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Chen Y, Ye Z, Lin M, Zhu L, Xu L, Wang X. Deciphering the Epigenetic Landscape: Placental Development and Its Role in Pregnancy Outcomes. Stem Cell Rev Rep 2024; 20:996-1014. [PMID: 38457061 DOI: 10.1007/s12015-024-10699-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 03/09/2024]
Abstract
The placenta stands out as a unique, transitory, and multifaceted organ, essential to the optimal growth and maturation of the fetus. Functioning as a vital nexus between the maternal and fetal circulatory systems, it oversees the critical exchange of nutrients and waste. This exchange is facilitated by placental cells, known as trophoblasts, which adeptly invade and remodel uterine blood vessels. Deviations in placental development underpin a slew of pregnancy complications, notably fetal growth restriction (FGR), preeclampsia (PE), recurrent spontaneous abortions (RSA), and preterm birth. Central to placental function and development is epigenetic regulation. Despite its importance, the intricate mechanisms by which epigenetics influence the placenta are not entirely elucidated. Recently, the scientific community has turned its focus to parsing out the epigenetic alterations during placental development, such as variations in promoter DNA methylation, genomic imprints, and shifts in non-coding RNA expression. By establishing correlations between epigenetic shifts in the placenta and pregnancy complications, researchers are unearthing invaluable insights into the biology and pathophysiology of these conditions. This review seeks to synthesize the latest findings on placental epigenetic regulation, spotlighting its crucial role in shaping fetal growth trajectories and development. Through this lens, we underscore the overarching significance of the placenta in the larger narrative of gestational health.
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Affiliation(s)
- Yujia Chen
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- National Health Commission (NHC), Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Zhoujie Ye
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- National Health Commission (NHC), Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Meijia Lin
- Department of Pathology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Liping Zhu
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- National Health Commission (NHC), Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China.
| | - Xinrui Wang
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China.
- National Health Commission (NHC), Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, China.
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Lopez-Tello J, Yong HEJ, Sandovici I, Dowsett GKC, Christoforou ER, Salazar-Petres E, Boyland R, Napso T, Yeo GSH, Lam BYH, Constancia M, Sferruzzi-Perri AN. Fetal manipulation of maternal metabolism is a critical function of the imprinted Igf2 gene. Cell Metab 2023; 35:1195-1208.e6. [PMID: 37437545 DOI: 10.1016/j.cmet.2023.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 04/12/2023] [Accepted: 06/09/2023] [Indexed: 07/14/2023]
Abstract
Maternal-offspring interactions in mammals involve both cooperation and conflict. The fetus has evolved ways to manipulate maternal physiology to enhance placental nutrient transfer, but the mechanisms involved remain unclear. The imprinted Igf2 gene is highly expressed in murine placental endocrine cells. Here, we show that Igf2 deletion in these cells impairs placental endocrine signaling to the mother, without affecting placental morphology. Igf2 controls placental hormone production, including prolactins, and is crucial to establish pregnancy-related insulin resistance and to partition nutrients to the fetus. Consequently, fetuses lacking placental endocrine Igf2 are growth restricted and hypoglycemic. Mechanistically, Igf2 controls protein synthesis and cellular energy homeostasis, actions dependent on the placental endocrine cell type. Igf2 loss also has additional long-lasting effects on offspring metabolism in adulthood. Our study provides compelling evidence for an intrinsic fetal manipulation system operating in placenta that modifies maternal metabolism and fetal resource allocation, with long-term consequences for offspring metabolic health.
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Affiliation(s)
- Jorge Lopez-Tello
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK.
| | - Hannah E J Yong
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A(∗)STAR), 30 Medical Drive, Singapore 117609, Singapore
| | - Ionel Sandovici
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge CB2 0SW, UK; Medical Research Council (MRC) Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science and, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Georgina K C Dowsett
- Medical Research Council (MRC) Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science and, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Efthimia R Christoforou
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Esteban Salazar-Petres
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Rebecca Boyland
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; Royal Devon and Exeter Hospital NHS Trust, Barrack Rd, Exeter EX2 5DW, UK
| | - Tina Napso
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Giles S H Yeo
- Medical Research Council (MRC) Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science and, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Brian Y H Lam
- Medical Research Council (MRC) Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science and, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Miguel Constancia
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge CB2 0SW, UK; Medical Research Council (MRC) Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science and, University of Cambridge, Cambridge CB2 0QQ, UK.
| | - Amanda N Sferruzzi-Perri
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK.
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Yuen S, Ezard THG, Sobey AJ. Epigenetic opportunities for evolutionary computation. ROYAL SOCIETY OPEN SCIENCE 2023; 10:221256. [PMID: 37181799 PMCID: PMC10170609 DOI: 10.1098/rsos.221256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/20/2023] [Indexed: 05/16/2023]
Abstract
Evolutionary computation is a group of biologically inspired algorithms used to solve complex optimization problems. It can be split into evolutionary algorithms, which take inspiration from genetic inheritance, and swarm intelligence algorithms, that take inspiration from cultural inheritance. However, much of the modern evolutionary literature remains relatively unexplored. To understand which evolutionary mechanisms have been considered, and which have been overlooked, this paper breaks down successful bioinspired algorithms under a contemporary biological framework based on the extended evolutionary synthesis, an extension of the classical, genetics focused, modern synthesis. Although the idea of the extended evolutionary synthesis has not been fully accepted in evolutionary theory, it presents many interesting concepts that could provide benefits to evolutionary computation. The analysis shows that Darwinism and the modern synthesis have been incorporated into evolutionary computation but the extended evolutionary synthesis has been broadly ignored beyond: cultural inheritance, incorporated in the sub-set of swarm intelligence algorithms, evolvability, through covariance matrix adaptation evolution strategy (CMA-ES), and multilevel selection, through multilevel selection genetic algorithm (MLSGA). The framework shows a gap in epigenetic inheritance for evolutionary computation, despite being a key building block in modern interpretations of evolution. This leaves a diverse range of biologically inspired mechanisms as low hanging fruit that should be explored further within evolutionary computation and illustrates the potential of epigenetic based approaches through the recent benchmarks in the literature.
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Affiliation(s)
- Sizhe Yuen
- Maritime Engineering, University of Southampton, Southampton SO17 1BJ, UK
| | - Thomas H. G. Ezard
- Ocean and Earth Science, National Oceanography Centre Southampton, European Way, University of Southampton, Southampton SO14 3ZH, UK
| | - Adam J. Sobey
- Maritime Engineering, University of Southampton, Southampton SO17 1BJ, UK
- Marine and Maritime Group, Data-centric Engineering, The Alan Turing Institute, The British Library, London NW1 2DB, UK
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4
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Saini A, Varshney A, Saini A, Mani I. Insight into epigenetics and human diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:1-21. [PMID: 37019588 DOI: 10.1016/bs.pmbts.2023.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
The most eminent research of the 21st century whirls around the epigenetic and the variability of DNA sequences in humans. The reciprocity between the epigenetic changes and the exogenous factors drives an influence on the inheritance biology and gene expression both inter-generationally and trans-generationally. Chromatin level modifications like DNA methylation, histone modifications or changes in transcripts functions either at transcription level or translational level pave the way for certain diseases or cancer in humans. The ability of epigenetics to explain the processes of various diseases has been demonstrated by recent epigenetic studies. Multidisciplinary therapeutic strategies were developed in order to analyse how epigenetic elements interact with different disease pathways. In this chapter we summarize how an organism may be predisposed to certain diseases by exposure to environmental variables such as chemicals, medications, stress, or infections during particular, vulnerable phases of life, and the epigenetic component may influence some of the diseases in humans.
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Salmeri N, Carbone IF, Cavoretto PI, Farina A, Morano D. Epigenetics Beyond Fetal Growth Restriction: A Comprehensive Overview. Mol Diagn Ther 2022; 26:607-626. [PMID: 36028645 DOI: 10.1007/s40291-022-00611-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2022] [Indexed: 12/30/2022]
Abstract
Fetal growth restriction is a pathological condition occurring when the fetus does not reach the genetically determined growth potential. The etiology of fetal growth restriction is expected to be multifactorial and include fetal, maternal, and placental factors, the latter being the most frequent cause of isolated fetal growth restriction. Severe fetal growth restriction has been related to both an increased risk of perinatal morbidity and mortality, and also a greater susceptibility to developing diseases (especially cardio-metabolic and neurological disorders) later in life. In the last decade, emerging evidence has supported the hypothesis of the Developmental Origin of Health and Disease, which states that individual developmental 'programming' takes place via a delicate fine tuning of fetal genetic and epigenetic marks in response to a large variety of 'stressor' exposures during pregnancy. As the placenta is the maternal-fetal interface, it has a crucial role in fetal programming, such that any perturbation altering placental function interferes with both in-utero fetal growth and also with the adult life phenotype. Several epigenetic mechanisms have been highlighted in modulating the dynamic placental epigenome, including alterations in DNA methylation status, post-translational modification of histones, and non-coding RNAs. This review aims to provide a comprehensive and critical overview of the available literature on the epigenetic background of fetal growth restriction. A targeted research strategy was performed using PubMed, MEDLINE, Embase, and The Cochrane Library up to January 2022. A detailed and fully referenced synthesis of available literature following the Scale for the Assessment of Narrative Review Articles guidelines is provided. A variety of epigenetic marks predominantly interfering with placental development, function, and metabolism were found to be potentially associated with fetal growth restriction. Available evidence on the role of environmental exposures in shaping the placental epigenome and the fetal phenotype were also critically discussed. Because of the highly dynamic crosstalk between epigenetic mechanisms and the extra level of complexity in interpreting the final placental transcriptome, a full comprehension of these phenomenon is still lacking and advances in multi-omics approaches are urgently needed. Elucidating the role of epigenetics in the developmental origins of health and disease represents a new challenge for the coming years, with the goal of providing early interventions and prevention strategies and, hopefully, new treatment opportunities.
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Affiliation(s)
- Noemi Salmeri
- Gynecology/Obstetrics Unit, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Ilma Floriana Carbone
- Unit of Obstetrics, Department of Woman, Child and Neonate, Mangiagalli Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Paolo Ivo Cavoretto
- Gynecology/Obstetrics Unit, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Antonio Farina
- Division of Obstetrics and Prenatal Medicine, Department of Medicine and Surgery (DIMEC), IRCCS Sant'Orsola-Malpighi Hospital, University of Bologna, 40138, Bologna, Italy.
| | - Danila Morano
- Department of Morphology, Surgery and Experimental Medicine, Section of Obstetrics and Gynecology, Azienda Ospedaliero-Universitaria S. Anna, University of Ferrara, Cona, Ferrara, Italy
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6
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Blood-derived lncRNAs as biomarkers for cancer diagnosis: the Good, the Bad and the Beauty. NPJ Precis Oncol 2022; 6:40. [PMID: 35729321 PMCID: PMC9213432 DOI: 10.1038/s41698-022-00283-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 05/13/2022] [Indexed: 11/24/2022] Open
Abstract
Cancer ranks as one of the deadliest diseases worldwide. The high mortality rate associated with cancer is partially due to the lack of reliable early detection methods and/or inaccurate diagnostic tools such as certain protein biomarkers. Cell-free nucleic acids (cfNA) such as circulating long noncoding RNAs (lncRNAs) have been proposed as a new class of potential biomarkers for cancer diagnosis. The reported correlation between the presence of tumors and abnormal levels of lncRNAs in the blood of cancer patients has notably triggered a worldwide interest among clinicians and oncologists who have been actively investigating their potentials as reliable cancer biomarkers. In this report, we review the progress achieved (“the Good”) and challenges encountered (“the Bad”) in the development of circulating lncRNAs as potential biomarkers for early cancer diagnosis. We report and discuss the diagnostic performance of more than 50 different circulating lncRNAs and emphasize their numerous potential clinical applications (“the Beauty”) including therapeutic targets and agents, on top of diagnostic and prognostic capabilities. This review also summarizes the best methods of investigation and provides useful guidelines for clinicians and scientists who desire conducting their own clinical studies on circulating lncRNAs in cancer patients via RT-qPCR or Next Generation Sequencing (NGS).
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Heskett MB, Spellman PT, Thayer MJ. Differential Allelic Expression among Long Non-Coding RNAs. Noncoding RNA 2021; 7:ncrna7040066. [PMID: 34698262 PMCID: PMC8544735 DOI: 10.3390/ncrna7040066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/11/2021] [Accepted: 10/20/2021] [Indexed: 12/23/2022] Open
Abstract
Long non-coding RNAs (lncRNA) comprise a diverse group of non-protein-coding RNAs >200 bp in length that are involved in various normal cellular processes and disease states, and can affect coding gene expression through mechanisms in cis or in trans. Since the discovery of the first functional lncRNAs transcribed by RNA Polymerase II, H19 and Xist, many others have been identified and noted for their unusual transcriptional pattern, whereby expression from one chromosome homolog is strongly favored over the other, also known as mono-allelic or differential allelic expression. lncRNAs with differential allelic expression have been observed to play critical roles in developmental gene regulation, chromosome structure, and disease. Here, we will focus on known examples of differential allelic expression of lncRNAs and highlight recent research describing functional lncRNAs expressed from both imprinted and random mono-allelic expression domains.
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Affiliation(s)
- Michael B. Heskett
- Department of Genetics, Oregon Health & Science University, Portland, OR 97239, USA; (M.B.H.); (P.T.S.)
| | - Paul T. Spellman
- Department of Genetics, Oregon Health & Science University, Portland, OR 97239, USA; (M.B.H.); (P.T.S.)
| | - Mathew J. Thayer
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
- Correspondence:
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DNA methylation and histone variants in aging and cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:1-110. [PMID: 34507780 DOI: 10.1016/bs.ircmb.2021.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aging-related diseases such as cancer can be traced to the accumulation of molecular disorder including increased DNA mutations and epigenetic drift. We provide a comprehensive review of recent results in mice and humans on modifications of DNA methylation and histone variants during aging and in cancer. Accumulated errors in DNA methylation maintenance lead to global decreases in DNA methylation with relaxed repression of repeated DNA and focal hypermethylation blocking the expression of tumor suppressor genes. Epigenetic clocks based on quantifying levels of DNA methylation at specific genomic sites is proving to be a valuable metric for estimating the biological age of individuals. Histone variants have specialized functions in transcriptional regulation and genome stability. Their concentration tends to increase in aged post-mitotic chromatin, but their effects in cancer are mainly determined by their specialized functions. Our increased understanding of epigenetic regulation and their modifications during aging has motivated interventions to delay or reverse epigenetic modifications using the epigenetic clocks as a rapid readout for efficacity. Similarly, the knowledge of epigenetic modifications in cancer is suggesting new approaches to target these modifications for cancer therapy.
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Lee S, Kim YN, Im D, Cho SH, Kim J, Kim JH, Kim K. DNA Methylation and gene expression patterns are widely altered in fetal growth restriction and associated with FGR development. Anim Cells Syst (Seoul) 2021; 25:128-135. [PMID: 34262655 PMCID: PMC8253195 DOI: 10.1080/19768354.2021.1925741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Fetal growth restriction (FGR) is the failure of the fetus toachieve its genetically determined growth potential, which increasesrisks for a variety of genetic diseases, such as type 2 diabetes mellitus, coronary artery disease, and stroke, during the lifetime. The dysregulation of DNA methylationis known to interact with environmental fluctuations, affect gene expressions comprehensively, and be fatal to fetus development in specific cases. Therefore, we set out to find out epigenetic and transcriptomic alterations associated with FGR development. We found a set of differentially expressed genes associated with differentially methylated regions in placentae and cord blood samples. Using dimensional reduction analysis, the expression and methylation variables of the epigenetically altered genes classified the FGR samples from the controls. These genes were also enriched in the biological pathways such as metabolism and developmental processes related to FGR. Furthermore, three genes of INS, MEG3, and ZFP36L2 are implicated in epigenetic imprinting, which has been associated with FGR. These results strongly suggest that DNA methylation is highly dysregulated during FGR development, and abnormal DNA methylation patterns are likely to alter gene expression.
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Affiliation(s)
- Seoyeong Lee
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Young Nam Kim
- Department of Obstetrics and Gynecology, Busan Paik Hospital, Inje University, Busan, Republic of Korea
| | - DoHwa Im
- Department of Obstetrics and Gynecology, Busan Paik Hospital, Inje University, Busan, Republic of Korea
| | - Su Han Cho
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Jiyeon Kim
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Jeong-Hyun Kim
- Department of Medicine, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Kwoneel Kim
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea.,Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
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Villanueva-Hayes C, Millership SJ. Imprinted Genes Impact Upon Beta Cell Function in the Current (and Potentially Next) Generation. Front Endocrinol (Lausanne) 2021; 12:660532. [PMID: 33986727 PMCID: PMC8112240 DOI: 10.3389/fendo.2021.660532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/01/2021] [Indexed: 11/23/2022] Open
Abstract
Beta cell failure lies at the centre of the aetiology and pathogenesis of type 2 diabetes and the epigenetic control of the expression of critical beta cell genes appears to play a major role in this decline. One such group of epigenetically-controlled genes, termed 'imprinted' genes, are characterised by transgenerational monoallelic expression due to differential allelic DNA methylation and play key functional roles within beta cells. Here, we review the evidence for this functional importance of imprinted genes in beta cells as well as their nutritional regulation by the diet and their altered methylation and/or expression in rodent models of diabetes and in type 2 diabetic islets. We also discuss imprinted genes in the context of the next generation, where dietary overnutrition in the parents can lead to their deregulation in the offspring, alongside beta cell dysfunction and defective glucose handling. Both the modulation of imprinted gene expression and the likelihood of developing type 2 diabetes in adulthood are susceptible to the impact of nutritional status in early life. Imprinted loci, therefore, represent an excellent opportunity with which to assess epigenomic changes in beta cells due to the diet in both the current and next generation.
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Niaz K, Shah SZA, Khan F, Bule M. Ochratoxin A-induced genotoxic and epigenetic mechanisms lead to Alzheimer disease: its modulation with strategies. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:44673-44700. [PMID: 32424756 DOI: 10.1007/s11356-020-08991-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/22/2020] [Indexed: 06/11/2023]
Abstract
Ochratoxin A (OTA) is a naturally occurring mycotoxin mostly found in food items including grains and coffee beans. It induces DNA single-strand breaks and has been considered to be carcinogenic. It is recognized as a serious threat to reproductive health both in males and females. OTA is highly nephrotoxic and carcinogenic, and its potency changes evidently between species and sexes. There is a close association between OTA, mutagenicity, carcinogenicity, and genotoxicity, but the underlying mechanisms are not clear. Reports regarding genotoxic effects in relation to OTA which leads to the induction of DNA adduct formation, protein synthesis inhibition, perturbation of cellular energy production, initiation of oxidative stress, induction of apoptosis, influences on mitosis, induction of cell cycle arrest, and interference with cytokine pathways. All these mechanisms are associated with nephrotoxicity, hepatotoxicity, teratotoxicity, immunological toxicity, and neurotoxicity. OTA administration activates various mechanisms such as p38 MAPK, JNKs, and ERKs dysfunctions, BDNF disruption, TH overexpression, caspase-3 and 9 activation, and ERK-1/2 phosphorylation which ultimately lead to Alzheimer disease (AD) progression. The current review will focus on OTA in terms of recent discoveries in the field of molecular biology. The main aim is to investigate the underlying mechanisms of OTA in regard to genotoxicity and epigenetic modulations that lead to AD. Also, we will highlight the strategies for the purpose of attenuating the hazards posed by OTA exposure.
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Affiliation(s)
- Kamal Niaz
- Department of Pharmacology and Toxicology, Faculty of Bio-Sciences, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, 63100, Pakistan.
| | - Syed Zahid Ali Shah
- Department of Pathology, Faculty of Veterinary Science, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, 63100, Pakistan
| | - Fazlullah Khan
- The Institute of Pharmaceutical Sciences (TIPS), School of Pharmacy, International Campus, Tehran University of Medical Sciences (IC-TUMS), Tehran, 1417614411, Iran
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Science, Tehran, 1417614411, Iran
| | - Mohammed Bule
- Department of Pharmacy, College of Medicine and Health Sciences, Ambo University, Ambo, Oromia, Ethiopia
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12
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Orjuela S, Machlab D, Menigatti M, Marra G, Robinson MD. DAMEfinder: a method to detect differential allele-specific methylation. Epigenetics Chromatin 2020; 13:25. [PMID: 32487212 PMCID: PMC7268773 DOI: 10.1186/s13072-020-00346-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 05/21/2020] [Indexed: 12/15/2022] Open
Abstract
Background DNA methylation is a highly studied epigenetic signature that is associated with regulation of gene expression, whereby genes with high levels of promoter methylation are generally repressed. Genomic imprinting occurs when one of the parental alleles is methylated, i.e., when there is inherited allele-specific methylation (ASM). A special case of imprinting occurs during X chromosome inactivation in females, where one of the two X chromosomes is silenced, to achieve dosage compensation between the sexes. Another more widespread form of ASM is sequence dependent (SD-ASM), where ASM is linked to a nearby heterozygous single nucleotide polymorphism (SNP). Results We developed a method to screen for genomic regions that exhibit loss or gain of ASM in samples from two conditions (treatments, diseases, etc.). The method relies on the availability of bisulfite sequencing data from multiple samples of the two conditions. We leverage other established computational methods to screen for these regions within a new R package called DAMEfinder. It calculates an ASM score for all CpG sites or pairs in the genome of each sample, and then quantifies the change in ASM between conditions. It then clusters nearby CpG sites with consistent change into regions. In the absence of SNP information, our method relies only on reads to quantify ASM. This novel ASM score compares favorably to current methods that also screen for ASM. Not only does it easily discern between imprinted and non-imprinted regions, but also females from males based on X chromosome inactivation. We also applied DAMEfinder to a colorectal cancer dataset and observed that colorectal cancer subtypes are distinguishable according to their ASM signature. We also re-discover known cases of loss of imprinting. Conclusion We have designed DAMEfinder to detect regions of differential ASM (DAMEs), which is a more refined definition of differential methylation, and can therefore help in breaking down the complexity of DNA methylation and its influence in development and disease.
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Affiliation(s)
- Stephany Orjuela
- Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Dania Machlab
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Mirco Menigatti
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Giancarlo Marra
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Mark D Robinson
- Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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13
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Kuang Q, Wang Y, Li S. Detailed observation on expression dynamics of Polycomb group genes during rice early endosperm development in subspecies hybridization reveals their characteristics of parent-of-origin genes. RICE (NEW YORK, N.Y.) 2019; 12:64. [PMID: 31410597 PMCID: PMC6692421 DOI: 10.1186/s12284-019-0306-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/27/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND Parent-of-origin gene expression and its role in seed development have drown a great attention in recent years. Genome-wide analysis has identified hundreds of candidate imprinted genes, a major type of parent-of-origin genes, in rice hybrid endosperms at the stage of 5 days after pollination (dap). However, the expression of these genes in early endosperm have been never confirmed due to technique limitations and the behavior of the imprinted genes in different rice hybridizations are still largely unknown. RESULTS Here, based on our elaborate technique established previously, the expression patterns of PcG genes in the early stages of endosperm development (within 3 dap), were comprehensively analyzed. We revealed that the free nucleus stage of endosperm development is critical for parent-of-origin gene analysis. The expression of the imprinted genes are highly dynamic, likely corresponding to the critical developmental events during this period. Hybridizations between Oryza sativa japonica and indica showed that the expression patterns of the same imprinted gene could be varied by crossing with different parental cultivars, indicative of their parent-dependent character. There are strong alleles that often showed predominant expression over other alleles regardless of the parental origin, which provides a possible explanation for the cultivar-dependent predominant phenotype in crop hybridizations. In addition, we found that the transcripts of the same gene behave differently, with imprinting or non-imprinting patterns, suggesting the existence of not only imprinted and non-imprinted genes but also imprinted or non-imprinted transcripts, which reveals new aspects of the genomic imprinting. CONCLUSIONS These findings on the characters of parent-of-origin genes shed light on the understanding the real role of gene imprinting in endosperm development.
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Affiliation(s)
- Quan Kuang
- Department of Biology, Institute of Biotechnology, Nanchang Normal College, Nanchang, 330032, China
| | - Yinghua Wang
- College of Software, East China Jiao Tong University, Nanchang, 330013, China
| | - Shisheng Li
- Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Key Laboratories of Economic Forest Germplasm Improvement and Comprehensive Resources Utilization of Hubei province, College of Biology and Agricultural Resource, Huanggang Normal University, Huanggang, 438000, China.
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14
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Karami K, Zerehdaran S, Javadmanesh A, Shariati MM. Assessment of maternal and parent of origin effects in genetic variation of economic traits in Iranian native fowl. Br Poult Sci 2019; 60:486-492. [PMID: 31132866 DOI: 10.1080/00071668.2019.1621987] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
1. The objective of the study was to investigate the influence of maternal and parent of origin effects (POE) on genetic variation of Iranian native fowl on economic traits. 2. Studied traits were body weights at birth (BW0), at eight (BW8) and 12 weeks of age (BW12), age (ASM) and weight at sexual maturity (WSM), egg number (EN) and average egg weight (AEW). 3. Several models, including additive, maternal additive genetics, permanent environmental effects and POE were compared using Wombat software. Bayesian Information Criterion (BIC) was used to identify the best model for each trait. The chance of reranking of birds between models was investigated using Spearman correlation and Wilcoxon rank test. 4. Based on the best model, direct heritability estimates for BW0, BW8, BW12, ASM, WSM, EN and AEW traits were 0.05, 0.21, 0.23, 0.30, 0.39, 0.22 and 0.38, respectively. Proportion of variance due to paternal POE for BW8 was 4% and proportion of variance due to maternal POE for BW12 was 5%. 5. Estimated maternal heritability for BW0 was 0.30 and for BW8 and BW12 were 0.00 and 0.01, respectively, which shows that maternal heritability was reduced by age. 6. Based on the results, considering POE for BW8 and BW12 and maternal genetic effects for BW0 improved the accuracy of estimations and avoid reranking of birds for these traits.
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Affiliation(s)
- K Karami
- Department of Animal Science, Ferdowsi University of Mashhad , Mashhad , Iran
| | - S Zerehdaran
- Department of Animal Science, Ferdowsi University of Mashhad , Mashhad , Iran
| | - A Javadmanesh
- Department of Animal Science, Ferdowsi University of Mashhad , Mashhad , Iran
| | - M M Shariati
- Department of Animal Science, Ferdowsi University of Mashhad , Mashhad , Iran
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15
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Machtinger R, Zhong J, Mansur A, Adir M, Racowsky C, Hauser R, Brennan K, Karlsson O, Baccarelli AA. Placental lncRNA Expression Is Associated With Prenatal Phthalate Exposure. Toxicol Sci 2019; 163:116-122. [PMID: 29385630 DOI: 10.1093/toxsci/kfy013] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Phthalates are endocrine-disrupting chemicals that can cross the placenta and affect the fetal epigenome. Among various epigenetic regulators of gene expression, long noncoding RNAs (lncRNAs) are important players that may also be involved in the manifestation of endocrine-disrupting chemical toxicity. We sought to explore the association between maternal urinary phthalate metabolite concentrations and lncRNA expression in human placenta to better understand potential mechanisms through which lncRNAs participate in mediating phthalate toxicity. Ten patients with uncomplicated dichorionic diamniotic twin pregnancies at term were included in this study. Urinary (n = 10) and placenta samples (n = 20) were collected for all participants. Urinary samples were analyzed for 15 phthalate metabolites and 2 phthalate alternative metabolites. Real-time PCR arrays were used to identify and quantify 87 lncRNAs from the placental samples. We tested the Spearman correlation matrix to compare prenatal phthalate measures against placental lncRNA levels. lncRNA levels showed large variations across samples, with no significant differences in lncRNA expression within twin pairs. Mono-(carboxynonyl) phthalate demonstrated consistently strong correlations with most lncRNAs. The strongest correlation was observed between mono-hydroxyisobutyl phthalate and LOC91450 (Rspearman = 0.88, p < .001). This correlation remained significant after Bonferroni adjustment. Other strong correlations were observed between mono-isobutyl phthalate, DPP10 and HOTTIP (Rspearman = -0.91, p < .001). AIRN, DACT3.AS1, DLX6, DPP10, HOTTIP, LOC143666, and LOC91450 were strongly correlated with the greatest number of phthalate metabolites. Further studies are needed to validate these results and understand if the altered expression of lncRNAs in human placenta has clinical significance.
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Affiliation(s)
- Ronit Machtinger
- Sheba Medical Center, Ramat-Gan and Sackler School of Medicine, Tel-Aviv University, Israel
| | - Jia Zhong
- Department of Environmental Health Sciences, Columbia University, Mailman School of Public Health, New York City, New York, USA
| | - Abdallah Mansur
- Sheba Medical Center, Ramat-Gan and Sackler School of Medicine, Tel-Aviv University, Israel
| | - Michal Adir
- Sheba Medical Center, Ramat-Gan and Sackler School of Medicine, Tel-Aviv University, Israel
| | - Catherine Racowsky
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Russ Hauser
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Kasey Brennan
- Department of Environmental Health Sciences, Columbia University, Mailman School of Public Health, New York City, New York, USA
| | - Oskar Karlsson
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Columbia University, Mailman School of Public Health, New York City, New York, USA
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16
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Pegoraro M, Marshall H, Lonsdale ZN, Mallon EB. Do social insects support Haig's kin theory for the evolution of genomic imprinting? Epigenetics 2018; 12:725-742. [PMID: 28703654 PMCID: PMC5739101 DOI: 10.1080/15592294.2017.1348445] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Although numerous imprinted genes have been described in several lineages, the phenomenon of genomic imprinting presents a peculiar evolutionary problem. Several hypotheses have been proposed to explain gene imprinting, the most supported being Haig's kinship theory. This theory explains the observed pattern of imprinting and the resulting phenotypes as a competition for resources between related individuals, but despite its relevance it has not been independently tested. Haig's theory predicts that gene imprinting should be present in eusocial insects in many social scenarios. These lineages are therefore ideal for testing both the theory's predictions and the mechanism of gene imprinting. Here we review the behavioral evidence of genomic imprinting in eusocial insects, the evidence of a mechanism for genomic imprinting and finally we evaluate recent results showing parent of origin allele specific expression in honeybees in the light of Haig's theory.
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Affiliation(s)
- Mirko Pegoraro
- a Department of Genetics and Genome Biology , University of Leicester , UK
| | - Hollie Marshall
- a Department of Genetics and Genome Biology , University of Leicester , UK
| | - Zoë N Lonsdale
- a Department of Genetics and Genome Biology , University of Leicester , UK
| | - Eamonn B Mallon
- a Department of Genetics and Genome Biology , University of Leicester , UK
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17
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Hernandez A, Stohn JP. The Type 3 Deiodinase: Epigenetic Control of Brain Thyroid Hormone Action and Neurological Function. Int J Mol Sci 2018; 19:ijms19061804. [PMID: 29921775 PMCID: PMC6032375 DOI: 10.3390/ijms19061804] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/13/2018] [Accepted: 06/15/2018] [Indexed: 12/31/2022] Open
Abstract
Thyroid hormones (THs) influence multiple processes in the developing and adult central nervous system, and their local availability needs to be maintained at levels that are tailored to the requirements of their biological targets. The local complement of TH transporters, deiodinase enzymes, and receptors is critical to ensure specific levels of TH action in neural cells. The type 3 iodothyronine deiodinase (DIO3) inactivates THs and is highly present in the developing and adult brain, where it limits their availability and action. DIO3 deficiency in mice results in a host of neurodevelopmental and behavioral abnormalities, demonstrating the deleterious effects of TH excess, and revealing the critical role of DIO3 in the regulation of TH action in the brain. The fact the Dio3 is an imprinted gene and that its allelic expression pattern varies across brain regions and during development introduces an additional level of control to deliver specific levels of hormone action in the central nervous system (CNS). The sensitive epigenetic nature of the mechanisms controlling the genomic imprinting of Dio3 renders brain TH action particularly susceptible to disruption due to exogenous treatments and environmental exposures, with potential implications for the etiology of human neurodevelopmental disorders.
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Affiliation(s)
- Arturo Hernandez
- Center for Molecular Medicine, Maine Medical Center Research Institute, Maine Medical Center, Scarborough, ME 04074, USA.
- Graduate School for Biomedical Science and Engineering, University of Maine, Orono, ME 04469, USA.
- Department of Medicine, Tufts University School of Medicine, Boston, MA 02111, USA.
| | - J Patrizia Stohn
- Center for Molecular Medicine, Maine Medical Center Research Institute, Maine Medical Center, Scarborough, ME 04074, USA.
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18
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Zhou Z, Lin Z, Pang X, Tariq MA, Ao X, Li P, Wang J. Epigenetic regulation of long non-coding RNAs in gastric cancer. Oncotarget 2018; 9:19443-19458. [PMID: 29721215 PMCID: PMC5922409 DOI: 10.18632/oncotarget.23821] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 10/25/2017] [Indexed: 12/14/2022] Open
Abstract
Gastric cancer is one of the most common cancers and is the second leading cause of cancer mortality worldwide. Therefore, it is urgent to explore new molecular biomarkers for early diagnosis, early treatment and prognosis for gastric cancer patients. Recently, increasing evidence has shown that epigenetic changes, such as aberrant DNA methylation, histone modifications, and noncoding RNAs (ncRNAs) expression, play substantial roles in the development and progression of malignancies. Among these changes, long non-coding RNAs (lncRNAs), a novel class of ncRNAs, are emerging as highly versatile actors in a variety of cellular processes by regulating gene expression at the epigenetic level as well as at the transcriptional and post-transcriptional levels. Hundreds of lncRNAs become dysregulated in the various pathological processes of gastric cancer, and multiple lncRNAs have been reported to function as tumor-suppressors or oncogenes, although the underlying mechanisms are still under investigation. Here, we provide an overview of the epigenetic regulation of chromatin and the molecular functions of lncRNAs; we focus on lncRNA-mediated epigenetic regulation of cancer-related gene expression in gastric cancer, as well as discuss the clinical implications of lncRNAs on epigenetic-related cancer treatments, which may contribute helpful approaches for the development of new potential strategies for future diagnosis and therapeutic intervention in human cancers.
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Affiliation(s)
- Zhixia Zhou
- Center for Tumor Molecular Biology, Institute for Translational Medicine, Qingdao University, Qingdao 266021, China
| | - Zhijuan Lin
- Center for Tumor Molecular Biology, Institute for Translational Medicine, Qingdao University, Qingdao 266021, China
| | - Xin Pang
- Center for Tumor Molecular Biology, Institute for Translational Medicine, Qingdao University, Qingdao 266021, China
| | - Muhammad Akram Tariq
- Center for Tumor Molecular Biology, Institute for Translational Medicine, Qingdao University, Qingdao 266021, China
| | - Xiang Ao
- Center for Tumor Molecular Biology, Institute for Translational Medicine, Qingdao University, Qingdao 266021, China
| | - Peifeng Li
- Center for Tumor Molecular Biology, Institute for Translational Medicine, Qingdao University, Qingdao 266021, China
| | - Jianxun Wang
- Center for Tumor Molecular Biology, Institute for Translational Medicine, Qingdao University, Qingdao 266021, China
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19
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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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20
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Alteber Z, Sharbi-Yunger A, Pevsner-Fischer M, Blat D, Roitman L, Tzehoval E, Elinav E, Eisenbach L. The anti-inflammatory IFITM genes ameliorate colitis and partially protect from tumorigenesis by changing immunity and microbiota. Immunol Cell Biol 2018; 96:284-297. [PMID: 29356071 DOI: 10.1111/imcb.12000] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 12/04/2017] [Accepted: 12/06/2017] [Indexed: 12/19/2022]
Abstract
Inflammation plays pivotal roles in different stages of tumor development. Screening for predisposing genetic abnormalities and understanding the roles these genes play in the crosstalk between immune and cancer cells will provide new targets for cancer therapy and prevention. The interferon inducible transmembrane (IFITM) genes are involved in pathogenesis of the gastro-intestinal tract. We aimed at delineating the role of IFITM3 in colonic epithelial homeostasis, inflammation and colitis-associated tumorigenesis using IFITM3-deficient mice. Chemical induction of colitis in IFITM3-deficient mice results in significantly increased clinical signs of inflammation and induction of invasive tumorigenesis. Bone marrow transplantation showed that cells of the hematopoietic system are responsible for colitis deterioration. In these mice, impaired cytokine expression skewed inflammatory response toward pathogenic Th17 with reduced expression of the anti-inflammatory cytokine IL10 during the recovery phase. Intriguingly, mice lacking the entire IFITM locus developed spontaneous chronic colitis from the age of 14 weeks. Sequencing the 16S rRNA of naïve mice lacking IFITM3 gene, or the entire locus containing five IFITM genes, revealed these mice had significant bacterial differences from their wild-type littermates. Our novel results provide strong evidence for the essential role of IFITM genes in ameliorating colitis and colitis-associated tumorigenesis.
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Affiliation(s)
- Zoya Alteber
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Adi Sharbi-Yunger
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | | | - Dan Blat
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Lior Roitman
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Esther Tzehoval
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Eran Elinav
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Lea Eisenbach
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 76100, Israel
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21
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Wang L, Chang S, Wang Z, Wang S, Huo J, Ding G, Li R, Liu C, Shangguan S, Lu X, Zhang T, Qiu Z, Wu J. Altered GNAS imprinting due to folic acid deficiency contributes to poor embryo development and may lead to neural tube defects. Oncotarget 2017; 8:110797-110810. [PMID: 29340017 PMCID: PMC5762285 DOI: 10.18632/oncotarget.22731] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/29/2017] [Indexed: 01/28/2023] Open
Abstract
Disturbed epigenetic modifications have been linked to the pathogenesis of Neural Tube Defects (NTDs) in those with folate deficiency during pregnancy. However, evidence is lacking to delineate the critical region in epigenome regulated by parental folic acid and mechanisms by which folate deficiency affects normal embryogenesis. Our data from clinical samples revealed the presence of aberrant DNA methylation in GNAS imprinting cluster in NTD samples with low folate concentrations. Results from mouse models indicated that the establishment of GNAS imprinting was influenced by both maternal and paternal folate-deficient diets. Such aberrant GNAS imprinting was present prior to the gametogenesis period. Imprinting in Exon1A/GNAS gDMR was abolished in both spermatozoa and oocytes upon treating with a parental folate-deficient diet (3.6% in spermatozoa, 9.8% in oocytes). Interestingly, loss of imprinting in the GNAS gene cluster altered chromatin structure to an overwhelmingly open structure (58.48% in the folate-free medium group vs. 39.51% in the folate-normal medium group; P < 0.05), and led to a disturbed expression of genes in this region. Furthermore, an elevated cyclic AMP levels was observed in folate acid deficiency group. Our results imply that GNAS imprinting plays major roles in folic acid metabolism regulation during embryogenesis. Aberrant GNAS imprinting is an attribute to NTDs, providing a new perspective for explaining the molecular mechanisms by which folate supplementation in human pregnancy provides protection from NTDs.
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Affiliation(s)
- Li Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, P.R. China
| | - Shaoyan Chang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, P.R. China
| | - Zhen Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, P.R. China
| | - Shan Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, P.R. China
| | - Junsheng Huo
- National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing, P.R. China
| | - Gangqiang Ding
- National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing, P.R. China
| | - Rui Li
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, P.R. China
| | - Chi Liu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, P.R. China
| | - Shaofang Shangguan
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, P.R. China
| | - Xiaolin Lu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, P.R. China
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, P.R. China
| | - Zhiyong Qiu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, P.R. China
| | - Jianxin Wu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, P.R. China
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22
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Yan X, Himburg HA, Pohl K, Quarmyne M, Tran E, Zhang Y, Fang T, Kan J, Chao NJ, Zhao L, Doan PL, Chute JP. Deletion of the Imprinted Gene Grb10 Promotes Hematopoietic Stem Cell Self-Renewal and Regeneration. Cell Rep 2017; 17:1584-1594. [PMID: 27806297 DOI: 10.1016/j.celrep.2016.10.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 09/06/2016] [Accepted: 10/07/2016] [Indexed: 01/30/2023] Open
Abstract
Imprinted genes are differentially expressed by adult stem cells, but their functions in regulating adult stem cell fate are incompletely understood. Here we show that growth factor receptor-bound protein 10 (Grb10), an imprinted gene, regulates hematopoietic stem cell (HSC) self-renewal and regeneration. Deletion of the maternal allele of Grb10 in mice (Grb10m/+ mice) substantially increased HSC long-term repopulating capacity, as compared to that of Grb10+/+ mice. After total body irradiation (TBI), Grb10m/+ mice demonstrated accelerated HSC regeneration and hematopoietic reconstitution, as compared to Grb10+/+ mice. Grb10-deficient HSCs displayed increased proliferation after competitive transplantation or TBI, commensurate with upregulation of CDK4 and Cyclin E. Furthermore, the enhanced HSC regeneration observed in Grb10-deficient mice was dependent on activation of the Akt/mTORC1 pathway. This study reveals a function for the imprinted gene Grb10 in regulating HSC self-renewal and regeneration and suggests that the inhibition of Grb10 can promote hematopoietic regeneration in vivo.
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Affiliation(s)
- Xiao Yan
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA
| | - Heather A Himburg
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Katherine Pohl
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Mamle Quarmyne
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Evelyn Tran
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Yurun Zhang
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Tiancheng Fang
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA
| | - Jenny Kan
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Nelson J Chao
- Division of Hematologic Malignancies and Cellular Therapy, Duke University, Durham, NC 27710, USA
| | - Liman Zhao
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Phuong L Doan
- Division of Hematologic Malignancies and Cellular Therapy, Duke University, Durham, NC 27710, USA
| | - John P Chute
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA.
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23
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Sun W, Yang Y, Xu C, Guo J. Regulatory mechanisms of long noncoding RNAs on gene expression in cancers. Cancer Genet 2017; 216-217:105-110. [PMID: 29025584 DOI: 10.1016/j.cancergen.2017.06.003] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 06/25/2017] [Accepted: 06/27/2017] [Indexed: 02/06/2023]
Abstract
Long non-coding RNAs (lncRNAs) are a heterogeneous class of RNAs that are non-protein coding transcripts longer than 200 nucleotides. In this review, we introduce the mechanisms by which lncRNAs regulate gene expression in four parts, epigenetic regulation (genetic imprinting and chromatin remodeling), transcriptional regulation (molecular decoy), post-transcriptional regulation (splicing and mRNA decay), and translational regulation. H19, Xist, and others are involved in genomic imprinting. HOTAIR and ANRIL function in chromatin remodeling. GAS5 is degraded through an RNA decay pathway. NEAT1 and MALAT1 function not only in the regulation of transcription but also in splicing.
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Affiliation(s)
- Weiliang Sun
- Ningbo Yinzhou People's Hospital and the Affiliated Hospital, Medical School of Ningbo University, Ningbo 315040, PR China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, PR China
| | - Yunben Yang
- Medical School of Zhejiang University, Hangzhou, PR China
| | - Chunjing Xu
- Medical School of Zhejiang University, Hangzhou, PR China
| | - Junming Guo
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, PR China.
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24
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Developmental and Transmittable Origins of Obesity-Associated Health Disorders. Trends Genet 2017; 33:399-407. [PMID: 28438343 DOI: 10.1016/j.tig.2017.03.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/27/2017] [Accepted: 03/28/2017] [Indexed: 11/23/2022]
Abstract
The current global obesity pandemic is clearly linked to both the increasing prevalence of, and preference for, foods high in calories, specifically fat and sucrose, and declining levels of daily physical activity. A less commonly discussed possible explanation is that risk of obesity begins in utero as a result of developmental plasticity during early life. This idea fits into the broader Developmental Origins of Health and Diseases (DOHAD) hypothesis, which holds that stressful in utero exposure manifests as disease in adulthood. In this review, we highlight several studies that have revealed the role of epigenetics in multigenerational transmission of developmentally programmed obesity and associated cardiometabolic disease.
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Galbraith DA, Yi SV, Grozinger CM. Evaluation of Possible Proximate Mechanisms Underlying the Kinship Theory of Intragenomic Conflict in Social Insects. Integr Comp Biol 2016; 56:1206-1214. [DOI: 10.1093/icb/icw111] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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Rienecker KDA, Hill MJ, Isles AR. Methods of epigenome editing for probing the function of genomic imprinting. Epigenomics 2016; 8:1389-1398. [PMID: 27625199 DOI: 10.2217/epi-2016-0073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The curious patterns of imprinted gene expression draw interest from several scientific disciplines to the functional consequences of genomic imprinting. Methods of probing the function of imprinting itself have largely been indirect and correlational, relying heavily on conventional transgenics. Recently, the burgeoning field of epigenome editing has provided new tools and suggested strategies for asking causal questions with site specificity. This perspective article aims to outline how these new methods may be applied to questions of functional imprinting and, with this aim in mind, to suggest new dimensions for the expansion of these epigenome-editing tools.
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Affiliation(s)
- Kira DA Rienecker
- MRC Centre for Neuropsychiatric Genetics & Genomics, Department of Psychological Medicine & Clinical Neuroscience, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Matthew J Hill
- MRC Centre for Neuropsychiatric Genetics & Genomics, Department of Psychological Medicine & Clinical Neuroscience, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Anthony R Isles
- MRC Centre for Neuropsychiatric Genetics & Genomics, Department of Psychological Medicine & Clinical Neuroscience, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
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Aghakhanyan G, Bonanni P, Randazzo G, Nappi S, Tessarotto F, De Martin L, Frijia F, De Marchi D, De Masi F, Kuppers B, Lombardo F, Caramella D, Montanaro D. From Cortical and Subcortical Grey Matter Abnormalities to Neurobehavioral Phenotype of Angelman Syndrome: A Voxel-Based Morphometry Study. PLoS One 2016; 11:e0162817. [PMID: 27626634 PMCID: PMC5023118 DOI: 10.1371/journal.pone.0162817] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 08/29/2016] [Indexed: 12/14/2022] Open
Abstract
Angelman syndrome (AS) is a rare neurogenetic disorder due to loss of expression of maternal ubiquitin-protein ligase E3A (UBE3A) gene. It is characterized by severe developmental delay, speech impairment, movement or balance disorder and typical behavioral uniqueness. Affected individuals show normal magnetic resonance imaging (MRI) findings, although mild dysmyelination may be observed. In this study, we adopted a quantitative MRI analysis with voxel-based morphometry (FSL-VBM) method to investigate disease-related changes in the cortical/subcortical grey matter (GM) structures. Since 2006 to 2013 twenty-six AS patients were assessed by our multidisciplinary team. From those, sixteen AS children with confirmed maternal 15q11-q13 deletions (mean age 7.7 ± 3.6 years) and twenty-one age-matched controls were recruited. The developmental delay and motor dysfunction were assessed using Bayley III and Gross Motor Function Measure (GMFM). Principal component analysis (PCA) was applied to the clinical and neuropsychological datasets. High-resolution T1-weighted images were acquired and FSL-VBM approach was applied to investigate differences in the local GM volume and to correlate clinical and neuropsychological changes in the regional distribution of GM. We found bilateral GM volume loss in AS compared to control children in the striatum, limbic structures, insular and orbitofrontal cortices. Voxel-wise correlation analysis with the principal components of the PCA output revealed a strong relationship with GM volume in the superior parietal lobule and precuneus on the left hemisphere. The anatomical distribution of cortical/subcortical GM changes plausibly related to several clinical features of the disease and may provide an important morphological underpinning for clinical and neurobehavioral symptoms in children with AS.
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Affiliation(s)
- Gayane Aghakhanyan
- Unit of Neuroradiology, Fondazione CNR/Regione Toscana G. Monasterio, Pisa, Italy
| | - Paolo Bonanni
- Epilepsy and Clinical Neurophysiology Unit, E. Medea Scientific Institute, Conegliano (TV), Italy
| | - Giovanna Randazzo
- Epilepsy and Clinical Neurophysiology Unit, E. Medea Scientific Institute, Conegliano (TV), Italy
| | - Sara Nappi
- Epilepsy and Clinical Neurophysiology Unit, E. Medea Scientific Institute, Conegliano (TV), Italy
| | - Federica Tessarotto
- Epilepsy and Clinical Neurophysiology Unit, E. Medea Scientific Institute, Conegliano (TV), Italy
| | - Lara De Martin
- Epilepsy and Clinical Neurophysiology Unit, E. Medea Scientific Institute, Conegliano (TV), Italy
| | - Francesca Frijia
- Unit of Neuroradiology, Fondazione CNR/Regione Toscana G. Monasterio, Pisa, Italy
| | - Daniele De Marchi
- Unit of Neuroradiology, Fondazione CNR/Regione Toscana G. Monasterio, Pisa, Italy
| | - Francesco De Masi
- Division of Anesthesiology and Intensive Care, University Hospital of Pisa, Pisa, Italy
| | - Beate Kuppers
- Division of Anesthesiology and Intensive Care, University Hospital of Pisa, Pisa, Italy
| | - Francesco Lombardo
- Unit of Neuroradiology, Fondazione CNR/Regione Toscana G. Monasterio, Pisa, Italy
| | - Davide Caramella
- Diagnostic and Interventional Radiology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Domenico Montanaro
- Unit of Neuroradiology, Fondazione CNR/Regione Toscana G. Monasterio, Pisa, Italy
- * E-mail:
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Abstract
SEPT9 gene methylation has been implicated as a biomarker for colorectal cancer (CRC) for more than 10 years and has been used clinically for more than 6 years. Studies have proven it to be an accurate, reliable, fast, and convenient method for CRC. In this chapter, we will first provide the background on the role of septin9 protein and the theoretical basis of the SEPT9 gene methylation assay. We will then focus on the performance of SEPT9 gene methylation assay for CRC early detection and screening by analyzing the data obtained in clinical trials and comparing its performance with other methods or markers. Finally, we will discuss the future applications of the assay in monitoring cancer recurrence, evaluating surgery, chemotherapy, and predicting long-term survival. We hope this chapter can provide a full overview of the theoretical basis, development, validation, and clinical applications of the SEPT9 assay for both basic science researchers and clinical practitioners.
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Affiliation(s)
- Lele Song
- Department of Radiotherapy, The Chinese PLA 309 Hospital, Beijing, PR China; BioChain (Beijing) Science and Technology, Inc., Economic and Technological Development Area, Beijing, PR China.
| | - Yuemin Li
- Department of Radiotherapy, The Chinese PLA 309 Hospital, Beijing, PR China.
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Li Y, Song L, Gong Y, He B. Detection of colorectal cancer by DNA methylation biomarker SEPT9: past, present and future. Biomark Med 2015; 8:755-69. [PMID: 25123042 DOI: 10.2217/bmm.14.8] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Colorectal cancer has become the third most common cancer in the world. Early diagnosis and treatment can significantly reduce colorectal cancer mortality. The current routinely used fecal-based screening methods do not provide satisfactory sensitivity. Although colonoscopy provides macroscopic diagnosis, the compliance is low due to its inconvenience and complications. Hence, the development of new screening methods is needed urgently. Peripheral blood SEPT9 gene methylation assay has become a potential option with promising future for early detection and screening of colorectal cancer. It is shown to be convenient, reliable with good compliance by several clinical trials. This article will review the theoretical foundation and development of the assay, focusing on its clinical trials, comparing it with other screening methods and discussing its future applications.
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Affiliation(s)
- Yuemin Li
- The Chinese PLA 309 Hospital (General Hospital of the PLA General Staff Headquarters), No. 17, HeiShanHu Road, HaiDian District, Beijing 100091, PR China
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Fatima R, Akhade VS, Pal D, Rao SMR. Long noncoding RNAs in development and cancer: potential biomarkers and therapeutic targets. MOLECULAR AND CELLULAR THERAPIES 2015; 3:5. [PMID: 26082843 PMCID: PMC4469312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/19/2015] [Indexed: 11/21/2023]
Abstract
Long noncoding RNAs are emerging as key players in various fundamental biological processes. We highlight the varied molecular mechanisms by which lncRNAs modulate gene expression in diverse cellular contexts and their role in early mammalian development in this review. Furthermore, it is being increasingly recognized that altered expression of lncRNAs is specifically associated with tumorigenesis, tumor progression and metastasis. We discuss various lncRNAs implicated in different cancer types with a focus on their clinical applications as potential biomarkers and therapeutic targets in the pathology of diverse cancers.
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Affiliation(s)
- Roshan Fatima
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur, Bangalore 560064 India
| | - Vijay Suresh Akhade
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur, Bangalore 560064 India
| | - Debosree Pal
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur, Bangalore 560064 India
| | - Satyanarayana MR Rao
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur, Bangalore 560064 India
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Fatima R, Akhade VS, Pal D, Rao SM. Long noncoding RNAs in development and cancer: potential biomarkers and therapeutic targets. MOLECULAR AND CELLULAR THERAPIES 2015; 3:5. [PMID: 26082843 PMCID: PMC4469312 DOI: 10.1186/s40591-015-0042-6] [Citation(s) in RCA: 203] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/19/2015] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs are emerging as key players in various fundamental biological processes. We highlight the varied molecular mechanisms by which lncRNAs modulate gene expression in diverse cellular contexts and their role in early mammalian development in this review. Furthermore, it is being increasingly recognized that altered expression of lncRNAs is specifically associated with tumorigenesis, tumor progression and metastasis. We discuss various lncRNAs implicated in different cancer types with a focus on their clinical applications as potential biomarkers and therapeutic targets in the pathology of diverse cancers.
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Affiliation(s)
- Roshan Fatima
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur, Bangalore 560064 India
| | - Vijay Suresh Akhade
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur, Bangalore 560064 India
| | - Debosree Pal
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur, Bangalore 560064 India
| | - Satyanarayana Mr Rao
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur, Bangalore 560064 India
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Abstract
Most of what is known about the pathogenesis of inflammatory bowel disease (IBD) pertains to complex interplay between host genetics, immunity, and environmental factors. Epigenetic modifications play pivotal roles in intestinal immunity and mucosal homeostasis as well as mediating gene-environment interactions. In this article, we provide a historical account of epigenetic research either directly related or pertinent to the pathogenesis and management of IBD. We further collate emerging evidence supporting roles for epigenetic mechanisms in relevant aspects of IBD biology, including deregulated immunity, host-pathogen recognition and mucosal integrity. Finally, we highlight key epigenetic mechanisms that link chronic inflammation to specific IBD comorbidities, including colitis-associated cancer and discuss their potential utility as novel biomarkers or pharmacologic targets in IBD therapy.
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Lorenc A, Linnenbrink M, Montero I, Schilhabel MB, Tautz D. Genetic differentiation of hypothalamus parentally biased transcripts in populations of the house mouse implicate the Prader-Willi syndrome imprinted region as a possible source of behavioral divergence. Mol Biol Evol 2014; 31:3240-9. [PMID: 25172960 PMCID: PMC4245819 DOI: 10.1093/molbev/msu257] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Parentally biased expression of transcripts (genomic imprinting) in adult tissues, including the brain, can influence and possibly drive the evolution of behavioral traits. We have previously found that paternally determined cues are involved in population-specific mate choice decisions between two populations of the Western house mouse (Mus musculus domesticus). Here, we ask whether this could be mediated by genomically imprinted transcripts that are subject to fast differentiation between these populations. We focus on three organs that are of special relevance for mate choice and behavior: The vomeronasal organ (VNO), the hypothalamus, and the liver. To first identify candidate transcripts at a genome-wide scale, we used reciprocal crosses between M. m. domesticus and M. m. musculus inbred strains and RNA sequencing of the respective tissues. Using a false discovery cutoff derived from mock reciprocal cross comparisons, we find a total of 66 imprinted transcripts, 13 of which have previously not been described as imprinted. The largest number of imprinted transcripts were found in the hypothalamus; fewer were found in the VNO, and the least were found in the liver. To assess molecular differentiation and imprinting in the wild-derived M. m. domesticus populations, we sequenced the RNA of the hypothalamus from individuals of these populations. This confirmed the presence of the above identified transcripts also in wild populations and allowed us to search for those that show a high genetic differentiation between these populations. Our results identify the Ube3a–Snrpn imprinted region on chromosome 7 as a region that encompasses the largest number of previously not described transcripts with paternal expression bias, several of which are at the same time highly differentiated. For four of these, we confirmed their imprinting status via single nucleotide polymorphism-specific pyrosequencing assays with RNA from reciprocal crosses. In addition, we find the paternally expressed Peg13 transcript within the Trappc9 gene region on chromosome 15 to be highly differentiated. Interestingly, both regions have been implicated in Prader–Willi nervous system disorder phenotypes in humans. We suggest that these genomically imprinted regions are candidates for influencing the population-specific mate-choice in mice.
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Affiliation(s)
- Anna Lorenc
- Max-Planck Institute for Evolutionary Biology, Department Evolutionary Genetics, Plön, Germany
| | - Miriam Linnenbrink
- Max-Planck Institute for Evolutionary Biology, Department Evolutionary Genetics, Plön, Germany
| | - Inka Montero
- Max-Planck Institute for Evolutionary Biology, Department Evolutionary Genetics, Plön, Germany
| | - Markus B Schilhabel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Diethard Tautz
- Max-Planck Institute for Evolutionary Biology, Department Evolutionary Genetics, Plön, Germany
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Danchin E, Pocheville A. Inheritance is where physiology meets evolution. J Physiol 2014; 592:2307-17. [PMID: 24882815 PMCID: PMC4048090 DOI: 10.1113/jphysiol.2014.272096] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/08/2014] [Indexed: 01/05/2023] Open
Abstract
Physiology and evolutionary biology have developed as two separated disciplines, a separation that mirrored the hypothesis that the physiological and evolutionary processes could be decoupled. We argue that non-genetic inheritance shatters the frontier between physiology and evolution, and leads to the coupling of physiological and evolutionary processes to a point where there exists a continuum between accommodation by phenotypic plasticity and adaptation by natural selection. This approach is also profoundly affecting the definition of the concept of phenotypic plasticity, which should now be envisaged as a multi-scale concept. We further suggest that inclusive inheritance provides a quantitative way to help bridging infra-individual (i.e. physiology) with supra-individual (i.e. evolution) approaches, in a way that should help building the long sough inclusive evolutionary synthesis.
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Affiliation(s)
- Etienne Danchin
- CNRS, UPS, ENFA; EDB (Laboratoire Evolution & Diversité Biologique), UMR5174, 118 route de Narbonne, F-31062, Toulouse, France Université de Toulouse, UMR5174, F-31062, Toulouse, France
| | - Arnaud Pocheville
- Center for Philosophy of Science, University of Pittsburgh, 817 Cathedral of Learning, Pittsburgh, PA, 15260, USA
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Caliebe A, Richter J, Ammerpohl O, Kanber D, Beygo J, Bens S, Haake A, Jüttner E, Korn B, Mackay DJG, Martin-Subero JI, Nagel I, Sebire NJ, Seidmann L, Vater I, von Kaisenberg CS, Temple IK, Horsthemke B, Buiting K, Siebert R. A familial disorder of altered DNA-methylation. J Med Genet 2014; 51:407-12. [DOI: 10.1136/jmedgenet-2013-102149] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Endogenously imprinted genes in Drosophila melanogaster. Mol Genet Genomics 2014; 289:653-73. [DOI: 10.1007/s00438-014-0840-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 03/04/2014] [Indexed: 12/21/2022]
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Genome-wide histone state profiling of fibroblasts from the opossum, Monodelphis domestica, identifies the first marsupial-specific imprinted gene. BMC Genomics 2014; 15:89. [PMID: 24484454 PMCID: PMC3912494 DOI: 10.1186/1471-2164-15-89] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Accepted: 01/23/2014] [Indexed: 01/05/2023] Open
Abstract
Background Imprinted genes have been extensively documented in eutherian mammals and found to exhibit significant interspecific variation in the suites of genes that are imprinted and in their regulation between tissues and developmental stages. Much less is known about imprinted loci in metatherian (marsupial) mammals, wherein studies have been limited to a small number of genes previously known to be imprinted in eutherians. We describe the first ab initio search for imprinted marsupial genes, in fibroblasts from the opossum, Monodelphis domestica, based on a genome-wide ChIP-seq strategy to identify promoters that are simultaneously marked by mutually exclusive, transcriptionally opposing histone modifications. Results We identified a novel imprinted gene (Meis1) and two additional monoallelically expressed genes, one of which (Cstb) showed allele-specific, but non-imprinted expression. Imprinted vs. allele-specific expression could not be resolved for the third monoallelically expressed gene (Rpl17). Transcriptionally opposing histone modifications H3K4me3, H3K9Ac, and H3K9me3 were found at the promoters of all three genes, but differential DNA methylation was not detected at CpG islands at any of these promoters. Conclusions In generating the first genome-wide histone modification profiles for a marsupial, we identified the first gene that is imprinted in a marsupial but not in eutherian mammals. This outcome demonstrates the practicality of an ab initio discovery strategy and implicates histone modification, but not differential DNA methylation, as a conserved mechanism for marking imprinted genes in all therian mammals. Our findings suggest that marsupials use multiple epigenetic mechanisms for imprinting and support the concept that lineage-specific selective forces can produce sets of imprinted genes that differ between metatherian and eutherian lines.
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Matarazzo V, Muscatelli F. Natural breaking of the maternal silence at the mouse and human imprinted Prader-Willi locus: A whisper with functional consequences. Rare Dis 2013; 1:e27228. [PMID: 25003016 PMCID: PMC3978896 DOI: 10.4161/rdis.27228] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Revised: 11/15/2013] [Accepted: 11/15/2013] [Indexed: 12/22/2022] Open
Abstract
Genomic imprinting is a normal process of epigenetic regulation leading some autosomal genes to be expressed from one parental allele only, the other parental allele being silenced. The reasons why this mechanism has been selected throughout evolution are not clear; however, expression dosage is critical for imprinted genes. There is a paradox between the fact that genomic imprinting is a robust mechanism controlling the expression of specific genes and the fact that this mechanism is based on epigenetic regulation that, per se, should present some flexibility. The robustness has been well studied, revealing the epigenetic modifications at the imprinted locus, but the flexibility has been poorly investigated.
Prader-Willi syndrome is the best-studied disease involving imprinted genes caused by the absence of expression of paternally inherited alleles of genes located in the human 15q11-q13 region. Until now, the silencing of the maternally inherited alleles was like a dogma. Rieusset et al. showed that in absence of the paternal Ndn allele, in Ndn +m/-p mice, the maternal Ndn allele is expressed at an extremely low level with a high degree of non-genetic heterogeneity. In about 50% of these mutant mice, this stochastic expression reduces birth lethality and severity of the breathing deficiency, correlated with a reduction in the loss of serotonergic neurons. Furthermore, using several mouse models, they reveal a competition between non-imprinted Ndn promoters, which results in monoallelic (paternal or maternal) Ndn expression, suggesting that Ndn monoallelic expression occurs in the absence of imprinting regulation. Importantly, specific expression of the maternal NDN allele is also detected in post-mortem brain samples of PWS individuals. Here, similar expression of the Magel2 maternal allele is reported in Magel2 +m/-p mice, suggesting that this loss of imprinting can be extended to other PWS genes. These data reveal an unexpected epigenetic flexibility of PWS imprinted genes that could be exploited to reactivate the functional but dormant maternal alleles in PWS.
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Hannula-Jouppi K, Muurinen M, Lipsanen-Nyman M, Reinius LE, Ezer S, Greco D, Kere J. Differentially methylated regions in maternal and paternal uniparental disomy for chromosome 7. Epigenetics 2013; 9:351-65. [PMID: 24247273 PMCID: PMC4053454 DOI: 10.4161/epi.27160] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
DNA methylation is a hallmark of genomic imprinting and differentially methylated regions (DMRs) are found near and in imprinted genes. Imprinted genes are expressed only from the maternal or paternal allele and their normal balance can be disrupted by uniparental disomy (UPD), the inheritance of both chromosomes of a chromosome pair exclusively from only either the mother or the father. Maternal UPD for chromosome 7 (matUPD7) results in Silver-Russell syndrome (SRS) with typical features and growth retardation, but no gene has been conclusively implicated in SRS. In order to identify novel DMRs and putative imprinted genes on chromosome 7, we analyzed eight matUPD7 patients, a segmental matUPD7q31-qter, a rare patUPD7 case and ten controls on the Infinium HumanMethylation450K BeadChip with 30 017 CpG methylation probes for chromosome 7. Genome-scale analysis showed highly significant clustering of DMRs only on chromosome 7, including the known imprinted loci GRB10, SGCE/PEG10, and PEG/MEST. We found ten novel DMRs on chromosome 7, two DMRs for the predicted imprinted genes HOXA4 and GLI3 and one for the disputed imprinted gene PON1. Quantitative RT-PCR on blood RNA samples comparing matUPD7, patUPD7, and controls showed differential expression for three genes with novel DMRs, HOXA4, GLI3, and SVOPL. Allele specific expression analysis confirmed maternal only expression of SVOPL and imprinting of HOXA4 was supported by monoallelic expression. These results present the first comprehensive map of parent-of-origin specific DMRs on human chromosome 7, suggesting many new imprinted sites.
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Affiliation(s)
- Katariina Hannula-Jouppi
- Department of Medical Genetics; Haartman Institute; Molecular Neurology Program; Research Program's Unit; Folkhälsan Institute of Genetics; University of Helsinki; Helsinki, Finland; Department of Dermatology and Allergology; Skin and Allergy Hospital; Helsinki University Central Hospital; Helsinki University Hospital; Helsinki, Finland
| | - Mari Muurinen
- Department of Medical Genetics; Haartman Institute; Molecular Neurology Program; Research Program's Unit; Folkhälsan Institute of Genetics; University of Helsinki; Helsinki, Finland
| | - Marita Lipsanen-Nyman
- Children's Hospital; University of Helsinki and Helsinki University Central Hospital; Helsinki University Hospital; Helsinki, Finland
| | - Lovisa E Reinius
- Department of Biosciences and Nutrition; Center for Biosciences; Karolinska Institutet; Stockholm, Sweden
| | - Sini Ezer
- Department of Medical Genetics; Haartman Institute; Molecular Neurology Program; Research Program's Unit; Folkhälsan Institute of Genetics; University of Helsinki; Helsinki, Finland
| | - Dario Greco
- Department of Medical Genetics; Haartman Institute; Molecular Neurology Program; Research Program's Unit; Folkhälsan Institute of Genetics; University of Helsinki; Helsinki, Finland; Department of Biosciences and Nutrition; Center for Biosciences; Karolinska Institutet; Stockholm, Sweden; Unit of Systems Toxicology; Finnish Institute of Occupational Health (FIOH); Helsinki, Finland
| | - Juha Kere
- Department of Medical Genetics; Haartman Institute; Molecular Neurology Program; Research Program's Unit; Folkhälsan Institute of Genetics; University of Helsinki; Helsinki, Finland; Department of Biosciences and Nutrition; Center for Biosciences; Karolinska Institutet; Stockholm, Sweden; Science for Life Laboratory; Karolinska Institutet; Solna, Sweden
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Analysis of allele-specific expression in mouse liver by RNA-Seq: a comparison with Cis-eQTL identified using genetic linkage. Genetics 2013; 195:1157-66. [PMID: 24026101 DOI: 10.1534/genetics.113.153882] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We report an analysis of allele-specific expression (ASE) and parent-of-origin expression in adult mouse liver using next generation sequencing (RNA-Seq) of reciprocal crosses of heterozygous F1 mice from the parental strains C57BL/6J and DBA/2J. We found a 60% overlap between genes exhibiting ASE and putative cis-acting expression quantitative trait loci (cis-eQTL) identified in an intercross between the same strains. We discuss the various biological and technical factors that contribute to the differences. We also identify genes exhibiting parental imprinting and complex expression patterns. Our study demonstrates the importance of biological replicates to limit the number of false positives with RNA-Seq data.
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42
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Abstract
The heritability of specific phenotypical traits relevant for physical performance has been extensively investigated and discussed by experts from various research fields. By deciphering the complete human DNA sequence, the human genome project has provided impressive insights into the genomic landscape. The hope that this information would reveal the origin of phenotypical traits relevant for physical performance or disease risks has proven overly optimistic, and it is still premature to refer to a 'post-genomic' era of biological science. Linking genomic regions with functions, phenotypical traits and variation in disease risk is now a major experimental bottleneck. The recent deluge of genome-wide association studies (GWAS) generates extensive lists of sequence variants and genes potentially linked to phenotypical traits, but functional insight is at best sparse. The focus of this review is on the complex mechanisms that modulate gene expression. A large fraction of these mechanisms is integrated into the field of epigenetics, mainly DNA methylation and histone modifications, which lead to persistent effects on the availability of DNA for transcription. With the exceptions of genomic imprinting and very rare cases of epigenetic inheritance, epigenetic modifications are not inherited transgenerationally. Along with their susceptibility to external influences, epigenetic patterns are highly specific to the individual and may represent pivotal control centers predisposing towards higher or lower physical performance capacities. In that context, we specifically review how epigenetics combined with classical genetics could broaden our knowledge of genotype-phenotype interactions. We discuss some of the shortcomings of GWAS and explain how epigenetic influences can mask the outcome of quantitative genetic studies. We consider epigenetic influences, such as genomic imprinting and epigenetic inheritance, as well as the life-long variability of epigenetic modification patterns and their potential impact on phenotype with special emphasis on traits related to physical performance. We suggest that epigenetic effects may also play a considerable role in the determination of athletic potential and these effects will need to be studied using more sophisticated quantitative genetic models. In the future, epigenetic status and its potential influence on athletic performance will have to be considered, explored and validated using well controlled model systems before we can begin to extrapolate new findings to complex and heterogeneous human populations. A combination of the fields of genomics, epigenomics and transcriptomics along with improved bioinformatics tools and precise phenotyping, as well as a precise classification of the test populations is required for future research to better understand the inter-relations of exercise physiology, performance traits and also susceptibility towards diseases. Only this combined input can provide the overall outlook necessary to decode the molecular foundation of physical performance.
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Affiliation(s)
- Tobias Ehlert
- Johannes Gutenberg-Universität Mainz, Department of Sports Medicine, Disease Prevention and Rehabilitation, Mainz, Germany
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Renfree MB, Suzuki S, Kaneko-Ishino T. The origin and evolution of genomic imprinting and viviparity in mammals. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120151. [PMID: 23166401 DOI: 10.1098/rstb.2012.0151] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genomic imprinting is widespread in eutherian mammals. Marsupial mammals also have genomic imprinting, but in fewer loci. It has long been thought that genomic imprinting is somehow related to placentation and/or viviparity in mammals, although neither is restricted to mammals. Most imprinted genes are expressed in the placenta. There is no evidence for genomic imprinting in the egg-laying monotreme mammals, despite their short-lived placenta that transfers nutrients from mother to embryo. Post natal genomic imprinting also occurs, especially in the brain. However, little attention has been paid to the primary source of nutrition in the neonate in all mammals, the mammary gland. Differentially methylated regions (DMRs) play an important role as imprinting control centres in each imprinted region which usually comprises both paternally and maternally expressed genes (PEGs and MEGs). The DMR is established in the male or female germline (the gDMR). Comprehensive comparative genome studies demonstrated that two imprinted regions, PEG10 and IGF2-H19, are conserved in both marsupials and eutherians and that PEG10 and H19 DMRs emerged in the therian ancestor at least 160 Ma, indicating the ancestral origin of genomic imprinting during therian mammal evolution. Importantly, these regions are known to be deeply involved in placental and embryonic growth. It appears that most maternal gDMRs are always associated with imprinting in eutherian mammals, but emerged at differing times during mammalian evolution. Thus, genomic imprinting could evolve from a defence mechanism against transposable elements that depended on DNA methylation established in germ cells.
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Affiliation(s)
- Marilyn B Renfree
- Department of Zoology, The University of Melbourne, Victoria 3010, Australia.
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Eckardt S, Dinger TC, Kurosaka S, Leu NA, Müller AM, McLaughlin KJ. In vivo and in vitro differentiation of uniparental embryonic stem cells into hematopoietic and neural cell types. Organogenesis 2012; 4:33-41. [PMID: 19279713 DOI: 10.4161/org.6123] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Accepted: 04/16/2008] [Indexed: 12/12/2022] Open
Abstract
The biological role of genomic imprinting in adult tissue is central to the consideration of transplanting uniparental embryonic stem (ES) cell-derived tissues. We have recently shown that both maternal (parthenogenetic/gynogenetic) and paternal (androgenetic) uniparental ES cells can differentiate, both in vivo in chimeras and in vitro, into adult-repopulating hematopoietic stem and progenitor cells. This suggests that, at least in some tissues, the presence of two maternal or two paternal genomes does not interfere with stem cell function and tissue homeostasis in the adult. Here, we consider implications of the contribution of uniparental cells to hematopoiesis and to development of other organ systems, notably neural tissue for which consequences of genomic imprinting are associated with a known bias in development and behavioral disorders. Our findings so far indicate that there is little or no limit to the differentiation potential of uniparental ES cells outside the normal developmental paradigm. As a potentially donor MHC-matching source of tissue, uniparental transplants may provide not only a clinical resource but also a unique tool to investigate aspects of genomic imprinting in adults.
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Affiliation(s)
- Sigrid Eckardt
- Center for Animal Transgenesis and Germ Cell Research; New Bolton Center; University of Pennsylvania; Kennett Square, Pennsylvania USA
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Liang X, Ma J, Schatten H, Sun Q. Epigenetic changes associated with oocyte aging. SCIENCE CHINA-LIFE SCIENCES 2012; 55:670-6. [DOI: 10.1007/s11427-012-4354-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 06/19/2012] [Indexed: 11/29/2022]
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Kärst S, Vahdati AR, Brockmann GA, Hager R. Genomic imprinting and genetic effects on muscle traits in mice. BMC Genomics 2012; 13:408. [PMID: 22906226 PMCID: PMC3475036 DOI: 10.1186/1471-2164-13-408] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 07/13/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomic imprinting refers to parent-of-origin dependent gene expression caused by differential DNA methylation of the paternally and maternally derived alleles. Imprinting is increasingly recognized as an important source of variation in complex traits, however, its role in explaining variation in muscle and physiological traits, especially those of commercial value, is largely unknown compared with genetic effects. RESULTS We investigated both genetic and genomic imprinting effects on key muscle traits in mice from the Berlin Muscle Mouse population, a key model system to study muscle traits. Using a genome scan, we first identified loci with either imprinting or genetic effects on phenotypic variation. Next, we established the proportion of phenotypic variation explained by additive, dominance and imprinted QTL and characterized the patterns of effects. In total, we identified nine QTL, two of which show large imprinting effects on glycogen content and potential, and body weight. Surprisingly, all imprinting patterns were of the bipolar type, in which the two heterozygotes are different from each other but the homozygotes are not. Most QTL had pleiotropic effects and explained up to 40% of phenotypic variance, with individual imprinted loci accounting for 4-5% of variation alone. CONCLUSION Surprisingly, variation in glycogen content and potential was only modulated by imprinting effects. Further, in contrast to general assumptions, our results show that genomic imprinting can impact physiological traits measured at adult stages and that the expression does not have to follow the patterns of paternal or maternal expression commonly ascribed to imprinting effects.
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Affiliation(s)
- Stefan Kärst
- Department for Crop and Animal Sciences, Humboldt-University Berlin, Berlin, Germany
| | - Ali R Vahdati
- Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Gudrun A Brockmann
- Department for Crop and Animal Sciences, Humboldt-University Berlin, Berlin, Germany
| | - Reinmar Hager
- Department for Crop and Animal Sciences, Humboldt-University Berlin, Berlin, Germany
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Genomic imprinting absent in Drosophila melanogaster adult females. Cell Rep 2012; 2:69-75. [PMID: 22840398 DOI: 10.1016/j.celrep.2012.06.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 04/27/2012] [Accepted: 06/12/2012] [Indexed: 12/15/2022] Open
Abstract
Genomic imprinting occurs when expression of an allele differs based on the sex of the parent that transmitted the allele. In D. melanogaster, imprinting can occur, but its impact on allelic expression genome-wide is unclear. Here, we search for imprinted genes in D. melanogaster using RNA-seq to compare allele-specific expression between pools of 7- to 10-day-old adult female progeny from reciprocal crosses. We identified 119 genes with allelic expression consistent with imprinting, and these genes showed significant clustering within the genome. Surprisingly, additional analysis of several of these genes showed that either genomic heterogeneity or high levels of intrinsic noise caused imprinting-like allelic expression. Consequently, our data provide no convincing evidence of imprinting for D. melanogaster genes in their native genomic context. Elucidating sources of false-positive signals for imprinting in allele-specific RNA-seq data, as done here, is critical given the growing popularity of this method for identifying imprinted genes.
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Yan B, Wang Z. Long noncoding RNA: its physiological and pathological roles. DNA Cell Biol 2012; 31 Suppl 1:S34-41. [PMID: 22612272 DOI: 10.1089/dna.2011.1544] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are transcribed RNA molecules >200 nucleotides in length. They comprise a diverse class of transcripts that structurally resemble mRNAs, but do not encode proteins. The characterization of lncRNAs and their acceptance as crucial regulators of numerous developmental and biological pathways have suggested that the lncRNA study has gradually become one of the hot topics in the field of RNA biology. In this article, we will highlight recent progress regarding lncRNAs studies, including their classification, biological functional characterization, and their potential roles in disease development.
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Affiliation(s)
- Biao Yan
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China.
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Transgenic epigenetics: using transgenic organisms to examine epigenetic phenomena. GENETICS RESEARCH INTERNATIONAL 2012; 2012:689819. [PMID: 22567397 PMCID: PMC3335706 DOI: 10.1155/2012/689819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 12/19/2011] [Accepted: 01/02/2012] [Indexed: 01/21/2023]
Abstract
Non-model organisms are generally more difficult and/or time consuming to work with than model organisms. In addition, epigenetic analysis of model organisms is facilitated by well-established protocols, and commercially-available reagents and kits that may not be available for, or previously tested on, non-model organisms. Given the evolutionary conservation and widespread nature of many epigenetic mechanisms, a powerful method to analyze epigenetic phenomena from non-model organisms would be to use transgenic model organisms containing an epigenetic region of interest from the non-model. Interestingly, while transgenic Drosophila and mice have provided significant insight into the molecular mechanisms and evolutionary conservation of the epigenetic processes that target epigenetic control regions in other model organisms, this method has so far been under-exploited for non-model organism epigenetic analysis. This paper details several experiments that have examined the epigenetic processes of genomic imprinting and paramutation, by transferring an epigenetic control region from one model organism to another. These cross-species experiments demonstrate that valuable insight into both the molecular mechanisms and evolutionary conservation of epigenetic processes may be obtained via transgenic experiments, which can then be used to guide further investigations and experiments in the species of interest.
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Meirmans S, Meirmans PG, Kirkendall LR. The costs of sex: facing real-world complexities. QUARTERLY REVIEW OF BIOLOGY 2012; 87:19-40. [PMID: 22518931 DOI: 10.1086/663945] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Understanding the maintenance of sexual reproduction constitutes a difficult problem for evolutionary biologists because of the immediate costs that sex seems to incur. Typically, general benefits to sex and recombination are investigated that might outweigh these costs. However, several factors can strongly influence the complex balance between costs and benefits of sex; these include constraints on the evolution of asexuality, ecological differentiation, and certain lif-history traits. We review these factors and their empirical support for the first time in a unified framework and find that they can reduce the costs of sex, circumvent them, or make them inapplicable. These factors can even tip the scales to a net benefit for sex. The reviewed factors affect species and species groups differently, and we conclude consequently that understanding the maintenance of sex could turn out to be more species-specific than commonly assumed. Interestingly, our study suggests that, in some species, no general benefits to sex and recombination might be needed to understand the maintenance of sex, as in our case study of dandelions.
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Affiliation(s)
- Stephanie Meirmans
- Centre for the Study of the Sciences and the Humanities and Department of Biology, University of Bergen 5020 Bergen, Norway.
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