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Abubakar M, Hajjaj M, Naqvi ZEZ, Shanawaz H, Naeem A, Padakanti SSN, Bellitieri C, Ramar R, Gandhi F, Saleem A, Abdul Khader AHS, Faraz MA. Non-Coding RNA-Mediated Gene Regulation in Cardiovascular Disorders: Current Insights and Future Directions. J Cardiovasc Transl Res 2024; 17:739-767. [PMID: 38092987 DOI: 10.1007/s12265-023-10469-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/23/2023] [Indexed: 09/04/2024]
Abstract
Cardiovascular diseases (CVDs) pose a significant burden on global health. Developing effective diagnostic, therapeutic, and prognostic indicators for CVDs is critical. This narrative review explores the role of select non-coding RNAs (ncRNAs) and provides an in-depth exploration of the roles of miRNAs, lncRNAs, and circRNAs in different aspects of CVDs, offering insights into their mechanisms and potential clinical implications. The review also sheds light on the diverse functions of ncRNAs, including their modulation of gene expression, epigenetic modifications, and signaling pathways. It comprehensively analyzes the interplay between ncRNAs and cardiovascular health, paving the way for potential novel interventions. Finally, the review provides insights into the methodologies used to investigate ncRNA-mediated gene regulation in CVDs, as well as the implications and challenges associated with translating ncRNA research into clinical applications. Considering the broader implications, this research opens avenues for interdisciplinary collaborations, enhancing our understanding of CVDs across scientific disciplines.
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Affiliation(s)
- Muhammad Abubakar
- Department of Internal Medicine, Ameer-Ud-Din Medical College, Lahore General Hospital, Lahore, Punjab, Pakistan.
| | - Mohsin Hajjaj
- Department of Internal Medicine, Jinnah Hospital, Lahore, Punjab, Pakistan
| | - Zil E Zehra Naqvi
- Department of Internal Medicine, Jinnah Hospital, Lahore, Punjab, Pakistan
| | - Hameed Shanawaz
- Department of Internal Medicine, Windsor University School of Medicine, Cayon, Saint Kitts and Nevis
| | - Ammara Naeem
- Department of Cardiology, Heart & Vascular Institute, Dearborn, Michigan, USA
| | | | | | - Rajasekar Ramar
- Department of Internal Medicine, Rajah Muthiah Medical College, Chidambaram, Tamil Nadu, India
| | - Fenil Gandhi
- Department of Family Medicine, Lower Bucks Hospital, Bristol, PA, USA
| | - Ayesha Saleem
- Department of Internal Medicine, Jinnah Hospital, Lahore, Punjab, Pakistan
| | | | - Muhammad Ahmad Faraz
- Department of Forensic Medicine, Postgraduate Medical Institute, Lahore, Punjab, Pakistan
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2
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Kretschmer M, Fischer V, Gapp K. When Dad's Stress Gets under Kid's Skin-Impacts of Stress on Germline Cargo and Embryonic Development. Biomolecules 2023; 13:1750. [PMID: 38136621 PMCID: PMC10742275 DOI: 10.3390/biom13121750] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Multiple lines of evidence suggest that paternal psychological stress contributes to an increased prevalence of neuropsychiatric and metabolic diseases in the progeny. While altered paternal care certainly plays a role in such transmitted disease risk, molecular factors in the germline might additionally be at play in humans. This is supported by findings on changes to the molecular make up of germ cells and suggests an epigenetic component in transmission. Several rodent studies demonstrate the correlation between paternal stress induced changes in epigenetic modifications and offspring phenotypic alterations, yet some intriguing cases also start to show mechanistic links in between sperm and the early embryo. In this review, we summarise efforts to understand the mechanism of intergenerational transmission from sperm to the early embryo. In particular, we highlight how stress alters epigenetic modifications in sperm and discuss the potential for these modifications to propagate modified molecular trajectories in the early embryo to give rise to aberrant phenotypes in adult offspring.
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Affiliation(s)
- Miriam Kretschmer
- Laboratory of Epigenetics and Neuroendocrinology, Department of Health Sciences and Technology, Institute for Neuroscience, ETH Zürich, 8057 Zürich, Switzerland; (M.K.); (V.F.)
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, 8057 Zürich, Switzerland
| | - Vincent Fischer
- Laboratory of Epigenetics and Neuroendocrinology, Department of Health Sciences and Technology, Institute for Neuroscience, ETH Zürich, 8057 Zürich, Switzerland; (M.K.); (V.F.)
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, 8057 Zürich, Switzerland
| | - Katharina Gapp
- Laboratory of Epigenetics and Neuroendocrinology, Department of Health Sciences and Technology, Institute for Neuroscience, ETH Zürich, 8057 Zürich, Switzerland; (M.K.); (V.F.)
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, 8057 Zürich, Switzerland
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3
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Richer S, Tian Y, Schoenfelder S, Hurst L, Murrell A, Pisignano G. Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters. Genome Biol 2023; 24:40. [PMID: 36869353 PMCID: PMC9983196 DOI: 10.1186/s13059-023-02876-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 02/13/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND There is widespread interest in the three-dimensional chromatin conformation of the genome and its impact on gene expression. However, these studies frequently do not consider parent-of-origin differences, such as genomic imprinting, which result in monoallelic expression. In addition, genome-wide allele-specific chromatin conformation associations have not been extensively explored. There are few accessible bioinformatic workflows for investigating allelic conformation differences and these require pre-phased haplotypes which are not widely available. RESULTS We developed a bioinformatic pipeline, "HiCFlow," that performs haplotype assembly and visualization of parental chromatin architecture. We benchmarked the pipeline using prototype haplotype phased Hi-C data from GM12878 cells at three disease-associated imprinted gene clusters. Using Region Capture Hi-C and Hi-C data from human cell lines (1-7HB2, IMR-90, and H1-hESCs), we can robustly identify the known stable allele-specific interactions at the IGF2-H19 locus. Other imprinted loci (DLK1 and SNRPN) are more variable and there is no "canonical imprinted 3D structure," but we could detect allele-specific differences in A/B compartmentalization. Genome-wide, when topologically associating domains (TADs) are unbiasedly ranked according to their allele-specific contact frequencies, a set of allele-specific TADs could be defined. These occur in genomic regions of high sequence variation. In addition to imprinted genes, allele-specific TADs are also enriched for allele-specific expressed genes. We find loci that have not previously been identified as allele-specific expressed genes such as the bitter taste receptors (TAS2Rs). CONCLUSIONS This study highlights the widespread differences in chromatin conformation between heterozygous loci and provides a new framework for understanding allele-specific expressed genes.
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Affiliation(s)
- Stephen Richer
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Yuan Tian
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
- UCL Cancer Institute, University College London, Paul O'Gorman Building, London, UK
| | | | - Laurence Hurst
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Adele Murrell
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
| | - Giuseppina Pisignano
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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Vargas LN, Silveira MM, Franco MM. Epigenetic Reprogramming and Somatic Cell Nuclear Transfer. Methods Mol Biol 2023; 2647:37-58. [PMID: 37041328 DOI: 10.1007/978-1-0716-3064-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Epigenetics is an area of genetics that studies the heritable modifications in gene expression and phenotype that are not controlled by the primary sequence of DNA. The main epigenetic mechanisms are DNA methylation, post-translational covalent modifications in histone tails, and non-coding RNAs. During mammalian development, there are two global waves of epigenetic reprogramming. The first one occurs during gametogenesis and the second one begins immediately after fertilization. Environmental factors such as exposure to pollutants, unbalanced nutrition, behavioral factors, stress, in vitro culture conditions can negatively affect epigenetic reprogramming events. In this review, we describe the main epigenetic mechanisms found during mammalian preimplantation development (e.g., genomic imprinting, X chromosome inactivation). Moreover, we discuss the detrimental effects of cloning by somatic cell nuclear transfer on the reprogramming of epigenetic patterns and some molecular alternatives to minimize these negative impacts.
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Affiliation(s)
- Luna N Vargas
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
- Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Márcia M Silveira
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
- Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Maurício M Franco
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil.
- Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil.
- School of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil.
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Zhou W, Hinoue T, Barnes B, Mitchell O, Iqbal W, Lee SM, Foy KK, Lee KH, Moyer EJ, VanderArk A, Koeman JM, Ding W, Kalkat M, Spix NJ, Eagleson B, Pospisilik JA, Szabó PE, Bartolomei MS, Vander Schaaf NA, Kang L, Wiseman AK, Jones PA, Krawczyk CM, Adams M, Porecha R, Chen BH, Shen H, Laird PW. DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse. CELL GENOMICS 2022; 2:100144. [PMID: 35873672 PMCID: PMC9306256 DOI: 10.1016/j.xgen.2022.100144] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/20/2022] [Accepted: 05/20/2022] [Indexed: 05/21/2023]
Abstract
We have developed a mouse DNA methylation array that contains 296,070 probes representing the diversity of mouse DNA methylation biology. We present a mouse methylation atlas as a rich reference resource of 1,239 DNA samples encompassing distinct tissues, strains, ages, sexes, and pathologies. We describe applications for comparative epigenomics, genomic imprinting, epigenetic inhibitors, patient-derived xenograft assessment, backcross tracing, and epigenetic clocks. We dissect DNA methylation processes associated with differentiation, aging, and tumorigenesis. Notably, we find that tissue-specific methylation signatures localize to binding sites for transcription factors controlling the corresponding tissue development. Age-associated hypermethylation is enriched at regions of Polycomb repression, while hypomethylation is enhanced at regions bound by cohesin complex members. Apc Min/+ polyp-associated hypermethylation affects enhancers regulating intestinal differentiation, while hypomethylation targets AP-1 binding sites. This Infinium Mouse Methylation BeadChip (version MM285) is widely accessible to the research community and will accelerate high-sample-throughput studies in this important model organism.
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Affiliation(s)
- Wanding Zhou
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corresponding author
| | - Toshinori Hinoue
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Bret Barnes
- Illumina, Inc., Bioinformatics and Instrument Software Department, San Diego, CA 92122, USA
| | - Owen Mitchell
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Waleed Iqbal
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sol Moe Lee
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kelly K. Foy
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Kwang-Ho Lee
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ethan J. Moyer
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alexandra VanderArk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Julie M. Koeman
- Genomics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Wubin Ding
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Manpreet Kalkat
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Nathan J. Spix
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Bryn Eagleson
- Vivarium and Transgenics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | | | - Piroska E. Szabó
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Marisa S. Bartolomei
- Department of Cell and Developmental Biology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | | | - Liang Kang
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ashley K. Wiseman
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Peter A. Jones
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Connie M. Krawczyk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Marie Adams
- Genomics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Rishi Porecha
- Illumina, Inc., Bioinformatics and Instrument Software Department, San Diego, CA 92122, USA
| | | | - Hui Shen
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
- Corresponding author
| | - Peter W. Laird
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
- Corresponding author
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Mangiavacchi PM, Caldas-Bussiere MC, Mendonça MDS, Rumpf R, Lemos Júnior PES, Alves CS, Carneiro WDS, Dias AJB, Rios ÁFL. Multi-locus DNA methylation analysis of imprinted genes in cattle from somatic cell nuclear transfer. Theriogenology 2022; 186:95-107. [DOI: 10.1016/j.theriogenology.2022.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 10/18/2022]
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Shimansky VN, Ryzhova MV, Sultanov RA, Tanyashin SV, Galstyan SA, Telysheva EN, Karnaukhov VV. [The DNA methylation profiling in the study and treatment of patients with meningiomas of the craniovertebral junction]. Arkh Patol 2022; 84:47-51. [PMID: 36469717 DOI: 10.17116/patol20228406147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The paper presents the experience of using DNA methylation status in patients with meningiomas of the craniovertebral junction area in a neurosurgical clinic. A clinical case of combined treatment of a patient with meningioma of the craniovertebral junction and the choice of tactics based on the result of DNA methylation analysis of meningioma are described.
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Affiliation(s)
| | - M V Ryzhova
- Burdenko Neurosurgical Center, Moscow, Russia
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8
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Large parental differences in chromatin organization in pancreatic beta cell line explaining diabetes susceptibility effects. Nat Commun 2021; 12:4338. [PMID: 34267199 PMCID: PMC8282625 DOI: 10.1038/s41467-021-24635-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 06/28/2021] [Indexed: 12/26/2022] Open
Abstract
Previous GWAS studies identified non-coding loci with parent-of-origin-specific effects on Type 2 diabetes susceptibility. Here we report the molecular basis for one such locus near the KRTAP5-6 gene on chromosome 11. We determine the pattern of long-range contacts between an enhancer in this locus and the human INS promoter 460 kb away, in the human pancreatic β-cell line, EndoC-βH1. 3C long range contact experiments distinguish contacts on the two sister chromosomes. Coupling with allele-specific SNPs allows construction of maps revealing marked differences in organization of the two sister chromosomes in the entire region between KRTAP5-6 and INS. Further mapping distinguishes maternal and paternal alleles. This reveals a domain of parent-of-origin-specific chromatin structure extending in the telomeric direction from the INS locus. This suggests more generally that imprinted loci may extend their influence over gene expression beyond those loci through long range chromatin structure, resulting in parent-of-origin-biased expression patterns over great distances. A SNP distant from the human insulin (INS) gene near the KRTAP5-6 gene confers increased susceptibility to type 2 diabetes when present on the paternal allele while decreased susceptibility when on the maternal allele. Here the authors show that long-range contacts between the INS locus and the KRTAP5-6 gene locus distinguish paternal and maternal alleles.
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9
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Freitag CM, Chiocchetti AG, Haslinger D, Yousaf A, Waltes R. [Genetic risk factors and their influence on neural development in autism spectrum disorders]. ZEITSCHRIFT FUR KINDER-UND JUGENDPSYCHIATRIE UND PSYCHOTHERAPIE 2021; 50:187-202. [PMID: 34128703 DOI: 10.1024/1422-4917/a000803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Genetic risk factors and their influence on neural development in autism spectrum disorders Abstract. Abstract. Autism spectrum disorders are etiologically based on genetic and specific gene x biologically relevant environmental risk factors. They are diagnosed based on behavioral characteristics, such as impaired social communication and stereotyped, repetitive behavior and sensory as well as special interests. The genetic background is heterogeneous, i. e., it comprises diverse genetic risk factors across the disorder and high interindividual differences of specific genetic risk factors. Nevertheless, risk factors converge regarding underlying biological mechanisms and shared pathways, which likely cause the autism-specific behavioral characteristics. The current selective literature review summarizes differential genetic risk factors and focuses particularly on mechanisms and pathways currently being discussed by international research. In conclusion, clinically relevant aspects and open translational research questions are presented.
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Affiliation(s)
- Christine M Freitag
- Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, Universitätsklinikum Frankfurt, Goethe-Universität, Frankfurt am Main
| | - Andreas G Chiocchetti
- Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, Universitätsklinikum Frankfurt, Goethe-Universität, Frankfurt am Main
| | - Denise Haslinger
- Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, Universitätsklinikum Frankfurt, Goethe-Universität, Frankfurt am Main
| | - Afsheen Yousaf
- Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, Universitätsklinikum Frankfurt, Goethe-Universität, Frankfurt am Main
| | - Regina Waltes
- Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, Universitätsklinikum Frankfurt, Goethe-Universität, Frankfurt am Main
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10
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Fan Y, Gao Q, Guan JX, Liu L, Hong M, Jun L, Wang L, Ding HF, Jiang LH, Hou BY, Li M, Song ZQ, Sun DQ, Yan CQ, Ma L. DDAH2 (-449 G/C) G allele is positively associated with leukoaraiosis in northeastern China: a double-blind, intergroup comparison, case-control study. Neural Regen Res 2021; 16:1592-1597. [PMID: 33433489 PMCID: PMC8323672 DOI: 10.4103/1673-5374.303037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Cerebrovascular endothelial dysfunction is involved in the progression of leukoaraiosis. Asymmetric dimethylarginine is a competitive inhibitor of nitric oxide, which is highly expressed in patients with leukoaraiosis. Dimethylarginine dimethylaminohydrolase (DDAH) is a hydrolytic enzyme that is primarily responsible for eliminating asymmetric dimethylarginine, and it plays a role in the pathogenesis of cardiovascular and cerebrovascular diseases. The DDAH2 subtype is expressed in organs rich in induced nitric oxide synthase, including the heart, the placenta, and the cerebral endothelium during cerebral ischemia, in the stress state, or under neurotoxicity. Overexpression of the DDAH2 gene can inhibit asymmetric dimethylarginine-induced peripheral circulating endothelial cell dysfunction. However, it is unknown whether this polymorphism regulates plasma asymmetric dimethylarginine levels in patients with leukoaraiosis. In this double-blind study, we recruited 46 patients with leukoaraiosis and 46 healthy, matched controls. Plasma asymmetric dimethylarginine levels were determined using enzyme-linked immunoassays. Genomic DNA was isolated from whole blood samples, and polymerase chain reaction, SmaI restriction enzyme digestion, restriction fragment length polymorphisms, and agarose electrophoresis were used to detect DDAH2 (-449 G/C) gene polymorphisms. The results revealed that 95.65% of leukoaraiosis patients had recessive genetic models (GG and CG), while 89.13% of healthy control subjects had dominant genetic models (CC and CG). There was a significant difference in the genotype composition ratio between leukoaraiosis patients and healthy controls (P = 0.0002). The frequency of G alleles in the leukoaraiosis patients (71.74%) was significantly higher than in healthy controls, whereas the frequency of C alleles was lower (χ2= 13.9580, P = 0.0002). Furthermore, asymmetric dimethylarginine concentrations in subjects with the GG genotype were significantly higher than in subjects with the CG and CC genotypes (Kruskal–Wallis H = 24.5955, P < 0.0001). In addition, the GG genotype of DDAH2 (-449 G/C) was more common in patients with leukoaraiosis. These findings suggest that the G allele of DDAH2 (-449 G/C) is a risk factor for leukoaraiosis morbidity and is correlated with high levels of asymmetric dimethylarginine. This study was approved by the Institutional Ethics Committee of the 2nd Affiliated Hospital of Harbin Medical University of China (approval No. KY2016-177) on July 28, 2016.
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Affiliation(s)
- Ying Fan
- Department of Geriatrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Qiang Gao
- Department of Geriatrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Jia-Xin Guan
- Department of Geriatrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Lei Liu
- Department of Geriatrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Ming Hong
- Department of Geriatrics, Tongling Municipal Hospital, Tongling, Anhui Province, China
| | - Li Jun
- Department of Cardiovascular Medicine, Shanxi Cardiovascular Hospital, Taiyuan, Shanxi Province, China
| | - Li Wang
- Department of Geriatrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Hai-Feng Ding
- Department of Geriatrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Li-Hong Jiang
- Department of Geriatrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Bo-Yu Hou
- Department of Geriatrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Mei Li
- Department of Geriatrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Zhi-Qiang Song
- Department of Geriatrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - De-Qin Sun
- Department of Geriatrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Chao-Qi Yan
- Physical Examination Center, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Lan Ma
- Department of Geriatrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
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11
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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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12
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Xia L, Liu Y, Zhang S, Yang Y, Zhou Z, Tu J. Can Prohibitin 1 be a Safeguard against liver disease? Ann Hepatol 2020; 18:790-795. [PMID: 31558419 DOI: 10.1016/j.aohep.2019.07.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 07/11/2019] [Accepted: 07/11/2019] [Indexed: 02/04/2023]
Abstract
Prohibitin (PHB) 1 is involved in multiple regulatory pathways in liver disease to protect hepatocytes, and its function is associated with subcellular localization. PHB1 located in the nucleus, cytoplasm and the mitochondrial inner membrane has anti-oxidative stress and anti-inflammatory effects in hepatitis and cirrhosis, which can protect liver cells from damage caused by inflammatory factors and reactive oxygen species (ROS) stimulation. The low expression of PHB1 located in the nucleus of liver cancer cells inhibits the proliferation and metastasis of liver cancer; thus, PHB1 exhibits the function of a tumor suppressor gene. Understanding the mechanisms of PHB1 in liver diseases may be useful for further research on the disease and may provide new ideas for the development of targeted therapeutic drugs in the future. Therefore, this review puts forward an overview of the role of PHB1 and its protective mechanism in liver diseases.
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Affiliation(s)
- Lei Xia
- Institute of Pharmacy and Pharmacology, University of South China, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang, Hunan, China
| | - Yuling Liu
- Institute of Pharmacy and Pharmacology, University of South China, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang, Hunan, China
| | - Sujun Zhang
- Medical Research Center, University of South China, Hengyang, Hunan, China
| | - Yurong Yang
- Institute of Pharmacy and Pharmacology, University of South China, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang, Hunan, China
| | - Zhigang Zhou
- The First Affiliated Hospital, University of South China, Hengyang, Hunan, China.
| | - Jian Tu
- The First Affiliated Hospital, University of South China, Hengyang, Hunan, China; Institute of Pharmacy and Pharmacology, University of South China, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang, Hunan, China.
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13
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Patel M, Patel D, Datta S, Singh U. CGGBP1-regulated cytosine methylation at CTCF-binding motifs resists stochasticity. BMC Genet 2020; 21:84. [PMID: 32727353 PMCID: PMC7392725 DOI: 10.1186/s12863-020-00894-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/23/2020] [Indexed: 12/03/2022] Open
Abstract
Background The human CGGBP1 binds to GC-rich regions and interspersed repeats, maintains homeostasis of stochastic cytosine methylation and determines DNA-binding of CTCF. Interdependence between regulation of cytosine methylation and CTCF occupancy by CGGBP1 remains unknown. Results By analyzing methylated DNA-sequencing data obtained from CGGBP1-depleted cells, we report that some transcription factor-binding sites, including CTCF, resist stochastic changes in cytosine methylation. By analysing CTCF-binding sites we show that cytosine methylation changes at CTCF motifs caused by CGGBP1 depletion resist stochastic changes. These CTCF-binding sites are positioned at locations where the spread of cytosine methylation in cis depends on the levels of CGGBP1. Conclusion Our findings suggest that CTCF occupancy and functions are determined by CGGBP1-regulated cytosine methylation patterns.
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Affiliation(s)
- Manthan Patel
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, Gujarat, India
| | - Divyesh Patel
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, Gujarat, India
| | - Subhamoy Datta
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, Gujarat, India
| | - Umashankar Singh
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, Gujarat, India.
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14
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Zhao X, Chang S, Liu X, Wang S, Zhang Y, Lu X, Zhang T, Zhang H, Wang L. Imprinting aberrations of SNRPN, ZAC1 and INPP5F genes involved in the pathogenesis of congenital heart disease with extracardiac malformations. J Cell Mol Med 2020; 24:9898-9907. [PMID: 32693431 PMCID: PMC7520315 DOI: 10.1111/jcmm.15584] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/28/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
Congenital heart disease (CHD) with extracardiac malformations (EM) is the most common multiple malformation, resulting from the interaction between genetic abnormalities and environmental factors. Most studies have attributed the causes of CHD with EM to chromosomal abnormalities. However, multi‐system dysplasia is usually caused by both genetic mutations and epigenetic dysregulation. The epigenetic mechanisms underlying the pathogenesis of CHD with EM remain unclear. In this study, we investigated the mechanisms of imprinting alterations, including those of the Small nuclear ribonucleoprotein polypeptide N (SNRPN), PLAG1 like zinc finger 1 (ZAC1) and inositol polyphosphate‐5‐phosphatase F (INPP5F) genes, in the pathogenesis of CHD with EM. The methylation levels of SNRPN, ZAC1, and INPP5F genes were analysed by the MassARRAY platform in 24 children with CHD with EM and 20 healthy controls. The expression levels of these genes were detected by real‐time polymerase chain reaction (PCR). The correlation between methylation regulation and gene expression was confirmed using 5‐azacytidine (5‐Aza) treated cells. The methylation levels of SNRPN and ZAC1 genes were significantly increased in CHD with EM, while that of INPP5F was decreased. The methylation alterations of these genes were negatively correlated with expression. Risk analysis showed that abnormal hypermethylation of SNRPN and ZAC1 resulted in 5.545 and 7.438 times higher risks of CHD with EM, respectively, and the abnormal hypomethylation of INPP5F was 8.38 times higher than that of the control group. We concluded that abnormally high methylation levels of SNRPN and ZAC1 and decreased levels of INPP5F imply an increased risk of CHD with EM by altering their gene functions. This study provides evidence of imprinted regulation in the pathogenesis of multiple malformations.
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Affiliation(s)
- Xiaolei Zhao
- Department of Cardiac Surgery, The Capital Institute of Pediatrics, Beijing, China
| | - Shaoyan Chang
- Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
| | - Xinli Liu
- Department of Obstetrics and Gynecology, PLA Army General Hospital 263rd Clinical Department, Beijing, China
| | - Shuangxing Wang
- Department of Cardiac Surgery, The Capital Institute of Pediatrics, Beijing, China
| | - Yueran Zhang
- Department of Cardiac Surgery, The Capital Institute of Pediatrics, Beijing, China
| | - Xiaolin Lu
- Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
| | - Ting Zhang
- Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
| | - Hui Zhang
- Department of Cardiac Surgery, The Capital Institute of Pediatrics, Beijing, China
| | - Li Wang
- Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
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15
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Yoon SH, Choi J, Lee WJ, Do JT. Genetic and Epigenetic Etiology Underlying Autism Spectrum Disorder. J Clin Med 2020; 9:E966. [PMID: 32244359 PMCID: PMC7230567 DOI: 10.3390/jcm9040966] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/28/2020] [Accepted: 03/28/2020] [Indexed: 12/19/2022] Open
Abstract
Autism spectrum disorder (ASD) is a pervasive neurodevelopmental disorder characterized by difficulties in social interaction, language development delays, repeated body movements, and markedly deteriorated activities and interests. Environmental factors, such as viral infection, parental age, and zinc deficiency, can be plausible contributors to ASD susceptibility. As ASD is highly heritable, genetic risk factors involved in neurodevelopment, neural communication, and social interaction provide important clues in explaining the etiology of ASD. Accumulated evidence also shows an important role of epigenetic factors, such as DNA methylation, histone modification, and noncoding RNA, in ASD etiology. In this review, we compiled the research published to date and described the genetic and epigenetic epidemiology together with environmental risk factors underlying the etiology of the different phenotypes of ASD.
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Affiliation(s)
| | | | | | - Jeong Tae Do
- Department of Stem Cell and Regenerative Biotechnology, KU Institute of Technology, Konkuk University, Seoul 05029, Korea; (S.H.Y.); (J.C.); (W.J.L.)
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16
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Vasconcelos S, Ramalho C, Marques CJ, Doria S. Altered expression of epigenetic regulators and imprinted genes in human placenta and fetal tissues from second trimester spontaneous pregnancy losses. Epigenetics 2019; 14:1234-1244. [PMID: 31221015 PMCID: PMC6791697 DOI: 10.1080/15592294.2019.1634988] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/14/2019] [Accepted: 06/18/2019] [Indexed: 01/01/2023] Open
Abstract
Epigenetic mechanisms such as genomic imprinting have a fundamental role in embryo and fetal development. Hence, we here studied expression levels of epigenetic modifiers and imprinted genes in cases of ididopathic spontaneous abortion (SA). Thirty-five placental samples and 35 matched fetal tissues from second trimester SA were analysed; including 16 controls (placental and fetal infections as the known cause of spontaneous abortion) and 19 idiopathic SA cases. Transcript levels of epigenetic regulators and imprinted genes were measured by qRT-PCR and methylation at imprinted genes was studied by bisulfite genomic sequencing and MS-MLPA. Global DNA hydroxymethylation (5-hmC) levels were measured by an ELISA-based assay. We observed an upregulation of TET2 and TET3 in placental samples from idiopathic SA cases; however, no significant difference in global 5-hmC levels was observed. On the contrary, in fetal tissues, TET3 was markedly downregulated in idiopathic SA, showing an opposite trend to that observed in placental tissue. IGF2 and CDKN1C were upregulated and MEST downregulated in placentas from idiopathic SA cases; concordantly, IGF2 was also upregulated in fetal tissues from idiopathic SA cases. Although not reaching statistical significance, an increase in methylation levels of MEST, KvDMR1 and H19 DMRs was observed in idiopathic SA cases, concordantly with the observed changes in expression. Our study reveals, for the first time, deregulation of epigenetic modifiers and imprinted genes in both placental and fetal tissues from idiopathic SA cases in the second trimester of pregnancy, indicating a critical role during pregnancy.
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Affiliation(s)
- Sara Vasconcelos
- Department of Genetics, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Carla Ramalho
- Department of Obstetrics and Gynecology Hospital São João, Faculty of Medicine, Porto, Portugal
| | - C. Joana Marques
- Department of Genetics, Faculty of Medicine, University of Porto, Porto, Portugal
- I3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Sofia Doria
- Department of Genetics, Faculty of Medicine, University of Porto, Porto, Portugal
- I3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
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17
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Nechin J, Tunstall E, Raymond N, Hamagami N, Pathmanabhan C, Forestier S, Davis TL. Hemimethylation of CpG dyads is characteristic of secondary DMRs associated with imprinted loci and correlates with 5-hydroxymethylcytosine at paternally methylated sequences. Epigenetics Chromatin 2019; 12:64. [PMID: 31623686 PMCID: PMC6796366 DOI: 10.1186/s13072-019-0309-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/09/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In mammals, the regulation of imprinted genes is controlled by differential methylation at imprinting control regions which acquire parent of origin-specific methylation patterns during gametogenesis and retain differences in allelic methylation status throughout fertilization and subsequent somatic cell divisions. In addition, many imprinted genes acquire differential methylation during post-implantation development; these secondary differentially methylated regions appear necessary to maintain the imprinted expression state of individual genes. Despite the requirement for both types of differentially methylated sequence elements to achieve proper expression across imprinting clusters, methylation patterns are more labile at secondary differentially methylated regions. To understand the nature of this variability, we analyzed CpG dyad methylation patterns at both paternally and maternally methylated imprinted loci within multiple imprinting clusters. RESULTS We determined that both paternally and maternally methylated secondary differentially methylated regions associated with imprinted genes display high levels of hemimethylation, 29-49%, in comparison to imprinting control regions which exhibited 8-12% hemimethylation. To explore how hemimethylation could arise, we assessed the differentially methylated regions for the presence of 5-hydroxymethylcytosine which could cause methylation to be lost via either passive and/or active demethylation mechanisms. We found enrichment of 5-hydroxymethylcytosine at paternally methylated secondary differentially methylated regions, but not at the maternally methylated sites we analyzed in this study. CONCLUSIONS We found high levels of hemimethylation to be a generalizable characteristic of secondary differentially methylated regions associated with imprinted genes. We propose that 5-hydroxymethylcytosine enrichment may be responsible for the variability in methylation status at paternally methylated secondary differentially methylated regions associated with imprinted genes. We further suggest that the high incidence of hemimethylation at secondary differentially methylated regions must be counteracted by continuous methylation acquisition at these loci.
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Affiliation(s)
- Julianna Nechin
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA, 19010-2899, USA
| | - Emma Tunstall
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA, 19010-2899, USA
| | - Naideline Raymond
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA, 19010-2899, USA
| | - Nicole Hamagami
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA, 19010-2899, USA
| | - Chris Pathmanabhan
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA, 19010-2899, USA
| | - Samantha Forestier
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA, 19010-2899, USA
| | - Tamara L Davis
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA, 19010-2899, USA.
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18
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Lee HJ, Choi NY, Lee SW, Lee Y, Ko K, Kim GJ, Hwang HS, Ko K. Alteration of Genomic Imprinting Status of Human Parthenogenetic Induced Pluripotent Stem Cells during Neural Lineage Differentiation. Int J Stem Cells 2019; 12:31-42. [PMID: 30836722 PMCID: PMC6457707 DOI: 10.15283/ijsc18084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 11/19/2018] [Accepted: 12/29/2018] [Indexed: 12/16/2022] Open
Abstract
Background and Objectives Genomic imprinting modulates growth and development in mammals and is associated with genetic disorders. Although uniparental embryonic stem cells have been used to study genomic imprinting, there is an ethical issue associated with the destruction of human embryos. In this study, to investigate the genomic imprinting status in human neurodevelopment, we used human uniparental induced pluripotent stem cells (iPSCs) that possessed only maternal alleles and differentiated into neural cell lineages. Methods Human somatic iPSCs (hSiPSCs) and human parthenogenetic iPSCs (hPgiPSCs) were differentiated into neural stem cells (NSCs) and named hSi-NSCs and hPgi-NSCs respectively. DNA methylation and gene expression of imprinted genes related neurodevelopment was analyzed during reprogramming and neural lineage differentiation. Results The DNA methylation and expression of imprinted genes were altered or maintained after differentiation into NSCs. The imprinting status in NSCs were maintained after terminal differentiation into neurons and astrocytes. In contrast, gene expression was differentially presented in a cell type-specific manner. Conclusions This study suggests that genomic imprinting should be determined in each neural cell type because the genomic imprinting status can differ in a cell type-specific manner. In addition, the in vitro model established in this study would be useful for verifying the epigenetic alteration of imprinted genes which can be differentially changed during neurodevelopment in human and for screening novel imprinted genes related to neurodevelopment. Moreover, the confirmed genomic imprinting status could be used to find out an abnormal genomic imprinting status of imprinted genes related with neurogenetic disorders according to uniparental genotypes.
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Affiliation(s)
- Hye Jeong Lee
- Departement of Stem Cell Biology, Konkuk University School of Medicine, Seoul, Korea.,Center for Stem Cell Research, Institute of Advanced Biomedical Science, Konkuk University, Seoul, Korea
| | - Na Young Choi
- Departement of Stem Cell Biology, Konkuk University School of Medicine, Seoul, Korea.,Center for Stem Cell Research, Institute of Advanced Biomedical Science, Konkuk University, Seoul, Korea
| | - Seung-Wong Lee
- Departement of Stem Cell Biology, Konkuk University School of Medicine, Seoul, Korea.,Center for Stem Cell Research, Institute of Advanced Biomedical Science, Konkuk University, Seoul, Korea
| | - Yukyeong Lee
- Departement of Stem Cell Biology, Konkuk University School of Medicine, Seoul, Korea.,Center for Stem Cell Research, Institute of Advanced Biomedical Science, Konkuk University, Seoul, Korea
| | - Kisung Ko
- Departments of Medicine, College of Medicine, Chung-Ang University, Seoul, Korea
| | - Gwang Jun Kim
- Departments of Obstetrics and Gynecology, College of Medicine, Chung-Ang University, Seoul, Korea
| | - Han Sung Hwang
- Department of Obstetrics and Gynecology, Konkuk University School of Medicine, Seoul, Korea
| | - Kinarm Ko
- Departement of Stem Cell Biology, Konkuk University School of Medicine, Seoul, Korea.,Center for Stem Cell Research, Institute of Advanced Biomedical Science, Konkuk University, Seoul, Korea.,Research Institute of Medical Science, Konkuk University, Seoul, Korea
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19
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Artiles KL, Fire AZ, Frøkjær-Jensen C. Assessment and Maintenance of Unigametic Germline Inheritance for C. elegans. Dev Cell 2019; 48:827-839.e9. [PMID: 30799227 PMCID: PMC6435406 DOI: 10.1016/j.devcel.2019.01.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 11/06/2018] [Accepted: 01/21/2019] [Indexed: 12/22/2022]
Abstract
The recent work of Besseling and Bringmann (2016) identified a molecular intervention for C. elegans in which premature segregation of maternal and paternal chromosomes in the fertilized oocyte can produce viable animals exhibiting a non-Mendelian inheritance pattern. Overexpression in embryos of a single protein regulating chromosome segregation (GPR-1) provides a germline derived clonally from a single parental gamete. We present a collection of strains and cytological assays to consistently generate and track non-Mendelian inheritance. These tools allow reproducible and high-frequency (>80%) production of non-Mendelian inheritance, the facile and simultaneous homozygosis for all nuclear chromosomes in a single generation, the precise exchange of nuclear and mitochondrial genomes between strains, and the assessments of non-canonical mitosis events. We show the utility of these strains by demonstrating a rapid assessment of cell lineage requirements (AB versus P1) for a set of genes (lin-2, lin-3, lin-12, and lin-31) with roles in C. elegans vulval development.
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Affiliation(s)
- Karen L Artiles
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew Z Fire
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Christian Frøkjær-Jensen
- King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division, KAUST Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia.
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20
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Kaneshiro KR, Rechtsteiner A, Strome S. Sperm-inherited H3K27me3 impacts offspring transcription and development in C. elegans. Nat Commun 2019; 10:1271. [PMID: 30894520 PMCID: PMC6426959 DOI: 10.1038/s41467-019-09141-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/21/2019] [Indexed: 01/28/2023] Open
Abstract
Paternal epigenetic inheritance is gaining attention for its growing medical relevance. However, the form in which paternal epigenetic information is transmitted to offspring and how it influences offspring development remain poorly understood. Here we show that in C. elegans, sperm-inherited chromatin states transmitted to the primordial germ cells in offspring influence germline transcription and development. We show that sperm chromosomes inherited lacking the repressive histone modification H3K27me3 are maintained in that state by H3K36me3 antagonism. Inheritance of H3K27me3-lacking sperm chromosomes results in derepression in the germline of somatic genes, especially neuronal genes, predominantly from sperm-inherited alleles. This results in germ cells primed for losing their germ cell identity and adopting a neuronal fate. These data demonstrate that histone modifications are one mechanism through which epigenetic information from a father can shape offspring gene expression and development. The mechanisms of paternal epigenetic inheritance and its influence on offspring are still poorly understood. Here the authors provide evidence that in C. elegans, sperm-inherited chromatin states influence transcription and cell identity in the germ cells of offspring.
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Affiliation(s)
- Kiyomi Raye Kaneshiro
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Andreas Rechtsteiner
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Susan Strome
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA.
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21
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Abstract
PURPOSE OF REVIEW Sotos syndrome is among a growing list of disorders resulting from mutations in epigenetic machinery genes. These Mendelian disorders of the epigenetic machinery (MDEMs) exhibit phenotypic overlap broadly characterized by intellectual disability and atypical growth and behaviors. Manifestations of Sotos syndrome include a distinct facial appearance, overgrowth, intellectual disability, and behavioral issues. Herein we review key aspects of Sotos syndrome, focusing on the neurobehavioral phenotype. Additionally, we highlight recent advances in our understanding of molecular pathogenesis implicating epigenetic mechanisms. RECENT FINDINGS Increasing evidence suggests MDEMs account for ∼19% of intellectual disability and ∼45% of overgrowth combined with intellectual disability, with Sotos syndrome constituting most of the latter. Although the genetic cause of Sotos syndrome, disruption of the histone methyltransferase writer NSD1, is well established, recent studies have further delineated the neurobehavioral phenotype and provided insight into disease pathogenesis. Explicitly, NSD1 target genes accounting for a subset of Sotos syndrome features and a specific DNA methylation signature have been identified. SUMMARY Sotos syndrome is, therefore, a genetic disorder with epigenetic consequences. Its characteristic neurobehavioral phenotype and those of related MDEMs illustrate the essential role epigenetic mechanisms play in neurologic development. Improvement in our understanding of molecular pathogenesis has important implications for development of diagnostic tests and therapeutic interventions.
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22
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Wang HQ, Yang CY, Wang SY, Wang T, Han JL, Wei K, Liu FC, Xu JD, Peng XZ, Wang JM. Cell-free plasma hypermethylated CASZ1, CDH13 and ING2 are promising biomarkers of esophageal cancer. J Biomed Res 2018; 32:424-433. [PMID: 30355852 PMCID: PMC6283827 DOI: 10.7555/jbr.32.20170065] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Identifying sensitive and specific biomarkers for early detection of cancer is immensely imperative for early diagnosis and treatment and better clinical outcome of cancer patients. This study aimed to construct a specific DNA methylation pattern of cancer suppressor genes and explore the feasibility of applying cell-free DNA based methylation as a biomarker for early diagnosis of esophageal squamous cell carcinoma (ESCC). We recruited early stage ESCC patients from Yangzhong County, China. The Illumina Infinium 450K Methylation BeadChip was used to construct a genome-wide DNA methylation profile. Then, differentiated genes were selected for the validation study using the Sequenom MassARRAY platform. The frequency of methylation was compared between cancer tissues, matched cell-free DNAs and normal controls. The specific methylation profiles were constructed, and the sensitivity and specificity were calculated. Seven CG sites in three genes CASZ1, CDH13 and ING2 were significantly hypermethylated in ESCC as compared with normal controls. A significant correlation was found between the methylation of DNA extracted from cancer tissues and matched plasma cell-free DNA, either for individual CG site or for cumulative methylation analysis. The sensitivity and specificity reached 100% at an appropriate cut-point using these specific methylation biomarkers. This study revealed that aberrant DNA methylation is a promising biomarker for molecular diagnosis of esophageal cancer. Hypermethylation of CASZ1, CDH13 and ING2 detected in plasma cell-free DNA can be applied as a potential noninvasive biomarker for diagnosis of esophageal cancer.
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Affiliation(s)
- Huan-Qiang Wang
- Department of Public Health and Preventive Medicine, Kangda College of Nanjing Medical University, Lianyungang, Jiangsu 222000, China
| | - Cong-Ying Yang
- Department of Social Medicine and Health Education,School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Si-Yuan Wang
- Department of Clinical Medicine, Kangda College of Nanjing Medical University, Lianyungang, Jiangsu 222000, China
| | - Tian Wang
- Department of Public Health and Preventive Medicine, Kangda College of Nanjing Medical University, Lianyungang, Jiangsu 222000, China
| | - Jing-Ling Han
- Department of Public Health and Preventive Medicine, Kangda College of Nanjing Medical University, Lianyungang, Jiangsu 222000, China
| | - Kai Wei
- Department of Public Health and Preventive Medicine, Kangda College of Nanjing Medical University, Lianyungang, Jiangsu 222000, China
| | - Fu-Cun Liu
- Department of Public Health and Preventive Medicine, Kangda College of Nanjing Medical University, Lianyungang, Jiangsu 222000, China
| | - Ji-da Xu
- Department of Public Health and Preventive Medicine, Kangda College of Nanjing Medical University, Lianyungang, Jiangsu 222000, China
| | - Xian-Zhen Peng
- Department of Public Health and Preventive Medicine, Kangda College of Nanjing Medical University, Lianyungang, Jiangsu 222000, China.,Department of Epidemiology,, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Jian-Ming Wang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
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23
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Nishitani S, Parets SE, Haas BW, Smith AK. DNA methylation analysis from saliva samples for epidemiological studies. Epigenetics 2018; 13:352-362. [PMID: 29912612 DOI: 10.1080/15592294.2018.1461295] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Abstract
Saliva is a non-invasive, easily accessible tissue, which is regularly collected in large epidemiological studies to examine genetic questions. Recently, it is becoming more common to use saliva to assess DNA methylation. However, DNA extracted from saliva is a mixture of both bacterial and human DNA derived from epithelial and immune cells in the mouth. Thus, there are unique challenges to using salivary DNA in methylation studies that can influence data quality. This study assesses: (1) quantification of human DNA after extraction; (2) delineation of human and bacterial DNA; (3) bisulfite conversion (BSC); (4) quantification of BSC DNA; (5) PCR amplification of BSC DNA from saliva and; (6) quantitation of DNA methylation with a targeted assay. The framework proposed will allow saliva samples to be more widely used in targeted epigenetic studies.
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Affiliation(s)
- Shota Nishitani
- a Department of Gynecology and Obstetrics , Emory University School of Medicine , Atlanta , GA , USA.,b Department of Psychiatry and Behavioral Sciences , Emory University School of Medicine , Atlanta , GA , USA
| | - Sasha E Parets
- b Department of Psychiatry and Behavioral Sciences , Emory University School of Medicine , Atlanta , GA , USA
| | - Brian W Haas
- c Department of Psychology , University of Georgia , Athens , GA , USA
| | - Alicia K Smith
- a Department of Gynecology and Obstetrics , Emory University School of Medicine , Atlanta , GA , USA.,b Department of Psychiatry and Behavioral Sciences , Emory University School of Medicine , Atlanta , GA , USA
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24
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Ruggeri B, Macare C, Stopponi S, Jia T, Carvalho FM, Robert G, Banaschewski T, Bokde ALW, Bromberg U, Büchel C, Cattrell A, Conrod PJ, Desrivières S, Flor H, Frouin V, Gallinat J, Garavan H, Gowland P, Heinz A, Ittermann B, Martinot JL, Paillère Martinot ML, Nees F, Papadopoulos-Orfanos D, Paus T, Poustka L, Smolka MN, Vetter NC, Walter H, Whelan R, Sommer WH, Bakalkin G, Ciccocioppo R, Schumann G. Methylation of OPRL1 mediates the effect of psychosocial stress on binge drinking in adolescents. J Child Psychol Psychiatry 2018; 59:650-658. [PMID: 29197086 PMCID: PMC5975104 DOI: 10.1111/jcpp.12843] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/16/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND Nociceptin is a key regulator linking environmental stress and alcohol drinking. In a genome-wide methylation analysis, we recently identified an association of a methylated region in the OPRL1 gene with alcohol-use disorders. METHODS Here, we investigate the biological basis of this observation by analysing psychosocial stressors, methylation of the OPRL1 gene, brain response during reward anticipation and alcohol drinking in 660 fourteen-year-old adolescents of the IMAGEN study. We validate our findings in marchigian sardinian (msP) alcohol-preferring rats that are genetically selected for increased alcohol drinking and stress sensitivity. RESULTS We found that low methylation levels in intron 1 of OPRL1 are associated with higher psychosocial stress and higher frequency of binge drinking, an effect mediated by OPRL1 methylation. In individuals with low methylation of OPRL1, frequency of binge drinking is associated with stronger BOLD response in the ventral striatum during reward anticipation. In msP rats, we found that stress results in increased alcohol intake and decreased methylation of OPRL1 in the nucleus accumbens. CONCLUSIONS Our findings describe an epigenetic mechanism that helps to explain how psychosocial stress influences risky alcohol consumption and reward processing, thus contributing to the elucidation of biological mechanisms underlying risk for substance abuse.
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Affiliation(s)
- Barbara Ruggeri
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, UK,MRC Social, Genetic and Developmental Psychiatry (SGDP) Centre, London, UK
| | - Christine Macare
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, UK,MRC Social, Genetic and Developmental Psychiatry (SGDP) Centre, London, UK
| | | | - Tianye Jia
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, UK,MRC Social, Genetic and Developmental Psychiatry (SGDP) Centre, London, UK
| | - Fabiana M. Carvalho
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, UK,MRC Social, Genetic and Developmental Psychiatry (SGDP) Centre, London, UK
| | - Gabriel Robert
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, UK,MRC Social, Genetic and Developmental Psychiatry (SGDP) Centre, London, UK
| | - Tobias Banaschewski
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Arun LW Bokde
- Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
| | - Uli Bromberg
- Universitaetsklinikum Hamburg Eppendorf, Hamburg, Germany
| | | | - Anna Cattrell
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, UK,MRC Social, Genetic and Developmental Psychiatry (SGDP) Centre, London, UK
| | - Patricia J Conrod
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, UK,Department of Psychiatry, Université de Montreal, Canada
| | - Sylvane Desrivières
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, UK,MRC Social, Genetic and Developmental Psychiatry (SGDP) Centre, London, UK
| | - Herta Flor
- Department of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Heidelberg University, Mannheim, Germany
| | - Vincent Frouin
- Neurospin, Commissariat à l'Energie Atomique et aux Energies Alternatives, Paris, France
| | - Jürgen Gallinat
- Department of Psychiatry and Psychotherapy, Campus Charité Mitte, Charité – Universitätsmedizin Berlin, Germany
| | - Hugh Garavan
- Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland,Departments of Psychiatry and Psychology, University of Vermont, USA
| | | | - Andreas Heinz
- Department of Psychiatry and Psychotherapy, Campus Charité Mitte, Charité – Universitätsmedizin Berlin, Germany
| | - Bernd Ittermann
- Physikalisch-Technische Bundesanstalt (PTB), Braunschweig und Berlin, Germany
| | - Jean Luc Martinot
- Institut National de la Santé et de la Recherche Médicale, INSERM CEA Unit 1000 “Imaging & Psychiatry”, University Paris Sud, Orsay
| | - Marie-Laure Paillère Martinot
- Institut National de la Santé et de la Recherche Médicale, INSERM CEA Unit 1000 “Imaging & Psychiatry”, University Paris Sud, Orsay
| | - Frauke Nees
- Department of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Heidelberg University, Mannheim, Germany
| | | | - Tomáš Paus
- School of Psychology, University of Nottingham, UK,Rotman Research Institute, University of Toronto, Toronto, Canada,Child Mind Institute, New York, USA
| | - Luise Poustka
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Michael N Smolka
- Department of Psychiatry and Psychotherapy, Technische Universität Dresden, Germany
| | - Nora C. Vetter
- Department of Psychiatry and Psychotherapy, Technische Universität Dresden, Germany
| | - Henrik Walter
- Department of Psychiatry and Psychotherapy, Campus Charité Mitte, Charité – Universitätsmedizin Berlin, Germany
| | | | - Wolfgang H Sommer
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Georgy Bakalkin
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | | | - Gunter Schumann
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, UK,MRC Social, Genetic and Developmental Psychiatry (SGDP) Centre, London, UK
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25
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Tikhodeyev ON. The mechanisms of epigenetic inheritance: how diverse are they? Biol Rev Camb Philos Soc 2018; 93:1987-2005. [PMID: 29790249 DOI: 10.1111/brv.12429] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/22/2018] [Accepted: 04/27/2018] [Indexed: 12/18/2022]
Abstract
Although epigenetic inheritance (EI) is a rapidly growing field of modern biology, it still has no clear place in fundamental genetic concepts which are traditionally based on the hereditary role of DNA. Moreover, not all mechanisms of EI attract the same attention, with most studies focused on DNA methylation, histone modification, RNA interference and amyloid prionization, but relatively few considering other mechanisms such as stable inhibition of plastid translation. Herein, we discuss all known and some hypothetical mechanisms that can underlie the stable inheritance of phenotypically distinct hereditary factors that lack differences in DNA sequence. These mechanisms include (i) regulation of transcription by DNA methylation, histone modifications, and transcription factors, (ii) RNA splicing, (iii) RNA-mediated post-transcriptional silencing, (iv) organellar translation, (v) protein processing by truncation, (vi) post-translational chemical modifications, (vii) protein folding, and (viii) homologous and non-homologous protein interactions. The breadth of this list suggests that any or almost any regulatory mechanism that participates in gene expression or gene-product functioning, under certain circumstances, may produce EI. Although the modes of EI are highly variable, in many epigenetic systems, stable allelic variants can be distinguished. Irrespective of their nature, all such alleles have an underlying similarity: each is a bimodular hereditary unit, whose features depend on (i) a certain epigenetic mark (epigenetic determinant) in the DNA sequence or its product, and (ii) the DNA sequence itself (DNA determinant; if this is absent, the epigenetic allele fails to perpetuate). Thus, stable allelic epigenetic inheritance (SAEI) does not contradict the hereditary role of DNA, but involves additional molecular mechanisms with no or almost no limitations to their variety.
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Affiliation(s)
- Oleg N Tikhodeyev
- Department of Genetics & Biotechnology, Saint-Petersburg State University, Saint-Petersburg 199034, Russia
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26
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Daskalakis M, Brocks D, Sheng YH, Islam MS, Ressnerova A, Assenov Y, Milde T, Oehme I, Witt O, Goyal A, Kühn A, Hartmann M, Weichenhan D, Jung M, Plass C. Reactivation of endogenous retroviral elements via treatment with DNMT- and HDAC-inhibitors. Cell Cycle 2018; 17:811-822. [PMID: 29633898 DOI: 10.1080/15384101.2018.1442623] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Inhibitors of DNA methyltransferases (DNMTis) or histone deacetylases (HDACis) are epigenetic drugs which are investigated since decades. Several have been approved and are applied in the treatment of hematopoietic and lymphatic malignancies, although their mode of action has not been fully understood. Two recent findings improved mechanistic insights: i) activation of human endogenous retroviral elements (HERVs) with concomitant synthesis of double-stranded RNAs (dsRNAs), and ii) massive activation of promoters from long terminal repeats (LTRs) which originated from past HERV invasions. These dsRNAs activate an antiviral response pathway followed by apoptosis. LTR promoter activation leads to synthesis of non-annotated transcripts potentially encoding novel or cryptic proteins. Here, we discuss the current knowledge of the molecular effects exerted by epigenetic drugs with a focus on DNMTis and HDACis. We highlight the role in LTR activation and provide novel data from both in vitro and in vivo epigenetic drug treatment.
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Affiliation(s)
- Michael Daskalakis
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany.,f German Cancer Research Consortium (DKTK) , Heidelberg , Germany
| | - David Brocks
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Yi-Hua Sheng
- b School of Pharmacy, College of Medicine , National Taiwan University , Taipei , Taiwan
| | - Md Saiful Islam
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Alzbeta Ressnerova
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Yassen Assenov
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Till Milde
- c Translational Program, Hopp Children's Cancer Center at NCT Heidelberg (KiTZ) , Germany.,d CCU Pediatric Oncology , German Cancer Research Center (DKFZ) , Heidelberg , Germany.,e Department of Pediatric Oncology, Hematology and Immunology , University Hospital, and Clinical Cooperation Unit Pediatric Oncology, DKFZ , Heidelberg , Germany.,f German Cancer Research Consortium (DKTK) , Heidelberg , Germany
| | - Ina Oehme
- c Translational Program, Hopp Children's Cancer Center at NCT Heidelberg (KiTZ) , Germany.,d CCU Pediatric Oncology , German Cancer Research Center (DKFZ) , Heidelberg , Germany.,e Department of Pediatric Oncology, Hematology and Immunology , University Hospital, and Clinical Cooperation Unit Pediatric Oncology, DKFZ , Heidelberg , Germany.,f German Cancer Research Consortium (DKTK) , Heidelberg , Germany
| | - Olaf Witt
- c Translational Program, Hopp Children's Cancer Center at NCT Heidelberg (KiTZ) , Germany.,d CCU Pediatric Oncology , German Cancer Research Center (DKFZ) , Heidelberg , Germany.,e Department of Pediatric Oncology, Hematology and Immunology , University Hospital, and Clinical Cooperation Unit Pediatric Oncology, DKFZ , Heidelberg , Germany.,f German Cancer Research Consortium (DKTK) , Heidelberg , Germany
| | - Ashish Goyal
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Alexander Kühn
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Mark Hartmann
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany.,g Regulation of Cellular Differentiation Group , German Cancer Research Center , Heidelberg , Germany
| | - Dieter Weichenhan
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Manfred Jung
- h Institute of Pharmaceutical Sciences, University of Freiburg , Germany
| | - Christoph Plass
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany.,f German Cancer Research Consortium (DKTK) , Heidelberg , Germany
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27
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Forensic DNA methylation profiling from minimal traces: How low can we go? Forensic Sci Int Genet 2018; 33:17-23. [DOI: 10.1016/j.fsigen.2017.11.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/02/2017] [Accepted: 11/10/2017] [Indexed: 12/15/2022]
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28
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Sosnowski DW, Booth C, York TP, Amstadter AB, Kliewer W. Maternal prenatal stress and infant DNA methylation: A systematic review. Dev Psychobiol 2018; 60:127-139. [PMID: 29344930 DOI: 10.1002/dev.21604] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 11/20/2017] [Accepted: 11/20/2017] [Indexed: 01/08/2023]
Abstract
Maternal prenatal stress has been linked to a variety of infant postnatal outcomes, partially through alterations in fetal HPA axis functioning; yet the underlying pathobiology remains elusive. Current literature posits DNA methylation as a candidate mechanism through which maternal prenatal stress can influence fetal HPA axis functioning. The goal of this systematic review was to summarize the literature examining the associations among maternal prenatal stress, DNA methylation of commonly studied HPA axis candidate genes, and infant HPA axis functioning. Results from the review provided evidence for a link between various maternal prenatal stressors, NR3C1 methylation, and infant stress reactivity, but findings among other genes were limited, with mixed results. An original study quality review tool revealed that a majority of studies in the review are adequate, and emphasizes the need for future research to consider study quality when interpreting research findings.
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Affiliation(s)
- David W Sosnowski
- Department of Psychology, Virginia Commonwealth University, Richmond, Virginia
| | - Carolyn Booth
- Department of Psychology, Virginia Commonwealth University, Richmond, Virginia
| | - Timothy P York
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia
| | - Ananda B Amstadter
- Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Wendy Kliewer
- Department of Psychology, Virginia Commonwealth University, Richmond, Virginia
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29
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Irimie AI, Braicu C, Sonea L, Zimta AA, Cojocneanu-Petric R, Tonchev K, Mehterov N, Diudea D, Buduru S, Berindan-Neagoe I. A Looking-Glass of Non-coding RNAs in oral cancer. Int J Mol Sci 2017; 18:ijms18122620. [PMID: 29206174 PMCID: PMC5751223 DOI: 10.3390/ijms18122620] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 11/10/2017] [Accepted: 11/17/2017] [Indexed: 12/14/2022] Open
Abstract
Oral cancer is a multifactorial pathology and is characterized by the lack of efficient treatment and accurate diagnostic tools. This is mainly due the late diagnosis; therefore, reliable biomarkers for the timely detection of the disease and patient stratification are required. Non-coding RNAs (ncRNAs) are key elements in the physiological and pathological processes of various cancers, which is also reflected in oral cancer development and progression. A better understanding of their role could give a more thorough perspective on the future treatment options for this cancer type. This review offers a glimpse into the ncRNA involvement in oral cancer, which can help the medical community tap into the world of ncRNAs and lay the ground for more powerful diagnostic, prognostic and treatment tools for oral cancer that will ultimately help build a brighter future for these patients.
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Affiliation(s)
- Alexandra Iulia Irimie
- Department of Prosthetic dentistry and Dental materials, Division Dental Propaedeutics, Aesthetic, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Cornelia Braicu
- Research Center for Functional Genomics and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Laura Sonea
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu-Hatieganu, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Alina Andreea Zimta
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu-Hatieganu, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Roxana Cojocneanu-Petric
- Research Center for Functional Genomics and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Konstantin Tonchev
- Department of Maxillofacial Surgery, Medical University, 3 Hristo Botev Blvd, 4002 Plovdiv, Bulgaria.
- Clinic of Maxillofacial Surgery, University Hospital "St. George", 66 Peshtersko Shosse Blvd, 4002 Plovdiv, Bulgaria.
| | - Nikolay Mehterov
- Department of Medical Biology, Medical University Plovdiv, 15-А Vasil Aprilov Bul, 4002 Plovdiv, Bulgaria.
| | - Diana Diudea
- Department of Prosthetic dentistry and Dental materials, Division Dental Propaedeutics, Aesthetic, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Smaranda Buduru
- Prosthetics and Dental materials, Faculty of Dental Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, 32 Clinicilor Street, 400006 Cluj-Napoca, Romania.
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu-Hatieganu, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
- Department of Functional Genomics and Experimental Pathology, The Oncology Institute "Prof. Dr. Ion Chiricuta", Republicii 34th street, 400015 Cluj-Napoca, Romania.
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30
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Gapp K, Bohacek J. Epigenetic germline inheritance in mammals: looking to the past to understand the future. GENES BRAIN AND BEHAVIOR 2017; 17:e12407. [PMID: 28782190 DOI: 10.1111/gbb.12407] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 07/15/2017] [Accepted: 08/03/2017] [Indexed: 12/25/2022]
Abstract
Life experiences can induce epigenetic changes in mammalian germ cells, which can influence the developmental trajectory of the offspring and impact health and disease across generations. While this concept of epigenetic germline inheritance has long been met with skepticism, evidence in support of this route of information transfer is now overwhelming, and some key mechanisms underlying germline transmission of acquired information are emerging. This review focuses specifically on sperm RNAs as causal vectors of inheritance. We examine how they might become altered in the germline, and how different classes of sperm RNAs might interact with other epimodifications in germ cells or in the zygote. We integrate the latest findings with earlier pioneering work in this field, point out major questions and challenges, and suggest how new experiments could address them.
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Affiliation(s)
- K Gapp
- Gurdon Institute, University of Cambridge, Cambridge, UK.,Wellcome Trust Sanger Institute, Hinxton, UK
| | - J Bohacek
- Laboratory of Molecular and Behavioral Neuroscience, Department of Health Sciences and Technology of ETH Zurich, Neuroscience Center Zurich, Switzerland
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31
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Abraham JM, Meltzer SJ. Long Noncoding RNAs in the Pathogenesis of Barrett's Esophagus and Esophageal Carcinoma. Gastroenterology 2017; 153:27-34. [PMID: 28528706 PMCID: PMC5515484 DOI: 10.1053/j.gastro.2017.04.046] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 04/26/2017] [Accepted: 04/28/2017] [Indexed: 12/13/2022]
Abstract
For many years, only a small fraction of the human genome was believed to regulate cell function and development. This protein-coding portion composed only 1% to 2% of 3 billion human DNA base pairs-the remaining sequence was classified as junk DNA. Subsequent research has revealed that most of the genome is transcribed into a broad array of noncoding RNAs, ranging in size from microRNA (20-23 nucleotides) to long noncoding RNA (lncRNA, more than 200 nucleotides). These noncoding RNA classes have been shown to use diverse molecular mechanisms to control gene expression and organ system development. As anticipated, alterations in this large control system can contribute to disease pathogenesis and carcinogenesis. We review the involvement of noncoding RNAs, lncRNAs in particular, in development of Barrett's esophagus and esophageal carcinoma.
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32
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Guntrum M, Vlasova E, Davis TL. Asymmetric DNA methylation of CpG dyads is a feature of secondary DMRs associated with the Dlk1/ Gtl2 imprinting cluster in mouse. Epigenetics Chromatin 2017. [PMID: 28649282 PMCID: PMC5480104 DOI: 10.1186/s13072-017-0138-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Background Differential DNA methylation plays a critical role in the regulation of imprinted genes. The differentially methylated state of the imprinting control region is inherited via the gametes at fertilization, and is stably maintained in somatic cells throughout development, influencing the expression of genes across the imprinting cluster. In contrast, DNA methylation patterns are more labile at secondary differentially methylated regions which are established at imprinted loci during post-implantation development. To investigate the nature of these more variably methylated secondary differentially methylated regions, we adopted a hairpin linker bisulfite mutagenesis approach to examine CpG dyad methylation at differentially methylated regions associated with the murine Dlk1/Gtl2 imprinting cluster on both complementary strands. Results We observed homomethylation at greater than 90% of the methylated CpG dyads at the IG-DMR, which serves as the imprinting control element. In contrast, homomethylation was only observed at 67–78% of the methylated CpG dyads at the secondary differentially methylated regions; the remaining 22–33% of methylated CpG dyads exhibited hemimethylation. Conclusions We propose that this high degree of hemimethylation could explain the variability in DNA methylation patterns at secondary differentially methylated regions associated with imprinted loci. We further suggest that the presence of 5-hydroxymethylation at secondary differentially methylated regions may result in hemimethylation and methylation variability as a result of passive and/or active demethylation mechanisms. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0138-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Megan Guntrum
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA 19010-2899 USA
| | - Ekaterina Vlasova
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA 19010-2899 USA
| | - Tamara L Davis
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA 19010-2899 USA
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33
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Gebert C, Correia L, Li Z, Petrie HT, Love PE, Pfeifer K. Chromosome choice for initiation of V-(D)-J recombination is not governed by genomic imprinting. Immunol Cell Biol 2017; 95:473-477. [PMID: 28244489 PMCID: PMC5788196 DOI: 10.1038/icb.2017.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 12/16/2016] [Accepted: 12/18/2016] [Indexed: 01/04/2023]
Abstract
V-(D)-J recombination generates the antigen receptor diversity necessary for immune cell function, while allelic exclusion ensures that each cell expresses a single antigen receptor. V-(D)-J recombination of the Ig, Tcrb, Tcrg and Tcrd antigen receptor genes is ordered and sequential so that only one allele generates a productive rearrangement. The mechanism controlling sequential rearrangement of antigen receptor genes, in particular how only one allele is selected to initiate recombination while at least temporarily leaving the other intact, remains unresolved. Genomic imprinting, a widespread phenomenon wherein maternal or paternal allele inheritance determines allele activity, could represent a regulatory mechanism for controlling sequential V-(D)-J rearrangement. We used strain-specific single-nucleotide polymorphisms within antigen receptor genes to determine if maternal vs paternal inheritance could underlie chromosomal choice for the initiation of recombination. We found no parental chromosomal bias in the initiation of V-(D)-J recombination in T or B cells, eliminating genomic imprinting as a potential regulator for this tightly regulated process.
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Affiliation(s)
- Claudia Gebert
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 USA
| | - Lauren Correia
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 USA
| | - Zhenhu Li
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 USA
| | | | - Paul E Love
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 USA
| | - Karl Pfeifer
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 USA
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34
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Bouschet T, Dubois E, Reynès C, Kota SK, Rialle S, Maupetit-Méhouas S, Pezet M, Le Digarcher A, Nidelet S, Demolombe V, Cavelier P, Meusnier C, Maurizy C, Sabatier R, Feil R, Arnaud P, Journot L, Varrault A. In Vitro Corticogenesis from Embryonic Stem Cells Recapitulates the In Vivo Epigenetic Control of Imprinted Gene Expression. Cereb Cortex 2017; 27:2418-2433. [PMID: 27095822 DOI: 10.1093/cercor/bhw102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In vitro corticogenesis from embryonic stem cells (ESCs) is an attractive model of cortical development and a promising tool for cortical therapy. It is unknown to which extent epigenetic mechanisms crucial for cortex development and function, such as parental genomic imprinting, are recapitulated by in vitro corticogenesis. Here, using genome-wide transcriptomic and methylation analyses on hybrid mouse tissues and cells, we find a high concordance of imprinting status between in vivo and ESC-derived cortices. Notably, in vitro corticogenesis strictly reproduced the in vivo parent-of-origin-dependent expression of 41 imprinted genes (IGs), including Mest and Cdkn1c known to control corticogenesis. Parent-of-origin-dependent DNA methylation was also conserved at 14 of 18 imprinted differentially methylated regions. The least concordant imprinted locus was Gpr1-Zdbf2, where the aberrant bi-allelic expression of Zdbf2 and Adam23 was concomitant with a gain of methylation on the maternal allele in vitro. Combined, our data argue for a broad conservation of the epigenetic mechanisms at imprinted loci in cortical cells derived from ESCs. We propose that in vitro corticogenesis helps to define the still poorly understood mechanisms that regulate imprinting in the brain and the roles of IGs in cortical development.
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Affiliation(s)
- Tristan Bouschet
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France
| | - Emeric Dubois
- Montpellier GenomiX, BioCampus Montpellier, CNRS UMS3426, INSERM US009, Université de Montpellier, Montpellier, France
| | - Christelle Reynès
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France
| | - Satya K Kota
- Institute of Molecular Genetics (IGMM), CNRS UMR 5535, University of Montpellier, Montpellier, France
| | - Stéphanie Rialle
- Montpellier GenomiX, BioCampus Montpellier, CNRS UMS3426, INSERM US009, Université de Montpellier, Montpellier, France
| | - Stéphanie Maupetit-Méhouas
- GReD (Genetics, Reproduction and Development), CNRS UMR6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Mikael Pezet
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France
| | - Anne Le Digarcher
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France
| | - Sabine Nidelet
- Montpellier GenomiX, BioCampus Montpellier, CNRS UMS3426, INSERM US009, Université de Montpellier, Montpellier, France
| | - Vincent Demolombe
- Montpellier GenomiX, BioCampus Montpellier, CNRS UMS3426, INSERM US009, Université de Montpellier, Montpellier, France
| | - Patricia Cavelier
- Institute of Molecular Genetics (IGMM), CNRS UMR 5535, University of Montpellier, Montpellier, France
| | - Céline Meusnier
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France
| | - Chloé Maurizy
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France.,Institute of Molecular Genetics (IGMM), CNRS UMR 5535, University of Montpellier, Montpellier, France
| | - Robert Sabatier
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics (IGMM), CNRS UMR 5535, University of Montpellier, Montpellier, France
| | - Philippe Arnaud
- GReD (Genetics, Reproduction and Development), CNRS UMR6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Laurent Journot
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France.,Montpellier GenomiX, BioCampus Montpellier, CNRS UMS3426, INSERM US009, Université de Montpellier, Montpellier, France
| | - Annie Varrault
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France
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Liu Y, Tang Y, Ye D, Ma W, Feng S, Li X, Zhou X, Chen X, Chen S. Impact of Abnormal DNA Methylation of Imprinted Loci on Human Spontaneous Abortion. Reprod Sci 2017; 25:131-139. [PMID: 28443481 DOI: 10.1177/1933719117704906] [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] [Indexed: 12/27/2022]
Abstract
Currently, there is a growing concern regarding the safety of assisted reproductive technology (ART) due to increased risk of spontaneous abortion (SA) and imprinting disorders in ART-conceived offspring. Early investigations suggested that aberrant genetic imprinting may be related to pregnancy loss; however, few studies have used human tissue specimens. Here the DNA methylation patterns of 3 imprinted genes, including maternally inherited GRB10 and the paternally inherited IGF2 and PEG3 genes, were evaluated in human chorionic villus samples by pyrosequencing and bisulfite sequencing polymerase chain reaction. The samples were divided into 4 groups: (1) SA of natural conception (NC; n = 84), (2) induced abortion of NC (n = 94), (3) SA after ART (n = 73), and (4) fetal reduction after ART (n = 86). The methylation levels and the percentages of abnormal methylation of the IGF2, GRB10, and PEG3 genes between the ART group and the NC group showed no significant difference. Both IGF2 and GRB10 genes showed higher methylation levels in the SA group compared to the non-SA group. Additionally, determining the single-nucleotide polymorphisms of 4 loci, including IGF2 rs3741205, rs3741206, rs3741211, and GRB10 rs2237457, showed that the TC+CC genotype of IGF2 rs3741211 had a 1.91-fold increased risk of SA after ART. However, there was no association between the mutant genotype of IGF2 rs3741211 and the methylation levels of IGF2 and H19, and ART might not affect the distribution of the abovementioned genotypes. It provides support for the opinion that genetic imprinting defects may be associated with SA, which might not be due to ART treatments.
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Affiliation(s)
- Yudong Liu
- 1 Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Yan Tang
- 1 Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China.,2 Center of Reproductive Medicine, Zhongshan City People's Hospital, Zhongshan, People's Republic of China
| | - Desheng Ye
- 1 Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Weixu Ma
- 1 Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Shuxian Feng
- 1 Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Xuelan Li
- 1 Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Xingyu Zhou
- 1 Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Xin Chen
- 1 Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Shiling Chen
- 1 Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
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Sazhenova EA, Nikitina TV, Skryabin NA, Minaycheva LI, Ivanova TV, Nemtseva TN, Yuriev SY, Evtushenko ID, Lebedev IN. Epigenetic status of imprinted genes in placenta during recurrent pregnancy loss. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417020090] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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A guide to designing germline-dependent epigenetic inheritance experiments in mammals. Nat Methods 2017; 14:243-249. [DOI: 10.1038/nmeth.4181] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 01/08/2017] [Indexed: 12/13/2022]
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Liu Y, Zheng H, Guo P, Feng S, Zhou X, Ye D, Chen X, Chen S. DNA methyltransferase 3A promoter polymorphism is associated with the risk of human spontaneous abortion after assisted reproduction techniques and natural conception. J Assist Reprod Genet 2017; 34:245-252. [PMID: 27817038 PMCID: PMC5306405 DOI: 10.1007/s10815-016-0837-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/25/2016] [Indexed: 12/16/2022] Open
Abstract
PURPOSE The aim of this study was to explore the association of the DNA-methyltransferase (DNMT)-3A and DNMT3B promoter polymorphisms with the risk of human spontaneous abortion after assisted reproduction techniques (ARTs) and natural conception. METHODS We collected tissues from women who underwent abortion procedures: (a) chorionic villus samples (CVS) and muscle samples (MS) from spontaneous abortions conceived by ART and natural cycle (study group), n = 152; and (b) CVS and MS from normal early pregnancy and second trimester (control group), n = 155. The single-nucleotide polymorphism (SNP) -448A > G in the DNMT3A promoter region and -149C/T polymorphism of DNMT3B were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and confirmed by sequencing. RESULTS The allele frequency of -448A among pregnancy loss group and control group was 34.2 % vs. 16.5 %, respectively. Compared with GG carriers, the DNMT3A -448AA homozygotes had an about 16-fold increased risk of spontaneous abortion [odds ratio (OR) = 16.130, 95 % confidence interval (CI), 3.665-70.984], and AG heterozygotes had an OR of 2.027 (95 % CI, 1.247-3.293). However, the distribution of -448A > G in individuals derived from ART pregnancies was not statistically significantly compared with those derived from spontaneous pregnancies (P = 0.661). For DNMT3B, we observed genotype frequencies of 100 % (TT) in the study group and the control group. CONCLUSIONS The DNMT3A -448A > G polymorphism may be a novel functional SNP and contribute to its genetic susceptibility to spontaneous abortion in Chinese women, and ART may not affect the distribution of -448A > G in pregnancy loss and normal pregnancy. The observed TT genotype of DMNT3B suggests that this is the predominant genotype of this population. The findings provide new insights into the etiology of human spontaneous abortion.
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Affiliation(s)
- Yudong Liu
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, No. 1838 Guangzhou Northern Road, Guangzhou, 510515, People's Republic of China
| | - Haiyan Zheng
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, No. 1838 Guangzhou Northern Road, Guangzhou, 510515, People's Republic of China
- Center of Reproductive Medicine, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, People's Republic of China
| | - Pingping Guo
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, No. 1838 Guangzhou Northern Road, Guangzhou, 510515, People's Republic of China
| | - Shuxian Feng
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, No. 1838 Guangzhou Northern Road, Guangzhou, 510515, People's Republic of China
| | - Xingyu Zhou
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, No. 1838 Guangzhou Northern Road, Guangzhou, 510515, People's Republic of China
| | - Desheng Ye
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, No. 1838 Guangzhou Northern Road, Guangzhou, 510515, People's Republic of China
| | - Xin Chen
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, No. 1838 Guangzhou Northern Road, Guangzhou, 510515, People's Republic of China
| | - Shiling Chen
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, No. 1838 Guangzhou Northern Road, Guangzhou, 510515, People's Republic of China.
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Das Tumorepigenom – von der Genregulation über die Tumorklassifikation zum Therapietarget. MED GENET-BERLIN 2017. [DOI: 10.1007/s11825-016-0115-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Zusammenfassung
Epigenetische Regulationsmechanismen sind essenziell für den koordinierten Ablauf zahlreicher zellulärer Prozesse wie die Differenzierung und Entwicklung oder auch die Anpassung der Genaktivität an die herrschenden Umweltbedingungen. Insbesondere Tumorerkrankungen gehen mit oftmals umfangreichen Alterationen im Epigenom einher. Diese Veränderungen sind dabei vielfach charakteristisch entweder für die Tumorentität, das Stadium der Erkrankung oder aber das klinische Ansprechen des Tumors auf eine Therapie und damit die individuelle Prognose des Patienten. Nach einer kurzen Darstellung epigenetischer Marker und ihrer Bedeutung bei malignen Erkrankungen werden in diesem Artikel Alterationen im Tumorepigenom und ihre Nutzbarkeit im Rahmen einer individualisierten Medizin exemplarisch vorgestellt.
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Thakur A, Mackin SJ, Irwin RE, O’Neill KM, Pollin G, Walsh C. Widespread recovery of methylation at gametic imprints in hypomethylated mouse stem cells following rescue with DNMT3A2. Epigenetics Chromatin 2016; 9:53. [PMID: 27895716 PMCID: PMC5118886 DOI: 10.1186/s13072-016-0104-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/08/2016] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Imprinted loci are paradigms of epigenetic regulation and are associated with a number of genetic disorders in human. A key characteristic of imprints is the presence of a gametic differentially methylated region (gDMR). Previous studies have indicated that DNA methylation lost from gDMRs could not be restored by DNMT1, or the de novo enzymes DNMT3A or 3B in stem cells, indicating that imprinted regions must instead undergo passage through the germline for reprogramming. However, previous studies were non-quantitative, were unclear on the requirement for DNMT3A/B and showed some inconsistencies. In addition, new putative gDMR has recently been described, along with an improved delineation of the existing gDMR locations. We therefore aimed to re-examine the dependence of methylation at gDMRs on the activities of the methyltransferases in mouse embryonic stem cells (ESCs). RESULTS We examined the most complete current set of imprinted gDMRs that could be assessed using quantitative pyrosequencing assays in two types of ESCs: those lacking DNMT1 (1KO) and cells lacking a combination of DNMT3A and DNMT3B (3abKO). We further verified results using clonal analysis and combined bisulfite and restriction analysis. Our results showed that loss of methylation was approximately equivalent in both cell types. 1KO cells rescued with a cDNA-expressing DNMT1 could not restore methylation at the imprinted gDMRs, confirming some previous observations. However, nearly all gDMRs were remethylated in 3abKO cells rescued with a DNMT3A2 expression construct (3abKO + 3a2). Transcriptional activity at the H19/Igf2 locus also tracked with the methylation pattern, confirming functional reprogramming in the latter. CONCLUSIONS These results suggested (1) a vital role for DNMT3A/B in methylation maintenance at imprints, (2) that loss of DNMT1 and DNMT3A/B had equivalent effects, (3) that rescue with DNMT3A2 can restore imprints in these cells. This may provide a useful system in which to explore factors influencing imprint reprogramming.
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Affiliation(s)
- Avinash Thakur
- Genomic Medicine Research Group, Biomedical Sciences Research Institute, Centre for Molecular Biosciences, University of Ulster, Coleraine, BT52 1SA UK
- Terry Fox Laboratory, BC Cancer Agency, 675 W 10th Ave, Vancouver, BC V5Z 1G1 Canada
| | - Sarah-Jayne Mackin
- Genomic Medicine Research Group, Biomedical Sciences Research Institute, Centre for Molecular Biosciences, University of Ulster, Coleraine, BT52 1SA UK
| | - Rachelle E. Irwin
- Genomic Medicine Research Group, Biomedical Sciences Research Institute, Centre for Molecular Biosciences, University of Ulster, Coleraine, BT52 1SA UK
| | - Karla M. O’Neill
- Genomic Medicine Research Group, Biomedical Sciences Research Institute, Centre for Molecular Biosciences, University of Ulster, Coleraine, BT52 1SA UK
- Centre for Experimental Medicine, The Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, 97 Lisburn Road, Belfast, BT9 7AE UK
| | - Gareth Pollin
- Genomic Medicine Research Group, Biomedical Sciences Research Institute, Centre for Molecular Biosciences, University of Ulster, Coleraine, BT52 1SA UK
| | - Colum Walsh
- Genomic Medicine Research Group, Biomedical Sciences Research Institute, Centre for Molecular Biosciences, University of Ulster, Coleraine, BT52 1SA UK
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Da Costa NM, Visoni SBC, Dos Santos IL, Barja-Fidalgo TC, Ribeiro-Pinto LF. Maternal protein restriction during lactation modulated the expression and activity of rat offspring hepatic CYP1A1, CYP1A2, CYP2B1, CYP2B2, and CYP2E1 during development. ACTA ACUST UNITED AC 2016; 49:e5238. [PMID: 27828666 PMCID: PMC5112539 DOI: 10.1590/1414-431x20165238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 08/31/2016] [Indexed: 12/28/2022]
Abstract
Early nutrition plays a long-term role in the predisposition to chronic diseases and
influences the metabolism of several drugs. This may happen through cytochromes P450
(CYPs) regulation, which are the main enzymes responsible for the metabolism of
xenobiotics. Here, we analyzed the effects of maternal protein restriction (MPR) on
the expression and activity of hepatic offspring’s CYPs during 90 days after birth,
using Wistar rats as a mammal model. Hepatic CYP1A1, CYP1A2, CYP2B1, CYP2B2 and
CYP2E1 mRNA and protein expression, and associated catalytic activities (ECOD, EROD,
MROD, BROD, PROD and PNPH) were evaluated in 15-, 30-, 60-, and 90-day-old offspring
from dams fed with either a 0% protein (MPR groups) or a standard diet (C groups)
during the 10 first days of lactation. Results showed that most CYP
genes were induced in 60- and 90-day-old MPR offspring. The inductions detected in
MPR60 and MPR90 were of 5.0- and 2.0-fold (CYP1A2), 3.7- and
2.0-fold (CYP2B2) and 9.8- and 5.8– fold (CYP2E1),
respectively, and a 3.8-fold increase of CYP2B1 in MPR90. No major
alterations were detected in CYP protein expression. The most relevant CYP catalytic
activities’ alterations were observed in EROD, BROD and PNPH. Nevertheless, they did
not follow the same pattern observed for mRNA expression, except for an induction of
EROD in MPR90 (3.5-fold) and of PNPH in MPR60 (2.2-fold). Together, these results
suggest that MPR during lactation was capable of altering the expression and activity
of the hepatic CYP enzymes evaluated in the offspring along development.
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Affiliation(s)
- N Meireles Da Costa
- Laboratório de Toxicologia e Biologia Molecular, Departamento de Bioquímica, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - S B C Visoni
- Laboratório de Toxicologia e Biologia Molecular, Departamento de Bioquímica, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - I L Dos Santos
- Laboratório de Toxicologia e Biologia Molecular, Departamento de Bioquímica, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - T C Barja-Fidalgo
- Laboratório de Farmacologia Celular e Molecular, Departamento de Biologia Celular, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - L F Ribeiro-Pinto
- Laboratório de Toxicologia e Biologia Molecular, Departamento de Bioquímica, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
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Abstract
Genomic DNA methylation functions to repress gene expression by interfering with transcription factor binding and/or recruiting repressive chromatin machinery. Recent data support contribution of regulated DNA methylation to embryonic pluripotency, development, and tissue differentiation; this important epigenetic mark is chemically stable yet enzymatically reversible-and heritable through the germline. Importantly, all the major components involved in dynamic DNA methylation are conserved in zebrafish, including the factors that "write, read, and erase" this mark. Therefore, the zebrafish has become an excellent model for studying most biological processes associated with DNA methylation in mammals. Here we briefly review the zebrafish model for studying DNA methylation and describe a series of methods for performing genome-wide DNA methylation analysis. We address and provide methods for methylated DNA immunoprecipitation followed by sequencing (MeDIP-Seq), bisulfite sequencing (BS-Seq), and reduced representation bisulfite sequencing (RRBS-Seq).
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Affiliation(s)
- P J Murphy
- University of Utah School of Medicine, Salt Lake City, UT, United States
| | - B R Cairns
- University of Utah School of Medicine, Salt Lake City, UT, United States
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43
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Abstract
Genomic imprinting, an inherently epigenetic phenomenon defined by parent of origin-dependent gene expression, is observed in mammals and flowering plants. Genome-scale surveys of imprinted expression and the underlying differential epigenetic marks have led to the discovery of hundreds of imprinted plant genes and confirmed DNA and histone methylation as key regulators of plant imprinting. However, the biological roles of the vast majority of imprinted plant genes are unknown, and the evolutionary forces shaping plant imprinting remain rather opaque. Here, we review the mechanisms of plant genomic imprinting and discuss theories of imprinting evolution and biological significance in light of recent findings.
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Affiliation(s)
- Jessica A Rodrigues
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California 94720, USA
| | - Daniel Zilberman
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California 94720, USA
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Abstract
Long non-coding RNAs (lncRNAs) are a diverse class of RNAs that engage in numerous biological processes across every branch of life. Although initially discovered as mRNA-like transcripts that do not encode proteins, recent studies have revealed features of lncRNAs that further distinguish them from mRNAs. In this Review, we describe special events in the lifetimes of lncRNAs - before, during and after transcription - and discuss how these events ultimately shape the unique characteristics and functional roles of lncRNAs.
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Affiliation(s)
- Jeffrey J Quinn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Bioengineering, Stanford University School of Medicine and School of Engineering, Stanford, California 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305, USA
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Epigenome Editing: State of the Art, Concepts, and Perspectives. Trends Genet 2015; 32:101-113. [PMID: 26732754 DOI: 10.1016/j.tig.2015.12.001] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 11/28/2015] [Accepted: 12/01/2015] [Indexed: 12/21/2022]
Abstract
Epigenome editing refers to the directed alteration of chromatin marks at specific genomic loci by using targeted EpiEffectors which comprise designed DNA recognition domains (zinc finger, TAL effector, or modified CRISPR/Cas9 complex) and catalytic domains from a chromatin-modifying enzyme. Epigenome editing is a promising approach for durable gene regulation, with many applications in basic research including the investigation of the regulatory functions and logic of chromatin modifications and cellular reprogramming. From a clinical point of view, targeted regulation of disease-related genes offers novel therapeutic avenues for many diseases. We review here the progress made in this field and discuss open questions in epigenetic regulation and its stability, methods to increase the specificity of epigenome editing, and improved delivery methods for targeted EpiEffectors. Future work will reveal if the approach of epigenome editing fulfills its great promise in basic research and clinical applications.
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Lazarus J, Mather KA, Thalamuthu A, Kwok JBJ. Genetic factors and epigenetic mechanisms of longevity: current perspectives. Epigenomics 2015; 7:1339-49. [PMID: 26639084 DOI: 10.2217/epi.15.80] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The exceptional longevity phenotype, defined as living beyond the age of 95, results from complex interactions between environmental and genetic factors. Epigenetic mechanisms, such as DNA methylation and histone modifications, mediate the interaction of these factors. This review will provide an overview of animal model studies used to examine age-related epigenetic modifications. Key human studies will be used to illustrate the progress made in the identification of the genetic loci associated with exceptional longevity, including APOE and FOXO3 and genes/loci that are also differentially methylated between long-lived individuals and younger controls. Future studies should focus on elucidating whether identified longevity genetic loci directly influence epigenetic mechanisms, especially on differentially methylated regions associated with longevity.
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Affiliation(s)
- Jessica Lazarus
- Neuroscience Research Australia, Barker Street, Randwick, Sydney, NSW 2031, Australia.,School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Karen A Mather
- Centre for Healthy Brain Aging, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - Anbupalam Thalamuthu
- Centre for Healthy Brain Aging, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - John B J Kwok
- Neuroscience Research Australia, Barker Street, Randwick, Sydney, NSW 2031, Australia.,School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
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Epigenetic changes in the developing brain: Effects on behavior. Proc Natl Acad Sci U S A 2015; 112:6789-95. [PMID: 26034282 DOI: 10.1073/pnas.1501482112] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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48
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Maupetit-Méhouas S, Montibus B, Nury D, Tayama C, Wassef M, Kota SK, Fogli A, Cerqueira Campos F, Hata K, Feil R, Margueron R, Nakabayashi K, Court F, Arnaud P. Imprinting control regions (ICRs) are marked by mono-allelic bivalent chromatin when transcriptionally inactive. Nucleic Acids Res 2015; 44:621-35. [PMID: 26400168 PMCID: PMC4737186 DOI: 10.1093/nar/gkv960] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 09/12/2015] [Indexed: 01/10/2023] Open
Abstract
Parental allele-specific expression of imprinted genes is mediated by imprinting control regions (ICRs) that are constitutively marked by DNA methylation imprints on the maternal or paternal allele. Mono-allelic DNA methylation is strictly required for the process of imprinting and has to be faithfully maintained during the entire life-span. While the regulation of DNA methylation itself is well understood, the mechanisms whereby the opposite allele remains unmethylated are unclear. Here, we show that in the mouse, at maternally methylated ICRs, the paternal allele, which is constitutively associated with H3K4me2/3, is marked by default by H3K27me3 when these ICRs are transcriptionally inactive, leading to the formation of a bivalent chromatin signature. Our data suggest that at ICRs, chromatin bivalency has a protective role by ensuring that DNA on the paternal allele remains unmethylated and protected against spurious and unscheduled gene expression. Moreover, they provide the proof of concept that, beside pluripotent cells, chromatin bivalency is the default state of transcriptionally inactive CpG island promoters, regardless of the developmental stage, thereby contributing to protect cell identity.
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Affiliation(s)
- Stéphanie Maupetit-Méhouas
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Bertille Montibus
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - David Nury
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Chiharu Tayama
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Michel Wassef
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France
| | - Satya K Kota
- Institute of Molecular Genetics, CNRS UMR-5535 and University of Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Anne Fogli
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Fabiana Cerqueira Campos
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Robert Feil
- Institute of Molecular Genetics, CNRS UMR-5535 and University of Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Raphael Margueron
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Franck Court
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Philippe Arnaud
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
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Strong E, Butcher D, Singhania R, Mervis C, Morris C, De Carvalho D, Weksberg R, Osborne L. Symmetrical Dose-Dependent DNA-Methylation Profiles in Children with Deletion or Duplication of 7q11.23. Am J Hum Genet 2015; 97:216-27. [PMID: 26166478 DOI: 10.1016/j.ajhg.2015.05.019] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/27/2015] [Indexed: 12/11/2022] Open
Abstract
Epigenetic dysfunction has been implicated in a growing list of disorders that include cancer, neurodevelopmental disorders, and neurodegeneration. Williams syndrome (WS) and 7q11.23 duplication syndrome (Dup7) are rare neurodevelopmental disorders with broad phenotypic spectra caused by deletion and duplication, respectively, of a 1.5-Mb region that includes several genes with a role in epigenetic regulation. We have identified striking differences in DNA methylation across the genome between blood cells from children with WS or Dup7 and blood cells from typically developing (TD) children. Notably, regions that were differentially methylated in both WS and Dup7 displayed a significant and symmetrical gene-dose-dependent effect, such that WS typically showed increased and Dup7 showed decreased DNA methylation. Differentially methylated genes were significantly enriched with genes in pathways involved in neurodevelopment, autism spectrum disorder (ASD) candidate genes, and imprinted genes. Using alignment with ENCODE data, we also found the differentially methylated regions to be enriched with CCCTC-binding factor (CTCF) binding sites. These findings suggest that gene(s) within 7q11.23 alter DNA methylation at specific sites across the genome and result in dose-dependent DNA-methylation profiles in WS and Dup7. Given the extent of DNA-methylation changes and the potential impact on CTCF binding and chromatin regulation, epigenetic mechanisms most likely contribute to the complex neurological phenotypes of WS and Dup7. Our findings highlight the importance of DNA methylation in the pathogenesis of WS and Dup7 and provide molecular mechanisms that are potentially shared by WS, Dup7, and ASD.
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Dayeh T, Ling C. Does epigenetic dysregulation of pancreatic islets contribute to impaired insulin secretion and type 2 diabetes? Biochem Cell Biol 2015; 93:511-21. [PMID: 26369706 DOI: 10.1139/bcb-2015-0057] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
β cell dysfunction is central to the development and progression of type 2 diabetes (T2D). T2D develops when β cells are not able to compensate for the increasing demand for insulin caused by insulin resistance. Epigenetic modifications play an important role in establishing and maintaining β cell identity and function in physiological conditions. On the other hand, epigenetic dysregulation can cause a loss of β cell identity, which is characterized by reduced expression of genes that are important for β cell function, ectopic expression of genes that are not supposed to be expressed in β cells, and loss of genetic imprinting. Consequently, this may lead to β cell dysfunction and impaired insulin secretion. Risk factors that can cause epigenetic dysregulation include parental obesity, an adverse intrauterine environment, hyperglycemia, lipotoxicity, aging, physical inactivity, and mitochondrial dysfunction. These risk factors can affect the epigenome at different time points throughout the lifetime of an individual and even before an individual is conceived. The plasticity of the epigenome enables it to change in response to environmental factors such as diet and exercise, and also makes the epigenome a good target for epigenetic drugs that may be used to enhance insulin secretion and potentially treat diabetes.
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Affiliation(s)
- Tasnim Dayeh
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Jan Waldenströms gata 35, CRC 91:12, 205 02 Malmö, Sweden.,Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Jan Waldenströms gata 35, CRC 91:12, 205 02 Malmö, Sweden
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Jan Waldenströms gata 35, CRC 91:12, 205 02 Malmö, Sweden.,Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Jan Waldenströms gata 35, CRC 91:12, 205 02 Malmö, Sweden
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