1
|
Wang J, Zhou X, Han T, Zhang H. Epigenetic signatures of trophoblast lineage and their biological functions. Cells Dev 2024; 179:203934. [PMID: 38942294 DOI: 10.1016/j.cdev.2024.203934] [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: 11/15/2023] [Revised: 03/13/2024] [Accepted: 06/13/2024] [Indexed: 06/30/2024]
Abstract
Trophoblasts play a crucial role in embryo implantation and in interacting with the maternal uterus. The trophoblast lineage develops into a substantial part of the placenta, a temporary extra-embryonic organ, capable of undergoing distinctive epigenetic events during development. The critical role of trophoblast-specific epigenetic signatures in regulating placental development has become known, significantly advancing our understanding of trophoblast identity and lineage development. Scientific efforts are revealing how trophoblast-specific epigenetic signatures mediate stage-specific gene regulatory programming during the development of the trophoblast lineage. These epigenetic signatures have a significant impact on blastocyst formation, placental development, as well as the growth and survival of embryos and fetuses. In evolution, DNA hypomethylation in the trophoblast lineage is conserved, and there is a significant disparity in the control of epigenetic dynamics and the landscape of genomic imprinting. Scientists have used murine and human multipotent trophoblast cells as in vitro models to recapitulate the essential epigenetic processes of placental development. Here, we review the epigenetic signatures of the trophoblast lineage and their biological functions to enhance our understanding of placental evolution, development, and function.
Collapse
Affiliation(s)
- Jianqi Wang
- Chongqing Key Laboratory of Maternal and Fetal Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xiaobo Zhou
- Chongqing Key Laboratory of Maternal and Fetal Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Department of Reproductive Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Tingli Han
- Chongqing Key Laboratory of Maternal and Fetal Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, 400016, China; The Center for Reproductive Medicine, Obstetrics and Gynecology Department, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China.
| | - Hua Zhang
- Chongqing Key Laboratory of Maternal and Fetal Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, 400016, China.
| |
Collapse
|
2
|
Yi M, Asgenbaatar N, Wang X, Ulaangerel T, Shen Y, Wen X, Du M, Dong X, Dugarjav M, Bou G. Different expression patterns of DNA methyltransferases during horse testis development. Gene 2024; 920:148531. [PMID: 38705424 DOI: 10.1016/j.gene.2024.148531] [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: 02/22/2024] [Revised: 04/28/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
DNA methyltransferases (DNMTs) are important epigenetic modification during spermatogenesis. To further evaluate the pattern of DNMTs in horse testes during development, we investigated the expression and localization of DNMT1, DNMT3a and DNMT3b at different time points. The qRT-PCR results showed that DNMT1 expression was maintained in testes tissue from 6-month-old (0.5y) to 2-year-old (2y) of age and decreased after 3-year-old (3y) (P < 0.01). The expression levels of DNMT3a and DNMT3b peaked in testes tissue at 3y (P < 0.01). At 4-year-old (4y), the expression of DNMT3a and DNMT3b was decreased and became similar to that at 0.5y. Immunofluorescence of DNMT1, DNMT3a and DNMT3b on testis samples confirmed the differential expression and localization of these three DNA methylation transferases during horse development. Further molecular biological studies are needed to understand the implications of the expression patterns of these DNMTs in horse testes.
Collapse
Affiliation(s)
- Minna Yi
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China
| | - Nairag Asgenbaatar
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China; Da Bei Nong group rumination technology rumination acadamy Haidian District, Beijing, China
| | - Xisheng Wang
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China; Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
| | - Tseweendolmaa Ulaangerel
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China
| | - Yingchao Shen
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China
| | - Xin Wen
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China
| | - Ming Du
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaoling Dong
- Da Bei Nong group rumination technology rumination acadamy Haidian District, Beijing, China; China Agricultural University, Beijing, China
| | - Manglai Dugarjav
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China.
| | - Gerelchimeg Bou
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China.
| |
Collapse
|
3
|
Chen S, Liu S, Shi S, Yin H, Tang Y, Zhang J, Li W, Liu G, Qu K, Ding X, Wang Y, Liu J, Zhang S, Fang L, Yu Y. Cross-Species Comparative DNA Methylation Reveals Novel Insights into Complex Trait Genetics among Cattle, Sheep, and Goats. Mol Biol Evol 2024; 41:msae003. [PMID: 38266195 PMCID: PMC10834038 DOI: 10.1093/molbev/msae003] [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: 07/24/2023] [Revised: 12/28/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024] Open
Abstract
The cross-species characterization of evolutionary changes in the functional genome can facilitate the translation of genetic findings across species and the interpretation of the evolutionary basis underlying complex phenotypes. Yet, this has not been fully explored between cattle, sheep, goats, and other mammals. Here, we systematically characterized the evolutionary dynamics of DNA methylation and gene expression in 3 somatic tissues (i.e. brain, liver, and skeletal muscle) and sperm across 7 mammalian species, including 3 ruminant livestock species (cattle, sheep, and goats), humans, pigs, mice, and dogs, by generating and integrating 160 DNA methylation and transcriptomic data sets. We demonstrate dynamic changes of DNA hypomethylated regions and hypermethylated regions in tissue-type manner across cattle, sheep, and goats. Specifically, based on the phylo-epigenetic model of DNA methylome, we identified a total of 25,074 hypomethylated region extension events specific to cattle, which participated in rewiring tissue-specific regulatory network. Furthermore, by integrating genome-wide association studies of 50 cattle traits, we provided novel insights into the genetic and evolutionary basis of complex phenotypes in cattle. Overall, our study provides a valuable resource for exploring the evolutionary dynamics of the functional genome and highlights the importance of cross-species characterization of multiomics data sets for the evolutionary interpretation of complex phenotypes in cattle livestock.
Collapse
Affiliation(s)
- Siqian Chen
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shuli Liu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Shaolei Shi
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Hongwei Yin
- Agriculture Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yongjie Tang
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jinning Zhang
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wenlong Li
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Gang Liu
- National Animal Husbandry Service, Beijing 100125, China
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong 675000, China
| | - Xiangdong Ding
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yachun Wang
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jianfeng Liu
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shengli Zhang
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics (QGG), Aarhus University, Aarhus, Denmark
| | - Ying Yu
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| |
Collapse
|
4
|
Lea G, Hanna CW. Loss of DNA methylation disrupts syncytiotrophoblast development: Proposed consequences of aberrant germline gene activation. Bioessays 2024; 46:e2300140. [PMID: 37994176 DOI: 10.1002/bies.202300140] [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: 07/28/2023] [Revised: 09/26/2023] [Accepted: 10/24/2023] [Indexed: 11/24/2023]
Abstract
DNA methylation is a repressive epigenetic modification that is essential for development and its disruption is widely implicated in disease. Yet, remarkably, ablation of DNA methylation in transgenic mouse models has limited impact on transcriptional states. Across multiple tissues and developmental contexts, the predominant transcriptional signature upon loss of DNA methylation is the de-repression of a subset of germline genes, normally expressed in gametogenesis. We recently reported loss of de novo DNA methyltransferase DNMT3B resulted in up-regulation of germline genes and impaired syncytiotrophoblast formation in the murine placenta. This defect led to embryonic lethality. We hypothesize that de-repression of germline genes in the Dnmt3b knockout underpins aspects of the placental phenotype by interfering with normal developmental processes. Specifically, we discuss molecular mechanisms by which aberrant expression of the piRNA pathway, meiotic proteins or germline transcriptional regulators may disrupt syncytiotrophoblast development.
Collapse
Affiliation(s)
- Georgia Lea
- Department of Physiology Development and Neuroscience, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Courtney W Hanna
- Department of Physiology Development and Neuroscience, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| |
Collapse
|
5
|
Bulka CM, Everson TM, Burt AA, Marsit CJ, Karagas MR, Boyle KE, Niemiec S, Kechris K, Davidson EJ, Yang IV, Feinberg JI, Volk HE, Ladd-Acosta C, Breton CV, O’Shea TM, Fry RC. Sex-based differences in placental DNA methylation profiles related to gestational age: an NIH ECHO meta-analysis. Epigenetics 2023; 18:2179726. [PMID: 36840948 PMCID: PMC9980626 DOI: 10.1080/15592294.2023.2179726] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/08/2022] [Accepted: 12/21/2022] [Indexed: 02/26/2023] Open
Abstract
The placenta undergoes many changes throughout gestation to support the evolving needs of the foetus. There is also a growing appreciation that male and female foetuses develop differently in utero, with unique epigenetic changes in placental tissue. Here, we report meta-analysed sex-specific associations between gestational age and placental DNA methylation from four cohorts in the National Institutes of Health (NIH) Environmental influences on Child Health Outcomes (ECHO) Programme (355 females/419 males, gestational ages 23-42 weeks). We identified 407 cytosine-guanine dinucleotides (CpGs) in females and 794 in males where placental methylation levels were associated with gestational age. After cell-type adjustment, 55 CpGs in females and 826 in males were significant. These were enriched for biological processes critical to the immune system in females and transmembrane transport in males. Our findings are distinct between the sexes: in females, associations with gestational age are largely explained by differences in placental cellular composition, whereas in males, gestational age is directly associated with numerous alterations in methylation levels.
Collapse
Affiliation(s)
- Catherine M. Bulka
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- College of Public Health, University of South Florida, Tampa, FL, USA
| | - Todd M. Everson
- Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Amber A. Burt
- Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Carmen J. Marsit
- Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Margaret R. Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Kristen E. Boyle
- Section of Nutrition, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Colorado School of Public Health, The Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, Aurora, CO, USA
| | - Sierra Niemiec
- Colorado School of Public Health, The Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, Aurora, CO, USA
| | - Katerina Kechris
- Colorado School of Public Health, The Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, Aurora, CO, USA
- Department of Biostatistics & Informatics, Colorado School of Public Health, Aurora, CO, USA
| | | | - Ivana V. Yang
- Colorado School of Public Health, The Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, Aurora, CO, USA
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jason I. Feinberg
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, ML, USA
| | - Heather E. Volk
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, ML, USA
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, ML, USA
| | - Carrie V. Breton
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - T. Michael O’Shea
- Department of Pediatrics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rebecca C. Fry
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Institute for Environmental Health Solutions, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
6
|
Guo Z, Liu Y, Zhan S, Cao J, Wang L, Guo J, Li L, Zhang H, Zhong T. Expression patterns and DNA methylation profile of GTL2 gene in goats. Anim Biotechnol 2023; 34:3617-3625. [PMID: 36911908 DOI: 10.1080/10495398.2023.2184698] [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: 03/14/2023]
Abstract
Gene trap locus 2 (GTL2), a long non-coding paternal imprinting gene, participates in various biological processes, including cell proliferation, differentiation, and apoptosis, by regulating the transcription of target mRNA, which is tightly related to the growth of the organic and maintenance of function. In this study, DNA methylation patterns of CpG islands (CGI) of GTL2 were explored, and its expression level was quantified in six tissues, rumen epithelium cells, and skeletal muscle cells in goats. GTL2 expression levels were measured by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), and the methylation model was confirmed by bisulfite-sequencing PCR (BSP). CGI methylation of GTL2 indicated a moderate methylation (ranging from 81.42 to 86.83%) in the brain, heart, liver, kidney, lung, and longissimus dorsi. GTL2 is most highly expressed in brain tissues, but there is no significant difference in the other five tissues. In addition, in the rumen epithelium cell proliferation, GTL2 expression was highest at 60 h, followed by 72 h, and almost unchanged at 12-48 h. In the skeletal muscle cell differentiation, GTL2 expression was highest at 0 and 24 h, significantly decreasing at 72 and 128 h. Pearson correlation analysis did not indicate a clear relationship between methylation and GTL2 expression levels, suggesting that other regulatory factors may modulate GTL2 expression. This study will provide a better understanding of the expression regulation mechanism of genes in the delta-like homolog 1 gene (DLK1)-GTL2 domain.
Collapse
Affiliation(s)
- Ziwei Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yue Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Siyuan Zhan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiaxue Cao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Linjie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiazhong Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Li Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hongping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Tao Zhong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|
7
|
Sacco JC, Starr E, Weaver A, Dietz R, Spocter MA. Resequencing of the TMF-1 (TATA Element Modulatory Factor) regulated protein (TRNP1) gene in domestic and wild canids. Canine Med Genet 2023; 10:10. [PMID: 37968761 PMCID: PMC10647097 DOI: 10.1186/s40575-023-00133-0] [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: 07/06/2023] [Accepted: 10/27/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND Cortical folding is related to the functional organization of the brain. The TMF-1 regulated protein (TRNP1) regulates the expansion and folding of the mammalian cerebral cortex, a process that may have been accelerated by the domestication of dogs. The objectives of this study were to sequence the TRNP1 gene in dogs and related canid species, provide evidence of its expression in dog brain and compare the genetic variation within dogs and across the Canidae. The gene was located in silico to dog chromosome 2. The sequence was experimentally confirmed by amplifying and sequencing the TRNP1 exonic and promoter regions in 72 canids (36 purebred dogs, 20 Gy wolves and wolf-dog hybrids, 10 coyotes, 5 red foxes and 1 Gy fox). RESULTS A partial TRNP1 transcript was isolated from several regions in the dog brain. Thirty genetic polymorphisms were found in the Canis sp. with 17 common to both dogs and wolves, and only one unique to dogs. Seven polymorphisms were observed only in coyotes. An additional 9 variants were seen in red foxes. Dogs were the least genetically diverse. Several polymorphisms in the promoter and 3'untranslated region were predicted to alter TRNP1 function by interfering with the binding of transcriptional repressors and miRNAs expressed in neural precursors. A c.259_264 deletion variant that encodes a polyalanine expansion was polymorphic in all species studied except for dogs. A stretch of 15 nucleotides that is found in other mammalian sequences (corresponding to 5 amino acids located between Pro58 and Ala59 in the putative dog protein) was absent from the TRNP1 sequences of all 5 canid species sequenced. Both of these aforementioned coding sequence variations were predicted to affect the formation of alpha helices in the disordered region of the TRNP1 protein. CONCLUSIONS Potentially functionally important polymorphisms in the TRNP1 gene are found within and across various Canis species as well as the red fox, and unique differences in protein structure have evolved and been conserved in the Canidae compared to all other mammalian species.
Collapse
Affiliation(s)
- James C Sacco
- Ellis Pharmacogenomics Laboratory, College of Pharmacy and Health Sciences, Drake University, 50311, Des Moines, IA, USA.
| | - Emma Starr
- Ellis Pharmacogenomics Laboratory, College of Pharmacy and Health Sciences, Drake University, 50311, Des Moines, IA, USA
| | - Alyssa Weaver
- Ellis Pharmacogenomics Laboratory, College of Pharmacy and Health Sciences, Drake University, 50311, Des Moines, IA, USA
| | - Rachel Dietz
- Ellis Pharmacogenomics Laboratory, College of Pharmacy and Health Sciences, Drake University, 50311, Des Moines, IA, USA
| | - Muhammad A Spocter
- Department of Anatomy, Des Moines University, 50266, Des Moines, IA, USA
| |
Collapse
|
8
|
Ahn J, Hwang IS, Park MR, Hwang S, Lee K. Imprinting at the KBTBD6 locus involves species-specific maternal methylation and monoallelic expression in livestock animals. J Anim Sci Biotechnol 2023; 14:131. [PMID: 37817239 PMCID: PMC10565993 DOI: 10.1186/s40104-023-00931-3] [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: 06/02/2023] [Accepted: 08/21/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND The primary differentially methylated regions (DMRs) which are maternally hypermethylated serve as imprinting control regions (ICRs) that drive monoallelic gene expression, and these ICRs have been investigated due to their implications in mammalian development. Although a subset of genes has been identified as imprinted, in-depth comparative approach needs to be developed for identification of species-specific imprinted genes. Here, we examined DNA methylation status and allelic expression at the KBTBD6 locus across species and tissues and explored potential mechanisms of imprinting. RESULTS Using whole-genome bisulfite sequencing and RNA-sequencing on parthenogenetic and normal porcine embryos, we identified a maternally hypermethylated DMR between the embryos at the KBTBD6 promoter CpG island and paternal monoallelic expression of KBTBD6. Also, in analyzed domesticated mammals but not in humans, non-human primates and mice, the KBTBD6 promoter CpG islands were methylated in oocytes and/or allelically methylated in tissues, and monoallelic KBTBD6 expression was observed, indicating livestock-specific imprinting. Further analysis revealed that these CpG islands were embedded within transcripts in porcine and bovine oocytes which coexisted with an active transcription mark and DNA methylation, implying the presence of transcription-dependent imprinting. CONCLUSIONS In this study, our comparative approach revealed an imprinted expression of the KBTBD6 gene in domesticated mammals, but not in humans, non-human primates, and mice which implicates species-specific evolution of genomic imprinting.
Collapse
Affiliation(s)
- Jinsoo Ahn
- Department of Animal Sciences, The Ohio State University, Columbus, OH 43210 USA
| | - In-Sul Hwang
- Animal Biotechnology Division, Rural Development Administration, National Institute of Animal Science, Jeonbuk, 55365 Republic of Korea
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, Columbia University, New York, NY 10032 USA
| | - Mi-Ryung Park
- Animal Biotechnology Division, Rural Development Administration, National Institute of Animal Science, Jeonbuk, 55365 Republic of Korea
| | - Seongsoo Hwang
- Animal Welfare Research Team, National Institute of Animal Science, RDA, 1500, Kongjwipatjwi-ro, Jeollabuk-do, 55365 Republic of Korea
| | - Kichoon Lee
- Department of Animal Sciences, The Ohio State University, Columbus, OH 43210 USA
| |
Collapse
|
9
|
Pedroza M, Gassaloglu SI, Dias N, Zhong L, Hou TCJ, Kretzmer H, Smith ZD, Sozen B. Self-patterning of human stem cells into post-implantation lineages. Nature 2023; 622:574-583. [PMID: 37369348 PMCID: PMC10584676 DOI: 10.1038/s41586-023-06354-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 06/21/2023] [Indexed: 06/29/2023]
Abstract
Investigating human development is a substantial scientific challenge due to the technical and ethical limitations of working with embryonic samples. In the face of these difficulties, stem cells have provided an alternative to experimentally model inaccessible stages of human development in vitro1-13. Here we show that human pluripotent stem cells can be triggered to self-organize into three-dimensional structures that recapitulate some key spatiotemporal events of early human post-implantation embryonic development. Our system reproducibly captures spontaneous differentiation and co-development of embryonic epiblast-like and extra-embryonic hypoblast-like lineages, establishes key signalling hubs with secreted modulators and undergoes symmetry breaking-like events. Single-cell transcriptomics confirms differentiation into diverse cell states of the perigastrulating human embryo14,15 without establishing placental cell types, including signatures of post-implantation epiblast, amniotic ectoderm, primitive streak, mesoderm, early extra-embryonic endoderm, as well as initial yolk sac induction. Collectively, our system captures key features of human embryonic development spanning from Carnegie stage16 4-7, offering a reproducible, tractable and scalable experimental platform to understand the basic cellular and molecular mechanisms that underlie human development, including new opportunities to dissect congenital pathologies with high throughput.
Collapse
Affiliation(s)
- Monique Pedroza
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Seher Ipek Gassaloglu
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Nicolas Dias
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, USA
- Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Liangwen Zhong
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Tien-Chi Jason Hou
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, USA
- Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Zachary D Smith
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, USA
- Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Berna Sozen
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, USA.
- Yale Stem Cell Center, Yale University, New Haven, CT, USA.
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, Yale University, New Haven, CT, USA.
| |
Collapse
|
10
|
LaSalle JM. Epigenomic signatures reveal mechanistic clues and predictive markers for autism spectrum disorder. Mol Psychiatry 2023; 28:1890-1901. [PMID: 36650278 PMCID: PMC10560404 DOI: 10.1038/s41380-022-01917-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 01/18/2023]
Abstract
Autism spectrum disorder (ASD) comprises a heterogeneous group of neurodevelopmental outcomes in children with a commonality in deficits in social communication and language combined with repetitive behaviors and interests. The etiology of ASD is heterogeneous, as several hundred genes have been implicated as well as multiple in utero environmental exposures. Over the past two decades, epigenetic investigations, including DNA methylation, have emerged as a novel way to capture the complex interface of multivariate ASD etiologies. More recently, epigenome-wide association studies using human brain and surrogate accessible tissues have revealed some convergent genes that are epigenetically altered in ASD, many of which overlap with known genetic risk factors. Unlike transcriptomes, epigenomic signatures defined by DNA methylation from surrogate tissues such as placenta and cord blood can reflect past differences in fetal brain gene transcription, transcription factor binding, and chromatin. For example, the discovery of NHIP (neuronal hypoxia inducible, placenta associated) through an epigenome-wide association in placenta, identified a common genetic risk for ASD that was modified by prenatal vitamin use. While epigenomic signatures are distinct between different genetic syndromic causes of ASD, bivalent chromatin and some convergent gene pathways are consistently epigenetically altered in both syndromic and idiopathic ASD, as well as some environmental exposures. Together, these epigenomic signatures hold promising clues towards improved early prediction and prevention of ASD as well genes and gene pathways to target for pharmacological interventions. Future advancements in single cell and multi-omic technologies, machine learning, as well as non-invasive screening of epigenomic signatures during pregnancy or newborn periods are expected to continue to impact the translatability of the recent discoveries in epigenomics to precision public health.
Collapse
Affiliation(s)
- Janine M LaSalle
- Department of Medical Microbiology and Immunology, Perinatal Origins of Disparities Center, MIND Institute, Genome Center, Environmental Health Sciences Center, University of California Davis, Davis, CA, USA.
| |
Collapse
|
11
|
Klughammer J, Romanovskaia D, Nemc A, Posautz A, Seid CA, Schuster LC, Keinath MC, Lugo Ramos JS, Kosack L, Evankow A, Printz D, Kirchberger S, Ergüner B, Datlinger P, Fortelny N, Schmidl C, Farlik M, Skjærven K, Bergthaler A, Liedvogel M, Thaller D, Burger PA, Hermann M, Distel M, Distel DL, Kübber-Heiss A, Bock C. Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species. Nat Commun 2023; 14:232. [PMID: 36646694 PMCID: PMC9842680 DOI: 10.1038/s41467-022-34828-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 11/08/2022] [Indexed: 01/18/2023] Open
Abstract
Methylation of cytosines is a prototypic epigenetic modification of the DNA. It has been implicated in various regulatory mechanisms across the animal kingdom and particularly in vertebrates. We mapped DNA methylation in 580 animal species (535 vertebrates, 45 invertebrates), resulting in 2443 genome-scale DNA methylation profiles of multiple organs. Bioinformatic analysis of this large dataset quantified the association of DNA methylation with the underlying genomic DNA sequence throughout vertebrate evolution. We observed a broadly conserved link with two major transitions-once in the first vertebrates and again with the emergence of reptiles. Cross-species comparisons focusing on individual organs supported a deeply conserved association of DNA methylation with tissue type, and cross-mapping analysis of DNA methylation at gene promoters revealed evolutionary changes for orthologous genes. In summary, this study establishes a large resource of vertebrate and invertebrate DNA methylomes, it showcases the power of reference-free epigenome analysis in species for which no reference genomes are available, and it contributes an epigenetic perspective to the study of vertebrate evolution.
Collapse
Affiliation(s)
- Johanna Klughammer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria. .,Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Daria Romanovskaia
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Amelie Nemc
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Annika Posautz
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Charlotte A Seid
- Ocean Genome Legacy Center, Northeastern University Marine Science Center, Nahant, USA
| | - Linda C Schuster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Juan Sebastian Lugo Ramos
- Max Planck Research Group Behavioral Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Lindsay Kosack
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ann Evankow
- Ocean Genome Legacy Center, Northeastern University Marine Science Center, Nahant, USA
| | - Dieter Printz
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Stefanie Kirchberger
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Bekir Ergüner
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Paul Datlinger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Nikolaus Fortelny
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Christian Schmidl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Matthias Farlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Medical University of Vienna, Center for Pathophysiology Infectiology and Immunology, Institute of Hygiene and Applied Immunology, Vienna, Austria
| | - Miriam Liedvogel
- Max Planck Research Group Behavioral Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Institute of Avian Research, An der Vogelwarte, Wilhelmshaven, Germany
| | - Denise Thaller
- Department for Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Pamela A Burger
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Marcela Hermann
- Medical University of Vienna, Department of Medical Biochemistry, Vienna, Austria
| | - Martin Distel
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Daniel L Distel
- Ocean Genome Legacy Center, Northeastern University Marine Science Center, Nahant, USA
| | - Anna Kübber-Heiss
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria. .,Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Vienna, Austria.
| |
Collapse
|
12
|
Ravaei A, Emanuele M, Nazzaro G, Fadiga L, Rubini M. Placental DNA methylation profile as predicting marker for autism spectrum disorder (ASD). Mol Med 2023; 29:8. [PMID: 36647002 PMCID: PMC9843962 DOI: 10.1186/s10020-022-00593-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/15/2022] [Indexed: 01/18/2023] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder that impairs normal brain development and socio-cognitive abilities. The pathogenesis of this condition points out the involvement of genetic and environmental factors during in-utero life. Placenta, as an interface tissue between mother and fetus, provides developing fetus requirements and exposes it to maternal environment as well. Therefore, the alteration of DNA methylation as epigenetic consequence of gene-environmental interaction in the placenta could shed light on ASD pathogenesis. In this study, we reviewed the current findings on placental methylation status and its association with ASD. Differentially methylated regions (DMRs) in ASD-developing placenta were found to be mainly enriched in ASD gene loci affecting synaptogenesis, microtubule dynamics, neurogenesis and neuritogenesis. In addition, non-genic DMRs in ASD-placenta proposes an alternative contributing mechanism for ASD development. Our study highlights the importance of placental DNA methylation signature as a biomarker for ASD prediction.
Collapse
Affiliation(s)
- Amin Ravaei
- grid.8484.00000 0004 1757 2064Medical Genetics Laboratory, Department of Neuroscience and Rehabilitation, University of Ferrara, Via Fossato di Mortara 74, 44121 Ferrara, Italy
| | - Marco Emanuele
- grid.8484.00000 0004 1757 2064Section of Physiology, Department of Neuroscience and Rehabilitation, University of Ferrara, Ferrara, Italy ,grid.25786.3e0000 0004 1764 2907IIT@UniFe Center for Translational Neurophysiology of Speech and Communication (CTNSC), Istituto Italiano di Tecnologia, Ferrara, Italy
| | - Giovanni Nazzaro
- grid.8484.00000 0004 1757 2064Section of Physiology, Department of Neuroscience and Rehabilitation, University of Ferrara, Ferrara, Italy ,grid.25786.3e0000 0004 1764 2907IIT@UniFe Center for Translational Neurophysiology of Speech and Communication (CTNSC), Istituto Italiano di Tecnologia, Ferrara, Italy
| | - Luciano Fadiga
- grid.8484.00000 0004 1757 2064Section of Physiology, Department of Neuroscience and Rehabilitation, University of Ferrara, Ferrara, Italy ,grid.25786.3e0000 0004 1764 2907IIT@UniFe Center for Translational Neurophysiology of Speech and Communication (CTNSC), Istituto Italiano di Tecnologia, Ferrara, Italy
| | - Michele Rubini
- grid.8484.00000 0004 1757 2064Medical Genetics Laboratory, Department of Neuroscience and Rehabilitation, University of Ferrara, Via Fossato di Mortara 74, 44121 Ferrara, Italy
| |
Collapse
|
13
|
Carrasco-Wong I, González-Ortiz M, Araujo GG, Lima VV, Giachini FR, Stojanova J, Moller A, Martín SS, Escudero P, Damiano AE, Sosa-Macias M, Galaviz-Hernandez C, Teran E, Escudero C. The Placental Function Beyond Pregnancy: Insights from Latin America. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1428:287-307. [PMID: 37466779 DOI: 10.1007/978-3-031-32554-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Currently, more than 100,000 papers had been published studying the placenta in both physiological and pathological contexts. However, relevant health conditions affecting placental function, mostly found in low-income countries, should be evaluated deeper. This review will raise some - of what we think necessary - points of discussion regarding challenging topics not fully understood, including the paternal versus maternal contribution on placental genes imprinting, placenta-brain communication, and some environmental conditions affecting the placenta. The discussions are parts of an international effort to fulfil some gaps observed in this area, and Latin-American research groups currently evaluate that.
Collapse
Affiliation(s)
- Ivo Carrasco-Wong
- Cellular Signaling and Differentiation Laboratory (CSDL), School of Medical Technology, Medicine and Science Faculty, Universidad San Sebastián, Santiago, Chile
| | - Marcelo González-Ortiz
- Laboratorio de Investigación Materno-Fetal (LIMaF), Departamento de Obstetricia y Ginecología, Facultad de Medicina, Universidad de Concepción, Concepción, Chile
- Group of Research and Innovation in Vascular Health (GRIVAS Health), Chillan, Chile
| | - Gabriel Gomes Araujo
- Laboratory of Vascular Biology, Institute of Health Sciences and Health, Universidade Federal de Mato Grosso, Barra do Garcas, Brazil
| | - Victor V Lima
- Laboratory of Vascular Biology, Institute of Health Sciences and Health, Universidade Federal de Mato Grosso, Barra do Garcas, Brazil
| | - Fernanda R Giachini
- Laboratory of Vascular Biology, Institute of Health Sciences and Health, Universidade Federal de Mato Grosso, Barra do Garcas, Brazil
| | - Jana Stojanova
- Interdisciplinary Centre for Health Studies (CIESAL), Universidad de Valparaíso, Viña del Mar, Chile
| | - Alejandra Moller
- Escuela de Tecnología Médica, Facultad de Medicina, Universidad de Valparaíso, Viña del Mar, Chile
| | - Sebastián San Martín
- Group of Research and Innovation in Vascular Health (GRIVAS Health), Chillan, Chile
- Biomedical Research Centre, School of Medicine, Universidad de Valparaíso, Viña del Mar, Chile
| | - Pablo Escudero
- Faculty of Medicine, Universidad San Sebastian, Sede Concepcion, Chile
| | - Alicia E Damiano
- Laboratorio de Biología de la Reproducción, Instituto de Fisiología y Biofísica Bernardo Houssay (IFIBIO)- CONICET- Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
- Cátedra de Biología Celular y Molecular, Departamento de Ciencias Biológicas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Martha Sosa-Macias
- Genomics Academia, Instituto Politécnico Nacional-CIIDIR Durango, Durango, Mexico
| | | | - Enrique Teran
- Colegio de Ciencias de la Salud, Universidad San Francisco de Quito, Quito, Ecuador
| | - Carlos Escudero
- Group of Research and Innovation in Vascular Health (GRIVAS Health), Chillan, Chile.
- Vascular Physiology Laboratory, Basic Sciences Department, Faculty of Sciences, Universidad del Bio-Bio, Chillan, Chile.
| |
Collapse
|
14
|
Mechanisms of DNA methylation and histone modifications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:51-92. [PMID: 37019597 DOI: 10.1016/bs.pmbts.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The field of genetics has expanded a lot in the past few decades due to the accessibility of human genome sequences, but still, the regulation of transcription cannot be explicated exclusively by the sequence of DNA of an individual. The coordination and crosstalk between chromatin factors which are conserved is indispensable for all living creatures. The regulation of gene expression has been dependent on the methylation of DNA, post-translational modifications of histones, effector proteins, chromatin remodeler enzymes that affect the chromatin structure and function, and other cellular activities such as DNA replication, DNA repair, proliferation and growth. The mutation and deletion of these factors can lead to human diseases. Various studies are being performed to identify and understand the gene regulatory mechanisms in the diseased state. The information from these high throughput screening studies is able to aid the treatment developments based on the epigenetics regulatory mechanisms. This book chapter will discourse on various modifications and their mechanisms that take place on histones and DNA that regulate the transcription of genes.
Collapse
|
15
|
Laufer BI, Hasegawa Y, Zhang Z, Hogrefe CE, Del Rosso LA, Haapanen L, Hwang H, Bauman MD, Van de Water J, Taha AY, Slupsky CM, Golub MS, Capitanio JP, VandeVoort CA, Walker CK, LaSalle JM. Multi-omic brain and behavioral correlates of cell-free fetal DNA methylation in macaque maternal obesity models. Nat Commun 2022; 13:5538. [PMID: 36130949 PMCID: PMC9492781 DOI: 10.1038/s41467-022-33162-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 09/06/2022] [Indexed: 11/28/2022] Open
Abstract
Maternal obesity during pregnancy is associated with neurodevelopmental disorder (NDD) risk. We utilized integrative multi-omics to examine maternal obesity effects on offspring neurodevelopment in rhesus macaques by comparison to lean controls and two interventions. Differentially methylated regions (DMRs) from longitudinal maternal blood-derived cell-free fetal DNA (cffDNA) significantly overlapped with DMRs from infant brain. The DMRs were enriched for neurodevelopmental functions, methylation-sensitive developmental transcription factor motifs, and human NDD DMRs identified from brain and placenta. Brain and cffDNA methylation levels from a large region overlapping mir-663 correlated with maternal obesity, metabolic and immune markers, and infant behavior. A DUX4 hippocampal co-methylation network correlated with maternal obesity, infant behavior, infant hippocampal lipidomic and metabolomic profiles, and maternal blood measurements of DUX4 cffDNA methylation, cytokines, and metabolites. We conclude that in this model, maternal obesity was associated with changes in the infant brain and behavior, and these differences were detectable in pregnancy through integrative analyses of cffDNA methylation with immune and metabolic factors.
Collapse
Affiliation(s)
- Benjamin I Laufer
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, 95616, USA
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
- Department of OMNI Bioinformatics, Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Yu Hasegawa
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA
| | - Zhichao Zhang
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA
| | - Casey E Hogrefe
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
| | - Laura A Del Rosso
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
| | - Lori Haapanen
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
| | - Hyeyeon Hwang
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, 95616, USA
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
| | - Melissa D Bauman
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
- Department of Psychiatry and Behavioral Sciences, School of Medicine, University of California Davis, Davis, CA, 95616, USA
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA
| | - Judy Van de Water
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA
- Department of Internal Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Ameer Y Taha
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA
| | - Carolyn M Slupsky
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA
- Department of Nutrition, University of California Davis, Davis, CA, 95616, USA
| | - Mari S Golub
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
| | - John P Capitanio
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
- Department of Psychology, University of California Davis, Davis, CA, 95616, USA
| | - Catherine A VandeVoort
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
- Department of Obstetrics and Gynecology, School of Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Cheryl K Walker
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA
- Department of Obstetrics and Gynecology, School of Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, 95616, USA.
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA.
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA.
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA.
| |
Collapse
|
16
|
Dou JF, Middleton LYM, Zhu Y, Benke KS, Feinberg JI, Croen LA, Hertz-Picciotto I, Newschaffer CJ, LaSalle JM, Fallin D, Schmidt RJ, Bakulski KM. Prenatal vitamin intake in first month of pregnancy and DNA methylation in cord blood and placenta in two prospective cohorts. Epigenetics Chromatin 2022; 15:28. [PMID: 35918756 PMCID: PMC9344645 DOI: 10.1186/s13072-022-00460-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/21/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Prenatal vitamin use is recommended before and during pregnancies for normal fetal development. Prenatal vitamins do not have a standard formulation, but many contain calcium, folic acid, iodine, iron, omega-3 fatty acids, zinc, and vitamins A, B6, B12, and D, and usually they contain higher concentrations of folic acid and iron than regular multivitamins in the US Nutrient levels can impact epigenetic factors such as DNA methylation, but relationships between maternal prenatal vitamin use and DNA methylation have been relatively understudied. We examined use of prenatal vitamins in the first month of pregnancy in relation to cord blood and placenta DNA methylation in two prospective pregnancy cohorts: the Early Autism Risk Longitudinal Investigation (EARLI) and Markers of Autism Risk Learning Early Signs (MARBLES) studies. RESULTS In placenta, prenatal vitamin intake was marginally associated with -0.52% (95% CI -1.04, 0.01) lower mean array-wide DNA methylation in EARLI, and associated with -0.60% (-1.08, -0.13) lower mean array-wide DNA methylation in MARBLES. There was little consistency in the associations between prenatal vitamin intake and single DNA methylation site effect estimates across cohorts and tissues, with only a few overlapping sites with correlated effect estimates. However, the single DNA methylation sites with p-value < 0.01 (EARLI cord nCpGs = 4068, EARLI placenta nCpGs = 3647, MARBLES cord nCpGs = 4068, MARBLES placenta nCpGs = 9563) were consistently enriched in neuronal developmental pathways. CONCLUSIONS Together, our findings suggest that prenatal vitamin intake in the first month of pregnancy may be related to lower placental global DNA methylation and related to DNA methylation in brain-related pathways in both placenta and cord blood.
Collapse
Affiliation(s)
- John F Dou
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, USA
| | - Lauren Y M Middleton
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, USA
| | - Yihui Zhu
- Department of Public Health Sciences and the M.I.N.D. Institute, School of Medicine, University of California, Davis, CA, USA
| | - Kelly S Benke
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Jason I Feinberg
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Lisa A Croen
- Kaiser Permanente Northern California, Oakland, CA, USA
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences and the M.I.N.D. Institute, School of Medicine, University of California, Davis, CA, USA
| | - Craig J Newschaffer
- College of Health and Human Development, Penn State University, State College, PA, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology and the M.I.N.D. Institute, School of Medicine, University of California, Davis, CA, USA
| | - Daniele Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Rebecca J Schmidt
- Department of Public Health Sciences and the M.I.N.D. Institute, School of Medicine, University of California, Davis, CA, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, USA.
| |
Collapse
|
17
|
Islam M, Strawn M, Behura SK. Fetal origin of sex‐bias brain aging. FASEB J 2022; 36:e22463. [DOI: 10.1096/fj.202200255rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/30/2022] [Accepted: 07/11/2022] [Indexed: 02/01/2023]
Affiliation(s)
- Maliha Islam
- Division of Animal Sciences University of Missouri Columbia Missouri USA
| | - Monica Strawn
- Division of Animal Sciences University of Missouri Columbia Missouri USA
| | - Susanta K. Behura
- Division of Animal Sciences University of Missouri Columbia Missouri USA
- MU Institute for Data Science and Informatics University of Missouri Columbia Missouri USA
- Interdisciplinary Neuroscience Program University of Missouri Columbia Missouri USA
| |
Collapse
|
18
|
Wanigasuriya I, Kinkel SA, Beck T, Roper EA, Breslin K, Lee HJ, Keniry A, Ritchie ME, Blewitt ME, Gouil Q. Maternal SMCHD1 controls both imprinted Xist expression and imprinted X chromosome inactivation. Epigenetics Chromatin 2022; 15:26. [PMID: 35843975 PMCID: PMC9290310 DOI: 10.1186/s13072-022-00458-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 06/21/2022] [Indexed: 12/13/2022] Open
Abstract
Embryonic development is dependent on the maternal supply of proteins through the oocyte, including factors setting up the adequate epigenetic patterning of the zygotic genome. We previously reported that one such factor is the epigenetic repressor SMCHD1, whose maternal supply controls autosomal imprinted expression in mouse preimplantation embryos and mid-gestation placenta. In mouse preimplantation embryos, X chromosome inactivation is also an imprinted process. Combining genomics and imaging, we show that maternal SMCHD1 is required not only for the imprinted expression of Xist in preimplantation embryos, but also for the efficient silencing of the inactive X in both the preimplantation embryo and mid-gestation placenta. These results expand the role of SMCHD1 in enforcing the silencing of Polycomb targets. The inability of zygotic SMCHD1 to fully restore imprinted X inactivation further points to maternal SMCHD1’s role in setting up the appropriate chromatin environment during preimplantation development, a critical window of epigenetic remodelling.
Collapse
Affiliation(s)
- Iromi Wanigasuriya
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Sarah A Kinkel
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Tamara Beck
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Ellise A Roper
- The School of Biomedical Sciences and Pharmacy, The University of Newcastle, Newcastle, Australia
| | - Kelsey Breslin
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Heather J Lee
- The School of Biomedical Sciences and Pharmacy, The University of Newcastle, Newcastle, Australia
| | - Andrew Keniry
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Matthew E Ritchie
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia.,The Department of Mathematics and Statistics, The University of Melbourne, Parkville, Australia
| | - Marnie E Blewitt
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia. .,The Department of Medical Biology, The University of Melbourne, Parkville, Australia.
| | - Quentin Gouil
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia. .,The Department of Medical Biology, The University of Melbourne, Parkville, Australia.
| |
Collapse
|
19
|
Comparative parallel multi-omics analysis during the induction of pluripotent and trophectoderm states. Nat Commun 2022; 13:3475. [PMID: 35715410 PMCID: PMC9205865 DOI: 10.1038/s41467-022-31131-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/31/2022] [Indexed: 11/09/2022] Open
Abstract
Following fertilization, it is only at the 32-64-cell stage when a clear segregation between cells of the inner cell mass and trophectoderm is observed, suggesting a 'T'-shaped model of specification. Here, we examine whether the acquisition of these two states in vitro, by nuclear reprogramming, share similar dynamics/trajectories. Using a comparative parallel multi-omics analysis (i.e., bulk RNA-seq, scRNA-seq, ATAC-seq, ChIP-seq, RRBS and CNVs) on cells undergoing reprogramming to pluripotency and TSC state we show that each reprogramming system exhibits specific trajectories from the onset of the process, suggesting 'V'-shaped model. We describe in detail the various trajectories toward the two states and illuminate reprogramming stage-specific markers, blockers, facilitators and TSC subpopulations. Finally, we show that while the acquisition of the TSC state involves the silencing of embryonic programs by DNA methylation, during the acquisition of pluripotency these regions are initially defined but retain inactive by the elimination of H3K27ac.
Collapse
|
20
|
Abstract
Dramatic nuclear reorganization occurs during early development to convert terminally differentiated gametes to a totipotent zygote, which then gives rise to an embryo. Aberrant epigenome resetting severely impairs embryo development and even leads to lethality. How the epigenomes are inherited, reprogrammed, and reestablished in this critical developmental period has gradually been unveiled through the rapid development of technologies including ultrasensitive chromatin analysis methods. In this review, we summarize the latest findings on epigenetic reprogramming in gametogenesis and embryogenesis, and how it contributes to gamete maturation and parental-to-zygotic transition. Finally, we highlight the key questions that remain to be answered to fully understand chromatin regulation and nuclear reprogramming in early development.
Collapse
Affiliation(s)
- Zhenhai Du
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Ke Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| |
Collapse
|
21
|
Laufer BI, Neier K, Valenzuela AE, Yasui DH, Schmidt RJ, Lein PJ, LaSalle JM. Placenta and fetal brain share a neurodevelopmental disorder DNA methylation profile in a mouse model of prenatal PCB exposure. Cell Rep 2022; 38:110442. [PMID: 35235788 PMCID: PMC8941983 DOI: 10.1016/j.celrep.2022.110442] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/19/2021] [Accepted: 02/03/2022] [Indexed: 12/27/2022] Open
Abstract
Polychlorinated biphenyls (PCBs) are developmental neurotoxicants implicated as environmental risk factors for neurodevelopmental disorders (NDDs). Here, we report the effects of prenatal exposure to a human-relevant mixture of PCBs on the DNA methylation profiles of mouse placenta and fetal brain. Thousands of differentially methylated regions (DMRs) distinguish placenta and fetal brain from PCB-exposed mice from sex-matched vehicle controls. In both placenta and fetal brain, PCB-associated DMRs are enriched for functions related to neurodevelopment and cellular signaling and enriched within regions of bivalent chromatin. The placenta and brain PCB DMRs overlap significantly and map to a shared subset of genes enriched for Wnt signaling, Slit/Robo signaling, and genes differentially expressed in NDD models. The consensus PCB DMRs also significantly overlap with DMRs from human NDD brain and placenta. These results demonstrate that PCB-exposed placenta contains a subset of DMRs that overlap fetal brain DMRs relevant to an NDD.
Collapse
Affiliation(s)
- Benjamin I Laufer
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA; UC Davis Genome Center, University of California, Davis, Davis, CA 95616, USA; MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Kari Neier
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA; UC Davis Genome Center, University of California, Davis, Davis, CA 95616, USA; MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA; Perinatal Origins of Disparities Center, University of California, Davis, Davis, CA 95616, USA
| | - Anthony E Valenzuela
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Dag H Yasui
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA; UC Davis Genome Center, University of California, Davis, Davis, CA 95616, USA; MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Rebecca J Schmidt
- MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA; Perinatal Origins of Disparities Center, University of California, Davis, Davis, CA 95616, USA; Department of Public Health Sciences, School of Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Pamela J Lein
- MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA; Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA; UC Davis Genome Center, University of California, Davis, Davis, CA 95616, USA; MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA; Perinatal Origins of Disparities Center, University of California, Davis, Davis, CA 95616, USA.
| |
Collapse
|
22
|
Zhu Y, Gomez JA, Laufer BI, Mordaunt CE, Mouat JS, Soto DC, Dennis MY, Benke KS, Bakulski KM, Dou J, Marathe R, Jianu JM, Williams LA, Gutierrez Fugón OJ, Walker CK, Ozonoff S, Daniels J, Grosvenor LP, Volk HE, Feinberg JI, Fallin MD, Hertz-Picciotto I, Schmidt RJ, Yasui DH, LaSalle JM. Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism. Genome Biol 2022; 23:46. [PMID: 35168652 PMCID: PMC8848662 DOI: 10.1186/s13059-022-02613-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/16/2022] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) involves complex genetics interacting with the perinatal environment, complicating the discovery of common genetic risk. The epigenetic layer of DNA methylation shows dynamic developmental changes and molecular memory of in utero experiences, particularly in placenta, a fetal tissue discarded at birth. However, current array-based methods to identify novel ASD risk genes lack coverage of the most structurally and epigenetically variable regions of the human genome. RESULTS We use whole genome bisulfite sequencing in placenta samples from prospective ASD studies to discover a previously uncharacterized ASD risk gene, LOC105373085, renamed NHIP. Out of 134 differentially methylated regions associated with ASD in placental samples, a cluster at 22q13.33 corresponds to a 118-kb hypomethylated block that replicates in two additional cohorts. Within this locus, NHIP is functionally characterized as a nuclear peptide-encoding transcript with high expression in brain, and increased expression following neuronal differentiation or hypoxia, but decreased expression in ASD placenta and brain. NHIP overexpression increases cellular proliferation and alters expression of genes regulating synapses and neurogenesis, overlapping significantly with known ASD risk genes and NHIP-associated genes in ASD brain. A common structural variant disrupting the proximity of NHIP to a fetal brain enhancer is associated with NHIP expression and methylation levels and ASD risk, demonstrating a common genetic influence. CONCLUSIONS Together, these results identify and initially characterize a novel environmentally responsive ASD risk gene relevant to brain development in a hitherto under-characterized region of the human genome.
Collapse
Affiliation(s)
- Yihui Zhu
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - J Antonio Gomez
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Benjamin I Laufer
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Charles E Mordaunt
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Julia S Mouat
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Daniela C Soto
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, CA, USA
| | - Megan Y Dennis
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, CA, USA
| | - Kelly S Benke
- Department of Public Health Sciences, University of California, Davis, CA, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - John Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Ria Marathe
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Julia M Jianu
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Logan A Williams
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Orangel J Gutierrez Fugón
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Cheryl K Walker
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
- Department of Obstetrics and Gynecology, University of California, Davis, CA, USA
| | - Sally Ozonoff
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
- Department of Psychiatry and Behavioral Sciences, Davis, CA, USA
| | - Jason Daniels
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Luke P Grosvenor
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Heather E Volk
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
- Wendy Klag Center for Autism and Developmental Disabilities, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Jason I Feinberg
- Wendy Klag Center for Autism and Developmental Disabilities, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - M Daniele Fallin
- Wendy Klag Center for Autism and Developmental Disabilities, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Irva Hertz-Picciotto
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
- Department of Public Health Sciences, University of California, Davis, CA, USA
| | - Rebecca J Schmidt
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
- Department of Public Health Sciences, University of California, Davis, CA, USA
| | - Dag H Yasui
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA.
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA.
- Genome Center, University of California, Davis, CA, USA.
- MIND Institute, School of Medicine, University of California, Davis, CA, USA.
| |
Collapse
|
23
|
Cui G, Xu Y, Cao S, Shi K. Inducing somatic cells into pluripotent stem cells is an important platform to study the mechanism of early embryonic development. Mol Reprod Dev 2022; 89:70-85. [PMID: 35075695 DOI: 10.1002/mrd.23559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 12/16/2021] [Accepted: 01/10/2022] [Indexed: 01/24/2023]
Abstract
The early embryonic development starts with the totipotent zygote upon fertilization of differentiated sperm and egg, which undergoes a range of reprogramming and transformation to acquire pluripotency. Induced pluripotent stem cells (iPSCs), a nonclonal technique to produce stem cells, are originated from differentiated somatic cells via accomplishment of cell reprogramming, which shares common reprogramming process with early embryonic development. iPSCs are attractive in recent years due to the potentially significant applications in disease modeling, potential value in genetic improvement of husbandry animal, regenerative medicine, and drug screening. This review focuses on introducing the research advance of both somatic cell reprogramming and early embryonic development, indicating that the mechanisms of iPSCs also shares common features with that of early embryonic development in several aspects, such as germ cell factors, DNA methylation, histone modification, and/or X chromosome inactivation. As iPSCs can successfully avoid ethical concerns that are naturally present in the embryos and/or embryonic stem cells, the practicality of somatic cell reprogramming (iPSCs) could provide an insightful platform to elucidate the mechanisms underlying the early embryonic development.
Collapse
Affiliation(s)
- Guina Cui
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, China
| | - Yanwen Xu
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, China
| | - Shuyuan Cao
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, China
| | - Kerong Shi
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, China
| |
Collapse
|
24
|
Pastor WA, Kwon SY. Distinctive aspects of the placental epigenome and theories as to how they arise. Cell Mol Life Sci 2022; 79:569. [PMID: 36287261 PMCID: PMC9606139 DOI: 10.1007/s00018-022-04568-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 08/18/2022] [Accepted: 09/21/2022] [Indexed: 11/26/2022]
Abstract
The placenta has a methylome dramatically unlike that of any somatic cell type. Among other distinctions, it features low global DNA methylation, extensive “partially methylated domains” packed in dense heterochromatin and methylation of hundreds of CpG islands important in somatic development. These features attract interest in part because a substantial fraction of human cancers feature the exact same phenomena, suggesting parallels between epigenome formation in placentation and cancer. Placenta also features an expanded set of imprinted genes, some of which come about by distinctive developmental pathways. Recent discoveries, some from far outside the placental field, shed new light on how the unusual placental epigenetic state may arise. Nonetheless, key questions remain unresolved.
Collapse
Affiliation(s)
- William A Pastor
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada.
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, H3A 1A3, Canada.
| | - Sin Young Kwon
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada
| |
Collapse
|
25
|
Erbescu A, Papuc SM, Budisteanu M, Arghir A, Neagu M. Re-emerging concepts of immune dysregulation in autism spectrum disorders. Front Psychiatry 2022; 13:1006612. [PMID: 36339838 PMCID: PMC9626859 DOI: 10.3389/fpsyt.2022.1006612] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by communication and social interaction deficits, and by restricted interests and stereotyped, repetitive behavior patterns. ASD has a strong genetic component and a complex architecture characterized by the interplay of rare and common genetic variants. Recently, increasing evidence suggest a significant contribution of immune system dysregulation in ASD. The present paper reviews the latest updates regarding the altered immune landscape of this complex disorder highlighting areas with potential for biomarkers discovery as well as personalization of therapeutic approaches. Cross-talk between the central nervous system and immune system has long been envisaged and recent evidence brings insights into the pathways connecting the brain to the immune system. Disturbance of cytokine levels plays an important role in the establishment of a neuroinflammatory milieu in ASD. Several other immune molecules involved in antigen presentation and inflammatory cellular phenotypes are also at play in ASD. Maternal immune activation, the presence of brain-reactive antibodies and autoimmunity are other potential prenatal and postnatal contributors to ASD pathophysiology. The molecular players involved in oxidative-stress response and mitochondrial system function, are discussed as contributors to the pro-inflammatory pattern. The gastrointestinal inflammation pathways proposed to play a role in ASD are also discussed. Moreover, the body of evidence regarding some of the genetic factors linked to the immune system dysregulation is reviewed and discussed. Last, but not least, the epigenetic traits and their interactions with the immune system are reviewed as an expanding field in ASD research. Understanding the immune-mediated pathways that influence brain development and function, metabolism, and intestinal homeostasis, may lead to the identification of robust diagnostic or predictive biomarkers for ASD individuals. Thus, novel therapeutic approaches could be developed, ultimately aiming to improve their quality of life.
Collapse
Affiliation(s)
- Alina Erbescu
- Victor Babes National Institute of Pathology, Bucharest, Romania.,Faculty of Biology, Doctoral School, University of Bucharest, Bucharest, Romania
| | | | - Magdalena Budisteanu
- Victor Babes National Institute of Pathology, Bucharest, Romania.,Prof. Dr. Alex. Obregia Clinical Hospital of Psychiatry, Bucharest, Romania.,Faculty of Medicine, Titu Maiorescu University, Bucharest, Romania
| | - Aurora Arghir
- Victor Babes National Institute of Pathology, Bucharest, Romania
| | - Monica Neagu
- Victor Babes National Institute of Pathology, Bucharest, Romania.,Faculty of Biology, Doctoral School, University of Bucharest, Bucharest, Romania.,Colentina Clinical Hospital, Bucharest, Romania
| |
Collapse
|
26
|
Genomic imprinting in human placentation. Reprod Med Biol 2022; 21:e12490. [DOI: 10.1002/rmb2.12490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/25/2022] [Accepted: 11/10/2022] [Indexed: 12/02/2022] Open
|
27
|
Abstract
Transposable elements (TEs) are mobile sequences that engender widespread mutations and thus are a major hazard that must be silenced. The most abundant active class of TEs in mammalian genomes is long interspersed element class 1 (LINE1). Here, we report that LINE1 transposition is suppressed in the male germline by transcription factors encoded by a rapidly evolving X-linked homeobox gene cluster. LINE1 transposition is repressed by many members of this RHOX transcription factor family, including those with different patterns of expression during spermatogenesis. One family member-RHOX10-suppresses LINE1 transposition during fetal development in vivo when the germline would otherwise be susceptible to LINE1 activation because of epigenetic reprogramming. We provide evidence that RHOX10 suppresses LINE transposition by inducing Piwil2, which encodes a key component in the Piwi-interacting RNA pathway that protects against TEs. The ability of RHOX transcription factors to suppress LINE1 is conserved in humans but is lost in RHOXF2 mutants from several infertile human patients, raising the possibility that loss of RHOXF2 causes human infertility by allowing uncontrolled LINE1 expression in the germline. Together, our results support a model in which the Rhox gene cluster is in an evolutionary arms race with TEs, resulting in expansion of the Rhox gene cluster to suppress TEs in different biological contexts.
Collapse
|
28
|
Pérez RF, Tejedor JR, Santamarina-Ojeda P, Martínez VL, Urdinguio RG, Villamañán L, Candiota AP, Sarró NMV, Barradas M, Fernandez-Marcos PJ, Serrano M, Fernández AF, Fraga MF. Conservation of Aging and Cancer Epigenetic Signatures across Human and Mouse. Mol Biol Evol 2021; 38:3415-3435. [PMID: 33871658 PMCID: PMC8321527 DOI: 10.1093/molbev/msab112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aging and cancer are two interrelated processes, with aging being a major risk factor for the development of cancer. Parallel epigenetic alterations have been described for both, although differences, especially within the DNA hypomethylation scenario, have also been recently reported. Although many of these observations arise from the use of mouse models, there is a lack of systematic comparisons of human and mouse epigenetic patterns in the context of disease. However, such comparisons are significant as they allow to establish the extent to which some of the observed similarities or differences arise from pre-existing species-specific epigenetic traits. Here, we have used reduced representation bisulfite sequencing to profile the brain methylomes of young and old, tumoral and nontumoral brain samples from human and mouse. We first characterized the baseline epigenomic patterns of the species and subsequently focused on the DNA methylation alterations associated with cancer and aging. Next, we described the functional genomic and epigenomic context associated with the alterations, and finally, we integrated our data to study interspecies DNA methylation levels at orthologous CpG sites. Globally, we found considerable differences between the characteristics of DNA methylation alterations in cancer and aging in both species. Moreover, we describe robust evidence for the conservation of the specific cancer and aging epigenomic signatures in human and mouse. Our observations point toward the preservation of the functional consequences of these alterations at multiple levels of genomic regulation. Finally, our analyses reveal a role for the genomic context in explaining disease- and species-specific epigenetic traits.
Collapse
Affiliation(s)
- Raúl F Pérez
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain.,Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain.,Health Research Institute of Asturias (ISPA), University of Oviedo, Oviedo, Spain.,Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain.,Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII), Madrid, Spain
| | - Juan Ramón Tejedor
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain.,Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain.,Health Research Institute of Asturias (ISPA), University of Oviedo, Oviedo, Spain.,Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain.,Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII), Madrid, Spain
| | - Pablo Santamarina-Ojeda
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain.,Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain.,Health Research Institute of Asturias (ISPA), University of Oviedo, Oviedo, Spain.,Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain.,Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII), Madrid, Spain
| | - Virginia López Martínez
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain.,Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain.,Health Research Institute of Asturias (ISPA), University of Oviedo, Oviedo, Spain.,Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain.,Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII), Madrid, Spain
| | - Rocío G Urdinguio
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain.,Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain.,Health Research Institute of Asturias (ISPA), University of Oviedo, Oviedo, Spain.,Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain.,Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII), Madrid, Spain
| | - Lucía Villamañán
- Unitat de Bioquímica de Biociències, Departament de Bioquímica i Biologia Molecular, Edifici Cs, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ana Paula Candiota
- Unitat de Bioquímica de Biociències, Departament de Bioquímica i Biologia Molecular, Edifici Cs, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - N Mí Vidal Sarró
- Servicio Anatomía Patológica, Hospital Universitari de Bellvitge-IDIBELL, Hospitalet de Llobregat, Spain
| | - Marta Barradas
- Metabolic Syndrome Group-BIOPROMET, Madrid Institute for Advanced Studies-IMDEA Food, CEI UAM+CSIC, Madrid, Spain
| | - Pablo Jose Fernandez-Marcos
- Metabolic Syndrome Group-BIOPROMET, Madrid Institute for Advanced Studies-IMDEA Food, CEI UAM+CSIC, Madrid, Spain
| | - Manuel Serrano
- Tumour Suppression Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.,Cellular Plasticity and Disease Group, Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Agusín F Fernández
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain.,Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain.,Health Research Institute of Asturias (ISPA), University of Oviedo, Oviedo, Spain.,Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain.,Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII), Madrid, Spain
| | - Mario F Fraga
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain.,Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain.,Health Research Institute of Asturias (ISPA), University of Oviedo, Oviedo, Spain.,Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain.,Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII), Madrid, Spain
| |
Collapse
|
29
|
Bertozzi TM, Takahashi N, Hanin G, Kazachenka A, Ferguson-Smith AC. A spontaneous genetically induced epiallele at a retrotransposon shapes host genome function. eLife 2021; 10:e65233. [PMID: 33755012 PMCID: PMC8084528 DOI: 10.7554/elife.65233] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/22/2021] [Indexed: 12/14/2022] Open
Abstract
Intracisternal A-particles (IAPs) are endogenous retroviruses (ERVs) responsible for most insertional mutations in the mouse. Full-length IAPs harbour genes flanked by long terminal repeats (LTRs). Here, we identify a solo LTR IAP variant (Iap5-1solo) recently formed in the inbred C57BL/6J mouse strain. In contrast to the C57BL/6J full-length IAP at this locus (Iap5-1full), Iap5-1solo lacks DNA methylation and H3K9 trimethylation. The distinct DNA methylation levels between the two alleles are established during preimplantation development, likely due to loss of KRAB zinc finger protein binding at the Iap5-1solo variant. Iap5-1solo methylation increases and becomes more variable in a hybrid genetic background yet is unresponsive to maternal dietary methyl supplementation. Differential epigenetic modification of the two variants is associated with metabolic differences and tissue-specific changes in adjacent gene expression. Our characterisation of Iap5-1 as a genetically induced epiallele with functional consequences establishes a new model to study transposable element repression and host-element co-evolution.
Collapse
Affiliation(s)
- Tessa M Bertozzi
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Nozomi Takahashi
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Geula Hanin
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | | | | |
Collapse
|
30
|
Zhu L, Marjani SL, Jiang Z. The Epigenetics of Gametes and Early Embryos and Potential Long-Range Consequences in Livestock Species-Filling in the Picture With Epigenomic Analyses. Front Genet 2021; 12:557934. [PMID: 33747031 PMCID: PMC7966815 DOI: 10.3389/fgene.2021.557934] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 02/04/2021] [Indexed: 12/31/2022] Open
Abstract
The epigenome is dynamic and forged by epigenetic mechanisms, such as DNA methylation, histone modifications, chromatin remodeling, and non-coding RNA species. Increasing lines of evidence support the concept that certain acquired traits are derived from environmental exposure during early embryonic and fetal development, i.e., fetal programming, and can even be "memorized" in the germline as epigenetic information and transmitted to future generations. Advances in technology are now driving the global profiling and precise editing of germline and embryonic epigenomes, thereby improving our understanding of epigenetic regulation and inheritance. These achievements open new avenues for the development of technologies or potential management interventions to counteract adverse conditions or improve performance in livestock species. In this article, we review the epigenetic analyses (DNA methylation, histone modification, chromatin remodeling, and non-coding RNAs) of germ cells and embryos in mammalian livestock species (cattle, sheep, goats, and pigs) and the epigenetic determinants of gamete and embryo viability. We also discuss the effects of parental environmental exposures on the epigenetics of gametes and the early embryo, and evidence for transgenerational inheritance in livestock.
Collapse
Affiliation(s)
- Linkai Zhu
- AgCenter, School of Animal Sciences, Louisiana State University, Baton Rouge, LA, United States
| | - Sadie L Marjani
- Department of Biology, Central Connecticut State University, New Britain, CT, United States
| | - Zongliang Jiang
- AgCenter, School of Animal Sciences, Louisiana State University, Baton Rouge, LA, United States
| |
Collapse
|
31
|
Mulholland CB, Nishiyama A, Ryan J, Nakamura R, Yiğit M, Glück IM, Trummer C, Qin W, Bartoschek MD, Traube FR, Parsa E, Ugur E, Modic M, Acharya A, Stolz P, Ziegenhain C, Wierer M, Enard W, Carell T, Lamb DC, Takeda H, Nakanishi M, Bultmann S, Leonhardt H. Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals. Nat Commun 2020; 11:5972. [PMID: 33235224 PMCID: PMC7686362 DOI: 10.1038/s41467-020-19603-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
Genome-wide DNA demethylation is a unique feature of mammalian development and naïve pluripotent stem cells. Here, we describe a recently evolved pathway in which global hypomethylation is achieved by the coupling of active and passive demethylation. TET activity is required, albeit indirectly, for global demethylation, which mostly occurs at sites devoid of TET binding. Instead, TET-mediated active demethylation is locus-specific and necessary for activating a subset of genes, including the naïve pluripotency and germline marker Dppa3 (Stella, Pgc7). DPPA3 in turn drives large-scale passive demethylation by directly binding and displacing UHRF1 from chromatin, thereby inhibiting maintenance DNA methylation. Although unique to mammals, we show that DPPA3 alone is capable of inducing global DNA demethylation in non-mammalian species (Xenopus and medaka) despite their evolutionary divergence from mammals more than 300 million years ago. Our findings suggest that the evolution of Dppa3 facilitated the emergence of global DNA demethylation in mammals.
Collapse
Affiliation(s)
- Christopher B Mulholland
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Atsuya Nishiyama
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Joel Ryan
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Merve Yiğit
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ivo M Glück
- Physical Chemistry, Department of Chemistry, Center for Nanoscience, Nanosystems Initiative Munich and Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Carina Trummer
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Weihua Qin
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michael D Bartoschek
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Franziska R Traube
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Edris Parsa
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Enes Ugur
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Miha Modic
- The Francis Crick Institute and UCL Queen Square Institute of Neurology, London, UK
| | - Aishwarya Acharya
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Paul Stolz
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Christoph Ziegenhain
- Department of Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Wolfgang Enard
- Department of Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Thomas Carell
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience, Nanosystems Initiative Munich and Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Sebastian Bultmann
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
| | - Heinrich Leonhardt
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
| |
Collapse
|
32
|
Decato BE, Qu J, Ji X, Wagenblast E, Knott SRV, Hannon GJ, Smith AD. Characterization of universal features of partially methylated domains across tissues and species. Epigenetics Chromatin 2020; 13:39. [PMID: 33008446 PMCID: PMC7532633 DOI: 10.1186/s13072-020-00363-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Partially methylated domains (PMDs) are a hallmark of epigenomes in reproducible and specific biological contexts, including cancer cells, the placenta, and cultured cell lines. Existing methods for deciding whether PMDs exist in a sample, as well as their identification, are few, often tailored to specific biological questions, and require high coverage samples for accurate identification. RESULTS In this study, we outline a set of axioms that take a step towards a functional definition for PMDs, describe an improved method for comparable PMD detection across samples with substantially differing sequencing depths, and refine the decision criteria for whether a sample contains PMDs using a data-driven approach. Applying our method to 267 methylomes from 7 species, we corroborated recent results regarding the general association between replication timing and PMD state, and report identification of several reproducibly "escapee" genes within late-replicating domains that escape the reduced expression and hypomethylation of their immediate genomic neighborhood. We also explored the discordant PMD state of orthologous genes between human and mouse, and observed a directional association of PMD state with gene expression and local gene density. CONCLUSIONS Our improved method makes low sequencing depth, population-level studies of PMD variation possible and our results further refine the model of PMD formation as one where sequence context and regional epigenomic features both play a role in gradual genome-wide hypomethylation.
Collapse
Affiliation(s)
- Benjamin E. Decato
- Quantitative and Computational Biology Section, University of Southern California, Childs Way, Los Angeles, California USA
| | - Jianghan Qu
- Quantitative and Computational Biology Section, University of Southern California, Childs Way, Los Angeles, California USA
| | - Xiaojing Ji
- Quantitative and Computational Biology Section, University of Southern California, Childs Way, Los Angeles, California USA
| | - Elvin Wagenblast
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724 USA
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, M5G 1L7 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, M5G 1L7 Canada
| | - Simon R. V. Knott
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724 USA
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048 USA
| | - Gregory J. Hannon
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724 USA
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
- New York Genome Center, 101 6th Avenue, New York, NY 10013 USA
| | - Andrew D. Smith
- Quantitative and Computational Biology Section, University of Southern California, Childs Way, Los Angeles, California USA
| |
Collapse
|
33
|
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.
Collapse
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
| |
Collapse
|
34
|
Zhou Y, Liu S, Hu Y, Fang L, Gao Y, Xia H, Schroeder SG, Rosen BD, Connor EE, Li CJ, Baldwin RL, Cole JB, Van Tassell CP, Yang L, Ma L, Liu GE. Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns. BMC Biol 2020; 18:85. [PMID: 32631327 PMCID: PMC7339546 DOI: 10.1186/s12915-020-00793-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/12/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Efforts to improve animal health, and understand genetic bases for production, may benefit from a comprehensive analysis of animal genomes and epigenomes. Although DNA methylation has been well studied in humans and other model species, its distribution patterns and regulatory impacts in cattle are still largely unknown. Here, we present the largest collection of cattle DNA methylation epigenomic data to date. RESULTS Using Holstein cattle, we generated 29 whole genome bisulfite sequencing (WGBS) datasets for 16 tissues, 47 corresponding RNA-seq datasets, and 2 whole genome sequencing datasets. We did read mapping and DNA methylation calling based on two different cattle assemblies, demonstrating the high quality of the long-read-based assembly markedly improved DNA methylation results. We observed large differences across cattle tissues in the methylation patterns of global CpG sites, partially methylated domains (PMDs), hypomethylated regions (HMRs), CG islands (CGIs), and common repeats. We detected that each tissue had a distinct set of PMDs, which showed tissue-specific patterns. Similar to human PMD, cattle PMDs were often linked to a general decrease of gene expression and a decrease in active histone marks and related to long-range chromatin organizations, like topologically associated domains (TADs). We tested a classification of the HMRs based on their distributions relative to transcription start sites (TSSs) and detected tissue-specific TSS-HMRs and genes that showed strong tissue effects. When performing cross-species comparisons of paired genes (two opposite strand genes with their TSS located in the same HMR), we found out they were more consistently co-expressed among human, mouse, sheep, goat, yak, pig, and chicken, but showed lower consistent ratios in more divergent species. We further used these WGBS data to detect 50,023 experimentally supported CGIs across bovine tissues and found that they might function as a guard against C-to-T mutations for TSS-HMRs. Although common repeats were often heavily methylated, some young Bov-A2 repeats were hypomethylated in sperm and could affect the promoter structures by exposing potential transcription factor binding sites. CONCLUSIONS This study provides a comprehensive resource for bovine epigenomic research and enables new discoveries about DNA methylation and its role in complex traits.
Collapse
Affiliation(s)
- Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Shuli Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Yan Hu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Lingzhao Fang
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Han Xia
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Steven G. Schroeder
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Erin E. Connor
- Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716 USA
| | - Cong-jun Li
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Ransom L. Baldwin
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - John B. Cole
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Curtis P. Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| |
Collapse
|
35
|
Ivanova E, Canovas S, Garcia-Martínez S, Romar R, Lopes JS, Rizos D, Sanchez-Calabuig MJ, Krueger F, Andrews S, Perez-Sanz F, Kelsey G, Coy P. DNA methylation changes during preimplantation development reveal inter-species differences and reprogramming events at imprinted genes. Clin Epigenetics 2020; 12:64. [PMID: 32393379 PMCID: PMC7216732 DOI: 10.1186/s13148-020-00857-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/23/2020] [Indexed: 02/08/2023] Open
Abstract
Preimplantation embryos experience profound resetting of epigenetic information inherited from the gametes. Genome-wide analysis at single-base resolution has shown similarities but also species differences between human and mouse preimplantation embryos in DNA methylation patterns and reprogramming. Here, we have extended such analysis to two key livestock species, the pig and the cow. We generated genome-wide DNA methylation and whole-transcriptome datasets from gametes to blastocysts in both species. In oocytes from both species, a distinctive bimodal methylation landscape is present, with hypermethylated domains prevalent over hypomethylated domains, similar to human, while in the mouse the proportions are reversed.An oocyte-like pattern of methylation persists in the cleavage stages, albeit with some reduction in methylation level, persisting to blastocysts in cow, while pig blastocysts have a highly hypomethylated landscape. In the pig, there was evidence of transient de novo methylation at the 8-16 cell stages of domains unmethylated in oocytes, revealing a complex dynamic of methylation reprogramming. The methylation datasets were used to identify germline differentially methylated regions (gDMRs) of known imprinted genes and for the basis of detection of novel imprinted loci. Strikingly in the pig, we detected a consistent reduction in gDMR methylation at the 8-16 cell stages, followed by recovery to the blastocyst stage, suggesting an active period of imprint stabilization in preimplantation embryos. Transcriptome analysis revealed absence of expression in oocytes of both species of ZFP57, a key factor in the mouse for gDMR methylation maintenance, but presence of the alternative imprint regulator ZNF445. In conclusion, our study reveals species differences in DNA methylation reprogramming and suggests that porcine or bovine models may be closer to human in key aspects than in the mouse model.
Collapse
Affiliation(s)
- Elena Ivanova
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Sebastian Canovas
- Physiology of Reproduction Group, Departamento de Fisiología, Universidad de Murcia, Campus Mare Nostrum, 30100, Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria, IMIB-Arrixaca-UMU, 30120, Murcia, Spain
| | - Soledad Garcia-Martínez
- Physiology of Reproduction Group, Departamento de Fisiología, Universidad de Murcia, Campus Mare Nostrum, 30100, Murcia, Spain
| | - Raquel Romar
- Physiology of Reproduction Group, Departamento de Fisiología, Universidad de Murcia, Campus Mare Nostrum, 30100, Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria, IMIB-Arrixaca-UMU, 30120, Murcia, Spain
| | - Jordana S Lopes
- Physiology of Reproduction Group, Departamento de Fisiología, Universidad de Murcia, Campus Mare Nostrum, 30100, Murcia, Spain
| | | | | | - Felix Krueger
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Fernando Perez-Sanz
- Instituto Murciano de Investigación Biosanitaria, IMIB-Arrixaca-UMU, 30120, Murcia, Spain
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK.
| | - Pilar Coy
- Physiology of Reproduction Group, Departamento de Fisiología, Universidad de Murcia, Campus Mare Nostrum, 30100, Murcia, Spain.
- Instituto Murciano de Investigación Biosanitaria, IMIB-Arrixaca-UMU, 30120, Murcia, Spain.
| |
Collapse
|
36
|
Narapareddy L, Wildman DE, Armstrong DL, Weckle A, Bell AF, Patil CL, Tardif SD, Ross CN, Rutherford JN. Maternal weight affects placental DNA methylation of genes involved in metabolic pathways in the common marmoset monkey (Callithrix jacchus). Am J Primatol 2020; 82:e23101. [PMID: 32020652 PMCID: PMC7154656 DOI: 10.1002/ajp.23101] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 12/09/2019] [Accepted: 12/14/2019] [Indexed: 12/13/2022]
Abstract
Accumulating evidence suggests that dysregulation of placental DNA methylation (DNAm) is a mechanism linking maternal weight during pregnancy to metabolic programming outcomes. The common marmoset, Callithrix jaccus, is a platyrrhine primate species that has provided much insight into studies of the primate placenta, maternal condition, and metabolic programming, yet the relationships between maternal weight and placental DNAm are unknown. Here, we report genome‐wide DNAm from term marmoset placentas using reduced representation bisulfite sequencing. We identified 74 genes whose DNAm pattern is associated with maternal weight during gestation. These genes are predominantly involved in energy metabolism and homeostasis, including the regulation of glycolytic and lipid metabolic processes pathways. The placental DNA methylation (DNAm) landscape of the marmoset placenta presents unique differences and similarities with human placental methylation patterns. Maternal weight is associated with placental DNAm in genes that are predominantly involved in energy metabolism and homeostasis. The impact of altered placental DNAm on placental function and development may also contribute to the potential role of placental DNAm in developmental programming in the marmoset monkey.
Collapse
Affiliation(s)
- Laren Narapareddy
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, Georgia
| | - Derek E Wildman
- Genomics Program, College of Public Health, University of South Florida, Tampa, Florida
| | - Don L Armstrong
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Amy Weckle
- Illinois Water Resources Center, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Aleeca F Bell
- Department of Women, Children and Family Health Science, College of Nursing, University of Illinois at Chicago, Chicago, Illinois
| | - Crystal L Patil
- Department of Women, Children and Family Health Science, College of Nursing, University of Illinois at Chicago, Chicago, Illinois
| | - Suzette D Tardif
- Texas Biomedical Research Institute, Southwest National Primate Research Center, San Antonio, Texas
| | - Corinna N Ross
- Program of Biology, College of Arts and Sciences, Texas A&M University-San Antonio, San Antonio, Texas
| | - Julienne N Rutherford
- Department of Women, Children and Family Health Science, College of Nursing, University of Illinois at Chicago, Chicago, Illinois
| |
Collapse
|
37
|
Dwi Putra SE, Reichetzeder C, Hasan AA, Slowinski T, Chu C, Krämer BK, Kleuser B, Hocher B. Being Born Large for Gestational Age is Associated with Increased Global Placental DNA Methylation. Sci Rep 2020; 10:927. [PMID: 31969597 PMCID: PMC6976643 DOI: 10.1038/s41598-020-57725-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 12/31/2019] [Indexed: 02/01/2023] Open
Abstract
Being born small (SGA) or large for gestational age (LGA) is associated with adverse birth outcomes and metabolic diseases in later life of the offspring. It is known that aberrations in growth during gestation are related to altered placental function. Placental function is regulated by epigenetic mechanisms such as DNA methylation. Several studies in recent years have demonstrated associations between altered patterns of DNA methylation and adverse birth outcomes. However, larger studies that reliably investigated global DNA methylation are lacking. The aim of this study was to characterize global placental DNA methylation in relationship to size for gestational age. Global DNA methylation was assessed in 1023 placental samples by LC-MS/MS. LGA offspring displayed significantly higher global placental DNA methylation compared to appropriate for gestational age (AGA; p < 0.001). ANCOVA analyses adjusted for known factors impacting on DNA methylation demonstrated an independent association between placental global DNA methylation and LGA births (p < 0.001). Tertile stratification according to global placental DNA methylation levels revealed a significantly higher frequency of LGA births in the third tertile. Furthermore, a multiple logistic regression analysis corrected for known factors influencing birth weight highlighted an independent positive association between global placental DNA methylation and the frequency of LGA births (p = 0.001).
Collapse
Affiliation(s)
- S E Dwi Putra
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany.,Department of Nutritional Toxicology, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany.,Faculty of Biotechnology, University of Surabaya, Surabaya, Indonesia
| | - C Reichetzeder
- Department of Nutritional Toxicology, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany.
| | - A A Hasan
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany.,Department of Nutritional Toxicology, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany.,Department of Biochemistry, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt.,UP Transfer GmbH, University of Potsdam, Potsdam, Germany
| | - T Slowinski
- Department of Nephrology, Campus Charité Mitte, University Hospital Charité, Berlin, Germany
| | - C Chu
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany
| | - B K Krämer
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany
| | - B Kleuser
- Department of Nutritional Toxicology, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - B Hocher
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany. .,Department of Basic Medicine, Medical College of Hunan Normal University, Changsha, China. .,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.
| |
Collapse
|
38
|
Bergallo M, Marozio L, Botta G, Tancredi A, Daprà V, Galliano I, Montanari P, Coscia A, Benedetto C, Tovo PA. Human Endogenous Retroviruses Are Preferentially Expressed in Mononuclear Cells From Cord Blood Than From Maternal Blood and in the Fetal Part of Placenta. Front Pediatr 2020; 8:244. [PMID: 32478020 PMCID: PMC7240011 DOI: 10.3389/fped.2020.00244] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 04/20/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Placenta shows high transcription levels of human endogenous retroviruses (HERVs) that are overexpressed during embryonic and fetal development. Methods: In order to gather further information on the degree of HERV activation in maternal and fetal tissues we assessed the transcription levels of pol genes of HERV-H, -K, and -W in PBMCs of newborns and their mothers as well as in chorion (fetal part) and decidua basalis (maternal part) of the placenta using a real time PCR assay. Results: Transcripts of pol genes of the three HERV families were significantly higher in mononuclear cells from cord blood than from maternal blood and in the fetal part than in the maternal part of the placenta. Conclusions: The HERV over-expressions in cells and tissues of the offspring are further clues that they play pivotal physiologic roles during early life events and suggest that HERV-driven abnormalities of pregnancy and fetal development may derive mostly from the conceptus, not from the mother.
Collapse
Affiliation(s)
- Massimiliano Bergallo
- Pediatric Laboratory, Department of Pediatric Sciences and Public Health, University of Turin, Turin, Italy.,Department of Pediatric Sciences and Public Health, University of Turin, Turin, Italy
| | - Luca Marozio
- Department of Surgical Sciences, Obstetrics and Gynecology 1, University of Turin, Turin, Italy
| | - Giovanni Botta
- Department of Pathology AOU Città della Salute e della Scienza di Torino, Turin, Italy
| | - Annalisa Tancredi
- Department of Surgical Sciences, Obstetrics and Gynecology 1, University of Turin, Turin, Italy
| | - Valentina Daprà
- Pediatric Laboratory, Department of Pediatric Sciences and Public Health, University of Turin, Turin, Italy.,Department of Pediatric Sciences and Public Health, University of Turin, Turin, Italy
| | - Ilaria Galliano
- Pediatric Laboratory, Department of Pediatric Sciences and Public Health, University of Turin, Turin, Italy.,Department of Pediatric Sciences and Public Health, University of Turin, Turin, Italy
| | - Paola Montanari
- Pediatric Laboratory, Department of Pediatric Sciences and Public Health, University of Turin, Turin, Italy.,Department of Pediatric Sciences and Public Health, University of Turin, Turin, Italy
| | - Alessandra Coscia
- Neonatology Unit, Department of Pediatric Sciences and Public Health, University of Turin, Turin, Italy
| | - Chiara Benedetto
- Department of Surgical Sciences, Obstetrics and Gynecology 1, University of Turin, Turin, Italy
| | - Pier Angelo Tovo
- Department of Pediatric Sciences and Public Health, University of Turin, Turin, Italy
| |
Collapse
|
39
|
Bogutz AB, Brind'Amour J, Kobayashi H, Jensen KN, Nakabayashi K, Imai H, Lorincz MC, Lefebvre L. Evolution of imprinting via lineage-specific insertion of retroviral promoters. Nat Commun 2019; 10:5674. [PMID: 31831741 PMCID: PMC6908575 DOI: 10.1038/s41467-019-13662-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/14/2019] [Indexed: 01/09/2023] Open
Abstract
Imprinted genes are expressed from a single parental allele, with the other allele often silenced by DNA methylation (DNAme) established in the germline. While species-specific imprinted orthologues have been documented, the molecular mechanisms underlying the evolutionary switch from biallelic to imprinted expression are unknown. During mouse oogenesis, gametic differentially methylated regions (gDMRs) acquire DNAme in a transcription-guided manner. Here we show that oocyte transcription initiating in lineage-specific endogenous retroviruses (ERVs) is likely responsible for DNAme establishment at 4/6 mouse-specific and 17/110 human-specific imprinted gDMRs. The latter are divided into Catarrhini- or Hominoidea-specific gDMRs embedded within transcripts initiating in ERVs specific to these primate lineages. Strikingly, imprinting of the maternally methylated genes Impact and Slc38a4 was lost in the offspring of female mice harboring deletions of the relevant murine-specific ERVs upstream of these genes. Our work reveals an evolutionary mechanism whereby maternally silenced genes arise from biallelically expressed progenitors. Although many species-specific imprinted genes have been identified, how the evolutionary switch from biallelic to imprinted expression occurs is still unknown. Here authors find that lineage-specific ERVs active as oocyte promoters can induce de novo DNA methylation at gDMRs and imprinting.
Collapse
Affiliation(s)
- Aaron B Bogutz
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Julie Brind'Amour
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Hisato Kobayashi
- Department of Embryology, Nara Medical University, Kashihara, Nara, 634-8521, Japan
| | - Kristoffer N Jensen
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Kazuhiko Nakabayashi
- Division of Developmental Genomics, Research Institute, National Center for Child Health and Development, Setagaya, Tokyo, 157-8535, Japan
| | - Hiroo Imai
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan
| | - Matthew C Lorincz
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
| | - Louis Lefebvre
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
| |
Collapse
|
40
|
Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics Chromatin 2019; 12:62. [PMID: 31601251 PMCID: PMC6786280 DOI: 10.1186/s13072-019-0307-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/25/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methylation of active genes, also known as gene body methylation, is found in many animal and plant genomes. Despite this, the transcriptional and developmental role of such methylation remains poorly understood. Here, we explore the dynamic range of DNA methylation in honey bee, a model organism for gene body methylation. RESULTS Our data show that CG methylation in gene bodies globally fluctuates during honey bee development. However, these changes cause no gene expression alterations. Intriguingly, despite the global alterations, tissue-specific CG methylation patterns of complete genes or exons are rare, implying robust maintenance of genic methylation during development. Additionally, we show that CG methylation maintenance fluctuates in somatic cells, while reaching maximum fidelity in sperm cells. Finally, unlike universally present CG methylation, we discovered non-CG methylation specifically in bee heads that resembles such methylation in mammalian brain tissue. CONCLUSIONS Based on these results, we propose that gene body CG methylation can oscillate during development if it is kept to a level adequate to preserve function. Additionally, our data suggest that heightened non-CG methylation is a conserved regulator of animal nervous systems.
Collapse
Affiliation(s)
- Keith D Harris
- School of Plant Sciences and Food Security, Tel-Aviv University, 69978, Tel-Aviv, Israel
| | - James P B Lloyd
- Center for RNA Systems Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia
| | - Katherine Domb
- School of Plant Sciences and Food Security, Tel-Aviv University, 69978, Tel-Aviv, Israel
| | - Daniel Zilberman
- Department of Cell and Developmental Biology, John Innes Center, Norwich, UK.
| | - Assaf Zemach
- School of Plant Sciences and Food Security, Tel-Aviv University, 69978, Tel-Aviv, Israel.
| |
Collapse
|
41
|
Zhu Y, Mordaunt CE, Yasui DH, Marathe R, Coulson RL, Dunaway KW, Jianu JM, Walker CK, Ozonoff S, Hertz-Picciotto I, Schmidt RJ, LaSalle JM. Placental DNA methylation levels at CYP2E1 and IRS2 are associated with child outcome in a prospective autism study. Hum Mol Genet 2019; 28:2659-2674. [PMID: 31009952 PMCID: PMC6687952 DOI: 10.1093/hmg/ddz084] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/25/2019] [Accepted: 04/15/2019] [Indexed: 12/20/2022] Open
Abstract
DNA methylation acts at the interface of genetic and environmental factors relevant for autism spectrum disorder (ASD). Placenta, normally discarded at birth, is a potentially rich source of DNA methylation patterns predictive of ASD in the child. Here, we performed whole methylome analyses of placentas from a prospective study MARBLES (Markers of Autism Risk in Babies-Learning Early Signs) of high-risk pregnancies. A total of 400 differentially methylated regions (DMRs) discriminated placentas stored from children later diagnosed with ASD compared to typically developing controls. These ASD DMRs were significantly enriched at promoters, mapped to 596 genes functionally enriched in neuronal development, and overlapped genetic ASD risk. ASD DMRs at CYP2E1 and IRS2 reached genome-wide significance, replicated by pyrosequencing and correlated with expression differences in brain. Methylation at CYP2E1 associated with both ASD diagnosis and genotype within the DMR. In contrast, methylation at IRS2 was unaffected by within DMR genotype but modified by preconceptional maternal prenatal vitamin use. This study therefore identified two potentially useful early epigenetic markers for ASD in placenta.
Collapse
Affiliation(s)
- Yihui Zhu
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, University of California, Davis, CA, USA
| | - Charles E Mordaunt
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, University of California, Davis, CA, USA
| | - Dag H Yasui
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, University of California, Davis, CA, USA
| | - Ria Marathe
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, University of California, Davis, CA, USA
| | - Rochelle L Coulson
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, University of California, Davis, CA, USA
| | - Keith W Dunaway
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, University of California, Davis, CA, USA
| | - Julia M Jianu
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, University of California, Davis, CA, USA
| | - Cheryl K Walker
- Department of Obstetrics & Gynecology, School of Medicine, MIND Institute, University of California, Davis, 95616, USA
| | - Sally Ozonoff
- MIND Institute, University of California, Davis, CA, USA
- Department of Psychiatry and Behavioral Sciences, School of Medicine, University of California, Davis, CA, USA
| | - Irva Hertz-Picciotto
- MIND Institute, University of California, Davis, CA, USA
- Department of Public Health Sciences, University of California, Davis, CA, USA
| | - Rebecca J Schmidt
- MIND Institute, University of California, Davis, CA, USA
- Department of Public Health Sciences, University of California, Davis, CA, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, University of California, Davis, CA, USA
| |
Collapse
|
42
|
Fang L, Zhou Y, Liu S, Jiang J, Bickhart DM, Null DJ, Li B, Schroeder SG, Rosen BD, Cole JB, Van Tassell CP, Ma L, Liu GE. Integrating Signals from Sperm Methylome Analysis and Genome-Wide Association Study for a Better Understanding of Male Fertility in Cattle. EPIGENOMES 2019; 3:epigenomes3020010. [PMID: 34968233 PMCID: PMC8594688 DOI: 10.3390/epigenomes3020010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/03/2019] [Accepted: 05/11/2019] [Indexed: 01/18/2023] Open
Abstract
Decreased male fertility is a big concern in both human society and the livestock industry. Sperm DNA methylation is commonly believed to be associated with male fertility. However, due to the lack of accurate male fertility records (i.e., limited mating times), few studies have investigated the comprehensive impacts of sperm DNA methylation on male fertility in mammals. In this study, we generated 10 sperm DNA methylomes and performed a preliminary correlation analysis between signals from sperm DNA methylation and signals from large-scale (n = 27,214) genome-wide association studies (GWAS) of 35 complex traits (including 12 male fertility-related traits). We detected genomic regions, which experienced DNA methylation alterations in sperm and were associated with aging and extreme fertility phenotypes (e.g., sire-conception rate or SCR). In dynamic hypomethylated regions (HMRs) and partially methylated domains (PMDs), we found genes (e.g., HOX gene clusters and microRNAs) that were involved in the embryonic development. We demonstrated that genomic regions, which gained rather than lost methylations during aging, and in animals with low SCR were significantly and selectively enriched for GWAS signals of male fertility traits. Our study discovered 16 genes as the potential candidate markers for male fertility, including SAMD5 and PDE5A. Collectively, this initial effort supported a hypothesis that sperm DNA methylation may contribute to male fertility in cattle and revealed the usefulness of functional annotations in enhancing biological interpretation and genomic prediction for complex traits and diseases.
Collapse
Affiliation(s)
- Lingzhao Fang
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuli Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jicai Jiang
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Derek M. Bickhart
- Dairy Forage Research Center, Agricultural Research Service, USDA, Madison, WI 53718, USA
| | - Daniel J. Null
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Bingjie Li
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Steven G. Schroeder
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - John B. Cole
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Curtis P. Van Tassell
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
- Correspondence: (L.M.); (G.E.L.); Tel.: +1-301-405-1389 (L.M.); +1-301-504-9843 (G.E.L.); Fax: +1-301-504-8414 (G.E.L.)
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
- Correspondence: (L.M.); (G.E.L.); Tel.: +1-301-405-1389 (L.M.); +1-301-504-9843 (G.E.L.); Fax: +1-301-504-8414 (G.E.L.)
| |
Collapse
|
43
|
Sevane N, Martínez R, Bruford MW. Genome-wide differential DNA methylation in tropically adapted Creole cattle and their Iberian ancestors. Anim Genet 2018; 50:15-26. [DOI: 10.1111/age.12731] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2018] [Indexed: 12/15/2022]
Affiliation(s)
- N. Sevane
- School of Biosciences; Cardiff University; Cathays Park Cardiff CF10 3AX UK
| | - R. Martínez
- Corporación Colombiana De Investigación Agropecuaria (Corpoica); Centro de Investigaciones Tibaitatá; km 14 via Bogotá 250047 Mosquera Colombia
| | - M. W. Bruford
- School of Biosciences; Cardiff University; Cathays Park Cardiff CF10 3AX UK
- Sustainable Places Research Institute; Cardiff University; Cardiff CF10 3BA UK
| |
Collapse
|
44
|
Zhou Y, Connor EE, Bickhart DM, Li C, Baldwin RL, Schroeder SG, Rosen BD, Yang L, Van Tassell CP, Liu GE. Comparative whole genome DNA methylation profiling of cattle sperm and somatic tissues reveals striking hypomethylated patterns in sperm. Gigascience 2018; 7:4965117. [PMID: 29635292 PMCID: PMC5928411 DOI: 10.1093/gigascience/giy039] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/28/2018] [Indexed: 12/21/2022] Open
Abstract
Background Although sperm DNA methylation has been studied in humans and other species, its status in cattle is largely unknown. Results Using whole-genome bisulfite sequencing (WGBS), we profiled the DNA methylome of cattle sperm through comparison with three somatic tissues (mammary gland, brain, and blood). Large differences between cattle sperm and somatic cells were observed in the methylation patterns of global CpGs, pericentromeric satellites, partially methylated domains (PMDs), hypomethylated regions (HMRs), and common repeats. As expected, we observed low methylation in the promoter regions and high methylation in the bodies of active genes. We detected selective hypomethylation of megabase domains of centromeric satellite clusters, which may be related to chromosome segregation during meiosis and their rapid transcriptional activation upon fertilization. We found more PMDs in sperm cells than in somatic cells and identified meiosis-related genes such asKIF2B and REPIN1, which are hypomethylated in sperm but hypermethylated in somatic cells. In addition to the common HMRs around gene promoters, which showed substantial differences between sperm and somatic cells, the sperm-specific HMRs also targeted to distinct spermatogenesis-related genes, including BOLL, MAEL, ASZ1, SYCP3, CTCFL, MND1, SPATA22, PLD6, DDX4, RBBP8, FKBP6, and SYCE1. Although common repeats were heavily methylated in both sperm and somatic cells, some young Bov-A2 repeats, which belong to the SINE family, were hypomethylated in sperm and could affect the promoter structures by introducing new regulatory elements. Conclusions Our study provides a comprehensive resource for bovine sperm epigenomic research and enables new discoveries about DNA methylation and its role in male fertility.
Collapse
Affiliation(s)
- Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Erin E Connor
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Derek M Bickhart
- The Cell Wall Utilization and Biology Laboratory, US Department of Agriculture, Agriculture Research Service, Madison, WI, 53706, USA
| | - Congjun Li
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Ransom L Baldwin
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| |
Collapse
|
45
|
Bozack AK, Cardenas A, Quamruzzaman Q, Rahman M, Mostofa G, Christiani DC, Kile ML. DNA methylation in cord blood as mediator of the association between prenatal arsenic exposure and gestational age. Epigenetics 2018; 13:923-940. [PMID: 30175652 PMCID: PMC6284783 DOI: 10.1080/15592294.2018.1516453] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 08/06/2018] [Accepted: 08/22/2018] [Indexed: 01/08/2023] Open
Abstract
Prenatal arsenic exposure is associated with adverse birth outcomes and disease risk later in life, which could be mediated through epigenetic dysregulation. We evaluated the association between arsenic and gestational age (GA) that was mediated through DNA methylation (DNAm) using data from a Bangladeshi birth cohort. Arsenic exposure was measured in maternal drinking water at ≤16 weeks GA and maternal toenails collected ≤1 month postpartum. Cord blood DNAm was measured using Infinium HumanMethylation450 arrays (n = 44, discovery phase). Top loci identified in the discovery phase were then pyrosequenced in a second group (n = 569, validation phase). Structural equation models (SEM) evaluated the direct and indirect effects of arsenic and DNAm on GA. In the discovery phase, arsenic was associated with differential DNAm of 139 loci that were associated with GA (P < 1.10X10-6; |β regression|>0.10). Each doubling in water arsenic concentration decreased GA by 2 days, which was fully mediated through the main principal component of the top-ten CpGs (P < 0.001). In the validation phase, there were direct and indirect effects of miR214-3 and MCC DNAm on GA. In an adjusted SEM model, mediation of the association between arsenic and GA by miR124-3 was borderline significant (P = 0.061). This study therefore identified DNAm at specific loci in cord blood that mediated the effect of arsenic exposure on GA. Specifically, prenatal arsenic exposure was associated with lower methylation of miR124-3 that mediated the exposure-response of arsenic on GA. Future research should evaluate if these epigenetic changes are persistent and associated with disease risk.
Collapse
Affiliation(s)
- Anne K. Bozack
- Department of Environmental Health Sciences, Columbia University, New York, NY, USA
| | - Andres Cardenas
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | | | | | | | - David C. Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Molly L. Kile
- School of Biological and Population Health Sciences, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA
| |
Collapse
|
46
|
Salhab A, Nordström K, Gasparoni G, Kattler K, Ebert P, Ramirez F, Arrigoni L, Müller F, Polansky JK, Cadenas C, G Hengstler J, Lengauer T, Manke T, Walter J. A comprehensive analysis of 195 DNA methylomes reveals shared and cell-specific features of partially methylated domains. Genome Biol 2018; 19:150. [PMID: 30266094 PMCID: PMC6161375 DOI: 10.1186/s13059-018-1510-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 08/20/2018] [Indexed: 12/12/2022] Open
Abstract
Background Partially methylated domains are extended regions in the genome exhibiting a reduced average DNA methylation level. They cover gene-poor and transcriptionally inactive regions and tend to be heterochromatic. We present a comprehensive comparative analysis of partially methylated domains in human and mouse cells, to identify structural and functional features associated with them. Results Partially methylated domains are present in up to 75% of the genome in human and mouse cells irrespective of their tissue or cell origin. Each cell type has a distinct set of partially methylated domains, and genes expressed in such domains show a strong cell type effect. The methylation level varies between cell types with a more pronounced effect in differentiating and replicating cells. The lowest level of methylation is observed in highly proliferating and immortal cancer cell lines. A decrease of DNA methylation within partially methylated domains tends to be linked to an increase in heterochromatic histone marks and a decrease of gene expression. Characteristic combinations of heterochromatic signatures in partially methylated domains are linked to domains of early and middle S-phase and late S-G2 phases of DNA replication. Conclusions Partially methylated domains are prominent signatures of long-range epigenomic organization. Integrative analysis identifies them as important general, lineage- and cell type-specific topological features. Changes in partially methylated domains are hallmarks of cell differentiation, with decreased methylation levels and increased heterochromatic marks being linked to enhanced cell proliferation. In combination with broad histone marks, partially methylated domains demarcate distinct domains of late DNA replication. Electronic supplementary material The online version of this article (10.1186/s13059-018-1510-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Abdulrahman Salhab
- Department of Genetics, Saarland University, Campus Saarbrücken, Saarbrücken, 66123, Germany
| | - Karl Nordström
- Department of Genetics, Saarland University, Campus Saarbrücken, Saarbrücken, 66123, Germany
| | - Gilles Gasparoni
- Department of Genetics, Saarland University, Campus Saarbrücken, Saarbrücken, 66123, Germany
| | - Kathrin Kattler
- Department of Genetics, Saarland University, Campus Saarbrücken, Saarbrücken, 66123, Germany
| | - Peter Ebert
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, 66123, Germany
| | - Fidel Ramirez
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, 79108, Germany
| | - Laura Arrigoni
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, 79108, Germany
| | - Fabian Müller
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, 66123, Germany
| | - Julia K Polansky
- Berlin-Brandenburg Center for Regenerative Therapies at the Charité, Berlin, Germany.,University Medicine Berlin and German Rheumatism Research Centre, Berlin, Germany
| | - Cristina Cadenas
- Leibniz Research Center for working Environment and Human Factors IfADo, Dortmund, 44139, Germany
| | - Jan G Hengstler
- Leibniz Research Center for working Environment and Human Factors IfADo, Dortmund, 44139, Germany
| | - Thomas Lengauer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, 66123, Germany
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, 79108, Germany
| | | | - Jörn Walter
- Department of Genetics, Saarland University, Campus Saarbrücken, Saarbrücken, 66123, Germany.
| |
Collapse
|
47
|
Dunn-Fletcher CE, Muglia LM, Pavlicev M, Wolf G, Sun MA, Hu YC, Huffman E, Tumukuntala S, Thiele K, Mukherjee A, Zoubovsky S, Zhang X, Swaggart KA, Lamm KYB, Jones H, Macfarlan TS, Muglia LJ. Anthropoid primate-specific retroviral element THE1B controls expression of CRH in placenta and alters gestation length. PLoS Biol 2018; 16:e2006337. [PMID: 30231016 PMCID: PMC6166974 DOI: 10.1371/journal.pbio.2006337] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 10/01/2018] [Accepted: 09/10/2018] [Indexed: 01/22/2023] Open
Abstract
Pregnancy and parturition are intricately regulated to ensure successful reproductive outcomes. However, the factors that control gestational length in humans and other anthropoid primates remain poorly defined. Here, we show the endogenous retroviral long terminal repeat transposon-like human element 1B (THE1B) selectively controls placental expression of corticotropin-releasing hormone (CRH) that, in turn, influences gestational length and birth timing. Placental expression of CRH and subsequently prolonged gestational length were found in two independent strains of transgenic mice carrying a 180-kb human bacterial artificial chromosome (BAC) DNA that contained the full length of CRH and extended flanking regions, including THE1B. Restricted deletion of THE1B silenced placental CRH expression and normalized birth timing in these transgenic lines. Furthermore, we revealed an interaction at the 5′ insertion site of THE1B with distal-less homeobox 3 (DLX3), a transcription factor expressed in placenta. Together, these findings suggest that retroviral insertion of THE1B into the anthropoid primate genome may have initiated expression of CRH in placental syncytiotrophoblasts via DLX3 and that this placental CRH is sufficient to alter the timing of birth. The proper timing of delivery is critical during pregnancy; if too early or too late, the baby will be at risk of serious health problems and even death. Corticotropin-releasing hormone (CRH) is a protein that can be detected in maternal blood, and its concentration correlates with the timing of birth. In humans and other anthropoid primates, CRH is made by the placenta, whereas in other mammals, it is produced in a specialized region of the brain. To understand the regulation and evolution of this key protein, we inserted the human CRH gene and nearby regions into the mouse genome, which resulted in human CRH expression in the mouse placenta. Mouse litters that make CRH in their placentas are born later than control mice, showing that CRH can directly affect birth timing. Using our mouse model, we then selectively deleted a remnant of an ancient retrovirus that is normally found in the DNA of anthropoid primates and demonstrated that this specific region controls expression of CRH in the placenta. Deletion of this region also restored normal birth timing in the mice by eliminating CRH production from the placenta. We propose that retroviral regulation of CRH in the placenta may be a mechanism of controlling birth timing in humans and other anthropoid primates.
Collapse
Affiliation(s)
- Caitlin E. Dunn-Fletcher
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- * E-mail: (CED); (LJM)
| | - Lisa M. Muglia
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Mihaela Pavlicev
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Gernot Wolf
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ming-An Sun
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland, United States of America
| | - Yueh-Chiang Hu
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Elizabeth Huffman
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Shivani Tumukuntala
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Katri Thiele
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Amrita Mukherjee
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Sandra Zoubovsky
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Xuzhe Zhang
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Kayleigh A. Swaggart
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Katherine Y. Bezold Lamm
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Helen Jones
- Division of Pediatric Surgery, Cincinnati Children’s Hospital Medical Center, Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Todd S. Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland, United States of America
| | - Louis J. Muglia
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- * E-mail: (CED); (LJM)
| |
Collapse
|
48
|
Abstract
Epigenetic mechanisms allow the establishment and maintenance of multiple cellular phenotypes from a single genomic code. At the initiation of development, the oocyte and spermatozoa provide their fully differentiated chromatin that soon after fertilization undergo extensive remodeling, resulting in a totipotent state that can then drive cellular differentiation towards all cell types. These remodeling involves different epigenetic modifications, including DNA methylation, post-translational modifications of histones, non-coding RNAs, and large-scale chromatin conformation changes. Moreover, epigenetic remodeling is responsible for reprogramming somatic cells to totipotency upon somatic cell nuclear transfer/cloning, which is often incomplete and inefficient. Given that environmental factors, such as assisted reproductive techniques (ARTs), can affect epigenetic remodeling, there is interest in understanding the mechanisms driving these changes. We describe and discuss our current understanding of mechanisms responsible for the epigenetic remodeling that ensues during preimplantation development of mammals, presenting findings from studies of mouse embryos and when available comparing them to what is known for human and cattle embryos.
Collapse
Affiliation(s)
- Pablo J Ross
- Department of Animal Science, University of California Davis, Davis, CA, United States
| | - Rafael V Sampaio
- Department of Animal Science, University of California Davis, Davis, CA, United States.,Department of Animal Science, University of California Davis, Davis, CA, United States
| |
Collapse
|
49
|
Gamage TKJB, Schierding W, Tsai P, Ludgate JL, Chamley LW, Weeks RJ, Macaulay EC, James JL. Human trophoblasts are primarily distinguished from somatic cells by differences in the pattern rather than the degree of global CpG methylation. Biol Open 2018; 7:bio.034884. [PMID: 30026266 PMCID: PMC6124577 DOI: 10.1242/bio.034884] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The placenta is a fetal exchange organ connecting mother and baby that facilitates fetal growth in utero. DNA methylation is thought to impact placental development and function. Global DNA methylation studies using human placental lysates suggest that the placenta is uniquely hypomethylated compared to somatic tissue lysates, and this hypomethylation is thought to be important in conserving the unique placental gene expression patterns required for successful function. In the placental field, methylation has frequently been examined in tissue lysates, which contain mixed cell types that can confound results. To better understand how DNA methylation influences placentation, DNA from isolated first trimester trophoblast populations underwent reduced representation bisulfite sequencing and was compared to publicly available data of blastocyst-derived and somatic cell populations. First, this revealed that, unlike murine blastocysts, human trophectoderm and inner cell mass samples did not have significantly different levels of global methylation. Second, our work suggests that differences in global CpG methylation between trophoblasts and somatic cells are much smaller than previously reported. Rather, our findings suggest that different patterns of CpG methylation may be more important in epigenetically distinguishing the placenta from somatic cell populations, and these patterns of methylation may contribute to successful placental/trophoblast function. Summary: The placenta may not be as uniquely hypomethylated as previously reported, rather differences in the pattern of CpG methylation are what make it epigenetically distinct.
Collapse
Affiliation(s)
- Teena K J B Gamage
- Department of Obstetrics and Gynaecology, The University of Auckland, Auckland 1142, New Zealand
| | - William Schierding
- Department of Obstetrics and Gynaecology, The University of Auckland, Auckland 1142, New Zealand
| | - Peter Tsai
- Department of Obstetrics and Gynaecology, The University of Auckland, Auckland 1142, New Zealand
| | - Jackie L Ludgate
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Lawrence W Chamley
- Department of Obstetrics and Gynaecology, The University of Auckland, Auckland 1142, New Zealand
| | - Robert J Weeks
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Erin C Macaulay
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Joanna L James
- Department of Obstetrics and Gynaecology, The University of Auckland, Auckland 1142, New Zealand
| |
Collapse
|
50
|
Strakovsky RS, Schantz SL. Impacts of bisphenol A (BPA) and phthalate exposures on epigenetic outcomes in the human placenta. ENVIRONMENTAL EPIGENETICS 2018; 4:dvy022. [PMID: 30210810 PMCID: PMC6128378 DOI: 10.1093/eep/dvy022] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 05/18/2023]
Abstract
The placenta guides fetal growth and development. Bisphenol A (BPA) and phthalates are widespread environmental contaminants and endocrine disruptors, and the placental epigenetic response to these chemicals is an area of growing research interest. Therefore, our objective was to summarize research linking BPA or phthalate exposure to placental outcomes in human pregnancies, with a particular focus on epigenetic endpoints. In PubMed, studies were selected for review (without limiting start date and ending on 1 May 2018) if they reported any direct effects of BPA or phthalates on the placenta in humans. Collectively, available studies suggest that BPA and phthalate exposures are associated with changes to placental micro-RNA expression, DNA methylation, and genomic imprinting. Furthermore, several studies suggest that fetal sex may be an important modifier of placental outcomes in response to these chemicals. Studies in humans demonstrate associations of BPA and phthalate exposure with adverse placental outcomes. Moving forward, more studies should consider sex differences (termed "placental sex") in the measured outcomes, and should utilize appropriate statistical approaches to assess modification by fetal sex. Furthermore, more consistent sample collection and molecular outcome assessment paradigms will be indispensable for making progress in the field. These advances, together with improved non-invasive tools for measuring placental function and outcomes across pregnancy, will be critical for understanding the mechanisms driving placental epigenetic disruption in response to BPA and phthalates, and how these disruptions translate into placental and fetal health.
Collapse
Affiliation(s)
- Rita S Strakovsky
- The Department of Food Science and Human Nutrition, Michigan State University, 236C Trout Building, 469 Wilson Road, East Lansing, MI, USA
- Correspondence address. The Department of Food Science and Human Nutrition, Michigan State University, 236C Trout Building, 469 Wilson Road, East Lansing, MI 48823, USA. Tel: 517-353-3352; Fax: 517-353-8963; E-mail:
| | - Susan L Schantz
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, 405 N. Mathews Ave, Urbana, IL, USA
- Department of Comparative Biosciences, 2347 Beckman Institute, University of Illinois Urbana-Champaign, 405 N. Mathews Ave, Urbana, IL, USA
| |
Collapse
|