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Legault LM, Breton-Larrivée M, Langford-Avelar A, Lemieux A, McGraw S. Sex-based disparities in DNA methylation and gene expression in late-gestation mouse placentas. Biol Sex Differ 2024; 15:2. [PMID: 38183126 PMCID: PMC10770955 DOI: 10.1186/s13293-023-00577-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/18/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND The placenta is vital for fetal development and its contributions to various developmental issues, such as pregnancy complications, fetal growth restriction, and maternal exposure, have been extensively studied in mice. The placenta forms mainly from fetal tissue and therefore has the same biological sex as the fetus it supports. Extensive research has delved into the placenta's involvement in pregnancy complications and future offspring development, with a notable emphasis on exploring sex-specific disparities. However, despite these investigations, sex-based disparities in epigenetic (e.g., DNA methylation) and transcriptomic features of the late-gestation mouse placenta remain largely unknown. METHODS We collected male and female mouse placentas at late gestation (E18.5, n = 3/sex) and performed next-generation sequencing to identify genome-wide sex differences in transcription and DNA methylation. RESULTS Our comparison between male and female revealed 358 differentially expressed genes (DEGs) on autosomes, which were associated with signaling pathways involved in transmembrane transport and the responses to viruses and external stimuli. X chromosome DEGs (n = 39) were associated with different pathways, including those regulating chromatin modification and small GTPase-mediated signal transduction. Differentially methylated regions (DMRs) were more common on the X chromosomes (n = 3756) than on autosomes (n = 1705). Interestingly, while most X chromosome DMRs had higher DNA methylation levels in female placentas and tended to be included in CpG dinucleotide-rich regions, 73% of autosomal DMRs had higher methylation levels in male placentas and were distant from CpG-rich regions. Several DEGs were correlated with DMRs. A subset of the DMRs present in late-stage placentas were already established in mid-gestation (E10.5) placentas (n = 348 DMRs on X chromosome and 19 DMRs on autosomes), while others were acquired later in placental development. CONCLUSION Our study provides comprehensive lists of DEGs and DMRs between male and female that collectively cause profound differences in the DNA methylation and gene expression profiles of late-gestation mouse placentas. Our results demonstrate the importance of incorporating sex-specific analyses into epigenetic and transcription studies to enhance the accuracy and comprehensiveness of their conclusions and help address the significant knowledge gap regarding how sex differences influence placental function.
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Affiliation(s)
- Lisa-Marie Legault
- CHU Ste-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard‑Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Mélanie Breton-Larrivée
- CHU Ste-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard‑Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Alexandra Langford-Avelar
- CHU Ste-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard‑Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Anthony Lemieux
- CHU Ste-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
| | - Serge McGraw
- CHU Ste-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada.
- Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard‑Montpetit, Montréal, QC, H3T 1J4, Canada.
- Department of Obstetrics and Gynecology, Université de Montréal, 2900 Boulevard Edouard‑Montpetit, Montréal, QC, H3T 1J4, Canada.
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Karahan G, Martel J, Rahimi S, Farag M, Matias F, MacFarlane AJ, Chan D, Trasler J. Higher incidence of embryonic defects in mouse offspring conceived with assisted reproduction from fathers with sperm epimutations. Hum Mol Genet 2023; 33:48-63. [PMID: 37740387 PMCID: PMC10729866 DOI: 10.1093/hmg/ddad160] [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: 05/31/2023] [Revised: 08/30/2023] [Accepted: 09/13/2023] [Indexed: 09/24/2023] Open
Abstract
Assisted reproductive technologies (ART) account for 1-6% of births in developed countries. While most children conceived are healthy, increases in birth and genomic imprinting defects have been reported; such abnormal outcomes have been attributed to underlying parental infertility and/or the ART used. Here, we assessed whether paternal genetic and lifestyle factors, that are associated with male infertility and affect the sperm epigenome, can influence ART outcomes. We examined how paternal factors, haploinsufficiency for Dnmt3L, an important co-factor for DNA methylation reactions, and/or diet-induced obesity, in combination with ART (superovulation, in vitro fertilization, embryo culture and embryo transfer), could adversely influence embryo development and DNA methylation patterning in mice. While male mice fed high-fat diets (HFD) gained weight and showed perturbed metabolic health, their sperm DNA methylation was minimally affected by the diet. In contrast, Dnmt3L haploinsufficiency induced a marked loss of DNA methylation in sperm; notably, regions affected were associated with neurodevelopmental pathways and enriched in young retrotransposons, sequences that can have functional consequences in the next generation. Following ART, placental imprinted gene methylation and growth parameters were impacted by one or both paternal factors. For embryos conceived by natural conception, abnormality rates were similar for WT and Dnmt3L+/- fathers. In contrast, paternal Dnmt3L+/- genotype, as compared to WT fathers, resulted in a 3-fold increase in the incidence of morphological abnormalities in embryos generated by ART. Together, the results indicate that embryonic morphological and epigenetic defects associated with ART may be exacerbated in offspring conceived by fathers with sperm epimutations.
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Affiliation(s)
- Gurbet Karahan
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada
- Research Institute of the McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
| | - Josée Martel
- Research Institute of the McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
| | - Sophia Rahimi
- Research Institute of the McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
| | - Mena Farag
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada
| | - Fernando Matias
- Nutrition Research Division, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | | | - Donovan Chan
- Research Institute of the McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
| | - Jacquetta Trasler
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada
- Research Institute of the McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, H3G 1Y6, Canada
- Department of Pediatrics, McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
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Chen X, Lu Y, Wang L, Ma X, Pu J, Lin L, Deng Q, Li Y, Wang W, Jin Y, Hu Z, Zhou Z, Chen G, Jiang L, Wang H, Zhao X, He X, Fu J, Russ HA, Li W, Zhu S. A fast chemical reprogramming system promotes cell identity transition through a diapause-like state. Nat Cell Biol 2023; 25:1146-1156. [PMID: 37550515 DOI: 10.1038/s41556-023-01193-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 06/21/2023] [Indexed: 08/09/2023]
Abstract
Cellular reprogramming by only small molecules holds enormous potentials for regenerative medicine. However, chemical reprogramming remains a slow process and labour intensive, hindering its broad applications and the investigation of underlying molecular mechanisms. Here, through screening of over 21,000 conditions, we develop a fast chemical reprogramming (FCR) system, which significantly improves the kinetics of cell identity rewiring. We find that FCR rapidly goes through an interesting route for pluripotent reprogramming, uniquely transitioning through a developmentally diapause-like state. Furthermore, FCR critically enables comprehensive characterizations using multi-omics technologies, and has revealed unexpected important features including key regulatory factors and epigenetic dynamics. Particularly, activation of pluripotency-related endogenous retroviruses via inhibition of heterochromatin significantly enhances reprogramming. Our studies provide critical insights into how only environmental cues are sufficient to rapidly reinstate pluripotency in somatic cells, and make notable technical and conceptual advances for solving the puzzle of regeneration.
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Affiliation(s)
- Xi Chen
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Yunkun Lu
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Leyun Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Xiaojie Ma
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Jiaqi Pu
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Childhealth, Hangzhou, China
| | - Lianyu Lin
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Qian Deng
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Yuhan Li
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Weiyun Wang
- Institute of Regenerative Medicine and Orthopedics, Institutes of Health Central Plain, Xinxiang Medical University, Xinxiang, China
| | - Yan Jin
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Zhensheng Hu
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Ziyu Zhou
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Guo Chen
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Liling Jiang
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Hao Wang
- Hangzhou Women's Hospital, Prenatal Diagnosis Center, Hangzhou, China
| | - Xiaoyang Zhao
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiangwei He
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Junfen Fu
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Childhealth, Hangzhou, China
| | - Holger A Russ
- Department of Pharmacology and Therapeutics, School of Medicine, University of Florida, Gainesville, FL, USA
- Diabetes Institute, School of Medicine, University of Florida, Gainesville, FL, USA
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Saiyong Zhu
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China.
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Legault LM, Doiron K, Breton-Larrivée M, Langford-Avelar A, Lemieux A, Caron M, Jerome-Majewska LA, Sinnett D, McGraw S. Pre-implantation alcohol exposure induces lasting sex-specific DNA methylation programming errors in the developing forebrain. Clin Epigenetics 2021; 13:164. [PMID: 34425890 PMCID: PMC8381495 DOI: 10.1186/s13148-021-01151-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 08/11/2021] [Indexed: 12/26/2022] Open
Abstract
Background Prenatal alcohol exposure is recognized for altering DNA methylation profiles of brain cells during development, and to be part of the molecular basis underpinning Fetal Alcohol Spectrum Disorder (FASD) etiology. However, we have negligible information on the effects of alcohol exposure during pre-implantation, the early embryonic window marked with dynamic DNA methylation reprogramming, and on how this may rewire the brain developmental program. Results Using a pre-clinical in vivo mouse model, we show that a binge-like alcohol exposure during pre-implantation at the 8-cell stage leads to surge in morphological brain defects and adverse developmental outcomes during fetal life. Genome-wide DNA methylation analyses of fetal forebrains uncovered sex-specific alterations, including partial loss of DNA methylation maintenance at imprinting control regions, and abnormal de novo DNA methylation profiles in various biological pathways (e.g., neural/brain development). Conclusion These findings support that alcohol-induced DNA methylation programming deviations during pre-implantation could contribute to the manifestation of neurodevelopmental phenotypes associated with FASD. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01151-0.
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Affiliation(s)
- L M Legault
- CHU Sainte-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - K Doiron
- CHU Sainte-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
| | - M Breton-Larrivée
- CHU Sainte-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - A Langford-Avelar
- CHU Sainte-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - A Lemieux
- CHU Sainte-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - M Caron
- CHU Sainte-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
| | - L A Jerome-Majewska
- McGill University Health Centre Glen Site, 1001 Boulevard Décarie, Montréal, QC, H4A 3J1, Canada.,Department of Pediatrics, McGill University, 1001 Boulevard Décarie, Montréal, QC, H4A 3J1, Canada
| | - D Sinnett
- CHU Sainte-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada.,Department of Pediatrics, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - S McGraw
- CHU Sainte-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada. .,Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada. .,Department of Obstetrics and Gynecology, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada.
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5
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Legault LM, Doiron K, Lemieux A, Caron M, Chan D, Lopes FL, Bourque G, Sinnett D, McGraw S. Developmental genome-wide DNA methylation asymmetry between mouse placenta and embryo. Epigenetics 2020; 15:800-815. [PMID: 32056496 PMCID: PMC7518706 DOI: 10.1080/15592294.2020.1722922] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 01/03/2020] [Accepted: 01/15/2020] [Indexed: 12/27/2022] Open
Abstract
In early embryos, DNA methylation is remodelled to initiate the developmental program but for mostly unknown reasons, methylation marks are acquired unequally between embryonic and placental cells. To better understand this, we generated high-resolution DNA methylation maps of mouse mid-gestation (E10.5) embryo and placenta. We uncovered specific subtypes of differentially methylated regions (DMRs) that contribute directly to the developmental asymmetry existing between mid-gestation embryonic and placental DNA methylation patterns. We show that the asymmetry occurs rapidly during the acquisition of marks in the post-implanted conceptus (E3.5-E6.5), and that these patterns are long-lasting across subtypes of DMRs throughout prenatal development and in somatic tissues. We reveal that at the peri-implantation stages, the de novo methyltransferase activity of DNMT3B is the main driver of methylation marks on asymmetric DMRs, and that DNMT3B can largely compensate for lack of DNMT3A in the epiblast and extraembryonic ectoderm, whereas DNMT3A can only partially compensate in the absence of DNMT3B. However, as development progresses and as DNMT3A becomes the principal de novo methyltransferase, the compensatory DNA methylation mechanism of DNMT3B on DMRs becomes less effective.
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Affiliation(s)
- LM Legault
- Research Center of the CHU Sainte-Justine, Montreal, Canada
- Department of Biochemistry and Molecular Medicine, Université De Montréal, Montreal, Canada
| | - K Doiron
- Research Center of the CHU Sainte-Justine, Montreal, Canada
| | - A Lemieux
- Research Center of the CHU Sainte-Justine, Montreal, Canada
- Department of Biochemistry and Molecular Medicine, Université De Montréal, Montreal, Canada
| | - M Caron
- Research Center of the CHU Sainte-Justine, Montreal, Canada
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - D Chan
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - FL Lopes
- School of Veterinary Medicine, São Paulo State University (Unesp), Aracatuba, Brazil
| | - G Bourque
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
- Canadian Center for Computational Genomics, Montreal, Quebec, Canada
| | - D Sinnett
- Research Center of the CHU Sainte-Justine, Montreal, Canada
- Department of Pediatrics, Université De Montréal, Montreal, Canada
| | - S McGraw
- Research Center of the CHU Sainte-Justine, Montreal, Canada
- Department of Biochemistry and Molecular Medicine, Université De Montréal, Montreal, Canada
- Department of Obstetrics and Gynecology, Université De Montréal, Montreal, Canada
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