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Del Toro-De León G, van Boven J, Santos-González J, Jiao WB, Peng H, Schneeberger K, Köhler C. Epigenetic and transcriptional consequences in the endosperm of chemically induced transposon mobilization in Arabidopsis. Nucleic Acids Res 2024:gkae572. [PMID: 38967011 DOI: 10.1093/nar/gkae572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/13/2024] [Accepted: 06/26/2024] [Indexed: 07/06/2024] Open
Abstract
Genomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene expression, has independently evolved in the endosperm of flowering plants and the placenta of mammals-tissues crucial for nurturing embryos. While transposable elements (TEs) frequently colocalize with imprinted genes and are implicated in imprinting establishment, direct investigations of the impact of de novo TE transposition on genomic imprinting remain scarce. In this study, we explored the effects of chemically induced transposition of the Copia element ONSEN on genomic imprinting in Arabidopsis thaliana. Through the combination of chemical TE mobilization and doubled haploid induction, we generated a line with 40 new ONSEN copies. Our findings reveal a preferential targeting of maternally expressed genes (MEGs) for transposition, aligning with the colocalization of H2A.Z and H3K27me3 in MEGs-both previously identified as promoters of ONSEN insertions. Additionally, we demonstrate that chemically-induced DNA hypomethylation induces global transcriptional deregulation in the endosperm, leading to the breakdown of MEG imprinting. This study provides insights into the consequences of chemically induced TE remobilization in the endosperm, revealing that chemically-induced epigenome changes can have long-term consequences on imprinted gene expression.
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Affiliation(s)
- Gerardo Del Toro-De León
- Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
| | - Joram van Boven
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala 75007, Sweden
| | - Juan Santos-González
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala 75007, Sweden
| | - Wen-Biao Jiao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Haoran Peng
- Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
- Faculty for Biology, LMU Munich, Planegg-Martinsried 82152, Germany
- Cluster of Excellence on Plant Sciences, Heinrich-Heine University, Düsseldorf 40225, Germany
| | - Claudia Köhler
- Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala 75007, Sweden
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Verruma CG, Santos RS, Marchesi JAP, Sales SLA, Vila RA, Rios ÁFL, Furtado CLM, Ramos ES. Dynamic methylation pattern of H19DMR and KvDMR1 in bovine oocytes and preimplantation embryos. J Assist Reprod Genet 2024; 41:333-345. [PMID: 38231285 PMCID: PMC10894807 DOI: 10.1007/s10815-023-03011-7] [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: 08/09/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024] Open
Abstract
PURPOSE This study aimed to evaluate the epigenetic reprogramming of ICR1 (KvDMR1) and ICR2 (H19DMR) and expression of genes controlled by them as well as those involved in methylation, demethylation, and pluripotency. METHODS We collected germinal vesicle (GV) and metaphase II (MII) oocytes, and preimplantation embryos at five stages [zygote, 4-8 cells, 8-16 cells, morula, and expanded blastocysts (ExB)]. DNA methylation was assessed by BiSeq, and the gene expression was evaluated using qPCR. RESULTS H19DMR showed an increased DNA methylation from GV to MII oocytes (68.04% and 98.05%, respectively), decreasing in zygotes (85.83%) until morula (61.65%), and ExB (63.63%). H19 and IGF2 showed increased expression in zygotes, which decreased in further stages. KvDMR1 was hypermethylated in both GV (71.82%) and MII (69.43%) and in zygotes (73.70%) up to morula (77.84%), with a loss of methylation at the ExB (36.64%). The zygote had higher expression of most genes, except for CDKN1C and PHLDA2, which were highly expressed in MII and GV oocytes, respectively. DNMTs showed increased expression in oocytes, followed by a reduction in the earliest stages of embryo development. TET1 was downregulated until 4-8-cell and upregulated in 8-16-cell embryos. TET2 and TET3 showed higher expression in oocytes, and a downregulation in MII oocytes and 4-8-cell embryo. CONCLUSION We highlighted the heterogeneity in the DNA methylation of H19DMR and KvDMR1 and a dynamic expression pattern of genes controlled by them. The expression of DNMTs and TETs genes was also dynamic owing to epigenetic reprogramming.
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Affiliation(s)
- Carolina G Verruma
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Renan S Santos
- Postgraduate Program in Physiology and Pharmacology, Drug Research and Development Center (NPDM), Federal University of Ceara (UFC), Fortaleza, CE, 60430-275, Brazil
| | - Jorge A P Marchesi
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Sarah L A Sales
- Postgraduate Program in Physiology and Pharmacology, Drug Research and Development Center (NPDM), Federal University of Ceara (UFC), Fortaleza, CE, 60430-275, Brazil
| | - Reginaldo A Vila
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Álvaro F L Rios
- Biotechnology Laboratory, Center of Bioscience and Biotechnology, State University of North Fluminense Darcy Ribeiro, Goitacazes Campus, Rio de Janeiro, Brazil
| | - Cristiana L M Furtado
- Experimental Biology Center, Graduate Program in Medical Sciences, University of Fortaleza - UNIFOR, Fortaleza, CE, 60811-905, Brazil
- Drug Research and Development Center (NPDM), Postgraduate Program in Translational Medicine, Federal University of Ceara (UFC), Fortaleza, CE, 60430-275, Brazil
| | - Ester S Ramos
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil.
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3
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Ashokan M, Jayanthi KV, Elango K, Sneha K, Ramesha KP, Reshma RS, Saravanan KA, Naveen KGS. Biological methylation: redefining the link between genotype and phenotype. Anim Biotechnol 2023; 34:3174-3186. [PMID: 35468300 DOI: 10.1080/10495398.2022.2065999] [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: 11/01/2022]
Abstract
The central dogma of molecular biology is responsible for the crucial flow of genetic information from DNA to protein through the transcription and translation process. Although the sequence of DNA is constant in all organs, the difference in protein and variation in the phenotype is mainly due to the quality and quantity of tissue-specific gene expression and methylation pattern. The term methylation has been defined and redefined by various scientists in the last fifty years. There is always huge excitement around this field because the inheritance of something is beyond its DNA sequence. Advanced gene methylation studies have redefined molecular genetics and these tools are considered de novo in alleviating challenges of animal disease and production. Recent emerging evidence has shown that the impact of DNA, RNA, and protein methylation is crucial for embryonic development, cell proliferation, cell differentiation, and phenotype production. Currently, many researchers are focusing their work on methylation to understand its significant role in expression, disease-resistant traits, productivity, and longevity. The main aim of the present review is to provide an overview of DNA, RNA, and protein methylation, current research output from different sources, methodologies, factors responsible for methylation of genes, and future prospects in animal genetics.
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Affiliation(s)
- M Ashokan
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
| | - K V Jayanthi
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
| | - K Elango
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore, India
| | - Kadimetla Sneha
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
| | - K P Ramesha
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore, India
| | - Raj S Reshma
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore, India
| | - K A Saravanan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Kumar G S Naveen
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
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4
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Nuño de la Rosa L. Agency in Reproduction. Evol Dev 2023; 25:418-429. [PMID: 37243316 DOI: 10.1111/ede.12440] [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: 10/13/2022] [Revised: 03/22/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023]
Abstract
While niche construction theory and developmental approaches to evolution have brought to the front the active role of organisms as ecological and developmental agents, respectively, the role of agents in reproduction has been widely neglected by organismal perspectives of evolution. This paper addresses this problem by proposing an agential view of reproduction and shows that such a perspective has implications for the explanation of the origin of modes of reproduction, the evolvability of reproductive modes, and the coevolution between reproduction and social behavior. After introducing the two prevalent views of agency in evolutionary biology, namely those of organismal agency and selective agency, I contrast these two perspectives as applied to the evolution of animal reproduction. Taking eutherian pregnancy as a case study, I wonder whether organismal approaches to agency forged in the frame of niche construction and developmental plasticity theories can account for the goal-directed activities involved in reproductive processes. I conclude that the agential role of organisms in reproduction is irreducible to developmental and ecological agency, and that reproductive goals need to be included into our definitions of organismal agency. I then explore the evolutionary consequences of endorsing an agential approach to reproduction, showing how such an approach might illuminate our understanding of the evolutionary origination and developmental evolvability of reproductive modes. Finally, I analyze recent studies on the coevolution between viviparity and social behavior in vertebrates to suggest that an agential notion of reproduction can provide unforeseen links between developmental and ecological agency.
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Affiliation(s)
- Laura Nuño de la Rosa
- Department of Logic and Theoretical Philosophy, Complutense University of Madrid, Madrid, Spain
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5
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Bond DM, Ortega-Recalde O, Laird MK, Hayakawa T, Richardson KS, Reese FCB, Kyle B, McIsaac-Williams BE, Robertson BC, van Heezik Y, Adams AL, Chang WS, Haase B, Mountcastle J, Driller M, Collins J, Howe K, Go Y, Thibaud-Nissen F, Lister NC, Waters PD, Fedrigo O, Jarvis ED, Gemmell NJ, Alexander A, Hore TA. The admixed brushtail possum genome reveals invasion history in New Zealand and novel imprinted genes. Nat Commun 2023; 14:6364. [PMID: 37848431 PMCID: PMC10582058 DOI: 10.1038/s41467-023-41784-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 09/13/2023] [Indexed: 10/19/2023] Open
Abstract
Combining genome assembly with population and functional genomics can provide valuable insights to development and evolution, as well as tools for species management. Here, we present a chromosome-level genome assembly of the common brushtail possum (Trichosurus vulpecula), a model marsupial threatened in parts of their native range in Australia, but also a major introduced pest in New Zealand. Functional genomics reveals post-natal activation of chemosensory and metabolic genes, reflecting unique adaptations to altricial birth and delayed weaning, a hallmark of marsupial development. Nuclear and mitochondrial analyses trace New Zealand possums to distinct Australian subspecies, which have subsequently hybridised. This admixture allowed phasing of parental alleles genome-wide, ultimately revealing at least four genes with imprinted, parent-specific expression not yet detected in other species (MLH1, EPM2AIP1, UBP1 and GPX7). We find that reprogramming of possum germline imprints, and the wider epigenome, is similar to eutherian mammals except onset occurs after birth. Together, this work is useful for genetic-based control and conservation of possums, and contributes to understanding of the evolution of novel mammalian epigenetic traits.
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Affiliation(s)
- Donna M Bond
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | | | - Melanie K Laird
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, 060-0808, Japan
| | - Kyle S Richardson
- Department of Anatomy, University of Otago, Dunedin, New Zealand
- Biology Department, University of Montana Western, Dillon, MT, 59725, USA
| | - Finlay C B Reese
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Bruce Kyle
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | | | | | | | - Amy L Adams
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Wei-Shan Chang
- School of Life and Environmental Science, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
- Health and Biosecurity, CSIRO, Canberra, ACT, Australia
| | - Bettina Haase
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | | | | | - Joanna Collins
- Tree of Life, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Yasuhiro Go
- Graduate School of Information Science, Hyogo University, Hyogo, Japan
- Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Aichi, Japan
- Department of System Neuroscience, National Institute for Physiological Sciences, Aichi, Japan
| | - Francoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Nicholas C Lister
- School of Biotechnology and Biomolecular Science, Faculty of Science, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Paul D Waters
- School of Biotechnology and Biomolecular Science, Faculty of Science, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Erich D Jarvis
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, 10065, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Alana Alexander
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Timothy A Hore
- Department of Anatomy, University of Otago, Dunedin, New Zealand.
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6
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Ayache L, Bushell A, Lee J, Salminen I, Crespi B. Mother's warmth from maternal genes: genomic imprinting of brown adipose tissue. Evol Med Public Health 2023; 11:379-385. [PMID: 37928960 PMCID: PMC10621903 DOI: 10.1093/emph/eoad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/04/2023] [Indexed: 11/07/2023] Open
Abstract
Background and objectives Brown adipose tissue (BAT) plays key roles in mammalian physiology, most notably with regard to thermoregulation in infants and juveniles. Previous studies have suggested that intragenomic conflict, in the form of genomic imprinting, mediates BAT thermogenesis, because it represents a public good for groups of siblings, or a mother with her offspring, who huddle together to conserve warmth. By this hypothesis, maternally expressed imprinted genes should promote BAT, while paternally expressed genes should repress it. Methodology We systematically searched the literature using two curated lists of genes imprinted in humans and/or mice, in association with evidence regarding effects of perturbation to imprinted gene expression on BAT development or activity. Results Overall, enhanced BAT was associated with relatively higher expression of maternally expressed imprinted genes, and relatively lower expression of paternally expressed imprinted genes; this pattern was found for 16 of the 19 genes with sufficient information for robust ascertainment (Binomial test, P < 0.005, 2-tailed). Conclusions and implications These results support the kinship theory of imprinting and indicate that future studies of BAT, and its roles in human health and disease, may usefully focus on effects of imprinted genes and associated genomic conflicts.
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Affiliation(s)
- Lynn Ayache
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Aiden Bushell
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Jessica Lee
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Iiro Salminen
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Bernard Crespi
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
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7
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Shiura H, Kitazawa M, Ishino F, Kaneko-Ishino T. Roles of retrovirus-derived PEG10 and PEG11/RTL1 in mammalian development and evolution and their involvement in human disease. Front Cell Dev Biol 2023; 11:1273638. [PMID: 37842090 PMCID: PMC10570562 DOI: 10.3389/fcell.2023.1273638] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023] Open
Abstract
PEG10 and PEG11/RTL1 are paternally expressed, imprinted genes that play essential roles in the current eutherian developmental system and are therefore associated with developmental abnormalities caused by aberrant genomic imprinting. They are also presumed to be retrovirus-derived genes with homology to the sushi-ichi retrotransposon GAG and POL, further expanding our comprehension of mammalian evolution via the domestication (exaptation) of retrovirus-derived acquired genes. In this manuscript, we review the importance of PEG10 and PEG11/RTL1 in genomic imprinting research via their functional roles in development and human disease, including neurodevelopmental disorders of genomic imprinting, Angelman, Kagami-Ogata and Temple syndromes, and the impact of newly inserted DNA on the emergence of newly imprinted regions. We also discuss their possible roles as ancestors of other retrovirus-derived RTL/SIRH genes that likewise play important roles in the current mammalian developmental system, such as in the placenta, brain and innate immune system.
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Affiliation(s)
- Hirosuke Shiura
- Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi, Japan
| | - Moe Kitazawa
- School of BioSciences, Faculty of Science, The University of Melbourne, Melbourne, VIC, Australia
| | - Fumitoshi Ishino
- Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Tomoko Kaneko-Ishino
- Faculty of Nursing, School of Medicine, Tokai University, Isehara, Kanagawa, Japan
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8
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Di Michele F, Chillón I, Feil R. Imprinted Long Non-Coding RNAs in Mammalian Development and Disease. Int J Mol Sci 2023; 24:13647. [PMID: 37686455 PMCID: PMC10487962 DOI: 10.3390/ijms241713647] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023] Open
Abstract
Imprinted genes play diverse roles in mammalian development, homeostasis, and disease. Most imprinted chromosomal domains express one or more long non-coding RNAs (lncRNAs). Several of these lncRNAs are strictly nuclear and their mono-allelic expression controls in cis the expression of protein-coding genes, often developmentally regulated. Some imprinted lncRNAs act in trans as well, controlling target gene expression elsewhere in the genome. The regulation of imprinted gene expression-including that of imprinted lncRNAs-is susceptible to stochastic and environmentally triggered epigenetic changes in the early embryo. These aberrant changes persist during subsequent development and have long-term phenotypic consequences. This review focuses on the expression and the cis- and trans-regulatory roles of imprinted lncRNAs and describes human disease syndromes associated with their perturbed expression.
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Affiliation(s)
- Flavio Di Michele
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, 1919 Route de Mende, 34093 Montpellier, France
- University of Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
| | - Isabel Chillón
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, 1919 Route de Mende, 34093 Montpellier, France
- University of Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, 1919 Route de Mende, 34093 Montpellier, France
- University of Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
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9
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Sainty R, Silver MJ, Prentice AM, Monk D. The influence of early environment and micronutrient availability on developmental epigenetic programming: lessons from the placenta. Front Cell Dev Biol 2023; 11:1212199. [PMID: 37484911 PMCID: PMC10358779 DOI: 10.3389/fcell.2023.1212199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/27/2023] [Indexed: 07/25/2023] Open
Abstract
DNA methylation is the most commonly studied epigenetic mark in humans, as it is well recognised as a stable, heritable mark that can affect genome function and influence gene expression. Somatic DNA methylation patterns that can persist throughout life are established shortly after fertilisation when the majority of epigenetic marks, including DNA methylation, are erased from the pre-implantation embryo. Therefore, the period around conception is potentially critical for influencing DNA methylation, including methylation at imprinted alleles and metastable epialleles (MEs), loci where methylation varies between individuals but is correlated across tissues. Exposures before and during conception can affect pregnancy outcomes and health throughout life. Retrospective studies of the survivors of famines, such as those exposed to the Dutch Hunger Winter of 1944-45, have linked exposures around conception to later disease outcomes, some of which correlate with DNA methylation changes at certain genes. Animal models have shown more directly that DNA methylation can be affected by dietary supplements that act as cofactors in one-carbon metabolism, and in humans, methylation at birth has been associated with peri-conceptional micronutrient supplementation. However, directly showing a role of micronutrients in shaping the epigenome has proven difficult. Recently, the placenta, a tissue with a unique hypomethylated methylome, has been shown to possess great inter-individual variability, which we highlight as a promising target tissue for studying MEs and mixed environmental exposures. The placenta has a critical role shaping the health of the fetus. Placenta-associated pregnancy complications, such as preeclampsia and intrauterine growth restriction, are all associated with aberrant patterns of DNA methylation and expression which are only now being linked to disease risk later in life.
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Affiliation(s)
- Rebecca Sainty
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Matt J. Silver
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Andrew M. Prentice
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - David Monk
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
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10
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Booth W, Levine BA, Corush JB, Davis MA, Dwyer Q, De Plecker R, Schuett GW. Discovery of facultative parthenogenesis in a new world crocodile. Biol Lett 2023; 19:20230129. [PMID: 37282490 PMCID: PMC10244963 DOI: 10.1098/rsbl.2023.0129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/17/2023] [Indexed: 06/08/2023] Open
Abstract
Over the past two decades, there has been an astounding growth in the documentation of vertebrate facultative parthenogenesis (FP). This unusual reproductive mode has been documented in birds, non-avian reptiles-specifically lizards and snakes-and elasmobranch fishes. Part of this growth among vertebrate taxa is attributable to awareness of the phenomenon itself and advances in molecular genetics/genomics and bioinformatics, and as such our understanding has developed considerably. Nonetheless, questions remain as to its occurrence outside of these vertebrate lineages, most notably in Chelonia (turtles) and Crocodylia (crocodiles, alligators and gharials). The latter group is particularly interesting because unlike all previously documented cases of FP in vertebrates, crocodilians lack sex chromosomes and sex determination is controlled by temperature. Here, using whole-genome sequencing data, we provide, to our knowledge, the first evidence of FP in a crocodilian, the American crocodile, Crocodylus acutus. The data support terminal fusion automixis as the reproductive mechanism; a finding which suggests a common evolutionary origin of FP across reptiles, crocodilians and birds. With FP now documented in the two main branches of extant archosaurs, this discovery offers tantalizing insights into the possible reproductive capabilities of the extinct archosaurian relatives of crocodilians and birds, notably members of Pterosauria and Dinosauria.
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Affiliation(s)
- Warren Booth
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
- Chiricahua Desert Museum, Rodeo, NM 88056, USA
| | - Brenna A. Levine
- Chiricahua Desert Museum, Rodeo, NM 88056, USA
- Department of Biology, Kean University, Union, NJ 07083, USA
| | - Joel B. Corush
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Illinois, IL 61820, USA
| | - Mark A. Davis
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Illinois, IL 61820, USA
| | - Quetzal Dwyer
- Reptilandia Reptile Lagoon, Johnson City, TX 78636, USA
| | - Roel De Plecker
- Parque Reptilandia, Dominical 5000, Puntarenas Province, 11902, Costa Rica
| | - Gordon W. Schuett
- Chiricahua Desert Museum, Rodeo, NM 88056, USA
- Department of Biology, Neuroscience Institute, Georgia State University, Atlanta, GA 30302, USA
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11
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Hu Y, Yuan S, Du X, Liu J, Zhou W, Wei F. Comparative analysis reveals epigenomic evolution related to species traits and genomic imprinting in mammals. Innovation (N Y) 2023; 4:100434. [PMID: 37215528 PMCID: PMC10196708 DOI: 10.1016/j.xinn.2023.100434] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 04/25/2023] [Indexed: 05/24/2023] Open
Abstract
DNA methylation is an epigenetic modification that plays a crucial role in various regulatory processes, including gene expression regulation, transposable element repression, and genomic imprinting. However, most studies on DNA methylation have been conducted in humans and other model species, whereas the dynamics of DNA methylation across mammals remain poorly explored, limiting our understanding of epigenomic evolution in mammals and the evolutionary impacts of conserved and lineage-specific DNA methylation. Here, we generated and gathered comparative epigenomic data from 13 mammalian species, including two marsupial species, to demonstrate that DNA methylation plays critical roles in several aspects of gene evolution and species trait evolution. We found that the species-specific DNA methylation of promoters and noncoding elements correlates with species-specific traits such as body patterning, indicating that DNA methylation might help establish or maintain interspecies differences in gene regulation that shape phenotypes. For a broader view, we investigated the evolutionary histories of 88 known imprinting control regions across mammals to identify their evolutionary origins. By analyzing the features of known and newly identified potential imprints in all studied mammals, we found that genomic imprinting may function in embryonic development through the binding of specific transcription factors. Our findings show that DNA methylation and the complex interaction between the genome and epigenome have a significant impact on mammalian evolution, suggesting that evolutionary epigenomics should be incorporated to develop a unified evolutionary theory.
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Affiliation(s)
- Yisi Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Shenli Yuan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xin Du
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiang Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenliang Zhou
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
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12
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Cao W, Douglas KC, Samollow PB, VandeBerg JL, Wang X, Clark AG. Origin and Evolution of Marsupial-specific Imprinting Clusters Through Lineage-specific Gene Duplications and Acquisition of Promoter Differential Methylation. Mol Biol Evol 2023; 40:msad022. [PMID: 36721950 PMCID: PMC9937046 DOI: 10.1093/molbev/msad022] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/08/2023] [Accepted: 01/25/2023] [Indexed: 02/02/2023] Open
Abstract
Genomic imprinting is a parent-of-origin-specific expression phenomenon that plays fundamental roles in many biological processes. In animals, imprinting is only observed in therian mammals, with ∼200 imprinted genes known in humans and mice. The imprinting pattern in marsupials has been minimally investigated by examining orthologs to known eutherian imprinted genes. To identify marsupial-specific imprinting in an unbiased way, we performed RNA-seq studies on samples of fetal brain and placenta from the reciprocal cross progeny of two laboratory opossum stocks. We inferred allele-specific expression for >3,000 expressed genes and discovered/validated 13 imprinted genes, including three previously known imprinted genes, Igf2r, Peg10, and H19. We estimate that marsupials imprint ∼60 autosomal genes, which is a much smaller set compared with eutherians. Among the nine novel imprinted genes, three noncoding RNAs have no known homologs in eutherian mammals, while the remaining genes have important functions in pluripotency, transcription regulation, nucleolar homeostasis, and neural differentiation. Methylation analyses at promoter CpG islands revealed differentially methylated regions in five of these marsupial-specific imprinted genes, suggesting that differential methylation is a common mechanism in the epigenetic regulation of marsupial imprinting. Clustering and co-regulation were observed at marsupial imprinting loci Pou5f3-Npdc1 and Nkrfl-Ipncr2, but eutherian-type multi-gene imprinting clusters were not detected. Also differing from eutherian mammals, the brain and placenta imprinting profiles are remarkably similar in opossums, presumably due to the shared origin of these organs from the trophectoderm. Our results contribute to a fuller understanding of the origin, evolution, and mechanisms of genomic imprinting in therian mammals.
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Affiliation(s)
- Wenqi Cao
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
- Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn University Center for Advanced Science, Auburn, AL, USA
| | - Kory C Douglas
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Paul B Samollow
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - John L VandeBerg
- South Texas Diabetes and Obesity Institute and Department of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Xu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
- Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn University Center for Advanced Science, Auburn, AL, USA
- Scott-Ritchey Research Center, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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13
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Shi C, Yan Z, Zhang Y, Qin L, Wu W, Gao C, Gao L, Liu J, Cui Y. Effects of putrescine on the quality and epigenetic modification of mouse oocytes during in vitro maturation. Reprod Fertil Dev 2022; 34:957-970. [PMID: 36031717 DOI: 10.1071/rd22064] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 07/29/2022] [Indexed: 11/23/2022] Open
Abstract
CONTEXT Low ovarian putrescine levels and decreased peak values following luteinising hormone peaks are related to poor oocyte quantity and quality in ageing women. AIMS To investigate the effects of putrescine supplementation in in vitro maturation (IVM) medium on oocyte quality and epigenetic modification. METHODS Germinal vesicle oocytes retrieved from the ovaries of 8-week-old and 9-month-old mice were divided into four groups (the young, young+difluoromethylornithine (DFMO), ageing and ageing+putrescine groups) and cultured in IVM medium with or without 1mM putrescine or DFMO for 16h. The first polar body extrusion (PBE), cleavage and embryonic development were evaluated. Spindles, chromosomes, mitochondria and reactive oxygen species (ROS) were measured. The expression levels of SIRT1, H3K9ac, H3K9me2, H3K9me3, and 5mC levels were evaluated. Sirt1 and imprinted genes were detected. RESULTS The PBE was higher in the ageing+putrescine group than in the ageing group. Putrescine increased the total and inner cell mass cell numbers of blastocysts in ageing oocytes. Putrescine decreased aberrant spindles and chromosome aneuploidy, increased the mitochondrial membrane potential and decreased ROS levels. Putrescine increased SIRT1 expression and attenuated the upregulation of H3K9ac levels in ageing oocytes. Putrescine did not affect 5mC, H3K9me2 or H3K9me3 levels or imprinted gene expression. CONCLUSIONS Putrescine supplementation during IVM improved the maturation and quality of ageing oocytes and promoted embryonic development by decreasing ROS generation, maintaining mitochondrial and spindle function and correcting aberrant epigenetic modification. IMPLICATIONS Putrescine shows application potential for human-assisted reproduction, especially for IVM of oocytes from ageing women.
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Affiliation(s)
- Chennan Shi
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province 210029, China
| | - Zhengjie Yan
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province 210029, China
| | - Yuexin Zhang
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province 210029, China
| | - Lianju Qin
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province 210029, China
| | - Wei Wu
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province 210029, China
| | - Chao Gao
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province 210029, China
| | - Li Gao
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province 210029, China
| | - Jiayin Liu
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province 210029, China
| | - Yugui Cui
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province 210029, China
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14
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Ishihara T, Griffith OW, Suzuki S, Renfree MB. Placental imprinting of SLC22A3 in the IGF2R imprinted domain is conserved in therian mammals. Epigenetics Chromatin 2022; 15:32. [PMID: 36030241 PMCID: PMC9419357 DOI: 10.1186/s13072-022-00465-4] [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: 05/27/2022] [Accepted: 07/25/2022] [Indexed: 11/10/2022] Open
Abstract
Background The eutherian IGF2R imprinted domain is regulated by an antisense long non-coding RNA, Airn, which is expressed from a differentially methylated region (DMR) in mice. Airn silences two neighbouring genes, Solute carrier family 22 member 2 (Slc22a2) and Slc22a3, to establish the Igf2r imprinted domain in the mouse placenta. Marsupials also have an antisense non-coding RNA, ALID, expressed from a DMR, although the exact function of ALID is currently unknown. The eutherian IGF2R DMR is located in intron 2, while the marsupial IGF2R DMR is located in intron 12, but it is not yet known whether the adjacent genes SLC22A2 and/or SLC22A3 are also imprinted in the marsupial lineage. In this study, the imprinting status of marsupial SLC22A2 and SLC22A3 in the IGF2R imprinted domain in the chorio-vitelline placenta was examined in a marsupial, the tammar wallaby. Results In the tammar placenta, SLC22A3 but not SLC22A2 was imprinted. Tammar SLC22A3 imprinting was evident in placental tissues but not in the other tissues examined in this study. A putative promoter of SLC22A3 lacked DNA methylation, suggesting that this gene is not directly silenced by a DMR on its promoter as seen in the mouse. Based on immunofluorescence, we confirmed that the tammar SLC22A3 is localised in the endodermal cell layer of the tammar placenta where nutrient trafficking occurs. Conclusions Since SLC22A3 is imprinted in the tammar placenta, we conclude that this placental imprinting of SLC22A3 has been positively selected after the marsupial and eutherian split because of the differences in the DMR location. Since SLC22A3 is known to act as a transporter molecule for nutrient transfer in the eutherian placenta, we suggest it was strongly selected to control the balance between supply and demand of nutrients in marsupial as it does in eutherian placentas. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-022-00465-4.
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Affiliation(s)
- Teruhito Ishihara
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Oliver W Griffith
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia.,Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Shunsuke Suzuki
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, Nagano, 399-4598, Japan
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia.
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15
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Montgomery SA, Hisanaga T, Wang N, Axelsson E, Akimcheva S, Sramek M, Liu C, Berger F. Polycomb-mediated repression of paternal chromosomes maintains haploid dosage in diploid embryos of Marchantia. eLife 2022; 11:79258. [PMID: 35996955 PMCID: PMC9402228 DOI: 10.7554/elife.79258] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/18/2022] [Indexed: 02/06/2023] Open
Abstract
Complex mechanisms regulate gene dosage throughout eukaryotic life cycles. Mechanisms controlling gene dosage have been extensively studied in animals, however it is unknown how generalizable these mechanisms are to diverse eukaryotes. Here, we use the haploid plant Marchantia polymorpha to assess gene dosage control in its short-lived diploid embryo. We show that throughout embryogenesis, paternal chromosomes are repressed resulting in functional haploidy. The paternal genome is targeted for genomic imprinting by the Polycomb mark H3K27me3 starting at fertilization, rendering the maternal genome in control of embryogenesis. Maintaining haploid gene dosage by this new form of imprinting is essential for embryonic development. Our findings illustrate how haploid-dominant species can regulate gene dosage through paternal chromosome inactivation and initiates the exploration of the link between life cycle history and gene dosage in a broader range of organisms.
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Affiliation(s)
- Sean Akira Montgomery
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Tetsuya Hisanaga
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Nan Wang
- Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Elin Axelsson
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Svetlana Akimcheva
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Milos Sramek
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Chang Liu
- Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
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16
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Conflict and the evolution of viviparity in vertebrates. Behav Ecol Sociobiol 2022. [DOI: 10.1007/s00265-022-03171-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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17
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Kostiniuk D, Tamminen H, Mishra PP, Marttila S, Raitoharju E. Methylation pattern of polymorphically imprinted nc886 is not conserved across mammalia. PLoS One 2022; 17:e0261481. [PMID: 35294436 PMCID: PMC8926257 DOI: 10.1371/journal.pone.0261481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/02/2022] [Indexed: 12/17/2022] Open
Abstract
Background In humans, the nc886 locus is a polymorphically imprinted metastable epiallele. Periconceptional conditions have an effect on the methylation status of nc886, and further, this methylation status is associated with health outcomes in later life, in line with the Developmental Origins of Health and Disease (DOHaD) hypothesis. Animal models would offer opportunities to study the associations between periconceptional conditions, nc886 methylation status and metabolic phenotypes further. Thus, we set out to investigate the methylation pattern of the nc886 locus in non-human mammals. Data We obtained DNA methylation data from the data repository GEO for mammals, whose nc886 gene included all three major parts of nc886 and had sequency similarity of over 80% with the human nc886. Our final sample set consisted of DNA methylation data from humans, chimpanzees, bonobos, gorillas, orangutangs, baboons, macaques, vervets, marmosets and guinea pigs. Results In human data sets the methylation pattern of nc886 locus followed the expected bimodal distribution, indicative of polymorphic imprinting. In great apes, we identified a unimodal DNA methylation pattern with 50% methylation level in all individuals and in all subspecies. In Old World monkeys, the between individual variation was greater and methylation on average was close to 60%. In guinea pigs the region around the nc886 homologue was non-methylated. Results obtained from the sequence comparison of the CTCF binding sites flanking the nc886 gene support the results on the DNA methylation data. Conclusions Our results indicate that unlike in humans, nc886 is not a polymorphically imprinted metastable epiallele in non-human primates or in guinea pigs, thus implying that animal models are not applicable for nc886 research. The obtained data suggests that the nc886 region may be classically imprinted in great apes, and potentially also in Old World monkeys, but not in guinea pigs.
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Affiliation(s)
- Daria Kostiniuk
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Hely Tamminen
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Pashupati P. Mishra
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Centre, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Saara Marttila
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Gerontology Research Center, Tampere University, Tampere, Finland
| | - Emma Raitoharju
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Centre, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tampere University Hospital, Tampere, Finland
- * E-mail:
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18
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Renfree MB, Shaw G. Placentation in Marsupials. ADVANCES IN ANATOMY, EMBRYOLOGY, AND CELL BIOLOGY 2022; 234:41-60. [PMID: 34694477 DOI: 10.1007/978-3-030-77360-1_4] [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: 02/09/2023]
Abstract
It is sometimes implied that marsupials are "aplacental," on the presumption that the only mammals that have a placenta are the eponymous "placental" mammals. This misconception has persisted despite the interest in and descriptions of the marsupial placenta, even in Amoroso's definitive chapter. It was also said that marsupials had no maternal recognition of pregnancy and no placental hormone production. In addition, it was thought that genomic imprinting could not exist in marsupials because pregnancy was so short. We now know that none of these ideas have held true with extensive studies over the last four decades definitively showing that they are indeed mammals with a fully functional placenta, and with their own specializations.
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Affiliation(s)
- Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia.
| | - Geoff Shaw
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
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19
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Kaneko-Ishino T, Ishino F. The Evolutionary Advantage in Mammals of the Complementary Monoallelic Expression Mechanism of Genomic Imprinting and Its Emergence From a Defense Against the Insertion Into the Host Genome. Front Genet 2022; 13:832983. [PMID: 35309133 PMCID: PMC8928582 DOI: 10.3389/fgene.2022.832983] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/11/2022] [Indexed: 12/30/2022] Open
Abstract
In viviparous mammals, genomic imprinting regulates parent-of-origin-specific monoallelic expression of paternally and maternally expressed imprinted genes (PEGs and MEGs) in a region-specific manner. It plays an essential role in mammalian development: aberrant imprinting regulation causes a variety of developmental defects, including fetal, neonatal, and postnatal lethality as well as growth abnormalities. Mechanistically, PEGs and MEGs are reciprocally regulated by DNA methylation of germ-line differentially methylated regions (gDMRs), thereby exhibiting eliciting complementary expression from parental genomes. The fact that most gDMR sequences are derived from insertion events provides strong support for the claim that genomic imprinting emerged as a host defense mechanism against the insertion in the genome. Recent studies on the molecular mechanisms concerning how the DNA methylation marks on the gDMRs are established in gametes and maintained in the pre- and postimplantation periods have further revealed the close relationship between genomic imprinting and invading DNA, such as retroviruses and LTR retrotransposons. In the presence of gDMRs, the monoallelic expression of PEGs and MEGs confers an apparent advantage by the functional compensation that takes place between the two parental genomes. Thus, it is likely that genomic imprinting is a consequence of an evolutionary trade-off for improved survival. In addition, novel genes were introduced into the mammalian genome via this same surprising and complex process as imprinted genes, such as the genes acquired from retroviruses as well as those that were duplicated by retropositioning. Importantly, these genes play essential/important roles in the current eutherian developmental system, such as that in the placenta and/or brain. Thus, genomic imprinting has played a critically important role in the evolutionary emergence of mammals, not only by providing a means to escape from the adverse effects of invading DNA with sequences corresponding to the gDMRs, but also by the acquisition of novel functions in development, growth and behavior via the mechanism of complementary monoallelic expression.
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Affiliation(s)
- Tomoko Kaneko-Ishino
- School of Medicine, Tokai University, Isehara, Japan
- *Correspondence: Tomoko Kaneko-Ishino, ; Fumitoshi Ishino,
| | - Fumitoshi Ishino
- Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- *Correspondence: Tomoko Kaneko-Ishino, ; Fumitoshi Ishino,
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20
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Tanaka K, Besson V, Rivagorda M, Oury F, Marazzi G, Sassoon DA. Paternally expressed gene 3 (Pw1/Peg3) promotes sexual dimorphism in metabolism and behavior. PLoS Genet 2022; 18:e1010003. [PMID: 35025875 PMCID: PMC8791484 DOI: 10.1371/journal.pgen.1010003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 01/26/2022] [Accepted: 12/20/2021] [Indexed: 01/06/2023] Open
Abstract
The paternally expressed gene 3 (Pw1/Peg3) is a mammalian-specific parentally imprinted gene expressed in stem/progenitor cells of the brain and endocrine tissues. Here, we compared phenotypic characteristics in Pw1/Peg3 deficient male and female mice. Our findings indicate that Pw1/Peg3 is a key player for the determination of sexual dimorphism in metabolism and behavior. Mice carrying a paternally inherited Pw1/Peg3 mutant allele manifested postnatal deficits in GH/IGF dependent growth before weaning, sex steroid dependent masculinization during puberty, and insulin dependent fat accumulation in adulthood. As a result, Pw1/Peg3 deficient mice develop a sex-dependent global shift of body metabolism towards accelerated adiposity, diabetic-like insulin resistance, and fatty liver. Furthermore, Pw1/Peg3 deficient males displayed reduced social dominance and competitiveness concomitant with alterations in the vasopressinergic architecture in the brain. This study demonstrates that Pw1/Peg3 provides an epigenetic context that promotes male-specific characteristics through sex steroid pathways during postnatal development. Pw1/Peg3 is under parental specific epigenetic regulation. We propose that Pw1/Peg3 confers a selective advantage in mammals by regulating sexual dimorphism. To address this question, we examined the consequences of Pw1/Peg3 loss of function in mice in an age- and sex-dependent context and found that Pw1/Peg3 mutants display reduced sexual dimorphism in growth, metabolism and behaviors. Our findings support the intralocus sexual conflict model of genomic imprinting where it contributes in sexual differentiation. Furthermore, our observations provide a unifying role of sex steroid signaling as a common property of Pw1/Peg3 expressing stem/progenitor cells and differentiated endocrine cells, both of which remain proliferative in response to gonadal hormones in adult life.
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Affiliation(s)
- Karo Tanaka
- Stem Cells and Regenerative Medicine, Institute of Cardiometabolism and Nutrition (ICAN), INSERM U1166, University of Pierre and Marie Curie Paris VI, Paris, France
| | - Vanessa Besson
- Stem Cells and Regenerative Medicine, Institute of Cardiometabolism and Nutrition (ICAN), INSERM U1166, University of Pierre and Marie Curie Paris VI, Paris, France
| | - Manon Rivagorda
- Hormonal Regulation of Brain Development and Functions, INSERM U1151, Institut Necker Enfants Malades, Paris, France
| | - Franck Oury
- Hormonal Regulation of Brain Development and Functions, INSERM U1151, Institut Necker Enfants Malades, Paris, France
| | - Giovanna Marazzi
- Stem Cells and Regenerative Medicine, Institute of Cardiometabolism and Nutrition (ICAN), INSERM U1166, University of Pierre and Marie Curie Paris VI, Paris, France
| | - David A. Sassoon
- Stem Cells and Regenerative Medicine, Institute of Cardiometabolism and Nutrition (ICAN), INSERM U1166, University of Pierre and Marie Curie Paris VI, Paris, France
- * E-mail:
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21
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Saleh-Subaie N, Ramírez-Cruz GA, Zúñiga-Vega JJ. Examination of the Trexler-DeAngelis Model of Maternal Provisioning Reveals That Matrotrophy Is Costly. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.690430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The evolution of matrotrophy (post-fertilization maternal provisioning to developing embryos) has been explained through several hypotheses. Trexler and DeAngelis proposed in 2003 a theoretical model that defines the ecological conditions under which matrotrophy would be favored over lecithotrophy (pre-fertilization maternal provisioning). According to this model, matrotrophy offers a selective advantage in environments with abundant and constantly available food, whereas environments with limited and fluctuating food resources should instead promote a lecithotrophic mode of maternal provisioning. This model also proposes that matrotrophy entails the consequence of leaner reproductive females and in turn shorter lifespans. In this study, we examined the Trexler-DeAngelis model using data from 45 populations of five viviparous species from the fish genus Poeciliopsis (family Poeciliidae). We used the matrotrophy index (MI) as a measure of post-fertilization maternal provisioning, and the index of stomach fullness and individual body condition (BC) as proxies for food availability. We also estimated the magnitude of fluctuations in food availability by calculating the temporal variances of these two proxies. Neither abundant nor constantly available food were associated with greater degrees of matrotrophy, which fails to support the predictions of the Trexler-DeAngelis model with respect to the ecological drivers of increased post-fertilization provisioning to embryos. Nonetheless, in all five species we observed that females with greater degrees of matrotrophy had poorer BC compared to females that provided less nutrients to embryos after fertilization. This finding is consistent with one of the expected consequences of advanced matrotrophy according to the Trexler-DeAngelis model, namely, a detriment to the nutritional status of females. Our study provides compelling evidence that gestating females experience a trade-off between post-fertilization provisioning to embryos and self-maintenance, revealing in turn that matrotrophy is a costly reproductive strategy.
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22
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Jiang H, Guo D, Ye J, Gao Y, Liu H, Wang Y, Xue M, Yan Q, Chen J, Duan L, Li G, Li X, Xie L. Genome-wide analysis of genomic imprinting in the endosperm and allelic variation in flax. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1697-1710. [PMID: 34228847 DOI: 10.1111/tpj.15411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Genomic imprinting is an epigenetic phenomenon that causes biased expression of maternally and paternally inherited alleles. In flowering plants, genomic imprinting predominantly occurs in the triploid endosperm and plays a vital role in seed development. In this study, we identified 248 candidate imprinted genes including 114 maternally expressed imprinted genes (MEGs) and 134 paternally expressed imprinted genes (PEGs) in flax (Linum usitatissimum L.) endosperm using deep RNA sequencing. These imprinted genes were neither clustered in specific chromosomal regions nor well conserved among flax and other plant species. MEGs tended to be expressed specifically in the endosperm, whereas the expression of PEGs was not tissue-specific. Imprinted single nucleotide polymorphisms differentiated 200 flax cultivars into the oil flax, oil-fiber dual purpose flax and fiber flax subgroups, suggesting that genomic imprinting contributed to intraspecific variation in flax. The nucleotide diversity of imprinted genes in the oil flax subgroup was significantly higher than that in the fiber flax subgroup, indicating that some imprinted genes underwent positive selection during flax domestication from oil flax to fiber flax. Moreover, imprinted genes that underwent positive selection were related to flax functions. Thirteen imprinted genes related to flax seed size and weight were identified using a candidate gene-based association study. Therefore, our study provides information for further exploration of the function and genomic variation of imprinted genes in the flax population.
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Affiliation(s)
- Haixia Jiang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Dongliang Guo
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Jiali Ye
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanfang Gao
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Huiqing Liu
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Yue Wang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Min Xue
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Qingcheng Yan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Jiaxun Chen
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Lepeng Duan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Gongze Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Xiao Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Liqiong Xie
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
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23
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Rodrigues JA, Hsieh PH, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye X, Nguyen ND, Nijjar S, Ronald PC, Fischer RL, Zilberman D. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proc Natl Acad Sci U S A 2021; 118:e2104445118. [PMID: 34272287 PMCID: PMC8307775 DOI: 10.1073/pnas.2104445118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Parent-of-origin-dependent gene expression in mammals and flowering plants results from differing chromatin imprints (genomic imprinting) between maternally and paternally inherited alleles. Imprinted gene expression in the endosperm of seeds is associated with localized hypomethylation of maternally but not paternally inherited DNA, with certain small RNAs also displaying parent-of-origin-specific expression. To understand the evolution of imprinting mechanisms in Oryza sativa (rice), we analyzed imprinting divergence among four cultivars that span both japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted genes are imprinted across cultivars and enriched for functions in chromatin and transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted genes display divergent imprinting. Analyses of DNA methylation and small RNAs revealed that endosperm-specific 24-nt small RNA-producing loci show weak RNA-directed DNA methylation, frequently overlap genes, and are imprinted four times more often than genes. However, imprinting divergence most often correlated with local DNA methylation epimutations (9 of 17 assessable loci), which were largely stable within subspecies. Small insertion/deletion events and transposable element insertions accompanied 4 of the 9 locally epimutated loci and associated with imprinting divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic variation occurred at key regulatory regions-the promoter and transcription start site of maternally biased genes, and the promoter and gene body of paternally biased genes. Our results reinforce models for the role of maternal-specific DNA hypomethylation in imprinting of both maternally and paternally biased genes, and highlight the role of transposition and epimutation in rice imprinting evolution.
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Affiliation(s)
- Jessica A Rodrigues
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Ping-Hung Hsieh
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Deling Ruan
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Toshiro Nishimura
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Manoj K Sharma
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Rita Sharma
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - XinYi Ye
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Nicholas D Nguyen
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Sukhranjan Nijjar
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Pamela C Ronald
- Department of Plant Pathology, University of California, Davis, CA 95616
- The Genome Center, University of California, Davis, CA 95616
| | - Robert L Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720;
| | - Daniel Zilberman
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720;
- Department of Cell and Developmental Biology, The John Innes Centre, Norwich NR4 7UH, United Kingdom
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24
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Migliore L, Nicolì V, Stoccoro A. Gender Specific Differences in Disease Susceptibility: The Role of Epigenetics. Biomedicines 2021; 9:652. [PMID: 34200989 PMCID: PMC8228628 DOI: 10.3390/biomedicines9060652] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/02/2021] [Accepted: 06/05/2021] [Indexed: 01/08/2023] Open
Abstract
Many complex traits or diseases, such as infectious and autoimmune diseases, cancer, xenobiotics exposure, neurodevelopmental and neurodegenerative diseases, as well as the outcome of vaccination, show a differential susceptibility between males and females. In general, the female immune system responds more efficiently to pathogens. However, this can lead to over-reactive immune responses, which may explain the higher presence of autoimmune diseases in women, but also potentially the more adverse effects of vaccination in females compared with in males. Many clinical and epidemiological studies reported, for the SARS-CoV-2 infection, a gender-biased differential response; however, the majority of reports dealt with a comparable morbidity, with males, however, showing higher COVID-19 adverse outcomes. Although gender differences in immune responses have been studied predominantly within the context of sex hormone effects, some other mechanisms have been invoked: cellular mosaicism, skewed X chromosome inactivation, genes escaping X chromosome inactivation, and miRNAs encoded on the X chromosome. The hormonal hypothesis as well as other mechanisms will be examined and discussed in the light of the most recent epigenetic findings in the field, as the concept that epigenetics is the unifying mechanism in explaining gender-specific differences is increasingly emerging.
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Affiliation(s)
- Lucia Migliore
- Department of Translational Research and of New Surgical and Medical Technologies, Medical School, University of Pisa, 56126 Pisa, Italy; (V.N.); (A.S.)
- Department of Laboratory Medicine, Azienda Ospedaliero Universitaria Pisana, 56124 Pisa, Italy
| | - Vanessa Nicolì
- Department of Translational Research and of New Surgical and Medical Technologies, Medical School, University of Pisa, 56126 Pisa, Italy; (V.N.); (A.S.)
| | - Andrea Stoccoro
- Department of Translational Research and of New Surgical and Medical Technologies, Medical School, University of Pisa, 56126 Pisa, Italy; (V.N.); (A.S.)
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25
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Rong H, Yang W, Zhu H, Jiang B, Jiang J, Wang Y. Genomic imprinted genes in reciprocal hybrid endosperm of Brassica napus. BMC PLANT BIOLOGY 2021; 21:140. [PMID: 33726676 PMCID: PMC7968328 DOI: 10.1186/s12870-021-02908-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 02/28/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND Genomic imprinting results in the expression of parent-of-origin-specific alleles in the offspring. Brassica napus is an oil crop with research values in polyploidization. Identification of imprinted genes in B. napus will enrich the knowledge of genomic imprinting in dicotyledon plants. RESULTS In this study, we performed reciprocal crosses between B. napus L. cultivars Yangyou 6 (Y6) and Zhongshuang 11 (ZS11) to collect endosperm at 20 and 25 days after pollination (DAP) for RNA-seq. In total, we identified 297 imprinted genes, including 283 maternal expressed genes (MEGs) and 14 paternal expressed genes (PEGs) according to the SNPs between Y6 and ZS11. Only 36 genes (35 MEGs and 1 PEG) were continuously imprinted in 20 and 25 DAP endosperm. We found 15, 2, 5, 3, 10, and 25 imprinted genes in this study were also imprinted in Arabidopsis, rice, castor bean, maize, B. rapa, and other B. napus lines, respectively. Only 26 imprinted genes were specifically expressed in endosperm, while other genes were also expressed in root, stem, leaf and flower bud of B. napus. A total of 109 imprinted genes were clustered on rapeseed chromosomes. We found the LTR/Copia transposable elements (TEs) were most enriched in both upstream and downstream of the imprinted genes, and the TEs enriched around imprinted genes were more than non-imprinted genes. Moreover, the expression of 5 AGLs and 6 pectin-related genes in hybrid endosperm were significantly changed comparing with that in parent endosperm. CONCLUSION This research provided a comprehensive identification of imprinted genes in B. napus, and enriched the gene imprinting in dicotyledon plants, which would be useful in further researches on how gene imprinting regulates seed development.
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Affiliation(s)
- Hao Rong
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Wenjing Yang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Haotian Zhu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Bo Jiang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Jinjin Jiang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Youping Wang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou, 225009 China
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26
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Stenz L. The L1-dependant and Pol III transcribed Alu retrotransposon, from its discovery to innate immunity. Mol Biol Rep 2021; 48:2775-2789. [PMID: 33725281 PMCID: PMC7960883 DOI: 10.1007/s11033-021-06258-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/26/2021] [Indexed: 02/07/2023]
Abstract
The 300 bp dimeric repeats digestible by AluI were discovered in 1979. Since then, Alu were involved in the most fundamental epigenetic mechanisms, namely reprogramming, pluripotency, imprinting and mosaicism. These Alu encode a family of retrotransposons transcribed by the RNA Pol III machinery, notably when the cytosines that constitute their sequences are de-methylated. Then, Alu hijack the functions of ORF2 encoded by another transposons named L1 during reverse transcription and integration into new sites. That mechanism functions as a complex genetic parasite able to copy-paste Alu sequences. Doing that, Alu have modified even the size of the human genome, as well as of other primate genomes, during 65 million years of co-evolution. Actually, one germline retro-transposition still occurs each 20 births. Thus, Alu continue to modify our human genome nowadays and were implicated in de novo mutation causing diseases including deletions, duplications and rearrangements. Most recently, retrotransposons were found to trigger neuronal diversity by inducing mosaicism in the brain. Finally, boosted during viral infections, Alu clearly interact with the innate immune system. The purpose of that review is to give a condensed overview of all these major findings that concern the fascinating physiology of Alu from their discovery up to the current knowledge.
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Affiliation(s)
- Ludwig Stenz
- Department of Genetic Medicine and Development, Faculty of Medicine, Geneva University, Geneva, Switzerland. .,Swiss Centre for Applied Human Toxicology, University of Basel, Basel, Switzerland.
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27
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Yuan V, Hui D, Yin Y, Peñaherrera MS, Beristain AG, Robinson WP. Cell-specific characterization of the placental methylome. BMC Genomics 2021; 22:6. [PMID: 33407091 PMCID: PMC7788826 DOI: 10.1186/s12864-020-07186-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/26/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND DNA methylation (DNAm) profiling has emerged as a powerful tool for characterizing the placental methylome. However, previous studies have focused primarily on whole placental tissue, which is a mixture of epigenetically distinct cell populations. Here, we present the first methylome-wide analysis of first trimester (n = 9) and term (n = 19) human placental samples of four cell populations: trophoblasts, Hofbauer cells, endothelial cells, and stromal cells, using the Illumina EPIC methylation array, which quantifies DNAm at > 850,000 CpGs. RESULTS The most distinct DNAm profiles were those of placental trophoblasts, which are central to many pregnancy-essential functions, and Hofbauer cells, which are a rare fetal-derived macrophage population. Cell-specific DNAm occurs at functionally-relevant genes, including genes associated with placental development and preeclampsia. Known placental-specific methylation marks, such as those associated with genomic imprinting, repetitive element hypomethylation, and placental partially methylated domains, were found to be more pronounced in trophoblasts and often absent in Hofbauer cells. Lastly, we characterize the cell composition and cell-specific DNAm dynamics across gestation. CONCLUSIONS Our results provide a comprehensive analysis of DNAm in human placental cell types from first trimester and term pregnancies. This data will serve as a useful DNAm reference for future placental studies, and we provide access to this data via download from GEO (GSE159526), through interactive exploration from the web browser ( https://robinsonlab.shinyapps.io/Placental_Methylome_Browser/ ), and through the R package planet, which allows estimation of cell composition directly from placental DNAm data.
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Affiliation(s)
- Victor Yuan
- BC Children’s Hospital Research Institute, Vancouver, BC Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
| | - Desmond Hui
- BC Children’s Hospital Research Institute, Vancouver, BC Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
| | - Yifan Yin
- BC Children’s Hospital Research Institute, Vancouver, BC Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
| | - Maria S. Peñaherrera
- BC Children’s Hospital Research Institute, Vancouver, BC Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
| | - Alexander G. Beristain
- BC Children’s Hospital Research Institute, Vancouver, BC Canada
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC Canada
| | - Wendy P. Robinson
- BC Children’s Hospital Research Institute, Vancouver, BC Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
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28
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Antczak DF, Allen WRT. Placentation in Equids. ADVANCES IN ANATOMY, EMBRYOLOGY, AND CELL BIOLOGY 2021; 234:91-128. [PMID: 34694479 DOI: 10.1007/978-3-030-77360-1_6] [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: 01/15/2023]
Abstract
This chapter focuses on the early stages of placental development in horses and their relatives in the genus Equus and highlights unique features of equid reproductive biology. The equine placenta is classified as a noninvasive, epitheliochorial type. However, equids have evolved a minor component of invasive trophoblast, the chorionic girdle and endometrial cups, which links the equine placenta with the highly invasive hemochorial placentae of rodents and, particularly, with the primate placenta. Two types of fetus-to-mother signaling in equine pregnancy are mediated by the invasive equine trophoblast cells. First, endocrinological signaling mediated by equine chorionic gonadotrophin (eCG) drives maternal progesterone production to support the equine conceptus between days 40 and 100 of gestation. Only in primates and equids does the placenta produce a gonadotrophin, but the evolutionary paths taken by these two groups of mammals to produce this placental signal were very different. Second, florid expression of paternal major histocompatibility complex (MHC) class I molecules by invading chorionic girdle cells stimulates strong maternal anti-fetal antibody responses that may play a role in the development of immunological tolerance that protects the conceptus from destruction by the maternal immune system. In humans, invasive extravillous trophoblasts also express MHC class I molecules, but the loci involved, and their likely function, are different from those of the horse. Comparison of the cellular and molecular events in these disparate species provides outstanding examples of convergent evolution and co-option in mammalian pregnancy and highlights how studies of the equine placenta have produced new insights into reproductive strategies.
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Affiliation(s)
- Douglas F Antczak
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA.
| | - W R Twink Allen
- Sharjah Equine Hospital, Sharjah, United Arab Emirates
- Robinson College, University of Cambridge, Cambridge, UK
- The Paul Mellon Laboratory of Equine Reproduction, 'Brunswick', Newmarket, Suffolk, UK
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29
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Chan WY, Chung J, Peplow LM, Hoffmann AA, van Oppen MJH. Maternal effects in gene expression of interspecific coral hybrids. Mol Ecol 2020; 30:517-527. [PMID: 33179328 DOI: 10.1111/mec.15727] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 12/24/2022]
Abstract
Maternal effects have been well documented for offspring morphology and life history traits in plants and terrestrial animals, yet little is known about maternal effects in corals. Further, few studies have explored maternal effects in gene expression. In a previous study, F1 interspecific hybrid and purebred larvae of the coral species Acropora tenuis and Acropora loripes were settled and exposed to ambient or elevated temperature and pCO2 conditions for 7 months. At this stage, the hybrid coral recruits from both ocean conditions exhibited strong maternal effects in several fitness traits. We conducted RNA-sequencing on these corals and showed that gene expression of the hybrid Acropora also exhibited clear maternal effects. Only 40 genes were differentially expressed between hybrids and their maternal progenitor. In contrast, ~2000 differentially expressed genes were observed between hybrids and their paternal progenitors, and between the reciprocal F1 hybrids. These results indicate that maternal effects in coral gene expression can be long-lasting. Unlike findings from most short-term stress experiments in corals, no genes were differentially expressed in the hybrid nor purebred offspring after seven months of exposure to elevated temperature and pCO2 conditions.
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Affiliation(s)
- Wing Yan Chan
- Australian Institute of Marine Science, Townsville, QLD, Australia.,School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Jessica Chung
- Bio21 Institute, University of Melbourne, Parkville, VIC, Australia.,Melbourne Bioinformatics, University of Melbourne, Parkville, VIC, Australia
| | - Lesa M Peplow
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Ary A Hoffmann
- Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
| | - Madeleine J H van Oppen
- Australian Institute of Marine Science, Townsville, QLD, Australia.,School of BioSciences, University of Melbourne, Parkville, VIC, Australia
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The Landscape of Genomic Imprinting at the Porcine SGCE/ PEG10 Locus from Methylome and Transcriptome of Parthenogenetic Embryos. G3-GENES GENOMES GENETICS 2020; 10:4037-4047. [PMID: 32878957 PMCID: PMC7642923 DOI: 10.1534/g3.120.401425] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In mammals, imprinted genes often exist in the form of clusters in specific chromosome regions. However, in pigs, genomic imprinting of a relatively few genes and clusters has been identified, and genes within or adjacent to putative imprinted clusters need to be investigated including those at the SGCE/PEG10 locus. The objective of this study was to, using porcine parthenogenetic embryos, investigate imprinting status of genes within the genomic region spans between the COL1A2 and ASB4 genes in chromosome 9. Whole-genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) were conducted with normal and parthenogenetic embryos, and methylome and transcriptome were analyzed. As a result, differentially methylated regions (DMRs) between the embryos were identified, and parental allele-specific expressions of the SGCE and PEG10 genes were verified. The pig imprinted interval was limited between SGCE and PEG10, since both the COL1A2 and CASD1 genes at the centromere-proximal region and the genes between PPP1R9A and ASB4 toward the telomere were non-imprinted and biallelically expressed. Consequently, our combining analyses of methylome, transcriptome, and informative polymorphisms revealed the boundary of imprinting cluster at the SGCE/PEG10 locus in pig chromosome 9 and consolidated the landscape of genomic imprinting in pigs.
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31
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Fujita MK, Singhal S, Brunes TO, Maldonado JA. Evolutionary Dynamics and Consequences of Parthenogenesis in Vertebrates. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-011720-114900] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Parthenogenesis is asexual reproduction without any required participation from males and, as such, is a null model for sexual reproduction. In a comparative context, we can expand our understanding of the evolution and ecology of sex by investigating the consequences of parthenogenesis. In this review, we examine the theoretical predictions of and empirical results on the evolution of asexual reproduction in vertebrates, focusing on recent studies addressing the origins and geographic spread of parthenogenetic lineages and the genomic consequences of an asexual life history. With advances in computational methods and genome technologies, researchers are poised to make rapid and significant progress in studying the origin and evolution of parthenogenesis in vertebrates, thus providing an important perspective on understanding biodiversity patterns of both asexual and sexual populations.
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Affiliation(s)
- Matthew K. Fujita
- Amphibian and Reptile Diversity Research Center and Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Sonal Singhal
- Department of Biology, California State University, Dominguez Hills, Carson, California 90747, USA
| | - Tuliana O. Brunes
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Jose A. Maldonado
- Amphibian and Reptile Diversity Research Center and Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
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32
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Edwards CA, Takahashi N, Corish JA, Ferguson-Smith AC. The origins of genomic imprinting in mammals. Reprod Fertil Dev 2020; 31:1203-1218. [PMID: 30615843 DOI: 10.1071/rd18176] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 10/01/2018] [Indexed: 12/13/2022] Open
Abstract
Genomic imprinting is a process that causes genes to be expressed according to their parental origin. Imprinting appears to have evolved gradually in two of the three mammalian subclasses, with no imprinted genes yet identified in prototheria and only six found to be imprinted in marsupials to date. By interrogating the genomes of eutherian suborders, we determine that imprinting evolved at the majority of eutherian specific genes before the eutherian radiation. Theories considering the evolution of imprinting often relate to resource allocation and recently consider maternal-offspring interactions more generally, which, in marsupials, places a greater emphasis on lactation. In eutherians, the imprint memory is retained at least in part by zinc finger protein 57 (ZFP57), a Kruppel associated box (KRAB) zinc finger protein that binds specifically to methylated imprinting control regions. Some imprints are less dependent on ZFP57invivo and it may be no coincidence that these are the imprints that are found in marsupials. Because marsupials lack ZFP57, this suggests another more ancestral protein evolved to regulate imprints in non-eutherian subclasses, and contributes to imprinting control in eutherians. Hence, understanding the mechanisms acting at imprinting control regions across mammals has the potential to provide valuable insights into our understanding of the origins and evolution of genomic imprinting.
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Affiliation(s)
- Carol A Edwards
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Nozomi Takahashi
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Jennifer A Corish
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Anne C Ferguson-Smith
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
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33
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Kaneko-Ishino T, Ishino F. Evolution of viviparity in mammals: what genomic imprinting tells us about mammalian placental evolution. Reprod Fertil Dev 2020; 31:1219-1227. [PMID: 30625287 DOI: 10.1071/rd18127] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 10/01/2018] [Indexed: 01/12/2023] Open
Abstract
Genomic imprinting is an epigenetic mechanism of regulating parent-of-origin-specific monoallelic expression of imprinted genes in viviparous therian mammals such as eutherians and marsupials. In this review we discuss several issues concerning the relationship between mammalian viviparity and genomic imprinting, as well as the domestication of essential placental genes: why has the genomic imprinting mechanism been so widely conserved despite the evident developmental disadvantages originating from monoallelic expression? How have genomic imprinted regions been established in the course of mammalian evolution? What drove the evolution of mammalian viviparity and how have genomic imprinting and domesticated genes contributed to this process? In considering the regulatory mechanism of imprinted genes, reciprocal expression of paternally and maternally expressed genes (PEGs and MEGs respectively) and the presence of several essential imprinted genes for placental formation and maintenance, it is likely that complementary, thereby monoallelic, expression of PEGs and MEGs is an evolutionary trade-off for survival. The innovation in novel imprinted regions was associated with the emergence of imprinting control regions, suggesting that genomic imprinting arose as a genome defence mechanism against the insertion of exogenous DNA. Mammalian viviparity emerged in the period when the atmospheric oxygen concentration was the lowest (~12%) during the last 550 million years (the Phanerozoic eon), implying this low oxygen concentration was a key factor in promoting mammalian viviparity as a response to a major evolutionary pressure. Because genomic imprinting and gene domestication from retrotransposons or retroviruses are effective measures of changing genomic function in therian mammals, they are likely to play critical roles in the emergence of viviparity for longer gestation periods.
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Affiliation(s)
- Tomoko Kaneko-Ishino
- School of Health Sciences, Tokai University, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Fumitoshi Ishino
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
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Xu H, Zhao L, Feng X, Ma Y, Chen W, Zou L, Yang Q, Sun J, Yu H, Jiao B. Landscape of genomic imprinting and its functions in the mouse mammary gland. J Mol Cell Biol 2020; 12:857-869. [PMID: 32369566 PMCID: PMC7883822 DOI: 10.1093/jmcb/mjaa020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 04/12/2020] [Accepted: 04/20/2020] [Indexed: 11/17/2022] Open
Abstract
Genomic imprinting is an epigenetic modification of DNA, whereby gene expression is restricted to either maternally or paternally inherited alleles. Imprinted genes (IGs) in the placenta and embryo are essential for growth regulation and nutrient supply. However, despite being an important nutrition delivery organ, studies on mammary gland genomic imprinting remain limited. In this study, we found that both the number of IGs and their expression levels decreased during development of the mouse mammary gland. IG expression was lineage-specific and related to mammary gland development and lactation. Meta-analysis of single-cell RNA sequencing data revealed that mammary gland IGs were co-expressed in a network that regulated cell stemness and differentiation, which was confirmed by our functional studies. Accordingly, our data indicated that IGs were essential for the self-renewal of mammary gland stem cells and IG decline was correlated with mammary gland maturity. Taken together, our findings revealed the importance of IGs in a poorly studied nutrition-related organ, i.e. the mammary gland, thus providing a reference for further studies on genomic imprinting.
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Affiliation(s)
- Haibo Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650223, China
| | - Lina Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650223, China
| | - Xu Feng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yujie Ma
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Wei Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Li Zou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Qin Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Jihong Sun
- Department of Radiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Hong Yu
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Baowei Jiao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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Laird MK, Hansen VL, McAllan BM, Murphy CR, Thompson MB. Uterine epithelial remodelling during pregnancy in the marsupial Monodelphis domestica (Didelphidae): Implications for mammalian placental evolution. J Anat 2020; 236:1126-1136. [PMID: 32052440 DOI: 10.1111/joa.13162] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/19/2019] [Accepted: 01/15/2020] [Indexed: 12/15/2022] Open
Abstract
Mammalian pregnancy involves remodelling of the uterine epithelium to enable placentation. In marsupials, such remodelling has probably played a key role in the transition from ancestral invasive placentation to non-invasive placentation. Identifying uterine alterations that are unique to marsupials with non-invasive placentation can thus elucidate mechanisms of marsupial placental evolution. We identified apical alterations to uterine epithelial cells prior to implantation in Monodelphis domestica, a member of the least derived living marsupial clade (Didelphidae) with invasive (endotheliochorial) placentation. We then compared these traits with those of Macropus eugenii (Macropodidae) and Trichosurus vulpecula (Phalangeridae), both with non-invasive placentation, to identify which alterations to the uterine epithelium are ancestral and which facilitate secondarily evolved non-invasive placentation. In M. domestica, remodelling of the uterine epithelium involves reduced cellular heterogeneity and development of uterodome-like cells, suggesting that similar alterations may also have occurred in the marsupial common ancestor. These alterations also overlap with those of both T. vulpecula and Ma. eugenii, suggesting that the placental shift from invasive to non-invasive placentation in marsupials involves essential, conserved characteristics, irrespective of placental mode. However, unique apical alterations of both T. vulpecula and Ma. eugenii, relative to M. domestica, imply that lineage-specific alterations underpin the evolutionary shift to non-invasive placentation in marsupials.
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Affiliation(s)
- Melanie K Laird
- Department of Anatomy, University of Otago, Dunedin, Aotearoa, New Zealand.,School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Victoria L Hansen
- Animal BioScience and Biotechnology Laboratory, United States Department of Agriculture Agricultural Research Service, Beltsville, MD, USA
| | - Bronwyn M McAllan
- Discipline of Physiology, Faculty of Medicine, University of Sydney, Sydney, NSW, Australia
| | - Christopher R Murphy
- Discipline of Anatomy and Histology, Faculty of Medicine, University of Sydney, Sydney, NSW, Australia
| | - Michael B Thompson
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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Deyssenroth MA, Marsit CJ, Chen J, Lambertini L. In-depth characterization of the placental imprintome reveals novel differentially methylated regions across birth weight categories. Epigenetics 2020; 15:47-60. [PMID: 31403346 PMCID: PMC6961688 DOI: 10.1080/15592294.2019.1647945] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 06/11/2019] [Accepted: 06/18/2019] [Indexed: 01/05/2023] Open
Abstract
Imprinted genes play a pivotal role in placental processes underlying fetal development, and much interest centers on discerning whether these loci, via changes in DNA methylation and/or gene expression, inform disruptions in appropriate fetal growth. In this study, we comprehensively profiled DNA methylation across the placental imprintome and assessed the relationship with gene expression levels and aberrant fetal growth.Placental DNA methylation across 153 imprinted loci, including imprint control regions (ICR) and surrounding non-ICR regions, was surveyed using the Nimblegen TruSeq bisulfite sequencing platform among participants enrolled in the Rhode Island Child Health Study (RICHS, n = 163). Methylation and gene expression associations were assessed using eQTM analysis. Differential methylation analysis contrasting small (SGA) and large for gestational age (LGA) infants against appropriate for gestational age (AGA) infants was assessed using the DMRcate R package.We identified 34 SGA-related differentially methylated regions (DMRs) and 9 LGA-related DMRs (FDR<0.05), and these BW-DMRs predominated in promoter and intronic regions. We observed overall hypomethylation among SGA-DMRs overlapping maternally expressed (paternally imprinted) genes while no parent-of-origin effect was observed among LGA DMRs. Three BW-DMRs, mapping to GABRG3, IGF1R and MEST, were common to SGA and LGA placenta. We did not observe significant correlations between BW-DMR-associated CpG methylation and gene expression levels.We report the first in-depth characterization of the placental imprintome in a population-wide setting. Our findings reveal growth-related differences in methylation without concomitant expression differences in regions that extend beyond typically interrogated imprinted loci, highlighting potentially novel placental biomarkers of growth and development.
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Affiliation(s)
- Maya A. Deyssenroth
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carmen J. Marsit
- Environmental Health at Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Jia Chen
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Luca Lambertini
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Farhadova S, Gomez-Velazquez M, Feil R. Stability and Lability of Parental Methylation Imprints in Development and Disease. Genes (Basel) 2019; 10:genes10120999. [PMID: 31810366 PMCID: PMC6947649 DOI: 10.3390/genes10120999] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/25/2019] [Accepted: 11/27/2019] [Indexed: 02/06/2023] Open
Abstract
DNA methylation plays essential roles in mammals. Of particular interest are parental methylation marks that originate from the oocyte or the sperm, and bring about mono-allelic gene expression at defined chromosomal regions. The remarkable somatic stability of these parental imprints in the pre-implantation embryo—where they resist global waves of DNA demethylation—is not fully understood despite the importance of this phenomenon. After implantation, some methylation imprints persist in the placenta only, a tissue in which many genes are imprinted. Again here, the underlying epigenetic mechanisms are not clear. Mouse studies have pinpointed the involvement of transcription factors, covalent histone modifications, and histone variants. These and other features linked to the stability of methylation imprints are instructive as concerns their conservation in humans, in which different congenital disorders are caused by perturbed parental imprints. Here, we discuss DNA and histone methylation imprints, and why unravelling maintenance mechanisms is important for understanding imprinting disorders in humans.
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Kim J, Frey WD, Sharma K, Ghimire S, Teruyama R, Stubbs L. Allele-specific enhancer interaction at the Peg3 imprinted domain. PLoS One 2019; 14:e0224287. [PMID: 31639176 PMCID: PMC6804975 DOI: 10.1371/journal.pone.0224287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 10/09/2019] [Indexed: 12/20/2022] Open
Abstract
The parental allele specificity of mammalian imprinted genes has been evolutionarily well conserved, although its functional constraints and associated mechanisms are not fully understood. In the current study, we generated a mouse mutant with switched active alleles driving the switch from paternal-to-maternal expression for Peg3 and the maternal-to-paternal expression for Zim1. The expression levels of Peg3 and Zim1, but not the spatial expression patterns, within the brain showed clear differences between wild type and mutant animals. We identified putative enhancers localized upstream of Peg3 that displayed allele-biased DNA methylation, and that also participate in allele-biased chromosomal conformations with regional promoters. Most importantly, these data suggest for the first time that long-distance enhancers may contribute to allelic expression within imprinted domains through allele-biased interactions with regional promoters.
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Affiliation(s)
- Joomyeong Kim
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- * E-mail:
| | - Wesley D. Frey
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Kaustubh Sharma
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Subash Ghimire
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Ryoichi Teruyama
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Lisa Stubbs
- Cell and Developmental Biology, Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
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Apicella C, Ruano CSM, Méhats C, Miralles F, Vaiman D. The Role of Epigenetics in Placental Development and the Etiology of Preeclampsia. Int J Mol Sci 2019; 20:ijms20112837. [PMID: 31212604 PMCID: PMC6600551 DOI: 10.3390/ijms20112837] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/03/2019] [Accepted: 06/03/2019] [Indexed: 12/12/2022] Open
Abstract
In this review, we comprehensively present the function of epigenetic regulations in normal placental development as well as in a prominent disease of placental origin, preeclampsia (PE). We describe current progress concerning the impact of DNA methylation, non-coding RNA (with a special emphasis on long non-coding RNA (lncRNA) and microRNA (miRNA)) and more marginally histone post-translational modifications, in the processes leading to normal and abnormal placental function. We also explore the potential use of epigenetic marks circulating in the maternal blood flow as putative biomarkers able to prognosticate the onset of PE, as well as classifying it according to its severity. The correlation between epigenetic marks and impacts on gene expression is systematically evaluated for the different epigenetic marks analyzed.
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Affiliation(s)
- Clara Apicella
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Camino S M Ruano
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Céline Méhats
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Francisco Miralles
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Daniel Vaiman
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
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Lazniewski M, Dawson WK, Rusek AM, Plewczynski D. One protein to rule them all: The role of CCCTC-binding factor in shaping human genome in health and disease. Semin Cell Dev Biol 2019; 90:114-127. [PMID: 30096365 PMCID: PMC6642822 DOI: 10.1016/j.semcdb.2018.08.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 08/06/2018] [Indexed: 12/12/2022]
Abstract
The eukaryotic genome, constituting several billion base pairs, must be contracted to fit within the volume of a nucleus where the diameter is on the scale of μm. The 3D structure and packing of such a long sequence cannot be left to pure chance, as DNA must be efficiently used for its primary roles as a matrix for transcription and replication. In recent years, methods like chromatin conformation capture (including 3C, 4C, Hi-C, ChIA-PET and Multi-ChIA) and optical microscopy have advanced substantially and have shed new light on how eukaryotic genomes are hierarchically organized; first into 10-nm fiber, next into DNA loops, topologically associated domains and finally into interphase or mitotic chromosomes. This knowledge has allowed us to revise our understanding regarding the mechanisms governing the process of DNA organization. Mounting experimental evidence suggests that the key element in the formation of loops is the binding of the CCCTC-binding factor (CTCF) to DNA; a protein that can be referred to as the chief organizer of the genome. However, CTCF does not work alone but in cooperation with other proteins, such as cohesin or Yin Yang 1 (YY1). In this short review, we briefly describe our current understanding of the structure of eukaryotic genomes, how they are established and how the formation of DNA loops can influence gene expression. We discuss the recent discoveries describing the 3D structure of the CTCF-DNA complex and the role of CTCF in establishing genome structure. Finally, we briefly explain how various genetic disorders might arise as a consequence of mutations in the CTCF target sequence or alteration of genomic imprinting.
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Affiliation(s)
- Michal Lazniewski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland
| | - Wayne K Dawson
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 103-8657, Japan
| | - Anna Maria Rusek
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; Clinical Molecular Biology Department, Medical University of Bialystok, Bialystok, Poland
| | - Dariusz Plewczynski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; Centre for Innovative Research, Medical University of Bialystok, Bialystok, Poland; Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland.
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Liu J, Li J, Liu HF, Fan SH, Singh S, Zhou XR, Hu ZY, Wang HZ, Hua W. Genome-wide screening and analysis of imprinted genes in rapeseed (Brassica napus L.) endosperm. DNA Res 2019; 25:629-640. [PMID: 30272113 PMCID: PMC6289790 DOI: 10.1093/dnares/dsy030] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/09/2018] [Indexed: 12/28/2022] Open
Abstract
Species-specific genomic imprinting is an epigenetic phenomenon leading to parent-of-origin-specific differential expression of maternally and paternally inherited alleles. To date, no studies of imprinting have been reported in rapeseed, a tetraploid species. Here, we analysed global patterns of allelic gene expression in developing rapeseed endosperms from reciprocal crosses between inbred lines YN171 and 93275. A total of 183 imprinted genes, consisting of 167 maternal expressed genes (MEGs) and 16 paternal expressed genes (PEGs), were identified from 14,394 genes found to harbour diagnostic SNPs between the parental lines. Some imprinted genes were validated in different endosperm stages and other parental combinations by RT-PCR analysis. A clear clustering of imprinted genes throughout the rapeseed genome was identified, which was different from most other plants. Methylation analysis of 104 out of the 183 imprinted genes showed that 11 genes (7 MEGs and 4 PEGs) harboured differentially methylated regions (DMRs). Unexpectedly, only 1 MEG out of these 11 genes had a DMR that exhibited high CG methylation rate in paternal allele and had big difference between parent alleles. These results extend our understanding of gene imprinting in plants and provide potential avenues for further research in imprinted genes.
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Affiliation(s)
- Jing Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, P.R. China
| | - Jun Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, P.R. China
| | - Hong-Fang Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, P.R. China
| | - Shi-Hang Fan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, P.R. China
| | - Surinder Singh
- Agriculture and Food Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, Australia
| | - Xue-Rong Zhou
- Agriculture and Food Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, Australia
| | - Zhi-Yong Hu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, P.R. China
| | - Han-Zhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, P.R. China
| | - Wei Hua
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, P.R. China
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Malnou EC, Umlauf D, Mouysset M, Cavaillé J. Imprinted MicroRNA Gene Clusters in the Evolution, Development, and Functions of Mammalian Placenta. Front Genet 2019; 9:706. [PMID: 30713549 PMCID: PMC6346411 DOI: 10.3389/fgene.2018.00706] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 12/14/2018] [Indexed: 12/27/2022] Open
Abstract
In mammals, the expression of a subset of microRNA (miRNA) genes is governed by genomic imprinting, an epigenetic mechanism that confers monoallelic expression in a parent-of-origin manner. Three evolutionarily distinct genomic intervals contain the vast majority of imprinted miRNA genes: the rodent-specific, paternally expressed C2MC located in intron 10 of the Sfmbt2 gene, the primate-specific, paternally expressed C19MC positioned at human Chr.19q13.4 and the eutherian-specific, maternally expressed miRNAs embedded within the imprinted Dlk1-Dio3 domains at human 14q32 (also named C14MC in humans). Interestingly, these imprinted miRNA genes form large clusters composed of many related gene copies that are co-expressed with a marked, or even exclusive, localization in the placenta. Here, we summarize our knowledge on the evolutionary, molecular, and physiological relevance of these epigenetically-regulated, recently-evolved miRNAs, by focusing on their roles in placentation and possibly also in pregnancy diseases (e.g., preeclampsia, intrauterine growth restriction, preterm birth).
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Affiliation(s)
- E Cécile Malnou
- Centre de Physiopathologie de Toulouse Purpan, Université de Toulouse, CNRS, INSERM, UPS, Toulouse, France
| | - David Umlauf
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Maïlys Mouysset
- Centre de Physiopathologie de Toulouse Purpan, Université de Toulouse, CNRS, INSERM, UPS, Toulouse, France
| | - Jérôme Cavaillé
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, CNRS, UPS, Université de Toulouse, Toulouse, France
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Kim J, Perera BPU, Ghimire S. Enhancer-driven alternative promoters of imprinted genes. PLoS One 2018; 13:e0208421. [PMID: 30500864 PMCID: PMC6267961 DOI: 10.1371/journal.pone.0208421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/17/2018] [Indexed: 11/24/2022] Open
Abstract
In the current study, we characterized the expression and histone modification profiles of the alternative promoters found within imprinted Igf2r, Mest, Zac1, Peg3, Snrpn and non-imprinted Myc loci. In terms of expression pattern, the alternative promoters are highly tissue-specific, which is in a stark contrast to the ubiquitous expression of the corresponding main promoters. The alternative promoters are associated with the histone modification mark H3K4me1, but not with H3K4me3, which is frequently associated with the main promoters. Phylogenetic analyses also indicated that the majority of the alternative promoters are unique to the mammalian lineage, further suggesting the recent formation of these promoters during mammalian evolution. Overall, this study suggests that the alternative promoters of imprinted loci may have been derived from enhancers in recent evolutionary times and co-evolved with the genomic imprinting mechanism.
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Affiliation(s)
- Joomyeong Kim
- Department of Biological Sciences, Louisiana State University, Baton Rouge, United States of America
- * E-mail:
| | - Bambarendage P. U. Perera
- Department of Biological Sciences, Louisiana State University, Baton Rouge, United States of America
| | - Subash Ghimire
- Department of Biological Sciences, Louisiana State University, Baton Rouge, United States of America
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Suzuki S, Shaw G, Renfree MB. Identification of a novel antisense noncoding RNA, ALID, transcribed from the putative imprinting control region of marsupial IGF2R. Epigenetics Chromatin 2018; 11:55. [PMID: 30268152 PMCID: PMC6162910 DOI: 10.1186/s13072-018-0227-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/25/2018] [Indexed: 12/20/2022] Open
Abstract
Background Genomic imprinting leads to maternal expression of IGF2R in both mouse and opossum. In mouse, the antisense long noncoding (lnc) RNA Airn, which is paternally expressed from the differentially methylated region (DMR) in the second intron of Igf2r, is required to silence the paternal Igf2r. In opossum, however, intriguingly, the DMR was reported to be in a different downstream intron (intron 11) and there was no antisense lncRNA detected in previous analyses. Therefore, clarifying the imprinting mechanism of marsupial IGF2R is of great relevance for understanding the origin and evolution of genomic imprinting in the IGF2R locus. Thus, the antisense lncRNA associated with the marsupial DMR can be considered as the ‘missing link’. In this study, we identified a novel antisense lncRNA, ALID, after detailed analysis of the IGF2R locus in an Australian marsupial, the tammar wallaby, Macropus eugenii, and compared it to that of the grey short-tailed opossum, Monodelphis domestica. Results Tammar IGF2R showed maternal expression and had a maternally methylated CpG island (CGI) in intron 12 as well as a promoter CGI without differential methylation, but none in the second intron. Re-analysis of the IGF2R of opossum detected the CGI in intron 12, not intron 11, as previously reported, confirming that the DMR in intron 12 is conserved between these marsupials and so is the putative imprinting control region of marsupial IGF2R. ALID is paternally expressed from the middle of the DMR and is approximately 650 bp long with a single exon structure that is extremely short compared to Airn. Hence, the lncRNA transcriptional overlap of the IGF2R promoter, which is essential for the Igf2r silencing in the mouse, is likely absent in tammar. This suggests that fundamental differences in the lncRNA-based silencing mechanisms evolved in eutherian and marsupial IGF2R and may reflect the lack of differential methylation in the promoter CGI of marsupial IGF2R. Conclusions Our study thus provides the best candidate factor for establishing paternal silencing of marsupial IGF2R without transcriptional overlap, which is distinct from the Igf2r silencing mechanism of Airn, but which may be analogous to the mode of action for the flanking Slc22a2 and Slc22a3 gene silencing in the mouse placenta. Electronic supplementary material The online version of this article (10.1186/s13072-018-0227-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shunsuke Suzuki
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, Nagano, 399-4598, Japan.,Department of Interdisciplinary Genome Sciences and Cell Metabolism, Institute for Biomedical Sciences, ICCER, Shinshu University, Nagano, 399-4598, Japan
| | - Geoffrey Shaw
- School of BioSciences, The University of Melbourne, Victoria, 3010, Australia
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Victoria, 3010, Australia.
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Huntriss J, Balen AH, Sinclair KD, Brison DR, Picton HM. Epigenetics and Reproductive Medicine. BJOG 2018; 125:e43-e54. [DOI: 10.1111/1471-0528.15240] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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46
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Khamlichi AA, Feil R. Parallels between Mammalian Mechanisms of Monoallelic Gene Expression. Trends Genet 2018; 34:954-971. [PMID: 30217559 DOI: 10.1016/j.tig.2018.08.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/06/2018] [Accepted: 08/16/2018] [Indexed: 02/06/2023]
Abstract
Different types of monoallelic gene expression are present in mammals, some of which are highly flexible, whereas others are more rigid. These include allelic exclusion at antigen receptor loci, the expression of olfactory receptor genes, genomic imprinting, X-chromosome inactivation, and random monoallelic expression (MAE). Although these processes play diverse biological roles, and arose through different selective pressures, the underlying epigenetic mechanisms show striking resemblances. Regulatory transcriptional events are important in all systems, particularly in the specification of MAE. Combined with comparative studies between species, this suggests that the different MAE systems found in mammals may have evolved from analogous ancestral processes.
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Affiliation(s)
- Ahmed Amine Khamlichi
- Institute of Pharmacology and Structural Biology (IPBS), Centre National de la Recherche Scientifique (CNRS) and Paul Sabatier University (UPS), 205 route de Narbonne, 31077 Toulouse, France.
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS and the University of Montpellier, 1919 route de Mende, 34293 Montpellier, France.
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47
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Pathak R, Feil R. Environmental effects on chromatin repression at imprinted genes and endogenous retroviruses. Curr Opin Chem Biol 2018; 45:139-147. [DOI: 10.1016/j.cbpa.2018.04.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/05/2018] [Accepted: 04/24/2018] [Indexed: 12/26/2022]
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48
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Pegoraro M, Marshall H, Lonsdale ZN, Mallon EB. Do social insects support Haig's kin theory for the evolution of genomic imprinting? Epigenetics 2018; 12:725-742. [PMID: 28703654 PMCID: PMC5739101 DOI: 10.1080/15592294.2017.1348445] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Although numerous imprinted genes have been described in several lineages, the phenomenon of genomic imprinting presents a peculiar evolutionary problem. Several hypotheses have been proposed to explain gene imprinting, the most supported being Haig's kinship theory. This theory explains the observed pattern of imprinting and the resulting phenotypes as a competition for resources between related individuals, but despite its relevance it has not been independently tested. Haig's theory predicts that gene imprinting should be present in eusocial insects in many social scenarios. These lineages are therefore ideal for testing both the theory's predictions and the mechanism of gene imprinting. Here we review the behavioral evidence of genomic imprinting in eusocial insects, the evidence of a mechanism for genomic imprinting and finally we evaluate recent results showing parent of origin allele specific expression in honeybees in the light of Haig's theory.
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Affiliation(s)
- Mirko Pegoraro
- a Department of Genetics and Genome Biology , University of Leicester , UK
| | - Hollie Marshall
- a Department of Genetics and Genome Biology , University of Leicester , UK
| | - Zoë N Lonsdale
- a Department of Genetics and Genome Biology , University of Leicester , UK
| | - Eamonn B Mallon
- a Department of Genetics and Genome Biology , University of Leicester , UK
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49
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Jue NK, Foley RJ, Reznick DN, O'Neill RJ, O'Neill MJ. Tissue-Specific Transcriptome for Poeciliopsis prolifica Reveals Evidence for Genetic Adaptation Related to the Evolution of a Placental Fish. G3 (BETHESDA, MD.) 2018; 8:2181-2192. [PMID: 29720394 PMCID: PMC6027864 DOI: 10.1534/g3.118.200270] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 04/11/2018] [Indexed: 11/18/2022]
Abstract
The evolution of the placenta is an excellent model to examine the evolutionary processes underlying adaptive complexity due to the recent, independent derivation of placentation in divergent animal lineages. In fishes, the family Poeciliidae offers the opportunity to study placental evolution with respect to variation in degree of post-fertilization maternal provisioning among closely related sister species. In this study, we present a detailed examination of a new reference transcriptome sequence for the live-bearing, matrotrophic fish, Poeciliopsis prolifica, from multiple-tissue RNA-seq data. We describe the genetic components active in liver, brain, late-stage embryo, and the maternal placental/ovarian complex, as well as associated patterns of positive selection in a suite of orthologous genes found in fishes. Results indicate the expression of many signaling transcripts, "non-coding" sequences and repetitive elements in the maternal placental/ovarian complex. Moreover, patterns of positive selection in protein sequence evolution were found associated with live-bearing fishes, generally, and the placental P. prolifica, specifically, that appear independent of the general live-bearer lifestyle. Much of the observed patterns of gene expression and positive selection are congruent with the evolution of placentation in fish functionally converging with mammalian placental evolution and with the patterns of rapid evolution facilitated by the teleost-specific whole genome duplication event.
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Affiliation(s)
- Nathaniel K Jue
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
| | - Robert J Foley
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
| | - David N Reznick
- Department of Biology, University of California, Riverside, CA 92521
| | - Rachel J O'Neill
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
| | - Michael J O'Neill
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
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50
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Mackin SJ, Thakur A, Walsh CP. Imprint stability and plasticity during development. Reproduction 2018; 156:R43-R55. [PMID: 29743259 DOI: 10.1530/rep-18-0051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/08/2018] [Indexed: 12/20/2022]
Abstract
There have been a number of recent insights in the area of genomic imprinting, the phenomenon whereby one of two autosomal alleles is selected for expression based on the parent of origin. This is due in part to a proliferation of new techniques for interrogating the genome that are leading researchers working on organisms other than mouse and human, where imprinting has been most studied, to become interested in looking for potential imprinting effects. Here, we recap what is known about the importance of imprints for growth and body size, as well as the main types of locus control. Interestingly, work from a number of labs has now shown that maintenance of the imprint post implantation appears to be a more crucial step than previously appreciated. We ask whether imprints can be reprogrammed somatically, how many loci there are and how conserved imprinted regions are in other species. Finally, we survey some of the methods available for examining DNA methylation genome-wide and look to the future of this burgeoning field.
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Affiliation(s)
- Sarah-Jayne Mackin
- Genomic Medicine Research GroupSchool of Biomedical Sciences, Ulster University, Northern Ireland, UK
| | - Avinash Thakur
- Genomic Medicine Research GroupSchool of Biomedical Sciences, Ulster University, Northern Ireland, UK
| | - Colum P Walsh
- Genomic Medicine Research GroupSchool of Biomedical Sciences, Ulster University, Northern Ireland, UK
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