024] [Revised: 06/10/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024] Open
Abstract
Human tumors progress in part by accumulating epigenetic alterations, which include gains and losses of DNA methylation in different parts of the cancer cell genome. Recent work has revealed a link between these two opposite alterations by showing that DNA hypomethylation in tumors can induce the expression of transcripts that overlap downstream gene promoters and thereby induce their hypermethylation. Preliminary in silico evidence prompted us to investigate if this mechanism applies to the locus harboring AGO1, a gene that plays a central role in miRNA biogenesis and RNA interference. Inspection of public RNA-Seq datasets and RT-qPCR experiments show that an alternative transcript starting 13.4 kb upstream of AGO1 (AGO1-V2) is expressed specifically in testicular germ cells, and becomes aberrantly activated in different types of tumors, particularly in tumors of the esophagus, stomach, and lung. This expression pattern classifies AGO1-V2 into the group of "Cancer-Germline" (CG) genes. Analysis of transcriptomic and methylomic datasets provided evidence that transcriptional activation of AGO1-V2 depends on DNA demethylation of its promoter region. Western blot experiments revealed that AGO1-V2 encodes a shortened isoform of AGO1, corresponding to a truncation of 75 aa in the N-terminal domain, and which we therefore referred to as "∆NAGO1". Interestingly, significant correlations between hypomethylation/activation of AGO1-V2 and hypermethylation/repression of AGO1 were observed upon examination of tumor cell lines and tissue datasets. Overall, our study reveals the existence of a process of interdependent epigenetic alterations in the AGO1 locus, which promotes swapping between two AGO1 protein-coding mRNA isoforms in tumors.
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Affiliation(s)
- Jean S. Fain
- Group of Genetics and Epigenetics, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.S.F.); (C.W.)
| | - Camille Wangermez
- Group of Genetics and Epigenetics, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.S.F.); (C.W.)
| | - Axelle Loriot
- Group of Computational Biology and Bioinformatics, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Claudia Denoue
- Group of Genetics and Epigenetics, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.S.F.); (C.W.)
| | - Charles De Smet
- Group of Genetics and Epigenetics, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.S.F.); (C.W.)
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8
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Kuhl H, Tan WH, Klopp C, Kleiner W, Koyun B, Ciorpac M, Feron R, Knytl M, Kloas W, Schartl M, Winkler C, Stöck M. A candidate sex determination locus in amphibians which evolved by structural variation between X- and Y-chromosomes. Nat Commun 2024; 15:4781. [PMID: 38839766 PMCID: PMC11153619 DOI: 10.1038/s41467-024-49025-2] [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: 10/20/2023] [Accepted: 05/17/2024] [Indexed: 06/07/2024] Open
Abstract
Most vertebrates develop distinct females and males, where sex is determined by repeatedly evolved environmental or genetic triggers. Undifferentiated sex chromosomes and large genomes have caused major knowledge gaps in amphibians. Only a single master sex-determining gene, the dmrt1-paralogue (dm-w) of female-heterogametic clawed frogs (Xenopus; ZW♀/ZZ♂), is known across >8740 species of amphibians. In this study, by combining chromosome-scale female and male genomes of a non-model amphibian, the European green toad, Bufo(tes) viridis, with ddRAD- and whole genome pool-sequencing, we reveal a candidate master locus, governing a male-heterogametic system (XX♀/XY♂). Targeted sequencing across multiple taxa uncovered structural X/Y-variation in the 5'-regulatory region of the gene bod1l, where a Y-specific non-coding RNA (ncRNA-Y), only expressed in males, suggests that this locus initiates sex-specific differentiation. Developmental transcriptomes and RNA in-situ hybridization show timely and spatially relevant sex-specific ncRNA-Y and bod1l-gene expression in primordial gonads. This coincided with differential H3K4me-methylation in pre-granulosa/pre-Sertoli cells, pointing to a specific mechanism of amphibian sex determination.
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Affiliation(s)
- Heiner Kuhl
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Müggelseedamm 301 & 310, 12587, Berlin, Germany
| | - Wen Hui Tan
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Block S1A, Level 6, Singapore, 117543, Singapore
| | - Christophe Klopp
- SIGENAE, Plate-forme Bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRAe, 31326, Castanet-Tolosan, France
| | - Wibke Kleiner
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Müggelseedamm 301 & 310, 12587, Berlin, Germany
| | - Baturalp Koyun
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Müggelseedamm 301 & 310, 12587, Berlin, Germany
- Department of Molecular Biology and Genetics, Genetics, Faculty of Science, Bilkent University, SB Building, Ankara, 06800, Turkey
| | - Mitica Ciorpac
- Danube Delta National Institute for Research and Development, Tulcea, 820112, Romania
- Advanced Research and Development Center for Experimental Medicine-CEMEX, "Grigore T. Popa", University of Medicine and Pharmacy, Mihail Kogălniceanu Street 9-13, Iasi, 700259, Romania
| | - Romain Feron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Martin Knytl
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 12843, Czech Republic
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Ontario, ON, Canada
| | - Werner Kloas
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Müggelseedamm 301 & 310, 12587, Berlin, Germany
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Wuerzburg, Am Hubland, 97074, Wuerzburg, Germany
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, 78666, USA
| | - Christoph Winkler
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Block S1A, Level 6, Singapore, 117543, Singapore.
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Müggelseedamm 301 & 310, 12587, Berlin, Germany.
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9
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Shen S, Wang M, Li X, Wang B, Hong W, Li W, Xu B, Guo Z, Han R, Yi S, Wu Z, He X, Wang L, Zhu Q, Yang G, Wang H, Deng Q, Chen J, Gao S, Jiang C, Gao R. The gonadal niche safeguards human fetal germline cell development following maternal SARS-CoV-2 infection. Cell Rep Med 2024; 5:101515. [PMID: 38631348 PMCID: PMC11148563 DOI: 10.1016/j.xcrm.2024.101515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/08/2024] [Accepted: 03/21/2024] [Indexed: 04/19/2024]
Abstract
During pregnancy, germline development is vital for maintaining the continuation of species. Recent studies have shown increased pregnancy risks in COVID-19 patients at the perinatal stage. However, the potential consequence of infection for reproductive quality in developing fetuses remains unclear. Here, we analyze the transcriptome and DNA methylome of the fetal germline following maternal severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We find that infection at early gestational age, a critical period of human primordial germ cell specification and epigenetic reprogramming, trivially affects fetal germ cell (FGC) development. Additionally, FGC-niche communications are not compromised by maternal infection. Strikingly, both general and SARS-CoV-2-specific immune pathways are greatly activated in gonadal niche cells to protect FGCs from maternal infection. Notably, there occurs an "in advance" development tendency in FGCs after maternal infection. Our study provides insights into the impacts of maternal SARS-CoV-2 infection on fetal germline development and serves as potential clinical guidance for future pandemics.
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Affiliation(s)
- Shijun Shen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Mengting Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Xiaocui Li
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China.
| | - Beiying Wang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China
| | - Wei Hong
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China
| | - Wei Li
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Ben Xu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Zhenxiang Guo
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Ruichen Han
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shanru Yi
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Zhiping Wu
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China
| | - Xiaoying He
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China
| | - Liping Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Qianshu Zhu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Guang Yang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Hong Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Qiaolin Deng
- Department of Physiology and Pharmacology, Biomedicum B5, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, 17177 Stockholm, Sweden
| | - Jiayu Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Cizhong Jiang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Rui Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
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10
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Cevik SE, Skaar DA, Jima DD, Liu AJ, Østbye T, Whitson HE, Jirtle RL, Hoyo C, Planchart A. DNA methylation of imprint control regions associated with Alzheimer's disease in non-Hispanic Blacks and non-Hispanic Whites. Clin Epigenetics 2024; 16:58. [PMID: 38658973 PMCID: PMC11043040 DOI: 10.1186/s13148-024-01672-4] [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: 11/09/2023] [Accepted: 04/13/2024] [Indexed: 04/26/2024] Open
Abstract
Alzheimer's disease (AD) prevalence is twice as high in non-Hispanic Blacks (NHBs) as in non-Hispanic Whites (NHWs). The objective of this study was to determine whether aberrant methylation at imprint control regions (ICRs) is associated with AD. Differentially methylated regions (DMRs) were bioinformatically identified from whole-genome bisulfite sequenced DNA derived from brain tissue of 9 AD (5 NHBs and 4 NHWs) and 8 controls (4 NHBs and 4 NHWs). We identified DMRs located within 120 regions defined as candidate ICRs in the human imprintome ( https://genome.ucsc.edu/s/imprintome/hg38.AD.Brain_track ). Eighty-one ICRs were differentially methylated in NHB-AD, and 27 ICRs were differentially methylated in NHW-AD, with two regions common to both populations that are proximal to the inflammasome gene, NLRP1, and a known imprinted gene, MEST/MESTIT1. These findings indicate that early developmental alterations in DNA methylation of regions regulating genomic imprinting may contribute to AD risk and that this epigenetic risk differs between NHBs and NHWs.
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Affiliation(s)
- Sebnem E Cevik
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - David A Skaar
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Andy J Liu
- Department of Neurology, School of Medicine, Duke University, Durham, NC, USA
| | - Truls Østbye
- Department of Family Medicine and Community Health, Duke University, Durham, NC, USA
| | - Heather E Whitson
- Department of Medicine, School of Medicine, Duke University, Durham, NC, USA
- Duke Center for the Study of Aging and Human Development, Durham, NC, USA
- Duke/UNC Alzheimer's Disease Research Center (ADRC), Durham, NC, USA
| | - Randy L Jirtle
- Toxicology Program, North Carolina State University, Raleigh, NC, USA.
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.
| | - Cathrine Hoyo
- Toxicology Program, North Carolina State University, Raleigh, NC, USA.
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.
| | - Antonio Planchart
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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11
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Ren P, Tong X, Li J, Jiang H, Liu S, Li X, Lai M, Yang W, Rong Y, Zhang Y, Jin J, Ma Y, Pan W, Fan HY, Zhang S, Zhang YL. CRL4 DCAF13 E3 ubiquitin ligase targets MeCP2 for degradation to prevent DNA hypermethylation and ensure normal transcription in growing oocytes. Cell Mol Life Sci 2024; 81:165. [PMID: 38578457 PMCID: PMC10997554 DOI: 10.1007/s00018-024-05185-4] [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: 01/29/2023] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 04/06/2024]
Abstract
The DNA methylation is gradually acquired during oogenesis, a process sustained by successful follicle development. However, the functional roles of methyl-CpG-binding protein 2 (MeCP2), an epigenetic regulator displaying specifical binding with methylated DNA, remains unknown in oogenesis. In this study, we found MeCP2 protein was highly expressed in primordial and primary follicle, but was almost undetectable in secondary follicles. However, in aged ovary, MeCP2 protein is significantly increased in both oocyte and granulosa cells. Overexpression of MeCP2 in growing oocyte caused transcription dysregulation, DNA hypermethylation, and genome instability, ultimately leading to follicle growth arrest and apoptosis. MeCP2 is targeted by DCAF13, a substrate recognition adaptor of the Cullin 4-RING (CRL4) E3 ligase, and polyubiquitinated for degradation in both cells and oocytes. Dcaf13-null oocyte exhibited an accumulation of MeCP2 protein, and the partial rescue of follicle growth arrest induced by Dcaf13 deletion was observed following MeCP2 knockdown. The RNA-seq results revealed that large amounts of genes were regulated by the DCAF13-MeCP2 axis in growing oocytes. Our study demonstrated that CRL4DCAF13 E3 ubiquitin ligase targets MeCP2 for degradation to ensure normal DNA methylome and transcription in growing oocytes. Moreover, in aged ovarian follicles, deceased DCAF13 and DDB1 protein were observed, indicating a potential novel mechanism that regulates ovary aging.
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Affiliation(s)
- Peipei Ren
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China
| | - Xiaomei Tong
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China
| | - Junjian Li
- College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Huifang Jiang
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China
| | - Siya Liu
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China
| | - Xiang Li
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China
| | - Mengru Lai
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China
| | - Weijie Yang
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China
| | - Yan Rong
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China
| | - Yingyi Zhang
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China
| | - Jiamin Jin
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China
| | - Yerong Ma
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China
| | - Weiwei Pan
- Department of Cell Biology, College of Medicine, Jiaxing University, Jiaxing, 314001, China
| | - Heng-Yu Fan
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Songying Zhang
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China.
| | - Yin-Li Zhang
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Hangzhou, China.
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12
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Aanniz T, Bouyahya A, Balahbib A, El Kadri K, Khalid A, Makeen HA, Alhazmi HA, El Omari N, Zaid Y, Wong RSY, Yeo CI, Goh BH, Bakrim S. Natural bioactive compounds targeting DNA methyltransferase enzymes in cancer: Mechanisms insights and efficiencies. Chem Biol Interact 2024; 392:110907. [PMID: 38395253 DOI: 10.1016/j.cbi.2024.110907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/06/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024]
Abstract
The regulation of gene expression is fundamental to health and life and is essentially carried out at the promoter region of the DNA of each gene. Depending on the molecular context, this region may be accessible or non-accessible (possibility of integration of RNA polymerase or not at this region). Among enzymes that control this process, DNA methyltransferase enzymes (DNMTs), are responsible for DNA demethylation at the CpG islands, particularly at the promoter regions, to regulate transcription. The aberrant activity of these enzymes, i.e. their abnormal expression or activity, can result in the repression or overactivation of gene expression. Consequently, this can generate cellular dysregulation leading to instability and tumor development. Several reports highlighted the involvement of DNMTs in human cancers. The inhibition or activation of DNMTs is a promising therapeutic approach in many human cancers. In the present work, we provide a comprehensive and critical summary of natural bioactive molecules as primary inhibitors of DNMTs in human cancers. The active compounds hold the potential to be developed as anti-cancer epidrugs targeting DNMTs.
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Affiliation(s)
- Tarik Aanniz
- Medical Biotechnology Laboratory, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat, B.P, 6203, Morocco.
| | - Abdelhakim Bouyahya
- Laboratory of Human Pathologies Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, 10106, Morocco.
| | - Abdelaali Balahbib
- High Institute of Nursing Professions and Health Techniques of Errachidia, Errachidia, Morocco.
| | - Kawtar El Kadri
- High Institute of Nursing Professions and Health Techniques of Errachidia, Errachidia, Morocco
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box: 114, Jazan, Saudi Arabia; Medicinal and Aromatic Plants Research Institute, National Center for Research, P.O. Box: 2424, Khartoum, 11111, Sudan.
| | - Hafiz A Makeen
- Pharmacy Practice Research Unit, Clinical Pharmacy Department, Faculty of Pharmacy, Jazan University, Jazan, Saudi Arabia.
| | - Hassan A Alhazmi
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box: 114, Jazan, Saudi Arabia; Pharmacy Practice Research Unit, Clinical Pharmacy Department, Faculty of Pharmacy, Jazan University, Jazan, Saudi Arabia.
| | - Nasreddine El Omari
- High Institute of Nursing Professions and Health Techniques of Tetouan, Tetouan, Morocco.
| | - Younes Zaid
- Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Morocco.
| | - Rebecca Shin-Yee Wong
- Sunway Biofunctional Molecules Discovery Centre, School of Medical and Life Sciences, Sunway University Malaysia, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia; Department of Medical Education, School of Medical and Life Sciences, Sunway University Malaysia, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia.
| | - Chien Ing Yeo
- Sunway Biofunctional Molecules Discovery Centre, School of Medical and Life Sciences, Sunway University Malaysia, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia.
| | - Bey Hing Goh
- Sunway Biofunctional Molecules Discovery Centre, School of Medical and Life Sciences, Sunway University Malaysia, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia; Biofunctional Molecule Exploratory Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway, 47500, Malaysia; College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
| | - Saad Bakrim
- Geo-Bio-Environment Engineering and Innovation Laboratory, Molecular Engineering, Biotechnology and Innovation Team, Polydisciplinary Faculty of Taroudant, Ibn Zohr University, Agadir, 80000, Morocco.
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13
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Hutton SJ, Siddiqui S, Pedersen EI, Markgraf CY, Segarra A, Hladik ML, Connon RE, Brander SM. Multigenerational, Indirect Exposure to Pyrethroids Demonstrates Potential Compensatory Response and Reduced Toxicity at Higher Salinity in Estuarine Fish. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:2224-2235. [PMID: 38267018 PMCID: PMC10851936 DOI: 10.1021/acs.est.3c06234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/26/2024]
Abstract
Estuarine environments are critical to fish species and serve as nurseries for developing embryos and larvae. They also undergo daily fluctuations in salinity and act as filters for pollutants. Additionally, global climate change (GCC) is altering salinity regimes within estuarine systems through changes in precipitation and sea level rise. GCC is also likely to lead to an increased use of insecticides to prevent pests from damaging agricultural crops as their habitats and mating seasons change from increased temperatures. This underscores the importance of understanding how insecticide toxicity to fish changes under different salinity conditions. In this study, larval Inland Silversides (Menidia beryllina) were exposed to bifenthrin (1.1 ng/L), cyfluthrin (0.9 ng/L), or cyhalothrin (0.7 ng/L) at either 6 or 10 practical salinity units (PSU) for 96 h during hatching, with a subset assessed for end points relevant to neurotoxicity and endocrine disruption by testing behavior, gene expression of a select suite of genes, reproduction, and growth. At both salinities, directly exposed F0 larvae were hypoactive relative to the F0 controls; however, the indirectly exposed F1 larvae were hyperactive relative to the F1 control. This could be evidence of a compensatory response to environmentally relevant concentrations of pyrethroids in fish. Effects on development, gene expression, and growth were also observed. Overall, exposure to pyrethroids at 10 PSU resulted in fewer behavioral and endocrine disruptive effects relative to those observed in organisms at 6 PSU.
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Affiliation(s)
- Sara J. Hutton
- Department
of Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon 97331, United States
| | - Samreen Siddiqui
- Department
of Fisheries, Wildlife, and Conservation Sciences, Coastal Oregon
Marine Experiment Station, Oregon State
University, Newport, Oregon 97365, United States
| | - Emily I. Pedersen
- Department
of Fisheries, Wildlife, and Conservation Sciences, Coastal Oregon
Marine Experiment Station, Oregon State
University, Newport, Oregon 97365, United States
| | - Christopher Y. Markgraf
- Department
of Biochemistry and Biophysics, Oregon State
University, Corvallis, Oregon 97331, United States
| | - Amelie Segarra
- Department
of Anatomy, Physiology, and Cell Biology, University of California, Davis, California 95616, United States
| | - Michelle L. Hladik
- U.S.
Geological Survey, California Water Science
Center, Sacramento, California 95819, United States
| | - Richard E. Connon
- Department
of Anatomy, Physiology, and Cell Biology, University of California, Davis, California 95616, United States
| | - Susanne M. Brander
- Department
of Fisheries, Wildlife, and Conservation Sciences, Coastal Oregon
Marine Experiment Station, Oregon State
University, Newport, Oregon 97365, United States
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14
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Meza-León A, Montoya-Estrada A, Reyes-Muñoz E, Romo-Yáñez J. Diabetes Mellitus and Pregnancy: An Insight into the Effects on the Epigenome. Biomedicines 2024; 12:351. [PMID: 38397953 PMCID: PMC10886464 DOI: 10.3390/biomedicines12020351] [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: 11/16/2023] [Revised: 12/17/2023] [Accepted: 01/08/2024] [Indexed: 02/25/2024] Open
Abstract
Worldwide, diabetes mellitus represents a growing health problem. If it occurs during pregnancy, it can increase the risk of various abnormalities in early and advanced life stages of exposed individuals due to fetal programming occurring in utero. Studies have determined that maternal conditions interfere with the genotypes and phenotypes of offspring. Researchers are now uncovering the mechanisms by which epigenetic alterations caused by diabetes affect the expression of genes and, therefore, the development of various diseases. Among the numerous possible epigenetic changes in this regard, the most studied to date are DNA methylation and hydroxymethylation, as well as histone acetylation and methylation. This review article addresses critical findings in epigenetic studies involving diabetes mellitus, including variations reported in the expression of specific genes and their transgenerational effects.
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Affiliation(s)
| | | | | | - José Romo-Yáñez
- Coordinación de Endocrinología Ginecológica y Perinatal, Instituto Nacional de Perinatología, Montes Urales 800, Lomas Virreyes, Mexico City 11000, Mexico
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15
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Krumpolec P, Kodada D, Hadžega D, Petrovič O, Babišová K, Dosedla E, Turcsányiová Z, Minárik G. Changes in DNA methylation associated with a specific mode of delivery: a pilot study. Front Med (Lausanne) 2024; 11:1291429. [PMID: 38314203 PMCID: PMC10835804 DOI: 10.3389/fmed.2024.1291429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 01/05/2024] [Indexed: 02/06/2024] Open
Abstract
Background The mode of delivery represents an epigenetic factor with potential to affect further development of the individual by multiple mechanisms. DNA methylation may be one of them, representing a major epigenetic mechanism involving direct chemical modification of the individual's DNA. This pilot study aims to examine whether a specific mode of delivery induces changes of DNA methylation by comparing the umbilical cord blood and peripheral blood of the newborns. Methods Blood samples from infants born by vaginal delivery and caesarean section were analysed to prepare the Methylseq library according to NEBNext enzymatic Methyl-seq Methylation Library Preparation Kit with further generation of target-enriched DNA libraries using the Twist Human Methylome Panel. DNA methylation status was determined using Illumina next-generation sequencing (NGS). Results We identified 168 differentially methylated regions in umbilical cord blood samples and 157 regions in peripheral blood samples. These were associated with 59 common biological, metabolic and signalling pathways for umbilical cord and peripheral blood samples. Conclusion Caesarean section is likely to represent an important epigenetic factor with the potential to induce changes in the genome that could play an important role in development of a broad spectrum of disorders. Our results could contribute to the elucidation of how epigenetic factors, such as a specific mode of delivery, could have adverse impact on health of an individual later in their life.
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Affiliation(s)
| | - Dominik Kodada
- Medirex Group Academy n.o., Nitra, Slovakia
- Department of Clinical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia
| | | | | | | | - Erik Dosedla
- Department of Gynaecology and Obstetrics, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
| | - Zuzana Turcsányiová
- Department of Gynaecology and Obstetrics, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
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16
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Shacfe G, Turko R, Syed HH, Masoud I, Tahmaz Y, Samhan LM, Alkattan K, Shafqat A, Yaqinuddin A. A DNA Methylation Perspective on Infertility. Genes (Basel) 2023; 14:2132. [PMID: 38136954 PMCID: PMC10743303 DOI: 10.3390/genes14122132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 11/24/2023] [Accepted: 11/25/2023] [Indexed: 12/24/2023] Open
Abstract
Infertility affects a significant number of couples worldwide and its incidence is increasing. While assisted reproductive technologies (ART) have revolutionized the treatment landscape of infertility, a significant number of couples present with an idiopathic cause for their infertility, hindering effective management. Profiling the genome and transcriptome of infertile men and women has revealed abnormal gene expression. Epigenetic modifications, which comprise dynamic processes that can transduce environmental signals into gene expression changes, may explain these findings. Indeed, aberrant DNA methylation has been widely characterized as a cause of abnormal sperm and oocyte gene expression with potentially deleterious consequences on fertilization and pregnancy outcomes. This review aims to provide a concise overview of male and female infertility through the lens of DNA methylation alterations.
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Affiliation(s)
| | | | | | | | | | | | | | - Areez Shafqat
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (G.S.); (R.T.); (H.H.S.); (I.M.); (Y.T.); (L.M.S.); (K.A.); (A.Y.)
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Ju X, Wang Z, Cai D, Bello SF, Nie Q. DNA methylation in poultry: a review. J Anim Sci Biotechnol 2023; 14:138. [PMID: 37925454 PMCID: PMC10625706 DOI: 10.1186/s40104-023-00939-9] [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: 04/27/2023] [Accepted: 09/10/2023] [Indexed: 11/06/2023] Open
Abstract
As an important epigenetic modification, DNA methylation is involved in many biological processes such as animal cell differentiation, embryonic development, genomic imprinting and sex chromosome inactivation. As DNA methylation sequencing becomes more sophisticated, it becomes possible to use it to solve more zoological problems. This paper reviews the characteristics of DNA methylation, with emphasis on the research and application of DNA methylation in poultry.
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Affiliation(s)
- Xing Ju
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, 510642, China
| | - Zhijun Wang
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, 666 Wusu Road, Lin'an, 311300, China
| | - Danfeng Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, 510642, China
| | - Semiu Folaniyi Bello
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, 510642, China
| | - Qinghua Nie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, 510642, China.
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Behluli L, Fontanilla AM, Andessner-Angleitner L, Tolar N, Molina JM, Gahurova L. Expression analysis suggests that DNMT3L is required for oocyte de novo DNA methylation only in Muridae and Cricetidae rodents. Epigenetics Chromatin 2023; 16:43. [PMID: 37924163 PMCID: PMC10625200 DOI: 10.1186/s13072-023-00518-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND During early mammalian development, DNA methylation undergoes two waves of reprogramming, enabling transitions between somatic cells, oocyte and embryo. The first wave of de novo DNA methylation establishment occurs in oocytes. Its molecular mechanisms have been studied in mouse, a classical mammalian model. Current model describes DNA methyltransferase 3A (DNMT3A) and its cofactor DNMT3L as two essential factors for oocyte DNA methylation-the ablation of either leads to nearly complete abrogation of DNA methylation. However, DNMT3L is not expressed in human oocytes, suggesting that the mechanism uncovered in mouse is not universal across mammals. RESULTS We analysed available RNA-seq data sets from oocytes of multiple mammals, including our novel data sets of several rodent species, and revealed that Dnmt3l is expressed only in the oocytes of mouse, rat and golden hamster, and at a low level in guinea pigs. We identified a specific promoter sequence recognised by an oocyte transcription factor complex associated with strong Dnmt3l activity and demonstrated that it emerged in the rodent clade Eumuroida, comprising the families Muridae (mice, rats, gerbils) and Cricetidae (hamsters). In addition, an evolutionarily novel promoter emerged in the guinea pig, driving weak Dnmt3l expression, likely without functional relevance. Therefore, Dnmt3l is expressed and consequently plays a role in oocyte de novo DNA methylation only in a small number of rodent species, instead of being an essential pan-mammalian factor. In contrast to somatic cells, where catalytically inactive DNMT3B interacts with DNMT3A, forming a heterotetramer, we did not find evidence for the expression of such inactive Dnmt3b isoforms in the oocytes of the tested species. CONCLUSIONS The analysis of RNA-seq data and genomic sequences revealed that DNMT3L is likely to play a role in oocytes de novo DNA methylation only in mice, rats, gerbils and hamsters. The mechanism governing de novo DNA methylation in the oocytes of most mammalian species, including humans, occurs through a yet unknown mechanism that differs from the current model discovered in mouse.
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Affiliation(s)
- Lirik Behluli
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
| | - Alyssa M Fontanilla
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
| | - Laura Andessner-Angleitner
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
| | - Nikolas Tolar
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
| | - Julia M Molina
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
- Department of Biological Sciences, Faculty of Sciences and Languages, São Paulo State University "Júlio de Mesquita Filho" - UNESP, Assis, São Paulo, Brazil
| | - Lenka Gahurova
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic.
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Momeni A, Haghpanah T, Nematollahi-Mahani SN, Ashourzadeh S, Eftekhar-Vaghefi SH. Comparing the effects of vitrification, before and after mouse oocyte in vitro maturation on developmental competence, changes in epigenetic regulators and stress oxidative response. Biochem Biophys Res Commun 2023; 679:179-190. [PMID: 37703761 DOI: 10.1016/j.bbrc.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/13/2023] [Accepted: 09/02/2023] [Indexed: 09/15/2023]
Abstract
Since the developmental stage of oocyte is a challenging issue in the success of vitrification, this study investigated the effects of vitrification, before and after in vitro maturation, on the survival and maturation rates, developmental competence and the expression levels of genes involved in apoptosis, oxidative stress and epigenetic modifications. Mouse germinal vesicle (GV) oocytes were divided into four groups: fresh in vitro matured oocytes without vitrification (fIVM), in vitro matured oocytes after vitrification (vIVM), in vitro matured oocytes before vitrification (IVMv). In addition, in vivo matured oocytes (MII) were used as control. After oocytes collection, maturation and survival rates as well as the intracellular reactive oxygen species (ROS) level were evaluated. Also, the expression level of various genes was analyzed by qRT-PCR. In addition, following artificial activation (parthenogenesis), the developmental competence of oocytes to the blastocyst stage was evaluated. A significant decrease in maturation rate and survival of vIVM oocytes was observed compared to fIVM and IVMv oocytes. Intracellular ROS levels were significantly increased in both vitrified groups compared to the fIVM group, and no significant difference between vitrified groups. Pro-apoptotic genes; BAX and Bcl2 as well as genes related to oxidative stress response Hsp1a, Hsp1b and SOD1were significantly increased in the vIVM group compared to the IVMv group. Interestingly, epigenetic regulators genes DNMT1, DNMT3a and DNMT3b were highly expressed in IVMv oocytes along with a decrease in the artificial activation rate compared to the vIVM oocytes. Our results indicated that despite observing more negative effects of vitrification before IVM on the survival rate and maturation as well as apoptosis status, less epigenetic changes in vIVM oocytes can make this process a better option in the treatment of infertility than IVM of oocytes followed by vitrification, a hypothesis that needs to be investigation in human oocytes.
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Affiliation(s)
- Asma Momeni
- Anatomical Sciences Department, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Tahereh Haghpanah
- Anatomical Sciences Department, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran.
| | | | - Sareh Ashourzadeh
- Afzalipour Clinical Center for Infertility, Kerman University of Medical Sciences, Afzalipour Hospital, Kerman, Iran
| | - Seyed Hassan Eftekhar-Vaghefi
- Anatomical Sciences Department, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran; Department of Anatomy, Kerman Branch, Islamic Azad University, Kerman, Iran.
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Zhao J, Wang W, Zhang L, Zhang J, Sturmey R, Zhang J. Dynamic metabolism during early mammalian embryogenesis. Development 2023; 150:dev202148. [PMID: 37877936 DOI: 10.1242/dev.202148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Dynamic metabolism is exhibited by early mammalian embryos to support changing cell fates during development. It is widely acknowledged that metabolic pathways not only satisfy cellular energetic demands, but also play pivotal roles in the process of cell signalling, gene regulation, cell proliferation and differentiation. Recently, various new technological advances have been made in metabolomics and computational analysis, deepening our understanding of the crucial role of dynamic metabolism during early mammalian embryogenesis. In this Review, we summarize recent studies on oocyte and embryo metabolism and its regulation, with a particular focus on its association with key developmental events such as fertilization, zygote genome activation and cell fate determination. In addition, we discuss the mechanisms of certain metabolites that, in addition to serving as energy sources, contribute to epigenetic modifications.
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Affiliation(s)
- Jing Zhao
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Wenjie Wang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou 310058, China
| | - Ling Zhang
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Jia Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou 310058, China
| | - Roger Sturmey
- Biomedical Institute for Multimorbidity, Hull York Medical School, University of Hull, Hull HU6 7RX, UK
| | - Jin Zhang
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou 310058, China
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Perez M, Aroh O, Sun Y, Lan Y, Juniper SK, Young CR, Angers B, Qian PY. Third-Generation Sequencing Reveals the Adaptive Role of the Epigenome in Three Deep-Sea Polychaetes. Mol Biol Evol 2023; 40:msad172. [PMID: 37494294 PMCID: PMC10414810 DOI: 10.1093/molbev/msad172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/16/2023] [Accepted: 07/17/2023] [Indexed: 07/28/2023] Open
Abstract
The roles of DNA methylation in invertebrates are poorly characterized, and critical data are missing for the phylum Annelida. We fill this knowledge gap by conducting the first genome-wide survey of DNA methylation in the deep-sea polychaetes dominant in deep-sea vents and seeps: Paraescarpia echinospica, Ridgeia piscesae, and Paralvinella palmiformis. DNA methylation calls were inferred from Oxford Nanopore sequencing after assembling high-quality genomes of these animals. The genomes of these worms encode all the key enzymes of the DNA methylation metabolism and possess a mosaic methylome similar to that of other invertebrates. Transcriptomic data of these polychaetes support the hypotheses that gene body methylation strengthens the expression of housekeeping genes and that promoter methylation acts as a silencing mechanism but not the hypothesis that DNA methylation suppresses the activity of transposable elements. The conserved epigenetic profiles of genes responsible for maintaining homeostasis under extreme hydrostatic pressure suggest DNA methylation plays an important adaptive role in these worms.
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Affiliation(s)
- Maeva Perez
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, China
- Department of Biological Sciences, Université de Montréal, Montréal, Canada
| | - Oluchi Aroh
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Yanan Sun
- Laboratory of Marine Organism Taxonomy and Phylogeny, Chinese Academy of Sciences, Institute of Oceanology, Qingdao, China
| | - Yi Lan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, China
| | - Stanley Kim Juniper
- School of Earth and Ocean Sciences, University of Victoria, Victoria, Canada
| | | | - Bernard Angers
- Department of Biological Sciences, Université de Montréal, Montréal, Canada
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, China
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22
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Berteli TS, Wang F, Navarro PA, Kohlrausch FB, Keefe DL. A pilot study of LINE-1 copy number and telomere length with aging in human sperm. J Assist Reprod Genet 2023; 40:1845-1854. [PMID: 37382785 PMCID: PMC10371944 DOI: 10.1007/s10815-023-02857-1] [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: 03/27/2023] [Accepted: 06/03/2023] [Indexed: 06/30/2023] Open
Abstract
PURPOSE Unlike other cells in the body, in sperm, telomere length (TL) increases with age. TL can regulate nearby genes, and the subtelomeric region is rich in retrotransposons. We hypothesized that age-related telomere lengthening in sperm might suppress Long Interspersed Element 1 (LINE-1/L1), the only competent retrotransposon in humans. METHODS We measured L1 copy number (L1-CN) and sperm telomere length (STL) from young and older men to evaluate the relationship between age, TL and L1-CN. We also evaluated L1-CN and TL in individual sperm to determine whether these variables influence sperm morphology. STL was assayed by Multiplex quantitative polymerase chain reaction method (mmqPCR) and L1-CN by Quantitative polymerase chain reaction (qPCR). RESULTS We found that STL increased, and L1-CN decreased significantly with paternal age. STL in normal single sperm was significantly higher than in abnormal sperm. L1-CN did not differ between normal and abnormal sperm. Furthermore, morphologically normal sperm have longer telomeres than abnormal sperm. CONCLUSIONS Elongation of telomeres in the male germline could repress retrotransposition, which tends to increase with cellular aging. More studies in larger cohorts across a wide age span are needed to confirm our conclusions and explore their biological and clinical significance.
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Affiliation(s)
- Thalita S Berteli
- Department of Obstetrics and Gynecology, Langone Medical Center, New York University, 462, 1st Avenue, New York, NY, 10016, USA.
- Human Reproduction Division, Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, Brazil.
| | - Fang Wang
- Department of Obstetrics and Gynecology, Langone Medical Center, New York University, 462, 1st Avenue, New York, NY, 10016, USA
| | - Paula A Navarro
- Human Reproduction Division, Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Fabiana B Kohlrausch
- Department of Obstetrics and Gynecology, Langone Medical Center, New York University, 462, 1st Avenue, New York, NY, 10016, USA
- Human Genetics Laboratory, Fluminense Federal University, Niteroi, RJ, Brazil
| | - David L Keefe
- Department of Obstetrics and Gynecology, Langone Medical Center, New York University, 462, 1st Avenue, New York, NY, 10016, USA
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Wu X, Wu X, Xie W. Activation, decommissioning, and dememorization: enhancers in a life cycle. Trends Biochem Sci 2023; 48:673-688. [PMID: 37221124 DOI: 10.1016/j.tibs.2023.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 05/25/2023]
Abstract
Spatiotemporal regulation of cell type-specific gene expression is essential to convert a zygote into a complex organism that contains hundreds of distinct cell types. A class of cis-regulatory elements called enhancers, which have the potential to enhance target gene transcription, are crucial for precise gene expression programs during development. Following decades of research, many enhancers have been discovered and how enhancers become activated has been extensively studied. However, the mechanisms underlying enhancer silencing are less well understood. We review current understanding of enhancer decommissioning and dememorization, both of which enable enhancer silencing. We highlight recent progress from genome-wide perspectives that have revealed the life cycle of enhancers and how its dynamic regulation underlies cell fate transition, development, cell regeneration, and epigenetic reprogramming.
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Affiliation(s)
- Xiaotong Wu
- Tsinghua-Peking Center for Life Sciences, New Cornerstone Science Laboratory, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China; Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xi Wu
- Tsinghua-Peking Center for Life Sciences, New Cornerstone Science Laboratory, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wei Xie
- Tsinghua-Peking Center for Life Sciences, New Cornerstone Science Laboratory, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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St John JC, Okada T, Andreas E, Penn A. The role of mtDNA in oocyte quality and embryo development. Mol Reprod Dev 2023; 90:621-633. [PMID: 35986715 PMCID: PMC10952685 DOI: 10.1002/mrd.23640] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/01/2022] [Accepted: 08/08/2022] [Indexed: 09/02/2023]
Abstract
The mitochondrial genome resides in the mitochondria present in nearly all cell types. The porcine (Sus scrofa) mitochondrial genome is circa 16.7 kb in size and exists in the multimeric format in cells. Individual cell types have different numbers of mitochondrial DNA (mtDNA) copy number based on their requirements for ATP produced by oxidative phosphorylation. The oocyte has the largest number of mtDNA of any cell type. During oogenesis, the oocyte sets mtDNA copy number in order that sufficient copies are available to support subsequent developmental events. It also initiates a program of epigenetic patterning that regulates, for example, DNA methylation levels of the nuclear genome. Once fertilized, the nuclear and mitochondrial genomes establish synchrony to ensure that the embryo and fetus can complete each developmental milestone. However, altering the oocyte's mtDNA copy number by mitochondrial supplementation can affect the programming and gene expression profiles of the developing embryo and, in oocytes deficient of mtDNA, it appears to have a positive impact on the embryo development rates and gene expression profiles. Furthermore, mtDNA haplotypes, which define common maternal origins, appear to affect developmental outcomes and certain reproductive traits. Nevertheless, the manipulation of the mitochondrial content of an oocyte might have a developmental advantage.
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Affiliation(s)
- Justin C. St John
- The Mitochondrial Genetics Group, The School of Biomedicine and The Robinson Research InstituteThe University of AdelaideAdelaideSouth AustraliaAustralia
| | - Takashi Okada
- The Mitochondrial Genetics Group, The School of Biomedicine and The Robinson Research InstituteThe University of AdelaideAdelaideSouth AustraliaAustralia
| | - Eryk Andreas
- The Mitochondrial Genetics Group, The School of Biomedicine and The Robinson Research InstituteThe University of AdelaideAdelaideSouth AustraliaAustralia
| | - Alexander Penn
- The Mitochondrial Genetics Group, The School of Biomedicine and The Robinson Research InstituteThe University of AdelaideAdelaideSouth AustraliaAustralia
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Tan K, Wilkinson MF. Developmental regulators moonlighting as transposons defense factors. Andrology 2023; 11:891-903. [PMID: 36895139 PMCID: PMC11162177 DOI: 10.1111/andr.13427] [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: 01/11/2023] [Revised: 02/17/2023] [Accepted: 03/04/2023] [Indexed: 03/11/2023]
Abstract
BACKGROUND The germline perpetuates genetic information across generations. To maintain the integrity of the germline, transposable elements in the genome must be silenced, as these mobile elements would otherwise engender widespread mutations passed on to subsequent generations. There are several well-established mechanisms that are dedicated to providing defense against transposable elements, including DNA methylation, RNA interference, and the PIWI-interacting RNA pathway. OBJECTIVES Recently, several studies have provided evidence that transposon defense is not only provided by factors dedicated to this purpose but also factors with other roles, including in germline development. Many of these are transcription factors. Our objective is to summarize what is known about these "bi-functional" transcriptional regulators. MATERIALS AND METHODS Literature search. RESULTS AND CONCLUSION We summarize the evidence that six transcriptional regulators-GLIS3, MYBL1, RB1, RHOX10, SETDB1, and ZBTB16-are both developmental regulators and transposable element-defense factors. These factors act at different stages of germ cell development, including in pro-spermatogonia, spermatogonial stem cells, and spermatocytes. Collectively, the data suggest a model in which specific key transcriptional regulators have acquired multiple functions over evolutionary time to influence developmental decisions and safeguard transgenerational genetic information. It remains to be determined whether their developmental roles were primordial and their transposon defense roles were co-opted, or vice versa.
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Affiliation(s)
- Kun Tan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
| | - Miles F. Wilkinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Institute of Genomic Medicine, University of California San Diego, La Jolla, California, USA
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Wiltshire A, Schaal R, Wang F, Tsou T, McKerrow W, Keefe D. Vitrification with Dimethyl Sulfoxide Induces Transcriptomic Alteration of Gene and Transposable Element Expression in Immature Human Oocytes. Genes (Basel) 2023; 14:1232. [PMID: 37372413 DOI: 10.3390/genes14061232] [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: 04/25/2023] [Revised: 05/24/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
Despite substantial advancements in the field of cryobiology, oocyte and embryo cryopreservation still compromise developmental competence. Furthermore, dimethyl sulfoxide (DMSO), one of the most commonly used cryoprotectants, has been found to exert potent effects on the epigenetic landscape of cultured human cells, as well as mouse oocytes and embryos. Little is known about its impact on human oocytes. Additionally, few studies investigate the effects of DMSO on transposable elements (TE), the control of which is essential for the maintenance of genomic instability. The objective of this study was to investigate the impact of vitrification with DMSO-containing cryoprotectant on the transcriptome, including on TEs, of human oocytes. Twenty-four oocytes at the GV stage were donated by four healthy women undergoing elective oocyte cryopreservation. Oocytes were paired such that half from each patient were vitrified with DMSO-containing cryoprotectant (Vitrified Cohort), while the other half were snap frozen in phosphate buffer, unexposed to DMSO (Non-Vitrified Cohort). All oocytes underwent RNA sequencing via a method with high fidelity for single cell analysis, and which allows for the analysis of TE expression through Switching Mechanism at the 5'-end of the RNA Transcript sequencing 2 (SMARTseq2), followed by functional enrichment analysis. Of the 27,837 genes identified by SMARTseq2, 7331 (26.3%) were differentially expressed (p < 0.05). There was a significant dysregulation of genes involved in chromatin and histone modification. Mitochondrial function, as well as the Wnt, insulin, mTOR, HIPPO, and MAPK signaling pathways were also altered. The expression of TEs was positively correlated with the expression of PIWIL2, DNMT3A, and DNMT3B, and negatively correlated with age. These findings suggest that the current standard process of oocyte vitrification, involving DMSO-containing cryoprotectant, induces significant transcriptome changes, including those involving TEs.
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Affiliation(s)
- Ashley Wiltshire
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, New York University Langone Fertility Center, 660 1st Avenue, New York, NY 10016, USA
| | - Renata Schaal
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, New York University Langone Fertility Center, 660 1st Avenue, New York, NY 10016, USA
| | - Fang Wang
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, New York University Langone Fertility Center, 660 1st Avenue, New York, NY 10016, USA
| | - Tiffany Tsou
- Institute for Systems Genetics, New York University Langone Medical Center, 550 1st Avenue, New York, NY 10016, USA
| | - Wilson McKerrow
- Institute for Systems Genetics, New York University Langone Medical Center, 550 1st Avenue, New York, NY 10016, USA
| | - David Keefe
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, New York University Langone Fertility Center, 660 1st Avenue, New York, NY 10016, USA
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Ben Maamar M, Wang Y, Nilsson EE, Beck D, Yan W, Skinner MK. Transgenerational sperm DMRs escape DNA methylation erasure during embryonic development and epigenetic inheritance. ENVIRONMENTAL EPIGENETICS 2023; 9:dvad003. [PMID: 37346491 PMCID: PMC10281242 DOI: 10.1093/eep/dvad003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/10/2023] [Accepted: 06/01/2023] [Indexed: 06/23/2023]
Abstract
Germline transmission of epigenetic information is a critical component of epigenetic inheritance. Previous studies have suggested that an erasure of DNA methylation is required to develop stem cells in the morula embryo. An exception involves imprinted genes that escape this DNA methylation erasure. Transgenerational differential DNA methylation regions (DMRs) have been speculated to be imprinted-like and escape this erasure. The current study was designed to assess if morula embryos escape the erasure of dichlorodiphenyltrichloroethane-induced transgenerational sperm DMR methylation. Observations demonstrate that the majority (98%) of transgenerational sperm DMR sites retain DNA methylation and are not erased, so appearing similar to imprinted-like sites. Interestingly, observations also demonstrate that the majority of low-density CpG genomic sites had a significant increase in DNA methylation in the morula embryo compared to sperm. This is in contrast to the previously observed DNA methylation erasure of higher-density CpG sites. The general erasure of DNA methylation during embryogenesis appears applicable to high-density DNA methylation sites (e.g. CpG islands) but neither to transgenerational DMR methylation sites nor to low-density CpG deserts, which constitute the vast majority of the genome's DNA methylation sites. The role of epigenetics during embryogenesis appears more dynamic than the simple erasure of DNA methylation.
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Affiliation(s)
- Millissia Ben Maamar
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Yue Wang
- David Geffen School of Medicine at UCLA, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Eric E Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Wei Yan
- David Geffen School of Medicine at UCLA, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
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Tompkins J, Lizhar E, Shokrani A, Wu X, Berley J, Kamali D, Hussey D, Cerneckis J, Kang TH, Wang J, Tsark W, Zeng D, Godatha S, Natarajan R, Riggs A. Engineering CpG island DNA methylation in pluripotent cells through synthetic CpG-free ssDNA insertion. CELL REPORTS METHODS 2023; 3:100465. [PMID: 37323577 PMCID: PMC10261899 DOI: 10.1016/j.crmeth.2023.100465] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 02/14/2023] [Accepted: 04/12/2023] [Indexed: 06/17/2023]
Abstract
Cellular differentiation requires global changes to DNA methylation (DNAme), where it functions to regulate transcription factor, chromatin remodeling activity, and genome interpretation. Here, we describe a simple DNAme engineering approach in pluripotent stem cells (PSCs) that stably extends DNAme across target CpG islands (CGIs). Integration of synthetic CpG-free single-stranded DNA (ssDNA) induces a target CpG island methylation response (CIMR) in multiple PSC lines, Nt2d1 embryonal carcinoma cells, and mouse PSCs but not in highly methylated CpG island hypermethylator phenotype (CIMP)+ cancer lines. MLH1 CIMR DNAme spanned the CGI, was precisely maintained through cellular differentiation, suppressed MLH1 expression, and sensitized derived cardiomyocytes and thymic epithelial cells to cisplatin. Guidelines for CIMR editing are provided, and initial CIMR DNAme is characterized at TP53 and ONECUT1 CGIs. Collectively, this resource facilitates CpG island DNAme engineering in pluripotency and the genesis of novel epigenetic models of development and disease.
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Affiliation(s)
- Joshua Tompkins
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Elizabeth Lizhar
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Alireza Shokrani
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Xiwei Wu
- Integrative Genomics Core, City of Hope, Duarte, CA 91010, USA
| | - Jordan Berley
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Diba Kamali
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Deborah Hussey
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Jonas Cerneckis
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Tae Hyuk Kang
- Integrative Genomics Core, City of Hope, Duarte, CA 91010, USA
| | - Jinhui Wang
- Integrative Genomics Core, City of Hope, Duarte, CA 91010, USA
| | - Walter Tsark
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Defu Zeng
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Swetha Godatha
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Arthur Riggs
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
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Serrano JB, Tabeling NC, de Winter-Korver CM, van Daalen SKM, van Pelt AMM, Mulder CL. Sperm DNA methylation is predominantly stable in mice offspring born after transplantation of long-term cultured spermatogonial stem cells. Clin Epigenetics 2023; 15:58. [PMID: 37029425 PMCID: PMC10080964 DOI: 10.1186/s13148-023-01469-x] [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: 09/15/2022] [Accepted: 03/21/2023] [Indexed: 04/09/2023] Open
Abstract
BACKGROUND Spermatogonial stem cell transplantation (SSCT) is proposed as a fertility therapy for childhood cancer survivors. SSCT starts with cryopreserving a testicular biopsy prior to gonadotoxic treatments such as cancer treatments. When the childhood cancer survivor reaches adulthood and desires biological children, the biopsy is thawed and SSCs are propagated in vitro and subsequently auto-transplanted back into their testis. However, culturing stress during long-term propagation can result in epigenetic changes in the SSCs, such as DNA methylation alterations, and might be inherited by future generations born after SSCT. Therefore, SSCT requires a detailed preclinical epigenetic assessment of the derived offspring before this novel cell therapy is clinically implemented. With this aim, the DNA methylation status of sperm from SSCT-derived offspring, with in vitro propagated SSCs, was investigated in a multi-generational mouse model using reduced-representation bisulfite sequencing. RESULTS Although there were some methylation differences, they represent less than 0.5% of the total CpGs and methylated regions, in all generations. Unsupervised clustering of all samples showed no distinct grouping based on their pattern of methylation differences. After selecting the few single genes that are significantly altered in multiple generations of SSCT offspring compared to control, we validated the results with quantitative Bisulfite Sanger sequencing and RT-qPCRin various organs. Differential methylation was confirmed only for Tal2, being hypomethylated in sperm of SSCT offspring and presenting higher gene expression in ovaries of SSCT F1 offspring compared to control F1. CONCLUSIONS We found no major differences in DNA methylation between SSCT-derived offspring and control, both in F1 and F2 sperm. The reassuring outcomes from our study are a prerequisite for promising translation of SSCT to the human situation.
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Affiliation(s)
- Joana B Serrano
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Nils C Tabeling
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Cindy M de Winter-Korver
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Saskia K M van Daalen
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Ans M M van Pelt
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Callista L Mulder
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
- Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands.
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30
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Hu J, Xu X, Li J, Jiang Y, Hong X, Rexrode KM, Wang G, Hu FB, Zhang H, Karmaus WJ, Wang X, Liang L. Sex differences in the intergenerational link between maternal and neonatal whole blood DNA methylation: a genome-wide analysis in 2 birth cohorts. Clin Epigenetics 2023; 15:51. [PMID: 36966332 PMCID: PMC10040137 DOI: 10.1186/s13148-023-01442-8] [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: 03/02/2022] [Accepted: 02/06/2023] [Indexed: 03/27/2023] Open
Abstract
BACKGROUND The mother-child inheritance of DNA methylation (DNAm) variations could contribute to the inheritance of disease susceptibility across generations. However, no study has investigated patterns of mother-child associations in DNAm at the genome-wide scale. It remains unknown whether there are sex differences in mother-child DNAm associations. RESULTS Using genome-wide DNAm profiling data (721,331 DNAm sites, including 704,552 on autosomes and 16,779 on the X chromosome) of 396 mother-newborn pairs (54.5% male) from the Boston Birth Cohort, we found significant sex differences in mother-newborn correlations in genome-wide DNAm patterns (Spearman's rho = 0.91-0.98; p = 4.0 × 10-8), with female newborns having stronger correlations. Sex differences in correlations were attenuated but remained significant after excluding X-chromosomal DNAm sites (Spearman's rho = 0.91-0.98; p = 0.035). Moreover, 89,267 DNAm sites (12.4% of all analyzed, including 88,051 [12.5% of analyzed] autosomal and 1,216 [7.2% of analyzed] X-chromosomal sites) showed significant mother-newborn associations in methylation levels, and the top autosomal DNAm sites had high heritability than the genome-wide background (e.g., the top 100 autosomal DNAm sites had a medium h2 of 0.92). Additionally, significant interactions between newborn sex and methylation levels were observed for 11 X-chromosomal and 4 autosomal DNAm sites that were mapped to genes that have been associated with sex-specific disease/traits or early development (e.g., EFHC2, NXY, ADCYAP1R1, and BMP4). Finally, 18,769 DNAm sites (14,482 [77.2%] on the X chromosome) showed mother-newborn differences in methylation levels that were significantly associated with newborn sex, and the top autosomal DNAm sites had relatively small heritability (e.g., the top 100 autosomal DNAm sites had a medium h2 of 0.23). These DNAm sites were mapped to 2,532 autosomal genes and 978 X-chromosomal genes with significant enrichment in pathways involved in neurodegenerative and psychological diseases, development, neurophysiological process, immune response, and sex-specific cancers. Replication analysis in the Isle of Wight birth cohort yielded consistent results. CONCLUSION In two independent birth cohorts, we demonstrated strong mother-newborn correlations in whole blood DNAm on both autosomes and ChrX, and such correlations vary substantially by sex. Future studies are needed to examine to what extent our findings contribute to developmental origins of pediatric and adult diseases with well-observed sex differences.
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Affiliation(s)
- Jie Hu
- Division of Women's Health, Department of Medicine, Bigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
| | - Xin Xu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
| | - Jun Li
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yu Jiang
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Xiumei Hong
- Center On the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Kathryn M Rexrode
- Division of Women's Health, Department of Medicine, Bigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Guoying Wang
- Center On the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Frank B Hu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Wilfried J Karmaus
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Xiaobin Wang
- Center On the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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Nandi S, Tripathi SK, Singh PK, Gupta PSP, Mondal S. Global DNA methylation, DNA methyltransferase and stress-related gene expression in ovine oocytes and embryos after exposure to metabolic stressors. Reprod Domest Anim 2023. [PMID: 36920043 DOI: 10.1111/rda.14341] [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: 01/25/2023] [Revised: 02/20/2023] [Accepted: 03/09/2023] [Indexed: 03/16/2023]
Abstract
DNA methylation, considered the most prominent epigenetic mark was important for the gene regulation in embryonic development. The present study aimed at evaluating the effects of metabolic stressors [Non-esterified fatty acid (NEFA), β-hydroxy-butyric acid (BHB), ammonia and urea] exposure during the in vitro ovine oocyte maturation, global DNA methylation, DNA methyltransferase and stress-related gene expression. Colorimetric analysis of global DNA methylation and the expression of the DNA methyltransferase genes (DNMT1, DNMT3A, and DNMT3B) were assessed in the matured oocytes, 2-cell embryos and blastocysts produced in vitro from oocytes exposed with the metabolic stressors during 24 h of the in vitro maturation (IVM). Further, the mRNA expression of the stress-related genes (SOD1, SOD2) in the matured oocytes, 2-cell embryos and blastocysts produced was assessed. Significant difference in global DNA methylation levels between all the treatments tested was observed when compared with control in oocytes, two-cell embryos and blastocysts. Elevated concentration of metabolic stressors resulted in increased expressions of several stress-related genes, i.e., SOD1, SOD2 and in mRNA expression of DNA methyltransferase genes. The present study is the first to report that the DNA methylation was sensitive to the effects of the metabolic stressors in ovine oocytes/embryos. The aberrant expressions of genes during oocyte development targeted in the present study can provide evidence for the early embryo developmental arrest and blastocysts quality. These results highlighted the sensitivity of the early embryogenesis and more precisely of the reprogramming period to metabolites challenges, in a realistic situation of elevated concentration of metabolic stressors.
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Affiliation(s)
- Sumanta Nandi
- Animal Biotechnology Laboratory, ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, 560030, India
| | - Shiv K Tripathi
- Animal Biotechnology Laboratory, ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, 560030, India
| | - Poonam K Singh
- Animal Biotechnology Laboratory, ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, 560030, India
| | - Paluru S P Gupta
- Animal Biotechnology Laboratory, ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, 560030, India
| | - Sukanta Mondal
- Animal Biotechnology Laboratory, ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, 560030, India
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The epigenetic regulatory mechanism of PIWI/piRNAs in human cancers. Mol Cancer 2023; 22:45. [PMID: 36882835 PMCID: PMC9990219 DOI: 10.1186/s12943-023-01749-3] [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: 07/25/2022] [Accepted: 02/16/2023] [Indexed: 03/09/2023] Open
Abstract
PIWI proteins have a strong correlation with PIWI-interacting RNAs (piRNAs), which are significant in development and reproduction of organisms. Recently, emerging evidences have indicated that apart from the reproductive function, PIWI/piRNAs with abnormal expression, also involve greatly in varieties of human cancers. Moreover, human PIWI proteins are usually expressed only in germ cells and hardly in somatic cells, so the abnormal expression of PIWI proteins in different types of cancer offer a promising opportunity for precision medicine. In this review, we discussed current researches about the biogenesis of piRNA, its epigenetic regulatory mechanisms in human cancers, such as N6-methyladenosine (m6A) methylation, histone modifications, DNA methylation and RNA interference, providing novel insights into the markers for clinical diagnosis, treatment and prognosis in human cancers.
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33
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Hayashi K, Alseekh S, Fernie AR. Genetic and epigenetic control of the plant metabolome. Proteomics 2023:e2200104. [PMID: 36781168 DOI: 10.1002/pmic.202200104] [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: 11/29/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023]
Abstract
Plant metabolites are mainly produced through chemical reactions catalysed by enzymes encoded in the genome. Mutations in enzyme-encoding or transcription factor-encoding genes can alter the metabolome by changing the enzyme's catalytic activity or abundance, respectively. Insertion of transposable elements into non-coding regions has also been reported to affect transcription and ultimately metabolite content. In addition to genetic mutations, transgenerational epigenetic variations have also been found to affect metabolic content by controlling the transcription of metabolism-related genes. However, the majority of cases reported so far, in which epigenetic mechanisms are associated with metabolism, are non-transgenerational, and are triggered by developmental signals or environmental stress. Although, accumulating research has provided evidence of strong genetic control of the metabolome, epigenetic control has been largely untouched. Here, we provide a review of the genetic and epigenetic control of metabolism with a focus on epigenetics. We discuss both transgenerational and non-transgenerational epigenetic marks regulating metabolism as well as prospects of the field of metabolic control where intricate interactions between genetics and epigenetics are involved.
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Affiliation(s)
- Koki Hayashi
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Center for Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Center for Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
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34
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Fallet M, Blanc M, Di Criscio M, Antczak P, Engwall M, Guerrero Bosagna C, Rüegg J, Keiter SH. Present and future challenges for the investigation of transgenerational epigenetic inheritance. ENVIRONMENT INTERNATIONAL 2023; 172:107776. [PMID: 36731188 DOI: 10.1016/j.envint.2023.107776] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Epigenetic pathways are essential in different biological processes and in phenotype-environment interactions in response to different stressors and they can induce phenotypic plasticity. They encompass several processes that are mitotically and, in some cases, meiotically heritable, so they can be transferred to subsequent generations via the germline. Transgenerational Epigenetic Inheritance (TEI) describes the phenomenon that phenotypic traits, such as changes in fertility, metabolic function, or behavior, induced by environmental factors (e.g., parental care, pathogens, pollutants, climate change), can be transferred to offspring generations via epigenetic mechanisms. Investigations on TEI contribute to deciphering the role of epigenetic mechanisms in adaptation, adversity, and evolution. However, molecular mechanisms underlying the transmission of epigenetic changes between generations, and the downstream chain of events leading to persistent phenotypic changes, remain unclear. Therefore, inter-, (transmission of information between parental and offspring generation via direct exposure) and transgenerational (transmission of information through several generations with disappearance of the triggering factor) consequences of epigenetic modifications remain major issues in the field of modern biology. In this article, we review and describe the major gaps and issues still encountered in the TEI field: the general challenges faced in epigenetic research; deciphering the key epigenetic mechanisms in inheritance processes; identifying the relevant drivers for TEI and implement a collaborative and multi-disciplinary approach to study TEI. Finally, we provide suggestions on how to overcome these challenges and ultimately be able to identify the specific contribution of epigenetics in transgenerational inheritance and use the correct tools for environmental science investigation and biomarkers identification.
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Affiliation(s)
- Manon Fallet
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden; Department of Biochemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Rd, Oxford OX1 3QU, United Kingdom.
| | - Mélanie Blanc
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, INRAE, Palavas, France
| | - Michela Di Criscio
- Department of Organismal Biology, Uppsala University, Norbyv. 18A, 75236 Uppsala, Sweden
| | - Philipp Antczak
- University of Cologne, Faculty of Medicine and Cologne University Hospital, Center for Molecular Medicine Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, University of Cologne, Cologne, Germany
| | - Magnus Engwall
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
| | | | - Joëlle Rüegg
- Department of Organismal Biology, Uppsala University, Norbyv. 18A, 75236 Uppsala, Sweden
| | - Steffen H Keiter
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
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35
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Tan DS, Cheung SL, Gao Y, Weinbuch M, Hu H, Shi L, Ti SC, Hutchins AP, Cojocaru V, Jauch R. The homeodomain of Oct4 is a dimeric binder of methylated CpG elements. Nucleic Acids Res 2023; 51:1120-1138. [PMID: 36631980 PMCID: PMC9943670 DOI: 10.1093/nar/gkac1262] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023] Open
Abstract
Oct4 is essential to maintain pluripotency and has a pivotal role in establishing the germline. Its DNA-binding POU domain was recently found to bind motifs with methylated CpG elements normally associated with epigenetic silencing. However, the mode of binding and the consequences of this capability has remained unclear. Here, we show that Oct4 binds to a compact palindromic DNA element with a methylated CpG core (CpGpal) in alternative states of pluripotency and during cellular reprogramming towards induced pluripotent stem cells (iPSCs). During cellular reprogramming, typical Oct4 bound enhancers are uniformly demethylated, with the prominent exception of the CpGpal sites where DNA methylation is often maintained. We demonstrate that Oct4 cooperatively binds the CpGpal element as a homodimer, which contrasts with the ectoderm-expressed POU factor Brn2. Indeed, binding to CpGpal is Oct4-specific as other POU factors expressed in somatic cells avoid this element. Binding assays combined with structural analyses and molecular dynamic simulations show that dimeric Oct4-binding to CpGpal is driven by the POU-homeodomain whilst the POU-specific domain is detached from DNA. Collectively, we report that Oct4 exerts parts of its regulatory function in the context of methylated DNA through a DNA recognition mechanism that solely relies on its homeodomain.
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Affiliation(s)
- Daisylyn Senna Tan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Shun Lai Cheung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ya Gao
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Maike Weinbuch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China,Institute for Molecular Medicine, Ulm University, Ulm, Germany
| | - Haoqing Hu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Liyang Shi
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shih-Chieh Ti
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Andrew P Hutchins
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Vlad Cojocaru
- STAR-UBB Institute, Babeş-Bolyai University, Cluj-Napoca, Romania,Computational Structural Biology Group, Utrecht University, The Netherlands,Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Ralf Jauch
- To whom correspondence should be addressed. Tel: +852 3917 9511; Fax: +852 28559730;
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36
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Vargas LN, Nochi ARF, de Castro PS, Cunha ATM, Silva TCF, Togawa RC, Silveira MM, Caetano AR, Franco MM. Differentially methylated regions identified in bovine embryos are not observed in adulthood. Anim Reprod 2023; 20:e20220076. [PMID: 36938311 PMCID: PMC10023072 DOI: 10.1590/1984-3143-ar2022-0076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/14/2023] [Indexed: 03/18/2023] Open
Abstract
The establishment of epigenetic marks during the reprogramming window is susceptible to environmental influences, and stimuli during this critical stage can cause altered DNA methylation in offspring. In a previous study, we found that low levels of sulphur and cobalt (low S/Co) in the diet offered to oocyte donors altered the DNA methylome of bovine embryos. However, due to the extensive epigenetic reprogramming that occurs during embryogenesis, we hypothesized that the different methylation regions (DMRs) identified in the blastocysts may not maintain in adulthood. Here, we aimed to characterize DMRs previously identified in embryos, in the blood and sperm of adult progenies of two groups of heifers (low S/Co and control). We used six bulls and characterized the DNA methylation levels of KDM2A, KDM5A, KMT2D, and DOT1L genes. Our results showed that all DMRs analysed in both groups and tissues were hypermethylated unlike that noticed in the embryonic methylome profiles. These results suggest that embryo DMRs were reprogrammed during the final stages of de novo methylation during embryogenesis or later in development. Therefore, due to the highly dynamic epigenetic state during early embryonic development, we suggest that is essential to validate the DMRs found in embryos in adult individuals.
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Affiliation(s)
- Luna Nascimento Vargas
- Laboratório de Reprodução Animal, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil
- Instituto de Biotecnologia, Universidade Federal de Uberlândia, Uberlândia, MG, Brasil
| | | | - Paloma Soares de Castro
- Laboratório de Reprodução Animal, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil
- Instituto de Biotecnologia, Universidade Federal de Uberlândia, Uberlândia, MG, Brasil
| | | | - Thainara Christie Ferreira Silva
- Laboratório de Reprodução Animal, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil
- Instituto de Biotecnologia, Universidade Federal de Uberlândia, Uberlândia, MG, Brasil
| | | | | | | | - Maurício Machaim Franco
- Laboratório de Reprodução Animal, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil
- Instituto de Biotecnologia, Universidade Federal de Uberlândia, Uberlândia, MG, Brasil
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil
- Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, MG, Brasil
- Corresponding author:
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Hu Q, Lian Z, Xia X, Tian H, Li Z. Integrated chromatin accessibility and DNA methylation analysis to reveal the critical epigenetic modification and regulatory mechanism in gonadal differentiation of the sequentially hermaphroditic fish, Monopterus albus. Biol Sex Differ 2022; 13:73. [PMID: 36539889 PMCID: PMC9764712 DOI: 10.1186/s13293-022-00484-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/11/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Monopterus albus is a hermaphroditic and economically farmed fish that undergoes sex reversal from ovary to testis via ovotestis during gonadal development. The epigenetic changes that are associated with gonadal development in this species remain unclear. METHODS We produced DNA methylome, transcriptome, and chromatin accessibility maps of the key stages of gonad development: ovary, ovotestis, and testis. The expression of the key candidate genes was detected using qRT-PCR and in situ hybridization and the methylation levels were analysed using bisulphite sequencing PCR. Promoter activity and regulation were assessed using dual-luciferase reporter assays. RESULTS Gonadal development exhibits highly dynamic transcriptomic, DNA methylation, and chromatin accessibility changes. We found that DNA methylation status, especially of the transcription start site, was significantly negatively correlated with gene expression while chromatin accessibility exhibited no correlation with gene expression during gonadal development. The epigenetic signatures revealed many novel regulatory elements and genes involved in sex reversal, which were validated. DNA methylation detection and site mutation of plastin-2 promoter, as a candidate gene, revealed that DNA methylation could impact the binding of transcription factor dmrt1 and foxl2 through methylation and demethylation to regulate plastin-2 expression during gonadal development. CONCLUSIONS These data provide novel insights into epigenetic modification and help elucidate the potential molecular mechanism by which dynamic modification of DNA methylation plays a crucial role in gonadal development.
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Affiliation(s)
- Qiaomu Hu
- grid.43308.3c0000 0000 9413 3760Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223 China
| | - Zitong Lian
- grid.43308.3c0000 0000 9413 3760Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223 China
| | - Xueping Xia
- grid.43308.3c0000 0000 9413 3760Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223 China
| | - Haifeng Tian
- grid.43308.3c0000 0000 9413 3760Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223 China
| | - Zhong Li
- grid.43308.3c0000 0000 9413 3760Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223 China
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Grandmaternal smoking during pregnancy is associated with differential DNA methylation in peripheral blood of their grandchildren. Eur J Hum Genet 2022; 30:1373-1379. [PMID: 35347270 PMCID: PMC9712525 DOI: 10.1038/s41431-022-01081-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 11/02/2021] [Accepted: 02/24/2022] [Indexed: 01/29/2023] Open
Abstract
The idea that information can be transmitted to subsequent generation(s) by epigenetic means has been studied for decades but remains controversial in humans. Epidemiological studies have established that grandparental exposures are associated with health outcomes in their grandchildren, often with sex-specific effects; however, the mechanism of transmission is still unclear. We conducted Epigenome Wide Association Studies (EWAS) to test whether grandmaternal smoking during pregnancy is associated with altered DNA methylation (DNAm) in peripheral blood from their adolescent grandchildren. We used data from a birth cohort, with discovery and replication datasets of up to 1225 and 708 individuals (respectively, for the maternal line), aged 15-17 years, and tested replication in the same individuals at birth and 7 years. We show for the first time that DNAm at a small number of loci in cord blood is associated with grandmaternal smoking in humans. In adolescents we see suggestive associations in regions of the genome which we hypothesised a priori could be involved in transgenerational transmission - we observe sex-specific associations at two sites on the X chromosome and one in an imprinting control region. All are within transcription factor binding sites (TFBSs), and we observe enrichment for TFBS among the CpG sites with the strongest associations; however, there is limited evidence that the associations we see replicate between timepoints. The implication of this work is that effects of smoking during pregnancy may induce DNAm changes in later generations and that these changes are often sex-specific, in line with epidemiological associations.
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Li TD, Murano K, Kitano T, Guo Y, Negishi L, Siomi H. TDP-43 safeguards the embryo genome from L1 retrotransposition. SCIENCE ADVANCES 2022; 8:eabq3806. [PMID: 36417507 PMCID: PMC9683724 DOI: 10.1126/sciadv.abq3806] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Transposable elements (TEs) are genomic parasites that propagate within the host genome and introduce mutations. Long interspersed nuclear element-1 (LINE-1 or L1) is the major TE class, which occupies nearly 20% of the mouse genome. L1 is highly active in mammalian preimplantation embryos, posing a major threat to genome integrity, but the mechanism of stage-specific protection against L1 retrotransposition is unknown. Here, we show that TAR DNA-binding protein 43 (TDP-43), mutations in which constitute a major risk factor for amyotrophic lateral sclerosis, inhibits L1 retrotransposition in mouse embryonic stem cells (mESCs) and preimplantation embryos. Knockdown of TDP-43 resulted in massive genomic L1 expansion and impaired cell growth in preimplantation embryos and ESCs. Functional analysis demonstrated that TDP-43 interacts with L1 open reading frame 1 protein (L1 ORF1p) to mediate genomic protection, and loss of this interaction led to derepression of L1 retrotransposition. Our results identify TDP-43 as a guardian of the embryonic genome.
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Affiliation(s)
- Ten D. Li
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kensaku Murano
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Tomohiro Kitano
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Youjia Guo
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Lumi Negishi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
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Abstract
BACKGROUND Autoimmune hepatitis has an unknown cause and genetic associations that are not disease-specific or always present. Clarification of its missing causality and heritability could improve prevention and management strategies. AIMS Describe the key epigenetic and genetic mechanisms that could account for missing causality and heritability in autoimmune hepatitis; indicate the prospects of these mechanisms as pivotal factors; and encourage investigations of their pathogenic role and therapeutic potential. METHODS English abstracts were identified in PubMed using multiple key search phases. Several hundred abstracts and 210 full-length articles were reviewed. RESULTS Environmental induction of epigenetic changes is the prime candidate for explaining the missing causality of autoimmune hepatitis. Environmental factors (diet, toxic exposures) can alter chromatin structure and the production of micro-ribonucleic acids that affect gene expression. Epistatic interaction between unsuspected genes is the prime candidate for explaining the missing heritability. The non-additive, interactive effects of multiple genes could enhance their impact on the propensity and phenotype of autoimmune hepatitis. Transgenerational inheritance of acquired epigenetic marks constitutes another mechanism of transmitting parental adaptations that could affect susceptibility. Management strategies could range from lifestyle adjustments and nutritional supplements to precision editing of the epigenetic landscape. CONCLUSIONS Autoimmune hepatitis has a missing causality that might be explained by epigenetic changes induced by environmental factors and a missing heritability that might reflect epistatic gene interactions or transgenerational transmission of acquired epigenetic marks. These unassessed or under-evaluated areas warrant investigation.
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Higham J, Kerr L, Zhang Q, Walker RM, Harris SE, Howard DM, Hawkins EL, Sandu AL, Steele JD, Waiter GD, Murray AD, Evans KL, McIntosh AM, Visscher PM, Deary IJ, Cox SR, Sproul D. Local CpG density affects the trajectory and variance of age-associated DNA methylation changes. Genome Biol 2022; 23:216. [PMID: 36253871 PMCID: PMC9575273 DOI: 10.1186/s13059-022-02787-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methylation is an epigenetic mark associated with the repression of gene promoters. Its pattern in the genome is disrupted with age and these changes can be used to statistically predict age with epigenetic clocks. Altered rates of aging inferred from these clocks are observed in human disease. However, the molecular mechanisms underpinning age-associated DNA methylation changes remain unknown. Local DNA sequence can program steady-state DNA methylation levels, but how it influences age-associated methylation changes is unknown. RESULTS We analyze longitudinal human DNA methylation trajectories at 345,895 CpGs from 600 individuals aged between 67 and 80 to understand the factors responsible for age-associated epigenetic changes at individual CpGs. We show that changes in methylation with age occur at 182,760 loci largely independently of variation in cell type proportions. These changes are especially apparent at 8322 low CpG density loci. Using SNP data from the same individuals, we demonstrate that methylation trajectories are affected by local sequence polymorphisms at 1487 low CpG density loci. More generally, we find that low CpG density regions are particularly prone to change and do so variably between individuals in people aged over 65. This differs from the behavior of these regions in younger individuals where they predominantly lose methylation. CONCLUSIONS Our results, which we reproduce in two independent groups of individuals, demonstrate that local DNA sequence influences age-associated DNA methylation changes in humans in vivo. We suggest that this occurs because interactions between CpGs reinforce maintenance of methylation patterns in CpG dense regions.
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Affiliation(s)
- Jonathan Higham
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Lyndsay Kerr
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Qian Zhang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- Present address: Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Present address: School of Psychology, University of Exeter, Edinburgh, UK
| | - Sarah E Harris
- Department of Psychology, Lothian Birth Cohorts Group, University of Edinburgh, Edinburgh, UK
| | - David M Howard
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Emma L Hawkins
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Anca-Larisa Sandu
- Aberdeen Biomedical Imaging Centre, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - J Douglas Steele
- Division of Imaging Science and Technology, Medical School, University of Dundee, Dundee, UK
| | - Gordon D Waiter
- Aberdeen Biomedical Imaging Centre, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Alison D Murray
- Aberdeen Biomedical Imaging Centre, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Peter M Visscher
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Ian J Deary
- Department of Psychology, Lothian Birth Cohorts Group, University of Edinburgh, Edinburgh, UK
| | - Simon R Cox
- Department of Psychology, Lothian Birth Cohorts Group, University of Edinburgh, Edinburgh, UK
| | - Duncan Sproul
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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Marttila S, Tamminen H, Rajić S, Mishra PP, Lehtimäki T, Raitakari O, Kähönen M, Kananen L, Jylhävä J, Hägg S, Delerue T, Peters A, Waldenberger M, Kleber ME, März W, Luoto R, Raitanen J, Sillanpää E, Laakkonen EK, Heikkinen A, Ollikainen M, Raitoharju E. Methylation status of VTRNA2-1/ nc886 is stable across populations, monozygotic twin pairs and in majority of tissues. Epigenomics 2022; 14:1105-1124. [PMID: 36200237 DOI: 10.2217/epi-2022-0228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aims & methods: The aim of this study was to characterize the methylation level of a polymorphically imprinted gene, VTRNA2-1/nc886, in human populations and somatic tissues.48 datasets, consisting of more than 30 tissues and >30,000 individuals, were used. Results: nc886 methylation status is associated with twin status and ethnic background, but the variation between populations is limited. Monozygotic twin pairs present concordant methylation, whereas ∼30% of dizygotic twin pairs present discordant methylation in the nc886 locus. The methylation levels of nc886 are uniform across somatic tissues, except in cerebellum and skeletal muscle. Conclusion: The nc886 imprint may be established in the oocyte, and, after implantation, the methylation status is stable, excluding a few specific tissues.
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Affiliation(s)
- Saara Marttila
- Molecular Epidemiology, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Gerontology Research Center, Tampere University, Tampere, 33014, Finland
| | - Hely Tamminen
- Molecular Epidemiology, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Sonja Rajić
- Molecular Epidemiology, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Finnish Cardiovascular Research Center Tampere, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Fimlab Laboratories, Arvo Ylpön katu 4, Tampere, 33520, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Finnish Cardiovascular Research Center Tampere, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Fimlab Laboratories, Arvo Ylpön katu 4, Tampere, 33520, Finland
| | - Olli Raitakari
- Centre for Population Health Research, University of Turku & Turku University Hospital, Turku, 20014, Finland.,Research Centre of Applied & Preventive Cardiovascular Medicine, University of Turku, Turku, 20014, Finland.,Department of Clinical Physiology & Nuclear Medicine, Turku University Hospital, Turku, 20014, Finland
| | - Mika Kähönen
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Department of Clinical Physiology, Tampere University Hospital, Tampere, 33521, Finland
| | - Laura Kananen
- Faculty of Medicine & Health Technology, & Gerontology Research Center, Tampere University, Arvo Ylpön katu 34, Tampere, 33520,Finland.,Department of Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, 171 77, Sweden.,Faculty of Social Sciences (Health Sciences), & Gerontology Research Center, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Juulia Jylhävä
- Department of Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, 171 77, Sweden.,Faculty of Social Sciences (Health Sciences), & Gerontology Research Center, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Sara Hägg
- Department of Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Thomas Delerue
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, D-85764,, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, D-85764, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, D-85764,, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, 68167, Germany.,SYNLAB MVZ Humangenetik Mannheim, Mannheim, Germany
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, 68167, Germany.,Competence Cluster for Nutrition & Cardiovascular Health (nutriCARD) Halle-Jena-Leipzig, Jena, 07743, Germany.,SYNLAB Academy, SYNLAB Holding Deutschland GmbH, Augsburg, 86156, Germany.,Clinical Institute of Medical & Chemical Laboratory Diagnostics, Medical University of Graz, Graz, 8010, Austria
| | - Riitta Luoto
- The Social Insurance Institute of Finland (Kela), Helsinki, 00250, Finland.,The UKK Institute for Health Promotion Research, Kaupinpuistonkatu 1, Tampere, 33500, Finland
| | - Jani Raitanen
- The UKK Institute for Health Promotion Research, Kaupinpuistonkatu 1, Tampere, 33500, Finland.,Faculty of Social Sciences (Health Sciences), Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Elina Sillanpää
- Gerontology Research Center & Faculty of Sport & Health Sciences, University of Jyväskylä, Jyväskylä, 40014, Finland.,Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Eija K Laakkonen
- Gerontology Research Center & Faculty of Sport & Health Sciences, University of Jyväskylä, Jyväskylä, 40014, Finland
| | - Aino Heikkinen
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Emma Raitoharju
- Molecular Epidemiology, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Finnish Cardiovascular Research Center Tampere, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
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Ma Y, Chen J, Li H, Xu F, Chong T, Wang Z, Zhang L. Immature rat testis sustained long-term development using an integrative model. Biol Res 2022; 55:30. [PMID: 36195947 PMCID: PMC9531454 DOI: 10.1186/s40659-022-00398-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/27/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Xenotransplantation has been primarily performed using fresh donor tissue to study testicular development for about 20 years, and whether the cultured tissue would be a suitable donor is unclear. In this study, we combined testicular culture and xenotransplantation into an integrative model and explored whether immature testicular tissue would survive and continue to develop in this model. METHODS In the new integrative model group, the testes of neonatal rats on postnatal day 8 (PND 8) were cultured for 4 days ex vivo and then were transplanted under the dorsal skin of castrated nude mice. The xenografted testes were resected on the 57th day after xenotransplantation and the testes of rats in the control group were harvested on PND 69. The survival state of testicular tissue was evaluated from morphological and functional perspectives including H&E staining, immunohistochemical staining of 8-OH-dG, immunofluorescence staining, TUNEL assay, ultrastructural study, gene expression and protein analysis. RESULTS (a) We found that complete spermatogenesis was established in the testes in the new integrative model group. Compared with the control in the same stage, the seminiferous epithelium in some tubules was a bit thinner and there were vacuoles in part of the tubules. Immunofluorescence staining revealed some ACROSIN-positive spermatids were present in seminiferous tubule of xenografted testes. TUNEL detection showed apoptotic cells and most of them were germ cells in the new integrative model group. 8-OH-dG immunohistochemistry showed strongly positive-stained in the seminiferous epithelium after xenotransplantation in comparison with the control group; (b) Compared with the control group, the expressions of FOXA3, DAZL, GFRα1, BOLL, SYCP3, CDC25A, LDHC, CREM and MKI67 in the new integrative model group were significantly elevated (P < 0.05), indicating that the testicular tissue was in an active differentiated and proliferative state; (c) Antioxidant gene detection showed that the expression of Nrf2, Keap1, NQO1 and SOD1 in the new integrative model group was significantly higher than those in the control group (P < 0.05), and DNA methyltransferase gene detection showed that the expression of DNMT3B was significantly elevated as well (P < 0.05). CONCLUSION The new integrative model could maintain the viability of immature testicular tissue and sustain the long-term survival in vivo with complete spermatogenesis. However, testicular genes expression was altered, vacuolation and thin seminiferous epithelium were still apparent in this model, manifesting that oxidative damage may contribute to the testicular development lesion and it needs further study in order to optimize this model.
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Affiliation(s)
- Yubo Ma
- Department of Urology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xi'an, 710004, China
| | - Juan Chen
- Department of Urology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xi'an, 710004, China
| | - Hecheng Li
- Department of Urology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xi'an, 710004, China
| | - Fangshi Xu
- Department of Urology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xi'an, 710004, China
| | - Tie Chong
- Department of Urology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xi'an, 710004, China
| | - Ziming Wang
- Department of Urology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xi'an, 710004, China.
| | - Liandong Zhang
- Department of Urology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xi'an, 710004, China.
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Li J, Xu J, Yang T, Chen J, Li F, Shen B, Fan C. Genome-wide methylation analyses of human sperm unravel novel differentially methylated regions in asthenozoospermia. Epigenomics 2022; 14:951-964. [PMID: 36004499 DOI: 10.2217/epi-2022-0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aims & objectives: To investigate DNA methylation patterns in asthenozoospermic and normozoospermic sperm and to explore the potential roles of differential methylations in the etiology of the disease. Materials & methods: The authors performed whole-genome bisulfite sequencing analysis between normozoospermic controls and asthenozoospermic individuals. Results: The authors identified 238 significant differentially methylated regions. These differentially methylated regions were annotated to 114 protein-coding genes, with many genes showing associations with spermatogenesis, sperm motility etc. Conclusion: There are plenty of genomic regions exhibiting altered DNA methylation in asthenozoospermia, a number of which are located within or adjacent to sperm-related genes, suggesting novel methylation markers of asthenozoospermia and potential epigenetic regulation mechanisms through DNA methylation in the disease.
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Affiliation(s)
- Jingjing Li
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Jinyan Xu
- Human Sperm Bank, Key Laboratory of Birth Defects & Related Diseases of Women & Children of Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, 610041, China
| | - Tingting Yang
- Human Sperm Bank, Key Laboratory of Birth Defects & Related Diseases of Women & Children of Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, 610041, China
| | - Jianhai Chen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Fuping Li
- Human Sperm Bank, Key Laboratory of Birth Defects & Related Diseases of Women & Children of Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, 610041, China
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Chuanzhu Fan
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
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Abstract
Over the course of a human lifespan, genome integrity erodes, leading to an increased abundance of several types of chromatin changes. The abundance of DNA lesions (chemical perturbations to nucleotides) increases with age, as does the number of genomic mutations and transcriptional disruptions caused by replication or transcription of those lesions, respectively. At the epigenetic level, precise DNA methylation patterns degrade, likely causing increasingly stochastic variations in gene expression. Similarly, the tight regulation of histone modifications begins to unravel. The genomic instability caused by these mechanisms allows transposon element reactivation and remobilization, further mutations, gene dysregulation, and cytoplasmic chromatin fragments. This cumulative genomic instability promotes cell signaling events that drive cell fate decisions and extracellular communications known to disrupt tissue homeostasis and regeneration. In this Review, we focus on age-related epigenetic changes and their interactions with age-related genomic changes that instigate these events.
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Affiliation(s)
- Carolina Soto-Palma
- Institute on the Biology of Aging and Metabolism
- Department of Biochemistry, Molecular Biology, and Biophysics
| | - Laura J. Niedernhofer
- Institute on the Biology of Aging and Metabolism
- Department of Biochemistry, Molecular Biology, and Biophysics
| | - Christopher D. Faulk
- Institute on the Biology of Aging and Metabolism
- Department of Animal Science, and
| | - Xiao Dong
- Institute on the Biology of Aging and Metabolism
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
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46
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Dvoran M, Nemcova L, Kalous J. An Interplay between Epigenetics and Translation in Oocyte Maturation and Embryo Development: Assisted Reproduction Perspective. Biomedicines 2022; 10:biomedicines10071689. [PMID: 35884994 PMCID: PMC9313063 DOI: 10.3390/biomedicines10071689] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/25/2022] [Accepted: 06/28/2022] [Indexed: 12/11/2022] Open
Abstract
Germ cell quality is a key prerequisite for successful fertilization and early embryo development. The quality is determined by the fine regulation of transcriptomic and proteomic profiles, which are prone to alteration by assisted reproduction technology (ART)-introduced in vitro methods. Gaining evidence shows the ART can influence preset epigenetic modifications within cultured oocytes or early embryos and affect their developmental competency. The aim of this review is to describe ART-determined epigenetic changes related to the oogenesis, early embryogenesis, and further in utero development. We confront the latest epigenetic, related epitranscriptomic, and translational regulation findings with the processes of meiotic maturation, fertilization, and early embryogenesis that impact the developmental competency and embryo quality. Post-ART embryo transfer, in utero implantation, and development (placentation, fetal development) are influenced by environmental and lifestyle factors. The review is emphasizing their epigenetic and ART contribution to fetal development. An epigenetic parallel among mouse, porcine, and bovine animal models and human ART is drawn to illustrate possible future mechanisms of infertility management as well as increase the awareness of the underlying mechanisms governing oocyte and embryo developmental complexity under ART conditions.
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47
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Qian J, Guo F. De novo programming: establishment of epigenome in mammalian oocytes. Biol Reprod 2022; 107:40-53. [PMID: 35552602 DOI: 10.1093/biolre/ioac091] [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: 12/20/2021] [Revised: 04/21/2022] [Accepted: 05/02/2022] [Indexed: 11/14/2022] Open
Abstract
Innovations in ultrasensitive and single-cell measurements enable us to study layers of genome regulation in the view of cellular and regulatory heterogeneity. Genome-scale mapping allows to evaluate epigenetic features and dynamics in different genomic contexts, including genebodies, CGIs, ICRs, promoters, PMDs, and repetitive elements. The epigenome of early embryos, fetal germ cells, and sperm has been extensively studied for the past decade, while oocytes remain less clear. Emerging evidence now supports the notion that transcription and chromatin accessibility precede de novo DNA methylation in both human and mouse oocytes. Recent studies also start to chart correlations among different histone modifications and DNA methylation. We discussed the potential mechanistic hierarchy by which shapes oocyte DNA methylome, also provided insights into the convergent and divergent features between human and mice.
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Affiliation(s)
- Jingjing Qian
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Fan Guo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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48
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Epigenetic Effect of Maternal Methyl-Group Donor Intake on Offspring’s Health and Disease. Life (Basel) 2022; 12:life12050609. [PMID: 35629277 PMCID: PMC9145757 DOI: 10.3390/life12050609] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/02/2022] [Accepted: 04/15/2022] [Indexed: 01/16/2023] Open
Abstract
Maternal exposure to some dietary and environmental factors during embryonic development can affect offspring’s phenotype and, furthermore, the risk of developing diseases later in life. One potential mechanism responsible for this early programming may be the modification of the epigenome, such as DNA methylation. Methyl-group donors are essential for DNA methylation and are shown to have an important role in fetal development and later health. The main goal of the present review is to summarize the available literature data on the epigenetic effect (DNA methylation) of maternal methyl-group donor availability on reproductivity, perinatal outcome, and later health of the offspring. In our literature search, we found evidence for the association between alterations in DNA methylation patterns caused by different maternal methyl-group donor (folate, choline, methionine, betaine) intake and reproductivity, birth weight, neural tube defect, congenital heart defect, cleft lip and palate, brain development, and the development of obesity and associated non-communicable diseases in later life. We can conclude that maternal methyl-group donor availability could affect offspring’s health via alterations in DNA methylation and may be a major link between early environmental exposure and the development of diseases in the offspring. However, still, further studies are necessary to confirm the associations and causal relationships.
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49
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Zhou S, Sakashita A, Yuan S, Namekawa SH. Retrotransposons in the Mammalian Male Germline. Sex Dev 2022:1-19. [PMID: 35231923 DOI: 10.1159/000520683] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 10/25/2021] [Indexed: 11/19/2022] Open
Abstract
Retrotransposons are a subset of DNA sequences that constitute a large part of the mammalian genome. They can translocate autonomously or non-autonomously, potentially jeopardizing the heritable germline genome. Retrotransposons coevolved with the host genome, and the germline is the prominent battlefield between retrotransposons and the host genome to maximize their mutual fitness. Host genomes have developed various mechanisms to suppress and control retrotransposons, including DNA methylation, histone modifications, and Piwi-interacting RNA (piRNA), for their own benefit. Thus, rapidly evolved retrotransposons often acquire positive functions, including gene regulation within the germline, conferring reproductive fitness in a species over the course of evolution. The male germline serves as an ideal model to examine the regulation and evolution of retrotransposons, resulting in genomic co-evolution with the host genome. In this review, we summarize and discuss the regulatory mechanisms of retrotransposons, stage-by-stage, during male germ cell development, with a particular focus on mice as an extensively studied mammalian model, highlighting suppression mechanisms and emerging functions of retrotransposons in the male germline.
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Affiliation(s)
- Shumin Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Akihiko Sakashita
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China
| | - Satoshi H Namekawa
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA
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50
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Janssen SM, Lorincz MC. Interplay between chromatin marks in development and disease. Nat Rev Genet 2022; 23:137-153. [PMID: 34608297 DOI: 10.1038/s41576-021-00416-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 02/07/2023]
Abstract
DNA methylation (DNAme) and histone post-translational modifications (PTMs) have important roles in transcriptional regulation. Although many reports have characterized the functions of such chromatin marks in isolation, recent genome-wide studies reveal surprisingly complex interactions between them. Here, we focus on the interplay between DNAme and methylation of specific lysine residues on the histone H3 tail. We describe the impact of genetic perturbation of the relevant methyltransferases in the mouse on the landscape of chromatin marks as well as the transcriptome. In addition, we discuss the specific neurodevelopmental growth syndromes and cancers resulting from pathogenic mutations in the human orthologues of these genes. Integrating these observations underscores the fundamental importance of crosstalk between DNA and histone H3 methylation in development and disease.
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Affiliation(s)
- Sanne M Janssen
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew C Lorincz
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada.
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