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Pliota P, Marvanova H, Koreshova A, Kaufman Y, Tikanova P, Krogull D, Hagmüller A, Widen SA, Handler D, Gokcezade J, Duchek P, Brennecke J, Ben-David E, Burga A. Selfish conflict underlies RNA-mediated parent-of-origin effects. Nature 2024; 628:122-129. [PMID: 38448590 PMCID: PMC10990930 DOI: 10.1038/s41586-024-07155-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/02/2024] [Indexed: 03/08/2024]
Abstract
Genomic imprinting-the non-equivalence of maternal and paternal genomes-is a critical process that has evolved independently in many plant and mammalian species1,2. According to kinship theory, imprinting is the inevitable consequence of conflictive selective forces acting on differentially expressed parental alleles3,4. Yet, how these epigenetic differences evolve in the first place is poorly understood3,5,6. Here we report the identification and molecular dissection of a parent-of-origin effect on gene expression that might help to clarify this fundamental question. Toxin-antidote elements (TAs) are selfish elements that spread in populations by poisoning non-carrier individuals7-9. In reciprocal crosses between two Caenorhabditis tropicalis wild isolates, we found that the slow-1/grow-1 TA is specifically inactive when paternally inherited. This parent-of-origin effect stems from transcriptional repression of the slow-1 toxin by the PIWI-interacting RNA (piRNA) host defence pathway. The repression requires PIWI Argonaute and SET-32 histone methyltransferase activities and is transgenerationally inherited via small RNAs. Remarkably, when slow-1/grow-1 is maternally inherited, slow-1 repression is halted by a translation-independent role of its maternal mRNA. That is, slow-1 transcripts loaded into eggs-but not SLOW-1 protein-are necessary and sufficient to counteract piRNA-mediated repression. Our findings show that parent-of-origin effects can evolve by co-option of the piRNA pathway and hinder the spread of selfish genes that require sex for their propagation.
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Affiliation(s)
- Pinelopi Pliota
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Hana Marvanova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Alevtina Koreshova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Yotam Kaufman
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Polina Tikanova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Daniel Krogull
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Andreas Hagmüller
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Sonya A Widen
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Dominik Handler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Joseph Gokcezade
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Peter Duchek
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Eyal Ben-David
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Alejandro Burga
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
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2
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Fang S, Chang KW, Lefebvre L. Roles of endogenous retroviral elements in the establishment and maintenance of imprinted gene expression. Front Cell Dev Biol 2024; 12:1369751. [PMID: 38505259 PMCID: PMC10948482 DOI: 10.3389/fcell.2024.1369751] [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: 01/12/2024] [Accepted: 02/26/2024] [Indexed: 03/21/2024] Open
Abstract
DNA methylation (DNAme) has long been recognized as a host defense mechanism, both in the restriction modification systems of prokaryotes as well as in the transcriptional silencing of repetitive elements in mammals. When DNAme was shown to be implicated as a key epigenetic mechanism in the regulation of imprinted genes in mammals, a parallel with host defense mechanisms was drawn, suggesting perhaps a common evolutionary origin. Here we review recent work related to this hypothesis on two different aspects of the developmental imprinting cycle in mammals that has revealed unexpected roles for long terminal repeat (LTR) retroelements in imprinting, both canonical and noncanonical. These two different forms of genomic imprinting depend on different epigenetic marks inherited from the mature gametes, DNAme and histone H3 lysine 27 trimethylation (H3K27me3), respectively. DNAme establishment in the maternal germline is guided by transcription during oocyte growth. Specific families of LTRs, evading silencing mechanisms, have been implicated in this process for specific imprinted genes. In noncanonical imprinting, maternally inherited histone marks play transient roles in transcriptional silencing during preimplantation development. These marks are ultimately translated into DNAme, notably over LTR elements, for the maintenance of silencing of the maternal alleles in the extraembryonic trophoblast lineage. Therefore, LTR retroelements play important roles in both establishment and maintenance of different epigenetic pathways leading to imprinted expression during development. Because such elements are mobile and highly polymorphic among different species, they can be coopted for the evolution of new species-specific imprinted genes.
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Affiliation(s)
| | | | - Louis Lefebvre
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
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3
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Wang Z, Liu N, Yang Y, Tu Z. The novel mechanism facilitating chronic hepatitis B infection: immunometabolism and epigenetic modification reprogramming. Front Immunol 2024; 15:1349867. [PMID: 38288308 PMCID: PMC10822934 DOI: 10.3389/fimmu.2024.1349867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/02/2024] [Indexed: 01/31/2024] Open
Abstract
Hepatitis B Virus (HBV) infections pose a global public health challenge. Despite extensive research on this disease, the intricate mechanisms underlying persistent HBV infection require further in-depth elucidation. Recent studies have revealed the pivotal roles of immunometabolism and epigenetic reprogramming in chronic HBV infection. Immunometabolism have identified as the process, which link cell metabolic status with innate immunity functions in response to HBV infection, ultimately contributing to the immune system's inability to resolve Chronic Hepatitis B (CHB). Within hepatocytes, HBV replication leads to a stable viral covalently closed circular DNA (cccDNA) minichromosome located in the nucleus, and epigenetic modifications in cccDNA enable persistence of infection. Additionally, the accumulation or depletion of metabolites not only directly affects the function and homeostasis of immune cells but also serves as a substrate for regulating epigenetic modifications, subsequently influencing the expression of antiviral immune genes and facilitating the occurrence of sustained HBV infection. The interaction between immunometabolism and epigenetic modifications has led to a new research field, known as metabolic epigenomics, which may form a mutually reinforcing relationship with CHB. Herein, we review the recent studies on immunometabolism and epigenetic reprogramming in CHB infection and discuss the potential mechanisms of persistent HBV infection. A deeper understanding of these mechanisms will offer novel insights and targets for intervention strategies against chronic HBV infection, thereby providing new hope for the treatment of related diseases.
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Affiliation(s)
- Zhengmin Wang
- Department of Hepatology, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Nan Liu
- Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun, China
| | - Yang Yang
- Department of Hepatology, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Zhengkun Tu
- Department of Hepatology, The First Hospital of Jilin University, Changchun, Jilin, China
- Institute of Liver Diseases, The First Hospital of Jilin University, Changchun, Jilin, China
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4
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Fafard-Couture É, Labialle S, Scott MS. The regulatory roles of small nucleolar RNAs within their host locus. RNA Biol 2024; 21:1-11. [PMID: 38626213 PMCID: PMC11028025 DOI: 10.1080/15476286.2024.2342685] [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] [Accepted: 04/08/2024] [Indexed: 04/18/2024] Open
Abstract
Small nucleolar RNAs (snoRNAs) are a class of conserved noncoding RNAs forming complexes with proteins to catalyse site-specific modifications on ribosomal RNA. Besides this canonical role, several snoRNAs are now known to regulate diverse levels of gene expression. While these functions are carried out in trans by mature snoRNAs, evidence has also been emerging of regulatory roles of snoRNAs in cis, either within their genomic locus or as longer transcription intermediates during their maturation. Herein, we review recent findings that snoRNAs can interact in cis with their intron to regulate the expression of their host gene. We also explore the ever-growing diversity of longer host-derived snoRNA extensions and their functional impact across the transcriptome. Finally, we discuss the role of snoRNA duplications into forging these new layers of snoRNA-mediated regulation, as well as their involvement in the genomic imprinting of their host locus.
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Affiliation(s)
- Étienne Fafard-Couture
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | | | - Michelle S Scott
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
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5
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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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6
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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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7
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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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8
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Liehr T. Uniparental disomy is a chromosomic disorder in the first place. Mol Cytogenet 2022; 15:5. [PMID: 35177099 PMCID: PMC8851757 DOI: 10.1186/s13039-022-00585-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 01/31/2022] [Indexed: 02/07/2023] Open
Abstract
Background Uniparental disomy (UPD) is well-known to be closely intermingled with imprinting disorders. Besides, UPD can lead to a disease by ‘activation’ of a recessive gene mutation or due to incomplete (cryptic) trisomic rescue. Corresponding to all common theories how UPD forms, it takes place as a consequence of a “chromosomic problem”, like an aneuploidy or a chromosomal rearrangement. Nonetheless, UPD is rarely considered as a cytogenetic, but most often as a molecular genetic problem. Results Here a review on the ~ 4900 published UPD-cases is provided, and even though being biased as discussed in the paper, the following insights have been given from that analysis: (1) the rate of maternal to paternal UPD is 2~3 to 1; (2) at most only ~ 0.03% of the available UPD cases are grasped scientifically, yet; (3) frequencies of single whole-chromosome UPDs are non-random, with UPD(16) and UPD(15) being most frequent in clinically healthy and diseased people, respectively; (4) there is a direct correlation of UPD frequency and known frequent first trimester trisomies, except for chromosomes 1, 5, 11 and 18 (which can be explained); (5) heterodisomy is under- and UPD-mosaicism is over-represented in recent reports; and (6) cytogenetics is not considered enough when a UPD is identified. Conclusions As UPD is diagnosed using molecular genetic approaches, and thus by specialists considering chromosomes at best as a whim of nature, most UPD reports lack the chromosomal aspect. Here it is affirmed and substantiated by corresponding data that UPD is a chromosomic disorder in the first place and cytogenetic analyses is indicated in each diagnosed UPD-case. Supplementary Information The online version contains supplementary material available at 10.1186/s13039-022-00585-2.
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Affiliation(s)
- Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, 07747, Jena, Germany.
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9
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Genomic imprinting in human placentation. Reprod Med Biol 2022; 21:e12490. [DOI: 10.1002/rmb2.12490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/25/2022] [Accepted: 11/10/2022] [Indexed: 12/02/2022] Open
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10
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Chen S, Liu S, Mi S, Li W, Zhang S, Ding X, Yu Y. Comparative Analyses of Sperm DNA Methylomes Among Three Commercial Pig Breeds Reveal Vital Hypomethylated Regions Associated With Spermatogenesis and Embryonic Development. Front Genet 2021; 12:740036. [PMID: 34691153 PMCID: PMC8527042 DOI: 10.3389/fgene.2021.740036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/08/2021] [Indexed: 12/12/2022] Open
Abstract
Identifying epigenetic changes is essential for an in-depth understanding of phenotypic diversity and pigs as the human medical model for anatomizing complex diseases. Abnormal sperm DNA methylation can lead to male infertility, fetal development failure, and affect the phenotypic traits of offspring. However, the whole genome epigenome map in pig sperm is lacking to date. In this study, we profiled methylation levels of cytosine in three commercial pig breeds, Landrace, Duroc, and Large White using whole-genome bisulfite sequencing (WGBS). The results showed that the correlation of methylation levels between Landrace and Large White pigs was higher. We found that 1,040-1,666 breed-specific hypomethylated regions (HMRs) were associated with embryonic developmental and economically complex traits for each breed. By integrating reduced representation bisulfite sequencing (RRBS) public data of pig testis, 1743 conservated HMRs between sperm and testis were defined, which may play a role in spermatogenesis. In addition, we found that the DNA methylation patterns of human and pig sperm showed high similarity by integrating public data from WGBS and chromatin immunoprecipitation sequencing (ChIP-seq) in other mammals, such as human and mouse. We identified 2,733 conserved HMRs between human and pig involved in organ development and brain-related traits, such as NLGN1 (neuroligin 1) containing a conserved-HMR between human and pig. Our results revealed the similarities and diversity of sperm methylation patterns among three commercial pig breeds and between human and pig. These findings are beneficial for elucidating the mechanism of male fertility, and the changes in commercial traits that undergo strong selection.
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Affiliation(s)
| | | | | | | | | | - Xiangdong Ding
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ying Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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11
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Germain ND, Chamberlain SJ. A protein regulated by UBE3A PEGs a potential biomarker. Cell Rep Med 2021; 2:100377. [PMID: 34467252 PMCID: PMC8385320 DOI: 10.1016/j.xcrm.2021.100377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
New research from Pandya and colleagues1 identifies PEG10 as a UBE3A-regulated protein that may underlie pathophysiology in Angelman syndrome neurons. PEG10 is a secreted protein, and this work suggests that it may be a potential biomarker for Angelman syndrome therapeutics under development.
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Affiliation(s)
- Noelle D. Germain
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA
| | - Stormy J. Chamberlain
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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12
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Singh P, Kairuz D, Arbuthnot P, Bloom K. Silencing hepatitis B virus covalently closed circular DNA: The potential of an epigenetic therapy approach. World J Gastroenterol 2021; 27:3182-3207. [PMID: 34163105 PMCID: PMC8218364 DOI: 10.3748/wjg.v27.i23.3182] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/23/2021] [Accepted: 05/07/2021] [Indexed: 02/06/2023] Open
Abstract
Global prophylactic vaccination programmes have helped to curb new hepatitis B virus (HBV) infections. However, it is estimated that nearly 300 million people are chronically infected and have a high risk of developing hepatocellular carcinoma. As such, HBV remains a serious health priority and the development of novel curative therapeutics is urgently needed. Chronic HBV infection has been attributed to the persistence of the covalently closed circular DNA (cccDNA) which establishes itself as a minichromosome in the nucleus of hepatocytes. As the viral transcription intermediate, the cccDNA is responsible for producing new virions and perpetuating infection. HBV is dependent on various host factors for cccDNA formation and the minichromosome is amenable to epigenetic modifications. Two HBV proteins, X (HBx) and core (HBc) promote viral replication by modulating the cccDNA epigenome and regulating host cell responses. This includes viral and host gene expression, chromatin remodeling, DNA methylation, the antiviral immune response, apoptosis, and ubiquitination. Elimination of the cccDNA minichromosome would result in a sterilizing cure; however, this may be difficult to achieve. Epigenetic therapies could permanently silence the cccDNA minichromosome and promote a functional cure. This review explores the cccDNA epigenome, how host and viral factors influence transcription, and the recent epigenetic therapies and epigenome engineering approaches that have been described.
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Affiliation(s)
- Prashika Singh
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg 2050, Gauteng, South Africa
| | - Dylan Kairuz
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg 2050, Gauteng, South Africa
| | - Patrick Arbuthnot
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg 2050, Gauteng, South Africa
| | - Kristie Bloom
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg 2050, Gauteng, South Africa
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Abstract
Genomic imprinting is the monoallelic expression of a gene based on parent of origin and is a consequence of differential epigenetic marking between the male and female germlines. Canonically, genomic imprinting is mediated by allelic DNA methylation. However, recently it has been shown that maternal H3K27me3 can result in DNA methylation-independent imprinting, termed "noncanonical imprinting." In this review, we compare and contrast what is currently known about the underlying mechanisms, the role of endogenous retroviral elements, and the conservation of canonical and noncanonical genomic imprinting.
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Affiliation(s)
- Courtney W Hanna
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
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14
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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: 4] [Impact Index Per Article: 1.3] [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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15
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16
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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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17
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Host Gene Regulation by Transposable Elements: The New, the Old and the Ugly. Viruses 2020; 12:v12101089. [PMID: 32993145 PMCID: PMC7650545 DOI: 10.3390/v12101089] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/14/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022] Open
Abstract
The human genome has been under selective pressure to evolve in response to emerging pathogens and other environmental challenges. Genome evolution includes the acquisition of new genes or new isoforms of genes and changes to gene expression patterns. One source of genome innovation is from transposable elements (TEs), which carry their own promoters, enhancers and open reading frames and can act as ‘controlling elements’ for our own genes. TEs include LINE-1 elements, which can retrotranspose intracellularly and endogenous retroviruses (ERVs) that represent remnants of past retroviral germline infections. Although once pathogens, ERVs also represent an enticing source of incoming genetic material that the host can then repurpose. ERVs and other TEs have coevolved with host genes for millions of years, which has allowed them to become embedded within essential gene expression programmes. Intriguingly, these host genes are often subject to the same epigenetic control mechanisms that evolved to combat the TEs that now regulate them. Here, we illustrate the breadth of host gene regulation through TEs by focusing on examples of young (The New), ancient (The Old), and disease-causing (The Ugly) TE integrants.
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18
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Abstract
In 1993, Denise Barlow proposed that genomic imprinting might have arisen from a host defense mechanism designed to inactivate retrotransposons. Although there were few examples at hand, she suggested that there should be maternal-specific and paternal-specific factors involved, with cognate imprinting boxes that they recognized; furthermore, the system should build on conserved biochemical factors, including DNA methylation, and maternal control should predominate for imprints. Here, we revisit this hypothesis in the light of recent advances in our understanding of host defense and DNA methylation and in particular, the link with Krüppel-associated box–zinc finger (KRAB-ZF) proteins.
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Affiliation(s)
- Miroslava Ondičová
- School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Rebecca J. Oakey
- Department of Medical & Molecular Genetics, King’s College London, Guy’s Hospital, London, United Kingdom
| | - Colum P. Walsh
- School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
- * E-mail:
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19
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Abstract
In this review, Batista and Köhler revisit the current models explaining imprinting regulation in plants, and discuss novel regulatory mechanisms that could function independently of parental DNA methylation asymmetries in the establishment of imprinting. Genomic imprinting is an epigenetic phenomenon leading to parentally biased gene expression. Throughout the years, extensive efforts have been made to characterize the epigenetic marks underlying imprinting in animals and plants. As a result, DNA methylation asymmetries between parental genomes emerged as the primary factor controlling the imprinting status of many genes. Nevertheless, the data accumulated so far suggest that this process cannot solely explain the imprinting of all genes. In this review, we revisit the current models explaining imprinting regulation in plants, and discuss novel regulatory mechanisms that could function independently of parental DNA methylation asymmetries in the establishment of imprinting.
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Affiliation(s)
- Rita A Batista
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala SE-750 07, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala SE-750 07, Sweden
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20
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Blake LE, Roux J, Hernando-Herraez I, Banovich NE, Perez RG, Hsiao CJ, Eres I, Cuevas C, Marques-Bonet T, Gilad Y. A comparison of gene expression and DNA methylation patterns across tissues and species. Genome Res 2020; 30:250-262. [PMID: 31953346 PMCID: PMC7050529 DOI: 10.1101/gr.254904.119] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 01/02/2020] [Indexed: 01/02/2023]
Abstract
Previously published comparative functional genomic data sets from primates using frozen tissue samples, including many data sets from our own group, were often collected and analyzed using nonoptimal study designs and analysis approaches. In addition, when samples from multiple tissues were studied in a comparative framework, individuals and tissues were confounded. We designed a multitissue comparative study of gene expression and DNA methylation in primates that minimizes confounding effects by using a balanced design with respect to species, tissues, and individuals. We also developed a comparative analysis pipeline that minimizes biases attributable to sequence divergence. Thus, we present the most comprehensive catalog of similarities and differences in gene expression and DNA methylation levels between livers, kidneys, hearts, and lungs, in humans, chimpanzees, and rhesus macaques. We estimate that overall, interspecies and inter-tissue differences in gene expression levels can only modestly be accounted for by corresponding differences in promoter DNA methylation. However, the expression pattern of genes with conserved inter-tissue expression differences can be explained by corresponding interspecies methylation changes more often. Finally, we show that genes whose tissue-specific regulatory patterns are consistent with the action of natural selection are highly connected in both gene regulatory and protein–protein interaction networks.
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Affiliation(s)
- Lauren E Blake
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Julien Roux
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.,Department of Biomedicine, University of Basel, 4031 Basel, Switzerland.,Swiss Institute of Bioinformatics, 4031 Basel, Switzerland
| | | | - Nicholas E Banovich
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Raquel Garcia Perez
- Universitat Pompeu Fabra, Institute of Evolutionary Biology, 88 08003 Barcelona, Spain
| | - Chiaowen Joyce Hsiao
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Ittai Eres
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Claudia Cuevas
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Tomas Marques-Bonet
- Universitat Pompeu Fabra, Institute of Evolutionary Biology, 88 08003 Barcelona, Spain.,Passeig de Lluís Companys, Catalan Institution of Research and Advanced Studies, 23 08010 Barcelona, Spain.,Barcelona Institute of Science and Technology, Centre for Genomic Regulation, 88 08003 Barcelona, Spain.,Universitat Autònoma de Barcelona, Institut Català de Paleontologia Miquel Crusafont, 08193 Barcelona, Spain
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.,Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
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21
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Bogutz AB, Brind'Amour J, Kobayashi H, Jensen KN, Nakabayashi K, Imai H, Lorincz MC, Lefebvre L. Evolution of imprinting via lineage-specific insertion of retroviral promoters. Nat Commun 2019; 10:5674. [PMID: 31831741 PMCID: PMC6908575 DOI: 10.1038/s41467-019-13662-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/14/2019] [Indexed: 01/09/2023] Open
Abstract
Imprinted genes are expressed from a single parental allele, with the other allele often silenced by DNA methylation (DNAme) established in the germline. While species-specific imprinted orthologues have been documented, the molecular mechanisms underlying the evolutionary switch from biallelic to imprinted expression are unknown. During mouse oogenesis, gametic differentially methylated regions (gDMRs) acquire DNAme in a transcription-guided manner. Here we show that oocyte transcription initiating in lineage-specific endogenous retroviruses (ERVs) is likely responsible for DNAme establishment at 4/6 mouse-specific and 17/110 human-specific imprinted gDMRs. The latter are divided into Catarrhini- or Hominoidea-specific gDMRs embedded within transcripts initiating in ERVs specific to these primate lineages. Strikingly, imprinting of the maternally methylated genes Impact and Slc38a4 was lost in the offspring of female mice harboring deletions of the relevant murine-specific ERVs upstream of these genes. Our work reveals an evolutionary mechanism whereby maternally silenced genes arise from biallelically expressed progenitors. Although many species-specific imprinted genes have been identified, how the evolutionary switch from biallelic to imprinted expression occurs is still unknown. Here authors find that lineage-specific ERVs active as oocyte promoters can induce de novo DNA methylation at gDMRs and imprinting.
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Affiliation(s)
- Aaron B Bogutz
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Julie Brind'Amour
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Hisato Kobayashi
- Department of Embryology, Nara Medical University, Kashihara, Nara, 634-8521, Japan
| | - Kristoffer N Jensen
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Kazuhiko Nakabayashi
- Division of Developmental Genomics, Research Institute, National Center for Child Health and Development, Setagaya, Tokyo, 157-8535, Japan
| | - Hiroo Imai
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan
| | - Matthew C Lorincz
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
| | - Louis Lefebvre
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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22
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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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23
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Fang L, Zhou Y, Liu S, Jiang J, Bickhart DM, Null DJ, Li B, Schroeder SG, Rosen BD, Cole JB, Van Tassell CP, Ma L, Liu GE. Integrating Signals from Sperm Methylome Analysis and Genome-Wide Association Study for a Better Understanding of Male Fertility in Cattle. EPIGENOMES 2019; 3:epigenomes3020010. [PMID: 34968233 PMCID: PMC8594688 DOI: 10.3390/epigenomes3020010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/03/2019] [Accepted: 05/11/2019] [Indexed: 01/18/2023] Open
Abstract
Decreased male fertility is a big concern in both human society and the livestock industry. Sperm DNA methylation is commonly believed to be associated with male fertility. However, due to the lack of accurate male fertility records (i.e., limited mating times), few studies have investigated the comprehensive impacts of sperm DNA methylation on male fertility in mammals. In this study, we generated 10 sperm DNA methylomes and performed a preliminary correlation analysis between signals from sperm DNA methylation and signals from large-scale (n = 27,214) genome-wide association studies (GWAS) of 35 complex traits (including 12 male fertility-related traits). We detected genomic regions, which experienced DNA methylation alterations in sperm and were associated with aging and extreme fertility phenotypes (e.g., sire-conception rate or SCR). In dynamic hypomethylated regions (HMRs) and partially methylated domains (PMDs), we found genes (e.g., HOX gene clusters and microRNAs) that were involved in the embryonic development. We demonstrated that genomic regions, which gained rather than lost methylations during aging, and in animals with low SCR were significantly and selectively enriched for GWAS signals of male fertility traits. Our study discovered 16 genes as the potential candidate markers for male fertility, including SAMD5 and PDE5A. Collectively, this initial effort supported a hypothesis that sperm DNA methylation may contribute to male fertility in cattle and revealed the usefulness of functional annotations in enhancing biological interpretation and genomic prediction for complex traits and diseases.
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Affiliation(s)
- Lingzhao Fang
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuli Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jicai Jiang
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Derek M. Bickhart
- Dairy Forage Research Center, Agricultural Research Service, USDA, Madison, WI 53718, USA
| | - Daniel J. Null
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Bingjie Li
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Steven G. Schroeder
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - John B. Cole
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Curtis P. Van Tassell
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
- Correspondence: (L.M.); (G.E.L.); Tel.: +1-301-405-1389 (L.M.); +1-301-504-9843 (G.E.L.); Fax: +1-301-504-8414 (G.E.L.)
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
- Correspondence: (L.M.); (G.E.L.); Tel.: +1-301-405-1389 (L.M.); +1-301-504-9843 (G.E.L.); Fax: +1-301-504-8414 (G.E.L.)
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24
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Li S, Zhang J, Huang S, He X. Genome-wide analysis reveals that exon methylation facilitates its selective usage in the human transcriptome. Brief Bioinform 2019; 19:754-764. [PMID: 28334074 DOI: 10.1093/bib/bbx019] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Indexed: 12/29/2022] Open
Abstract
DNA methylation, especially in promoter regions, is a well-characterized epigenetic marker related to gene expression regulation in eukaryotes. However, the role of intragenic DNA methylation in the usage of corresponding exons still remains elusive. In this study, we described the DNA methylome across 10 human tissues. The human genome showed both conserved and varied methylation levels among these tissues. We found that the methylation densities in promoters and first exons were negatively correlated with the corresponding gene expression level. Nevertheless, the methylation densities within introns, internal exons and down 1 kb regions showed weak correlation with gene expression levels. Importantly, we observed a remarkably positive relationship between methylation density and exon expression level of intragenic exons. Notably, skip-in exons were much more methylated than skip-out exons. We also identified 260 exons that showed both differential methylation levels and differential expression levels in lung cancer. Genes harboring these differentially regulated exons were significantly enriched in the cancer hallmark-related biological process. Moreover, a 10-exon signature was identified as a promising prognostic predictor for lung cancer. Our study illuminates the DNA methylome, describes its relationship with gene expression across human tissues and provides new insights into intragenic DNA methylation and exon usage during the transcriptional/alternative splicing process and in cancer.
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Affiliation(s)
- Shengli Li
- Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiwei Zhang
- Shanghai Medical College, Fudan University, Shanghai, China
| | - Shenglin Huang
- Shanghai Medical College, Fudan University, Shanghai, China
| | - Xianghuo He
- Shanghai Medical College, Fudan University, Shanghai, China
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25
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Fang L, Zhou Y, Liu S, Jiang J, Bickhart DM, Null DJ, Li B, Schroeder SG, Rosen BD, Cole JB, Van Tassell CP, Ma L, Liu GE. Comparative analyses of sperm DNA methylomes among human, mouse and cattle provide insights into epigenomic evolution and complex traits. Epigenetics 2019; 14:260-276. [PMID: 30810461 PMCID: PMC6557555 DOI: 10.1080/15592294.2019.1582217] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Sperm DNA methylation is crucial for fertility and viability of offspring but epigenome evolution in mammals is largely understudied. By comparing sperm DNA methylomes and large-scale genome-wide association study (GWAS) signals between human and cattle, we aimed to examine the DNA methylome evolution and its associations with complex phenotypes in mammals. Our analysis revealed that genes with conserved non-methylated promoters (e.g., ANKS1A and WNT7A) among human and cattle were involved in common system and embryo development, and enriched for GWAS signals of body conformation traits in both species, while genes with conserved hypermethylated promoters (e.g., TCAP and CD80) were engaged in immune responses and highlighted by immune-related traits. On the other hand, genes with human-specific hypomethylated promoters (e.g., FOXP2 and HYDIN) were engaged in neuron system development and enriched for GWAS signals of brain-related traits, while genes with cattle-specific hypomethylated promoters (e.g., LDHB and DGAT2) mainly participated in lipid storage and metabolism. We validated our findings using sperm-retained nucleosome, preimplantation transcriptome, and adult tissue transcriptome data, as well as sequence evolutionary features, including motif binding sites, mutation rates, recombination rates and evolution signatures. In conclusion, our results demonstrate important roles of epigenome evolution in shaping the genetic architecture underlying complex phenotypes, hence enhance signal prioritization in GWAS and provide valuable information for human neurological disorders and livestock genetic improvement.
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Affiliation(s)
- Lingzhao Fang
- a Animal Genomics and Improvement Laboratory, BARC , Agricultural Research Service, USDA , Beltsville , MD , USA.,b Department of Animal and Avian Sciences , University of Maryland , College Park , MD , USA
| | - Yang Zhou
- c Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China , Huazhong Agricultural University , Wuhan , Hubei , China
| | - Shuli Liu
- a Animal Genomics and Improvement Laboratory, BARC , Agricultural Research Service, USDA , Beltsville , MD , USA.,d Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology , China Agricultural University , Beijing , China
| | - Jicai Jiang
- b Department of Animal and Avian Sciences , University of Maryland , College Park , MD , USA
| | - Derek M Bickhart
- e Dairy Forage Research Center , Agricultural Research Service, USDA , Madison , WI , USA
| | - Daniel J Null
- a Animal Genomics and Improvement Laboratory, BARC , Agricultural Research Service, USDA , Beltsville , MD , USA
| | - Bingjie Li
- a Animal Genomics and Improvement Laboratory, BARC , Agricultural Research Service, USDA , Beltsville , MD , USA
| | - Steven G Schroeder
- a Animal Genomics and Improvement Laboratory, BARC , Agricultural Research Service, USDA , Beltsville , MD , USA
| | - Benjamin D Rosen
- a Animal Genomics and Improvement Laboratory, BARC , Agricultural Research Service, USDA , Beltsville , MD , USA
| | - John B Cole
- a Animal Genomics and Improvement Laboratory, BARC , Agricultural Research Service, USDA , Beltsville , MD , USA
| | - Curtis P Van Tassell
- a Animal Genomics and Improvement Laboratory, BARC , Agricultural Research Service, USDA , Beltsville , MD , USA
| | - Li Ma
- b Department of Animal and Avian Sciences , University of Maryland , College Park , MD , USA
| | - George E Liu
- a Animal Genomics and Improvement Laboratory, BARC , Agricultural Research Service, USDA , Beltsville , MD , USA
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26
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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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27
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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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28
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Anderson SN, Springer NM. Potential roles for transposable elements in creating imprinted expression. Curr Opin Genet Dev 2018; 49:8-14. [DOI: 10.1016/j.gde.2018.01.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/25/2018] [Accepted: 01/29/2018] [Indexed: 10/18/2022]
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29
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Liu H, Shang X, Zhu H. LncRNA/DNA binding analysis reveals losses and gains and lineage specificity of genomic imprinting in mammals. Bioinformatics 2018; 33:1431-1436. [PMID: 28052924 DOI: 10.1093/bioinformatics/btw818] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 12/20/2016] [Indexed: 11/14/2022] Open
Abstract
Motivation Genomic imprinting is regulated by lncRNAs and is important for embryogenesis, physiology and behaviour in mammals. Aberrant imprinting causes diseases and disorders. Experimental studies have examined genomic imprinting primarily in humans and mice, thus leaving some fundamental issues poorly addressed. The cost of experimentally examining imprinted genes in many tissues in diverse species makes computational analysis of lncRNAs' DNA binding sites valuable. Results We performed lncRNA/DNA binding analysis in imprinting clusters from multiple mammalian clades and discovered the following: (i) lncRNAs and imprinting sites show significant losses and gains and distinct lineage-specificity; (ii) binding of lncRNAs to promoters of imprinted genes may occur widely throughout the genome; (iii) a considerable number of imprinting sites occur in only evolutionarily more derived species; and (iv) multiple lncRNAs may bind to the same imprinting sites, and some lncRNAs have multiple DNA binding motifs. These results suggest that the occurrence of abundant lncRNAs in mammalian genomes makes genomic imprinting a mechanism of adaptive evolution at the epigenome level. Availability and Implementation The data and program are available at the database LongMan at lncRNA.smu.edu.cn. Contact zhuhao@smu.edu.cn. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Haihua Liu
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiaoxiao Shang
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Hao Zhu
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
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Hong X, Kim ES, Guo H. Epigenetic regulation of hepatitis B virus covalently closed circular DNA: Implications for epigenetic therapy against chronic hepatitis B. Hepatology 2017; 66:2066-2077. [PMID: 28833361 PMCID: PMC5696023 DOI: 10.1002/hep.29479] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/24/2017] [Accepted: 08/15/2017] [Indexed: 12/12/2022]
Abstract
Hepatitis B virus (HBV) infection represents a significant public health burden worldwide. Although current therapeutics manage to control the disease progression, lifelong treatment and surveillance are required because drug resistance develops during treatment and reactivations frequently occur following medication cessation. Thus, the occurrence of hepatocellular carcinoma is decreased, but not eliminated. One major reason for failure of HBV treatment is the inability to eradicate or inactivate the viral covalently closed circular DNA (cccDNA), which is a stable episomal form of the viral genome decorated with host histones and nonhistone proteins. Accumulating evidence suggests that epigenetic modifications of cccDNA contribute to viral replication and the outcome of chronic HBV infection. Here, we summarize current progress on HBV epigenetics research and the therapeutic implications for chronic HBV infection by learning from the epigenetic therapies for cancer and other viral diseases, which may open a new venue to cure chronic hepatitis B. (Hepatology 2017;66:2066-2077).
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Affiliation(s)
- Xupeng Hong
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC 20057, USA,Corresponding author: Haitao Guo, ; Xupeng Hong,
| | - Elena S. Kim
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Haitao Guo
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA,Corresponding author: Haitao Guo, ; Xupeng Hong,
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Zadora J, Singh M, Herse F, Przybyl L, Haase N, Golic M, Yung HW, Huppertz B, Cartwright JE, Whitley G, Johnsen GM, Levi G, Isbruch A, Schulz H, Luft FC, Müller DN, Staff AC, Hurst LD, Dechend R, Izsvák Z. Disturbed Placental Imprinting in Preeclampsia Leads to Altered Expression of DLX5, a Human-Specific Early Trophoblast Marker. Circulation 2017; 136:1824-1839. [PMID: 28904069 PMCID: PMC5671803 DOI: 10.1161/circulationaha.117.028110] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 08/28/2017] [Indexed: 01/23/2023]
Abstract
Supplemental Digital Content is available in the text. Background: Preeclampsia is a complex and common human-specific pregnancy syndrome associated with placental pathology. The human specificity provides both intellectual and methodological challenges, lacking a robust model system. Given the role of imprinted genes in human placentation and the vulnerability of imprinted genes to loss of imprinting changes, there has been extensive speculation, but no robust evidence, that imprinted genes are involved in preeclampsia. Our study aims to investigate whether disturbed imprinting contributes to preeclampsia. Methods: We first aimed to confirm that preeclampsia is a disease of the placenta by generating and analyzing genome-wide molecular data on well-characterized patient material. We performed high-throughput transcriptome analyses of multiple placenta samples from healthy controls and patients with preeclampsia. Next, we identified differentially expressed genes in preeclamptic placentas and intersected them with the list of human imprinted genes. We used bioinformatics/statistical analyses to confirm association between imprinting and preeclampsia and to predict biological processes affected in preeclampsia. Validation included epigenetic and cellular assays. In terms of human specificity, we established an in vitro invasion-differentiation trophoblast model. Our comparative phylogenetic analysis involved single-cell transcriptome data of human, macaque, and mouse preimplantation embryogenesis. Results: We found disturbed placental imprinting in preeclampsia and revealed potential candidates, including GATA3 and DLX5, with poorly explored imprinted status and no prior association with preeclampsia. As a result of loss of imprinting, DLX5 was upregulated in 69% of preeclamptic placentas. Levels of DLX5 correlated with classic preeclampsia markers. DLX5 is expressed in human but not in murine trophoblast. The DLX5high phenotype resulted in reduced proliferation, increased metabolism, and endoplasmic reticulum stress-response activation in trophoblasts in vitro. The transcriptional profile of such cells mimics the transcriptome of preeclamptic placentas. Pan-mammalian comparative analysis identified DLX5 as part of the human-specific regulatory network of trophoblast differentiation. Conclusions: Our analysis provides evidence of a true association among disturbed imprinting, gene expression, and preeclampsia. As a result of disturbed imprinting, the upregulated DLX5 affects trophoblast proliferation. Our in vitro model might fill a vital niche in preeclampsia research. Human-specific regulatory circuitry of DLX5 might help explain certain aspects of preeclampsia.
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Affiliation(s)
- Julianna Zadora
- From Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (J.Z., M.S., F.H., N.H., D.N.M., Z.I.); Experimental and Clinical Research Center, a joint cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Germany (J.Z., F.H., L.P., N.H., M.G., H.S., F.C.L., D.N.M., R.D.); Berlin Institute of Health, Germany (J.Z., F.H., L.P., N.H., M.G., F.C.L., D.N.M., R.D., Z.I.); Department of Obstetrics and Department of Gynecology, Charité-Universitätsmedizin Berlin, Germany (M.G.); German Centre for Cardiovascular Research, partner site Berlin, Germany (N.H., D.N.M.); Centre for Trophoblast Research, University of Cambridge, UK (H.W.Y.); Institute of Cell Biology, Histology and Embryology, Medical University of Graz, Austria (B.H.); Molecular and Clinical Sciences Research Institute, St George's University of London, UK (J.E.C., G.W.); Division of Obstetrics and Gynaecology, Oslo University Hospital, Norway (G.M.J., A.C.S.); University of Oslo, Norway (G.M.J., A.C.S.); Évolution des Régulations Endocriniennes, Muséum Nationale d'Histoire Naturelle, Paris, France (G.L.); HELIOS-Klinikum, Berlin, Germany (A.I., R.D.); Cologne Center for Genomics, University of Cologne, Germany (H.S.); and Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, UK (L.D.H.)
| | - Manvendra Singh
- From Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (J.Z., M.S., F.H., N.H., D.N.M., Z.I.); Experimental and Clinical Research Center, a joint cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Germany (J.Z., F.H., L.P., N.H., M.G., H.S., F.C.L., D.N.M., R.D.); Berlin Institute of Health, Germany (J.Z., F.H., L.P., N.H., M.G., F.C.L., D.N.M., R.D., Z.I.); Department of Obstetrics and Department of Gynecology, Charité-Universitätsmedizin Berlin, Germany (M.G.); German Centre for Cardiovascular Research, partner site Berlin, Germany (N.H., D.N.M.); Centre for Trophoblast Research, University of Cambridge, UK (H.W.Y.); Institute of Cell Biology, Histology and Embryology, Medical University of Graz, Austria (B.H.); Molecular and Clinical Sciences Research Institute, St George's University of London, UK (J.E.C., G.W.); Division of Obstetrics and Gynaecology, Oslo University Hospital, Norway (G.M.J., A.C.S.); University of Oslo, Norway (G.M.J., A.C.S.); Évolution des Régulations Endocriniennes, Muséum Nationale d'Histoire Naturelle, Paris, France (G.L.); HELIOS-Klinikum, Berlin, Germany (A.I., R.D.); Cologne Center for Genomics, University of Cologne, Germany (H.S.); and Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, UK (L.D.H.)
| | - Florian Herse
- From Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (J.Z., M.S., F.H., N.H., D.N.M., Z.I.); Experimental and Clinical Research Center, a joint cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Germany (J.Z., F.H., L.P., N.H., M.G., H.S., F.C.L., D.N.M., R.D.); Berlin Institute of Health, Germany (J.Z., F.H., L.P., N.H., M.G., F.C.L., D.N.M., R.D., Z.I.); Department of Obstetrics and Department of Gynecology, Charité-Universitätsmedizin Berlin, Germany (M.G.); German Centre for Cardiovascular Research, partner site Berlin, Germany (N.H., D.N.M.); Centre for Trophoblast Research, University of Cambridge, UK (H.W.Y.); Institute of Cell Biology, Histology and Embryology, Medical University of Graz, Austria (B.H.); Molecular and Clinical Sciences Research Institute, St George's University of London, UK (J.E.C., G.W.); Division of Obstetrics and Gynaecology, Oslo University Hospital, Norway (G.M.J., A.C.S.); University of Oslo, Norway (G.M.J., A.C.S.); Évolution des Régulations Endocriniennes, Muséum Nationale d'Histoire Naturelle, Paris, France (G.L.); HELIOS-Klinikum, Berlin, Germany (A.I., R.D.); Cologne Center for Genomics, University of Cologne, Germany (H.S.); and Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, UK (L.D.H.)
| | - Lukasz Przybyl
- From Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (J.Z., M.S., F.H., N.H., D.N.M., Z.I.); Experimental and Clinical Research Center, a joint cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Germany (J.Z., F.H., L.P., N.H., M.G., H.S., F.C.L., D.N.M., R.D.); Berlin Institute of Health, Germany (J.Z., F.H., L.P., N.H., M.G., F.C.L., D.N.M., R.D., Z.I.); Department of Obstetrics and Department of Gynecology, Charité-Universitätsmedizin Berlin, Germany (M.G.); German Centre for Cardiovascular Research, partner site Berlin, Germany (N.H., D.N.M.); Centre for Trophoblast Research, University of Cambridge, UK (H.W.Y.); Institute of Cell Biology, Histology and Embryology, Medical University of Graz, Austria (B.H.); Molecular and Clinical Sciences Research Institute, St George's University of London, UK (J.E.C., G.W.); Division of Obstetrics and Gynaecology, Oslo University Hospital, Norway (G.M.J., A.C.S.); University of Oslo, Norway (G.M.J., A.C.S.); Évolution des Régulations Endocriniennes, Muséum Nationale d'Histoire Naturelle, Paris, France (G.L.); HELIOS-Klinikum, Berlin, Germany (A.I., R.D.); Cologne Center for Genomics, University of Cologne, Germany (H.S.); and Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, UK (L.D.H.)
| | - Nadine Haase
- From Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (J.Z., M.S., F.H., N.H., D.N.M., Z.I.); Experimental and Clinical Research Center, a joint cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Germany (J.Z., F.H., L.P., N.H., M.G., H.S., F.C.L., D.N.M., R.D.); Berlin Institute of Health, Germany (J.Z., F.H., L.P., N.H., M.G., F.C.L., D.N.M., R.D., Z.I.); Department of Obstetrics and Department of Gynecology, Charité-Universitätsmedizin Berlin, Germany (M.G.); German Centre for Cardiovascular Research, partner site Berlin, Germany (N.H., D.N.M.); Centre for Trophoblast Research, University of Cambridge, UK (H.W.Y.); Institute of Cell Biology, Histology and Embryology, Medical University of Graz, Austria (B.H.); Molecular and Clinical Sciences Research Institute, St George's University of London, UK (J.E.C., G.W.); Division of Obstetrics and Gynaecology, Oslo University Hospital, Norway (G.M.J., A.C.S.); University of Oslo, Norway (G.M.J., A.C.S.); Évolution des Régulations Endocriniennes, Muséum Nationale d'Histoire Naturelle, Paris, France (G.L.); HELIOS-Klinikum, Berlin, Germany (A.I., R.D.); Cologne Center for Genomics, University of Cologne, Germany (H.S.); and Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, UK (L.D.H.)
| | - Michaela Golic
- From Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (J.Z., M.S., F.H., N.H., D.N.M., Z.I.); Experimental and Clinical Research Center, a joint cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Germany (J.Z., F.H., L.P., N.H., M.G., H.S., F.C.L., D.N.M., R.D.); Berlin Institute of Health, Germany (J.Z., F.H., L.P., N.H., M.G., F.C.L., D.N.M., R.D., Z.I.); Department of Obstetrics and Department of Gynecology, Charité-Universitätsmedizin Berlin, Germany (M.G.); German Centre for Cardiovascular Research, partner site Berlin, Germany (N.H., D.N.M.); Centre for Trophoblast Research, University of Cambridge, UK (H.W.Y.); Institute of Cell Biology, Histology and Embryology, Medical University of Graz, Austria (B.H.); Molecular and Clinical Sciences Research Institute, St George's University of London, UK (J.E.C., G.W.); Division of Obstetrics and Gynaecology, Oslo University Hospital, Norway (G.M.J., A.C.S.); University of Oslo, Norway (G.M.J., A.C.S.); Évolution des Régulations Endocriniennes, Muséum Nationale d'Histoire Naturelle, Paris, France (G.L.); HELIOS-Klinikum, Berlin, Germany (A.I., R.D.); Cologne Center for Genomics, University of Cologne, Germany (H.S.); and Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, UK (L.D.H.)
| | - Hong Wa Yung
- From Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (J.Z., M.S., F.H., N.H., D.N.M., Z.I.); Experimental and Clinical Research Center, a joint cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Germany (J.Z., F.H., L.P., N.H., M.G., H.S., F.C.L., D.N.M., R.D.); Berlin Institute of Health, Germany (J.Z., F.H., L.P., N.H., M.G., F.C.L., D.N.M., R.D., Z.I.); Department of Obstetrics and Department of Gynecology, Charité-Universitätsmedizin Berlin, Germany (M.G.); German Centre for Cardiovascular Research, partner site Berlin, Germany (N.H., D.N.M.); Centre for Trophoblast Research, University of Cambridge, UK (H.W.Y.); Institute of Cell Biology, Histology and Embryology, Medical University of Graz, Austria (B.H.); Molecular and Clinical Sciences Research Institute, St George's University of London, UK (J.E.C., G.W.); Division of Obstetrics and Gynaecology, Oslo University Hospital, Norway (G.M.J., A.C.S.); University of Oslo, Norway (G.M.J., A.C.S.); Évolution des Régulations Endocriniennes, Muséum Nationale d'Histoire Naturelle, Paris, France (G.L.); HELIOS-Klinikum, Berlin, Germany (A.I., R.D.); Cologne Center for Genomics, University of Cologne, Germany (H.S.); and Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, UK (L.D.H.)
| | - Berthold Huppertz
- From Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (J.Z., M.S., F.H., N.H., D.N.M., Z.I.); Experimental and Clinical Research Center, a joint cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Germany (J.Z., F.H., L.P., N.H., M.G., H.S., F.C.L., D.N.M., R.D.); Berlin Institute of Health, Germany (J.Z., F.H., L.P., N.H., M.G., F.C.L., D.N.M., R.D., Z.I.); Department of Obstetrics and Department of Gynecology, Charité-Universitätsmedizin Berlin, Germany (M.G.); German Centre for Cardiovascular Research, partner site Berlin, Germany (N.H., D.N.M.); Centre for Trophoblast Research, University of Cambridge, UK (H.W.Y.); Institute of Cell Biology, Histology and Embryology, Medical University of Graz, Austria (B.H.); Molecular and Clinical Sciences Research Institute, St George's University of London, UK (J.E.C., G.W.); Division of Obstetrics and Gynaecology, Oslo University Hospital, Norway (G.M.J., A.C.S.); University of Oslo, Norway (G.M.J., A.C.S.); Évolution des Régulations Endocriniennes, Muséum Nationale d'Histoire Naturelle, Paris, France (G.L.); HELIOS-Klinikum, Berlin, Germany (A.I., R.D.); Cologne Center for Genomics, University of Cologne, Germany (H.S.); and Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, UK (L.D.H.)
| | - Judith E Cartwright
- From Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (J.Z., M.S., F.H., N.H., D.N.M., Z.I.); Experimental and Clinical Research Center, a joint cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Germany (J.Z., F.H., L.P., N.H., M.G., H.S., F.C.L., D.N.M., R.D.); Berlin Institute of Health, Germany (J.Z., F.H., L.P., N.H., M.G., F.C.L., D.N.M., R.D., Z.I.); Department of Obstetrics and Department of Gynecology, Charité-Universitätsmedizin Berlin, Germany (M.G.); German Centre for Cardiovascular Research, partner site Berlin, Germany (N.H., D.N.M.); Centre for Trophoblast Research, University of Cambridge, UK (H.W.Y.); Institute of Cell Biology, Histology and Embryology, Medical University of Graz, Austria (B.H.); Molecular and Clinical Sciences Research Institute, St George's University of London, UK (J.E.C., G.W.); Division of Obstetrics and Gynaecology, Oslo University Hospital, Norway (G.M.J., A.C.S.); University of Oslo, Norway (G.M.J., A.C.S.); Évolution des Régulations Endocriniennes, Muséum Nationale d'Histoire Naturelle, Paris, France (G.L.); HELIOS-Klinikum, Berlin, Germany (A.I., R.D.); Cologne Center for Genomics, University of Cologne, Germany (H.S.); and Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, UK (L.D.H.)
| | - Guy Whitley
- From Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (J.Z., M.S., F.H., N.H., D.N.M., Z.I.); Experimental and Clinical Research Center, a joint cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Germany (J.Z., F.H., L.P., N.H., M.G., H.S., F.C.L., D.N.M., R.D.); Berlin Institute of Health, Germany (J.Z., F.H., L.P., N.H., M.G., F.C.L., D.N.M., R.D., Z.I.); Department of Obstetrics and Department of Gynecology, Charité-Universitätsmedizin Berlin, Germany (M.G.); German Centre for Cardiovascular Research, partner site Berlin, Germany (N.H., D.N.M.); Centre for Trophoblast Research, University of Cambridge, UK (H.W.Y.); Institute of Cell Biology, Histology and Embryology, Medical University of Graz, Austria (B.H.); Molecular and Clinical Sciences Research Institute, St George's University of London, UK (J.E.C., G.W.); Division of Obstetrics and Gynaecology, Oslo University Hospital, Norway (G.M.J., A.C.S.); University of Oslo, Norway (G.M.J., A.C.S.); Évolution des Régulations Endocriniennes, Muséum Nationale d'Histoire Naturelle, Paris, France (G.L.); HELIOS-Klinikum, Berlin, Germany (A.I., R.D.); Cologne Center for Genomics, University of Cologne, Germany (H.S.); and Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, UK (L.D.H.)
| | - Guro M Johnsen
- From Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (J.Z., M.S., F.H., N.H., D.N.M., Z.I.); Experimental and Clinical Research Center, a joint cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Germany (J.Z., F.H., L.P., N.H., M.G., H.S., F.C.L., D.N.M., R.D.); Berlin Institute of Health, Germany (J.Z., F.H., L.P., N.H., M.G., F.C.L., D.N.M., R.D., Z.I.); Department of Obstetrics and Department of Gynecology, Charité-Universitätsmedizin Berlin, Germany (M.G.); German Centre for Cardiovascular Research, partner site Berlin, Germany (N.H., D.N.M.); Centre for Trophoblast Research, University of Cambridge, UK (H.W.Y.); Institute of Cell Biology, Histology and Embryology, Medical University of Graz, Austria (B.H.); Molecular and Clinical Sciences Research Institute, St George's University of London, UK (J.E.C., G.W.); Division of Obstetrics and Gynaecology, Oslo University Hospital, Norway (G.M.J., A.C.S.); University of Oslo, Norway (G.M.J., A.C.S.); Évolution des Régulations Endocriniennes, Muséum Nationale d'Histoire Naturelle, Paris, France (G.L.); HELIOS-Klinikum, Berlin, Germany (A.I., R.D.); Cologne Center for Genomics, University of Cologne, Germany (H.S.); and Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, UK (L.D.H.)
| | - Giovanni Levi
- From Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (J.Z., M.S., F.H., N.H., D.N.M., Z.I.); Experimental and Clinical Research Center, a joint cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Germany (J.Z., F.H., L.P., N.H., M.G., H.S., F.C.L., D.N.M., R.D.); Berlin Institute of Health, Germany (J.Z., F.H., L.P., N.H., M.G., F.C.L., D.N.M., R.D., Z.I.); Department of Obstetrics and Department of Gynecology, Charité-Universitätsmedizin Berlin, Germany (M.G.); German Centre for Cardiovascular Research, partner site Berlin, Germany (N.H., D.N.M.); Centre for Trophoblast Research, University of Cambridge, UK (H.W.Y.); Institute of Cell Biology, Histology and Embryology, Medical University of Graz, Austria (B.H.); Molecular and Clinical Sciences Research Institute, St George's University of London, UK (J.E.C., G.W.); Division of Obstetrics and Gynaecology, Oslo University Hospital, Norway (G.M.J., A.C.S.); University of Oslo, Norway (G.M.J., A.C.S.); Évolution des Régulations Endocriniennes, Muséum Nationale d'Histoire Naturelle, Paris, France (G.L.); HELIOS-Klinikum, Berlin, Germany (A.I., R.D.); Cologne Center for Genomics, University of Cologne, Germany (H.S.); and Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, UK (L.D.H.)
| | - Annette Isbruch
- From Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (J.Z., M.S., F.H., N.H., D.N.M., Z.I.); Experimental and Clinical Research Center, a joint cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Germany (J.Z., F.H., L.P., N.H., M.G., H.S., F.C.L., D.N.M., R.D.); Berlin Institute of Health, Germany (J.Z., F.H., L.P., N.H., M.G., F.C.L., D.N.M., R.D., Z.I.); Department of Obstetrics and Department of Gynecology, Charité-Universitätsmedizin Berlin, Germany (M.G.); German Centre for Cardiovascular Research, partner site Berlin, Germany (N.H., D.N.M.); Centre for Trophoblast Research, University of Cambridge, UK (H.W.Y.); Institute of Cell Biology, Histology and Embryology, Medical University of Graz, Austria (B.H.); Molecular and Clinical Sciences Research Institute, St George's University of London, UK (J.E.C., G.W.); Division of Obstetrics and Gynaecology, Oslo University Hospital, Norway (G.M.J., A.C.S.); University of Oslo, Norway (G.M.J., A.C.S.); Évolution des Régulations Endocriniennes, Muséum Nationale d'Histoire Naturelle, Paris, France (G.L.); HELIOS-Klinikum, Berlin, Germany (A.I., R.D.); Cologne Center for Genomics, University of Cologne, Germany (H.S.); and Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, UK (L.D.H.)
| | - Herbert Schulz
- From Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (J.Z., M.S., F.H., N.H., D.N.M., Z.I.); Experimental and Clinical Research Center, a joint cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Germany (J.Z., F.H., L.P., N.H., M.G., H.S., F.C.L., D.N.M., R.D.); Berlin Institute of Health, Germany (J.Z., F.H., L.P., N.H., M.G., F.C.L., D.N.M., R.D., Z.I.); Department of Obstetrics and Department of Gynecology, Charité-Universitätsmedizin Berlin, Germany (M.G.); German Centre for Cardiovascular Research, partner site Berlin, Germany (N.H., D.N.M.); Centre for Trophoblast Research, University of Cambridge, UK (H.W.Y.); Institute of Cell Biology, Histology and Embryology, Medical University of Graz, Austria (B.H.); Molecular and Clinical Sciences Research Institute, St George's University of London, UK (J.E.C., G.W.); Division of Obstetrics and Gynaecology, Oslo University Hospital, Norway (G.M.J., A.C.S.); University of Oslo, Norway (G.M.J., A.C.S.); Évolution des Régulations Endocriniennes, Muséum Nationale d'Histoire Naturelle, Paris, France (G.L.); HELIOS-Klinikum, Berlin, Germany (A.I., R.D.); Cologne Center for Genomics, University of Cologne, Germany (H.S.); and Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, UK (L.D.H.)
| | - Friedrich C Luft
- From Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (J.Z., M.S., F.H., N.H., D.N.M., Z.I.); Experimental and Clinical Research Center, a joint cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Germany (J.Z., F.H., L.P., N.H., M.G., H.S., F.C.L., D.N.M., R.D.); Berlin Institute of Health, Germany (J.Z., F.H., L.P., N.H., M.G., F.C.L., D.N.M., R.D., Z.I.); Department of Obstetrics and Department of Gynecology, Charité-Universitätsmedizin Berlin, Germany (M.G.); German Centre for Cardiovascular Research, partner site Berlin, Germany (N.H., D.N.M.); Centre for Trophoblast Research, University of Cambridge, UK (H.W.Y.); Institute of Cell Biology, Histology and Embryology, Medical University of Graz, Austria (B.H.); Molecular and Clinical Sciences Research Institute, St George's University of London, UK (J.E.C., G.W.); Division of Obstetrics and Gynaecology, Oslo University Hospital, Norway (G.M.J., A.C.S.); University of Oslo, Norway (G.M.J., A.C.S.); Évolution des Régulations Endocriniennes, Muséum Nationale d'Histoire Naturelle, Paris, France (G.L.); HELIOS-Klinikum, Berlin, Germany (A.I., R.D.); Cologne Center for Genomics, University of Cologne, Germany (H.S.); and Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, UK (L.D.H.)
| | - Dominik N Müller
- From Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (J.Z., M.S., F.H., N.H., D.N.M., Z.I.); Experimental and Clinical Research Center, a joint cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Germany (J.Z., F.H., L.P., N.H., M.G., H.S., F.C.L., D.N.M., R.D.); Berlin Institute of Health, Germany (J.Z., F.H., L.P., N.H., M.G., F.C.L., D.N.M., R.D., Z.I.); Department of Obstetrics and Department of Gynecology, Charité-Universitätsmedizin Berlin, Germany (M.G.); German Centre for Cardiovascular Research, partner site Berlin, Germany (N.H., D.N.M.); Centre for Trophoblast Research, University of Cambridge, UK (H.W.Y.); Institute of Cell Biology, Histology and Embryology, Medical University of Graz, Austria (B.H.); Molecular and Clinical Sciences Research Institute, St George's University of London, UK (J.E.C., G.W.); Division of Obstetrics and Gynaecology, Oslo University Hospital, Norway (G.M.J., A.C.S.); University of Oslo, Norway (G.M.J., A.C.S.); Évolution des Régulations Endocriniennes, Muséum Nationale d'Histoire Naturelle, Paris, France (G.L.); HELIOS-Klinikum, Berlin, Germany (A.I., R.D.); Cologne Center for Genomics, University of Cologne, Germany (H.S.); and Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, UK (L.D.H.)
| | - Anne Cathrine Staff
- From Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (J.Z., M.S., F.H., N.H., D.N.M., Z.I.); Experimental and Clinical Research Center, a joint cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Germany (J.Z., F.H., L.P., N.H., M.G., H.S., F.C.L., D.N.M., R.D.); Berlin Institute of Health, Germany (J.Z., F.H., L.P., N.H., M.G., F.C.L., D.N.M., R.D., Z.I.); Department of Obstetrics and Department of Gynecology, Charité-Universitätsmedizin Berlin, Germany (M.G.); German Centre for Cardiovascular Research, partner site Berlin, Germany (N.H., D.N.M.); Centre for Trophoblast Research, University of Cambridge, UK (H.W.Y.); Institute of Cell Biology, Histology and Embryology, Medical University of Graz, Austria (B.H.); Molecular and Clinical Sciences Research Institute, St George's University of London, UK (J.E.C., G.W.); Division of Obstetrics and Gynaecology, Oslo University Hospital, Norway (G.M.J., A.C.S.); University of Oslo, Norway (G.M.J., A.C.S.); Évolution des Régulations Endocriniennes, Muséum Nationale d'Histoire Naturelle, Paris, France (G.L.); HELIOS-Klinikum, Berlin, Germany (A.I., R.D.); Cologne Center for Genomics, University of Cologne, Germany (H.S.); and Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, UK (L.D.H.)
| | - Laurence D Hurst
- From Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (J.Z., M.S., F.H., N.H., D.N.M., Z.I.); Experimental and Clinical Research Center, a joint cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Germany (J.Z., F.H., L.P., N.H., M.G., H.S., F.C.L., D.N.M., R.D.); Berlin Institute of Health, Germany (J.Z., F.H., L.P., N.H., M.G., F.C.L., D.N.M., R.D., Z.I.); Department of Obstetrics and Department of Gynecology, Charité-Universitätsmedizin Berlin, Germany (M.G.); German Centre for Cardiovascular Research, partner site Berlin, Germany (N.H., D.N.M.); Centre for Trophoblast Research, University of Cambridge, UK (H.W.Y.); Institute of Cell Biology, Histology and Embryology, Medical University of Graz, Austria (B.H.); Molecular and Clinical Sciences Research Institute, St George's University of London, UK (J.E.C., G.W.); Division of Obstetrics and Gynaecology, Oslo University Hospital, Norway (G.M.J., A.C.S.); University of Oslo, Norway (G.M.J., A.C.S.); Évolution des Régulations Endocriniennes, Muséum Nationale d'Histoire Naturelle, Paris, France (G.L.); HELIOS-Klinikum, Berlin, Germany (A.I., R.D.); Cologne Center for Genomics, University of Cologne, Germany (H.S.); and Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, UK (L.D.H.).
| | - Ralf Dechend
- From Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (J.Z., M.S., F.H., N.H., D.N.M., Z.I.); Experimental and Clinical Research Center, a joint cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Germany (J.Z., F.H., L.P., N.H., M.G., H.S., F.C.L., D.N.M., R.D.); Berlin Institute of Health, Germany (J.Z., F.H., L.P., N.H., M.G., F.C.L., D.N.M., R.D., Z.I.); Department of Obstetrics and Department of Gynecology, Charité-Universitätsmedizin Berlin, Germany (M.G.); German Centre for Cardiovascular Research, partner site Berlin, Germany (N.H., D.N.M.); Centre for Trophoblast Research, University of Cambridge, UK (H.W.Y.); Institute of Cell Biology, Histology and Embryology, Medical University of Graz, Austria (B.H.); Molecular and Clinical Sciences Research Institute, St George's University of London, UK (J.E.C., G.W.); Division of Obstetrics and Gynaecology, Oslo University Hospital, Norway (G.M.J., A.C.S.); University of Oslo, Norway (G.M.J., A.C.S.); Évolution des Régulations Endocriniennes, Muséum Nationale d'Histoire Naturelle, Paris, France (G.L.); HELIOS-Klinikum, Berlin, Germany (A.I., R.D.); Cologne Center for Genomics, University of Cologne, Germany (H.S.); and Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, UK (L.D.H.).
| | - Zsuzsanna Izsvák
- From Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (J.Z., M.S., F.H., N.H., D.N.M., Z.I.); Experimental and Clinical Research Center, a joint cooperation between the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Germany (J.Z., F.H., L.P., N.H., M.G., H.S., F.C.L., D.N.M., R.D.); Berlin Institute of Health, Germany (J.Z., F.H., L.P., N.H., M.G., F.C.L., D.N.M., R.D., Z.I.); Department of Obstetrics and Department of Gynecology, Charité-Universitätsmedizin Berlin, Germany (M.G.); German Centre for Cardiovascular Research, partner site Berlin, Germany (N.H., D.N.M.); Centre for Trophoblast Research, University of Cambridge, UK (H.W.Y.); Institute of Cell Biology, Histology and Embryology, Medical University of Graz, Austria (B.H.); Molecular and Clinical Sciences Research Institute, St George's University of London, UK (J.E.C., G.W.); Division of Obstetrics and Gynaecology, Oslo University Hospital, Norway (G.M.J., A.C.S.); University of Oslo, Norway (G.M.J., A.C.S.); Évolution des Régulations Endocriniennes, Muséum Nationale d'Histoire Naturelle, Paris, France (G.L.); HELIOS-Klinikum, Berlin, Germany (A.I., R.D.); Cologne Center for Genomics, University of Cologne, Germany (H.S.); and Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, UK (L.D.H.).
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Sato M. Early Origin and Evolution of the Angelman Syndrome Ubiquitin Ligase Gene Ube3a. Front Cell Neurosci 2017; 11:62. [PMID: 28326016 PMCID: PMC5339648 DOI: 10.3389/fncel.2017.00062] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/22/2017] [Indexed: 12/20/2022] Open
Abstract
The human Ube3a gene encodes an E3 ubiquitin ligase and exhibits brain-specific genomic imprinting. Genetic abnormalities that affect the maternal copy of this gene cause the neurodevelopmental disorder Angelman syndrome (AS), which is characterized by severe mental retardation, speech impairment, seizure, ataxia and some unique behavioral phenotypes. In this review article, I highlight the evolution of the Ube3a gene and its imprinting to provide evolutionary insights into AS. Recent comparative genomic studies have revealed that Ube3a is most phylogenetically similar to HECTD2 among the human HECT (homologous to the E6AP carboxyl terminus) family of E3 ubiquitin ligases, and its distant evolutionary origin can be traced to common ancestors of fungi and animals. Moreover, a gene more similar to Ube3a than HECTD2 is found in a range of eukaryotes from amoebozoans to basal metazoans, but is lost in later lineages. Unlike in mice and humans, Ube3a expression is biallelic in birds, monotremes, marsupials and insects. The imprinting domain that governs maternal expression of Ube3a was formed from non-imprinted elements following multiple chromosomal rearrangements after diversification of marsupials and placental mammals. Hence, the evolutionary origins of Ube3a date from long before the emergence of the nervous system, although its imprinted expression was acquired relatively recently. These observations suggest that exogenous expression and functional analyses of ancient Ube3a orthologs in mammalian neurons will facilitate the evolutionary understanding of AS.
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Affiliation(s)
- Masaaki Sato
- Graduate School of Science and Engineering and Brain and Body System Science Institute, Saitama UniversitySaitama, Japan
- RIKEN Brain Science InstituteWako, Japan
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Epigenetic events in male common urogenital organs cancer. JOURNAL OF CANCER RESEARCH AND PRACTICE 2016. [DOI: 10.1016/j.jcrpr.2016.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Wijenayake S, Storey KB. The role of DNA methylation during anoxia tolerance in a freshwater turtle (Trachemys scripta elegans). J Comp Physiol B 2016; 186:333-42. [PMID: 26843075 DOI: 10.1007/s00360-016-0960-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/05/2016] [Accepted: 01/15/2016] [Indexed: 11/24/2022]
Abstract
Oxygen deprivation is a lethal stress that only a few animals can tolerate for extended periods. This study focuses on analyzing the role of DNA methylation in aiding natural anoxia tolerance in a champion vertebrate anaerobe, the red-eared slider turtle (Trachemys scripta elegans). We examined the relative expression and total enzymatic activity of four DNA methyltransferases (DNMT1, DNMT2, DNMT3a and DNMT3b), two methyl-binding domain proteins (MBD1 and MBD2), and relative genomic levels of 5-methylcytosine under control, 5 h anoxic, and 20 h anoxic conditions in liver, heart, and white skeletal muscle (n = 4, p < 0.05). In liver, protein expression of DNMT1, DNMT2, MBD1, and MBD2 rose significantly by two- to fourfold after 5 h anoxic submergence compared to normoxic-control conditions. In heart, 5 h anoxia submergence resulted in a 1.4-fold increase in DNMT3a levels and a significant decrease in MBD1 and MBD2 levels to ~30 % of control values. In white muscle, DNMT3a and DNMT3b increased threefold and MBD1 levels increased by 50 % in response to 5 h anoxia. Total DNMT activity rose by 0.6-2.0-fold in liver and white muscle and likewise global 5mC levels significantly increased in liver and white muscle under 5 and 20 h anoxia. The results demonstrate an overall increase in DNA methylation, DNMT protein expression and enzymatic activity in response to 5 and 20 h anoxia in liver and white muscle indicating a potential downregulation of gene expression via this epigenetic mechanism during oxygen deprivation.
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Affiliation(s)
- Sanoji Wijenayake
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Kenneth B Storey
- Department of Biology, Department of Chemistry, Canada Research Chair in Molecular Physiology, Institute of Biochemistry, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
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Abstract
A fundamental initiative for evolutionary biologists is to understand the molecular basis underlying phenotypic diversity. A long-standing hypothesis states that species-specific traits may be explained by differences in gene regulation rather than differences at the protein level. Over the past few years, evolutionary studies have shifted from mere sequence comparisons to integrative analyses in which gene regulation is key to understanding species evolution. DNA methylation is an important epigenetic modification involved in the regulation of numerous biological processes. Nevertheless, the evolution of the human methylome and the processes driving such changes are poorly understood. Here, we review the close interplay between Cytosine-phosphate-Guanine (CpG) methylation and the underlying genome sequence, as well as its evolutionary impact. We also summarize the latest advances in the field, revisiting the main literature on human and nonhuman primates. We hope to encourage the scientific community to address the many challenges posed by the field of comparative epigenomics.
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Habibi L, Pedram M, AmirPhirozy A, Bonyadi K. Mobile DNA Elements: The Seeds of Organic Complexity on Earth. DNA Cell Biol 2015. [DOI: 10.1089/dna.2015.2938] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Laleh Habibi
- Department of Pharmaceutics, School of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Nutrition Department, School of Nutritional Science and Dietetics, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehrdad Pedram
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Akbar AmirPhirozy
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Khadijeh Bonyadi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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Prokopuk L, Western PS, Stringer JM. Transgenerational epigenetic inheritance: adaptation through the germline epigenome? Epigenomics 2015; 7:829-46. [PMID: 26367077 DOI: 10.2217/epi.15.36] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Epigenetic modifications direct the way DNA is packaged into the nucleus, making genes more or less accessible to transcriptional machinery and influencing genomic stability. Environmental factors have the potential to alter the epigenome, allowing genes that are silenced to be activated and vice versa. This ultimately influences disease susceptibility and health in an individual. Furthermore, altered chromatin states can be transmitted to subsequent generations, thus epigenetic modifications may provide evolutionary mechanisms that impact on adaptation to changed environments. However, the mechanisms involved in establishing and maintaining these epigenetic modifications during development remain unclear. This review discusses current evidence for transgenerational epigenetic inheritance, confounding issues associated with its study, and the biological relevance of altered epigenetic states for subsequent generations.
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Affiliation(s)
- Lexie Prokopuk
- Centre for Genetic Diseases, Hudson Institute of Medical Research, 27-31 Wright Street, Clayton, Victoria 3168, Australia.,Molecular & Translational Science, Monash University, Clayton, Victoria 3168, Australia
| | - Patrick S Western
- Centre for Genetic Diseases, Hudson Institute of Medical Research, 27-31 Wright Street, Clayton, Victoria 3168, Australia.,Molecular & Translational Science, Monash University, Clayton, Victoria 3168, Australia
| | - Jessica M Stringer
- Centre for Genetic Diseases, Hudson Institute of Medical Research, 27-31 Wright Street, Clayton, Victoria 3168, Australia.,Molecular & Translational Science, Monash University, Clayton, Victoria 3168, Australia
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A Mouse Model for Imprinting of the Human Retinoblastoma Gene. PLoS One 2015; 10:e0134672. [PMID: 26275142 PMCID: PMC4537222 DOI: 10.1371/journal.pone.0134672] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 07/13/2015] [Indexed: 12/21/2022] Open
Abstract
The human RB1 gene is imprinted due to integration of the PPP1R26P1 pseudogene into intron 2. PPP1R26P1 harbors the gametic differentially methylated region of the RB1 gene, CpG85, which is methylated in the female germ line. The paternally unmethylated CpG85 acts as promoter for the alternative transcript 2B of RB1, which interferes with expression of full-length RB1 in cis. In mice, PPP1R26P1 is not present in the Rb1 gene and Rb1 is not imprinted. Assuming that the mechanisms responsible for genomic imprinting are conserved, we investigated if imprinting of mouse Rb1 can be induced by transferring human PPP1R26P1 into mouse Rb1. We generated humanized Rb1_PPP1R26P1 knock-in mice that pass human PPP1R26P1 through the mouse germ line. We found that the function of unmethylated CpG85 as promoter for an alternative Rb1 transcript and as cis-repressor of the main Rb1 transcript is maintained in mouse tissues. However, CpG85 is not recognized as a gametic differentially methylated region in the mouse germ line. DNA methylation at CpG85 is acquired only in tissues of neuroectodermal origin, independent of parental transmission of PPP1R26P1. Absence of CpG85 methylation in oocytes and sperm implies a failure of imprint methylation establishment in the germ line. Our results indicate that site-specific integration of a proven human gametic differentially methylated region is not sufficient for acquisition of DNA methylation in the mouse germ line, even if promoter function of the element is maintained. This suggests a considerable dependency of DNA methylation induction on the surrounding sequence. However, our model is suited to determine the cellular function of the alternative Rb1 transcript.
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Barlow D. Denise Barlow: a career in epigenetics. RNA Biol 2015; 12:105-8. [PMID: 25779649 DOI: 10.1080/15476286.2015.1018711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Jeong CW, Park GT, Yun H, Hsieh TF, Choi YD, Choi Y, Lee JS. Control of Paternally Expressed Imprinted UPWARD CURLY LEAF1, a Gene Encoding an F-Box Protein That Regulates CURLY LEAF Polycomb Protein, in the Arabidopsis Endosperm. PLoS One 2015; 10:e0117431. [PMID: 25689861 PMCID: PMC4331533 DOI: 10.1371/journal.pone.0117431] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 12/22/2014] [Indexed: 12/22/2022] Open
Abstract
Genomic imprinting, an epigenetic process in mammals and flowering plants, refers to the differential expression of alleles of the same genes in a parent-of-origin-specific manner. In Arabidopsis, imprinting occurs primarily in the endosperm, which nourishes the developing embryo. Recent high-throughput sequencing analyses revealed that more than 200 loci are imprinted in Arabidopsis; however, only a few of these imprinted genes and their imprinting mechanisms have been examined in detail. Whereas most imprinted loci characterized to date are maternally expressed imprinted genes (MEGs), PHERES1 (PHE1) and ADMETOS (ADM) are paternally expressed imprinted genes (PEGs). Here, we report that UPWARD CURLY LEAF1 (UCL1), a gene encoding an E3 ligase that degrades the CURLY LEAF (CLF) polycomb protein, is a PEG. After fertilization, paternally inherited UCL1 is expressed in the endosperm, but not in the embryo. The expression pattern of a β-glucuronidase (GUS) reporter gene driven by the UCL1 promoter suggests that the imprinting control region (ICR) of UCL1 is adjacent to a transposable element in the UCL1 5′-upstream region. Polycomb Repressive Complex 2 (PRC2) silences the maternal UCL1 allele in the central cell prior to fertilization and in the endosperm after fertilization. The UCL1 imprinting pattern was not affected in paternal PRC2 mutants. We found unexpectedly that the maternal UCL1 allele is reactivated in the endosperm of Arabidopsis lines with mutations in cytosine DNA METHYLTRANSFERASE 1 (MET1) or the DNA glycosylase DEMETER (DME), which antagonistically regulate CpG methylation of DNA. By contrast, maternal UCL1 silencing was not altered in mutants with defects in non-CpG methylation. Thus, silencing of the maternal UCL1 allele is regulated by both MET1 and DME as well as by PRC2, suggesting that divergent mechanisms for the regulation of PEGs evolved in Arabidopsis.
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Affiliation(s)
- Cheol Woong Jeong
- School of Biological Sciences, Seoul National University, Seoul, Korea
| | - Guen Tae Park
- School of Biological Sciences, Seoul National University, Seoul, Korea
| | - Hyein Yun
- School of Biological Sciences, Seoul National University, Seoul, Korea
| | - Tzung-Fu Hsieh
- Plants for Human Health Institute & Department of Plant and Microbial Biology, North Carolina State University, Kannapolis, North Carolina, United State of America
| | - Yang Do Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Yeonhee Choi
- School of Biological Sciences, Seoul National University, Seoul, Korea
- * E-mail: (YC); (JSL)
| | - Jong Seob Lee
- School of Biological Sciences, Seoul National University, Seoul, Korea
- * E-mail: (YC); (JSL)
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Spencer HG, Clark AG. Non-conflict theories for the evolution of genomic imprinting. Heredity (Edinb) 2014; 113:112-8. [PMID: 24398886 PMCID: PMC4105448 DOI: 10.1038/hdy.2013.129] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/08/2013] [Accepted: 11/11/2013] [Indexed: 01/09/2023] Open
Abstract
Theories focused on kinship and the genetic conflict it induces are widely considered to be the primary explanations for the evolution of genomic imprinting. However, there have appeared many competing ideas that do not involve kinship/conflict. These ideas are often overlooked because kinship/conflict is entrenched in the literature, especially outside evolutionary biology. Here we provide a critical overview of these non-conflict theories, providing an accessible perspective into this literature. We suggest that some of these alternative hypotheses may, in fact, provide tenable explanations of the evolution of imprinting for at least some loci.
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Affiliation(s)
- H G Spencer
- Allan Wilson Centre for Molecular Ecology & Evolution and Gravida: National Centre for Growth & Development, Department of Zoology, University of Otago, Dunedin, New Zealand
| | - A G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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42
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Pires ND, Grossniklaus U. Different yet similar: evolution of imprinting in flowering plants and mammals. F1000PRIME REPORTS 2014; 6:63. [PMID: 25165562 PMCID: PMC4126536 DOI: 10.12703/p6-63] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Genomic imprinting refers to a form of epigenetic gene regulation whereby alleles are differentially expressed in a parent-of-origin-dependent manner. Imprinting evolved independently in flowering plants and in therian mammals in association with the elaboration of viviparity and a placental habit. Despite the striking differences in plant and animal reproduction, genomic imprinting shares multiple characteristics between them. In both groups, imprinted expression is controlled, at least in part, by DNA methylation and chromatin modifications in cis-regulatory regions, and many maternally and paternally expressed genes display complementary dosage-dependent effects during embryogenesis. This suggests that genomic imprinting evolved in response to similar selective pressures in flowering plants and mammals. Nevertheless, there are important differences between plant and animal imprinting. In particular, genomic imprinting has been shown to be more flexible and evolutionarily labile in plants. In mammals, imprinted genes are organized mainly in highly conserved clusters, whereas in plants they occur in isolation throughout the genome and are affected by local gene duplications. There is a large degree of intra- and inter-specific variation in imprinted gene expression in plants. These differences likely reflect the distinct life cycles and the different evolutionary dynamics that shape plant and animal genomes.
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Frésard L, Leroux S, Servin B, Gourichon D, Dehais P, Cristobal MS, Marsaud N, Vignoles F, Bed'hom B, Coville JL, Hormozdiari F, Beaumont C, Zerjal T, Vignal A, Morisson M, Lagarrigue S, Pitel F. Transcriptome-wide investigation of genomic imprinting in chicken. Nucleic Acids Res 2014; 42:3768-82. [PMID: 24452801 PMCID: PMC3973300 DOI: 10.1093/nar/gkt1390] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Genomic imprinting is an epigenetic mechanism by which alleles of some specific genes are expressed in a parent-of-origin manner. It has been observed in mammals and marsupials, but not in birds. Until now, only a few genes orthologous to mammalian imprinted ones have been analyzed in chicken and did not demonstrate any evidence of imprinting in this species. However, several published observations such as imprinted-like QTL in poultry or reciprocal effects keep the question open. Our main objective was thus to screen the entire chicken genome for parental-allele-specific differential expression on whole embryonic transcriptomes, using high-throughput sequencing. To identify the parental origin of each observed haplotype, two chicken experimental populations were used, as inbred and as genetically distant as possible. Two families were produced from two reciprocal crosses. Transcripts from 20 embryos were sequenced using NGS technology, producing ∼200 Gb of sequences. This allowed the detection of 79 potentially imprinted SNPs, through an analysis method that we validated by detecting imprinting from mouse data already published. However, out of 23 candidates tested by pyrosequencing, none could be confirmed. These results come together, without a priori, with previous statements and phylogenetic considerations assessing the absence of genomic imprinting in chicken.
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Affiliation(s)
- Laure Frésard
- INRA, UMR444 Laboratoire de Génétique Cellulaire, Castanet-Tolosan F-31326, France, ENVT, UMR444 Laboratoire de Génétique Cellulaire, Toulouse F-31076, France, INRA, PEAT Pôle d'Expérimentation Avicole de Tours, Nouzilly F- 37380, France, INRA, Sigenae UR875 Biométrie et Intelligence Artificielle, Castanet-Tolosan F-31326, France, INRA, GeT-PlaGe Genotoul, Castanet-Tolosan F-31326, France, INRA, UMR1313 Génétique animale et biologie intégrative, Jouy en Josas F-78350, France, AgroParisTech, UMR1313 Génétique animale et biologie intégrative, Jouy en Josas F-78350, France, Department of Computer Sciences, University of California, Los Angeles, CA 90095, USA, INRA, UR83 Recherche Avicoles, Nouzilly F- 37380, France and Agrocampus Ouest, UMR1348 Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Élevage, Animal Genetics Laboratory, Rennes F-35000, France
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Skaar DA, Li Y, Bernal AJ, Hoyo C, Murphy SK, Jirtle RL. The human imprintome: regulatory mechanisms, methods of ascertainment, and roles in disease susceptibility. ILAR J 2014; 53:341-58. [PMID: 23744971 DOI: 10.1093/ilar.53.3-4.341] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Imprinted genes form a special subset of the genome, exhibiting monoallelic expression in a parent-of-origin-dependent fashion. This monoallelic expression is controlled by parental-specific epigenetic marks, which are established in gametogenesis and early embryonic development and are persistent in all somatic cells throughout life. We define this specific set of cis-acting epigenetic regulatory elements as the imprintome, a distinct and specially tasked subset of the epigenome. Imprintome elements contain DNA methylation and histone modifications that regulate monoallelic expression by affecting promoter accessibility, chromatin structure, and chromatin configuration. Understanding their regulation is critical because a significant proportion of human imprinted genes are implicated in complex diseases. Significant species variation in the repertoire of imprinted genes and their epigenetic regulation, however, will not allow model organisms solely to be used for this crucial purpose. Ultimately, only the human will suffice to accurately define the human imprintome.
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Affiliation(s)
- David A Skaar
- Department of Oncology, Duke University Medical Center, Durham, North Carolina, USA
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Kanber D, Buiting K, Roos C, Gromoll J, Kaya S, Horsthemke B, Lohmann D. The origin of the RB1 imprint. PLoS One 2013; 8:e81502. [PMID: 24282601 PMCID: PMC3839921 DOI: 10.1371/journal.pone.0081502] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 10/23/2013] [Indexed: 11/19/2022] Open
Abstract
The human RB1 gene is imprinted due to a differentially methylated CpG island in intron 2. This CpG island is part of PPP1R26P1, a truncated retrocopy of PPP1R26, and serves as a promoter for an alternative RB1 transcript. We show here by in silico analyses that the parental PPP1R26 gene is present in the analysed members of Haplorrhini, which comprise Catarrhini (Old World Monkeys, Small apes, Great Apes and Human), Platyrrhini (New World Monkeys) and tarsier, and Strepsirrhini (galago). Interestingly, we detected the retrocopy, PPP1R26P1, in all Anthropoidea (Catarrhini and Platyrrhini) that we studied but not in tarsier or galago. Additional retrocopies are present in human and chimpanzee on chromosome 22, but their distinct composition indicates that they are the result of independent retrotransposition events. Chimpanzee and marmoset have further retrocopies on chromosome 8 and chromosome 4, respectively. To examine the origin of the RB1 imprint, we compared the methylation patterns of the parental PPP1R26 gene and its retrocopies in different primates (human, chimpanzee, orangutan, rhesus macaque, marmoset and galago). Methylation analysis by deep bisulfite sequencing showed that PPP1R26 is methylated whereas the retrocopy in RB1 intron 2 is differentially methylated in all primates studied. All other retrocopies are fully methylated, except for the additional retrocopy on marmoset chromosome 4, which is also differentially methylated. Using an informative SNP for the methylation analysis in marmoset, we could show that the differential methylation pattern of the retrocopy on chromosome 4 is allele-specific. We conclude that the epigenetic fate of a PPP1R26 retrocopy after integration depends on the DNA sequence and selective forces at the integration site.
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Affiliation(s)
- Deniz Kanber
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
- * E-mail:
| | - Karin Buiting
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
| | - Christian Roos
- Gene Bank of Primates und Abteilung Primatengenetik, Deutsches Primatenzentrum, Leibniz-Institut für Primatenforschung, Göttingen, Germany
| | - Jörg Gromoll
- Centrum für Reproduktionsmedizin und Andrologie, Universitätsklinikum Münster, Münster, Germany
| | - Sabine Kaya
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
| | | | - Dietmar Lohmann
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
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Holman L, Kokko H. The evolution of genomic imprinting: costs, benefits and long-term consequences. Biol Rev Camb Philos Soc 2013; 89:568-87. [DOI: 10.1111/brv.12069] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 09/15/2013] [Accepted: 09/26/2013] [Indexed: 12/23/2022]
Affiliation(s)
- Luke Holman
- Centre of Excellence in Biological Interactions, Division of Ecology, Evolution & Genetics; Research School of Biology, Australian National University; Daley Road, Canberra Australian Capital Territory 0200 Australia
| | - Hanna Kokko
- Centre of Excellence in Biological Interactions, Division of Ecology, Evolution & Genetics; Research School of Biology, Australian National University; Daley Road, Canberra Australian Capital Territory 0200 Australia
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Yoshida T, Kawabe A. Importance of gene duplication in the evolution of genomic imprinting revealed by molecular evolutionary analysis of the type I MADS-box gene family in Arabidopsis species. PLoS One 2013; 8:e73588. [PMID: 24039992 PMCID: PMC3764040 DOI: 10.1371/journal.pone.0073588] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 07/25/2013] [Indexed: 01/11/2023] Open
Abstract
The pattern of molecular evolution of imprinted genes is controversial and the entire picture is still to be unveiled. Recently, a relationship between the formation of imprinted genes and gene duplication was reported in genome-wide survey of imprinted genes in Arabidopsis thaliana. Because gene duplications influence the molecular evolution of the duplicated gene family, it is necessary to investigate both the pattern of molecular evolution and the possible relationship between gene duplication and genomic imprinting for a better understanding of evolutionary aspects of imprinted genes. In this study, we investigated the evolutionary changes of type I MADS-box genes that include imprinted genes by using relative species of Arabidopsis thaliana (two subspecies of A. lyrata and three subspecies of A. halleri). A duplicated gene family enables us to compare DNA sequences between imprinted genes and its homologs. We found an increased number of gene duplications within species in clades containing the imprinted genes, further supporting the hypothesis that local gene duplication is one of the driving forces for the formation of imprinted genes. Moreover, data obtained by phylogenetic analysis suggested “rapid evolution” of not only imprinted genes but also its closely related orthologous genes, which implies the effect of gene duplication on molecular evolution of imprinted genes.
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Affiliation(s)
- Takanori Yoshida
- Faculty of Life Science, Kyoto Sangyo University, Kyoto, Kyoto, Japan
| | - Akira Kawabe
- Faculty of Life Science, Kyoto Sangyo University, Kyoto, Kyoto, Japan
- * E-mail:
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Abstract
Imprinted gene expression--the biased expression of alleles dependent on their parent of origin--is an important type of epigenetic gene regulation in flowering plants and mammals. In plants, genes are imprinted primarily in the endosperm, the triploid placenta-like tissue that surrounds and nourishes the embryo during its development. Differential allelic expression is correlated with active DNA demethylation by DNA glycosylases and repressive targeting by the Polycomb group proteins. Imprinted gene expression is one consequence of a large-scale remodeling to the epigenome, primarily directed at transposable elements, that occurs in gametes and seeds. This remodeling could be important for maintaining the epigenome in the embryo as well as for establishing gene imprinting.
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Affiliation(s)
- Mary Gehring
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142;
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Shao J, Huang CH, Kalyanaraman B, Zhu BZ. Potent methyl oxidation of 5-methyl-2'-deoxycytidine by halogenated quinoid carcinogens and hydrogen peroxide via a metal-independent mechanism. Free Radic Biol Med 2013; 60:177-82. [PMID: 23376470 PMCID: PMC4476646 DOI: 10.1016/j.freeradbiomed.2013.01.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 12/28/2012] [Accepted: 01/17/2013] [Indexed: 10/27/2022]
Abstract
Halogenated quinones are a class of carcinogenic intermediates and are newly identified chlorination disinfection by-products in drinking water. We found recently that the highly reactive and biologically important hydroxyl radical ((•)OH) can be produced by halogenated quinones and H2O2 independent of transition metal ions. However, it is not clear whether these quinoid carcinogens and H2O2 can oxidize the nucleoside 5-methyl-2'-deoxycytidine (5mdC) to its methyl oxidation products and, if so, what the underlying molecular mechanism is. Here we show that three methyl oxidation products, 5-(hydroperoxymethyl)-, 5-(hydroxymethyl)-, and 5-formyl-2'-deoxycytidine, could be produced when 5mdC was treated with tetrachloro-1,4-benzoquinone (TCBQ) and H2O2. The formation of the oxidation products was markedly inhibited by typical (•)OH scavengers and under anaerobic conditions. Analogous effects were observed with other halogenated quinones and the classic Fenton system. Based on these data, we propose that the oxidation of 5mdC by TCBQ/H2O2 might be through the following mechanism: (•)OH produced by TCBQ/H2O2 may first abstract hydrogen from the methyl group of 5mdC, leading to the formation of 5-(2'-deoxycytidylyl)methyl radical, which may combine with O2 to form the peroxyl radical. The unstable peroxyl radical transforms into the corresponding hydroperoxide 5-(hydroperoxymethyl)-2'-deoxycytidine, which reacts with TCBQ and results in the formation of 5-(hydroxymethyl)-2'-deoxycytidine and 5-formyl-2'-deoxycytidine. This is the first report that halogenated quinoid carcinogens and H2O2 can induce potent methyl oxidation of 5mdC via a metal-independent mechanism, which may partly explain their potential carcinogenicity.
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Affiliation(s)
- Jie Shao
- State Key Laboratory of Environmental Chemistry and
Ecotoxicology, Research Center for Eco-Environmental Sciences, The Chinese Academy
of Sciences, Beijing 100085, China
| | - Chun-Hua Huang
- State Key Laboratory of Environmental Chemistry and
Ecotoxicology, Research Center for Eco-Environmental Sciences, The Chinese Academy
of Sciences, Beijing 100085, China
| | | | - Ben-Zhan Zhu
- Linus Pauling Institute, Oregon State University, Corvallis,
OR 97331, USA
- Department of Biophysics, Medical College of Wisconsin,
Milwaukee, WI 53226
- Addresses for Correspondence:
Ben-Zhan Zhu, Ph.D., Professor of Chemistry and Toxicology, State Key Laboratory
of Environmental Chemistry and Ecotoxicology, Research Center for
Eco-Environmental Sciences, The Chinese Academy of Sciences, P.O. Box 2871,
Beijing 100085, China, Phone: 86-10-62849030, Fax: 86-10-62923563,
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