1
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Holuka C, Grova N, Charalambous EG, Le Cléac H J, Turner JD, Mposhi A. Transgenerational impacts of early life adversity: from health determinants, implications to epigenetic consequences. Neurosci Biobehav Rev 2024; 164:105785. [PMID: 38945418 DOI: 10.1016/j.neubiorev.2024.105785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/09/2024] [Accepted: 06/23/2024] [Indexed: 07/02/2024]
Abstract
Exposure to different environmental factors, social and socioeconomic factors promotes development of the early-life adversity (ELA) phenotype. The persistence of this phenotype across generations is an interesting phenomenon that remains unexplored. Of late many studies have focused on disease-associated outcomes of ELA following exposure during childhood but the persistence of epigenetic imprints transmitted by ELA exposed parents to their offspring remains poorly described. It is possible that both parents are able to transmit ELA-associated genetic imprints to their offspring via transgenerational inheritance mechanisms. Here, we highlight the role of the mother and father in the biological process of conception, from epigenetic reprogramming cycles to later environmental exposures. We explain some of the known determinants of ELA (pollution, socioeconomic challenges, infections, etc.) and their disease-associated outcomes. Finally, we highlight the role of epigenetics, mitochondria and ncRNAs as mechanisms mediating transgenerational inheritance. Whether these transgenerational inheritance mechanisms occur in the human context remains unclear but there is a large body of suggestive evidence in non-human models that points out to its existence.
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Affiliation(s)
- Cyrielle Holuka
- Immune Endocrine Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health, Luxembourg; Faculty of Science, University of Luxembourg, Belval L-4365, Luxembourg
| | - Nathalie Grova
- Immune Endocrine Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health, Luxembourg; UMR Inserm 1256 nGERE, Nutrition-Génétique et exposition aux risques environnementaux, Institute of Medical Research (Pôle BMS) - University of Lorraine, B.P. 184, Nancy 54511, France
| | - Eleftheria G Charalambous
- Department of Psychiatry and Psychotherapy, University Medecine Greifswald, Ellernholzstr. 1-2, Greifswald 17489, Germany; Department of Psychology, University of Cyprus, Nicosia 2109, Cyprus
| | - Jeanne Le Cléac H
- Immune Endocrine Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health, Luxembourg; Faculty of Science, University of Luxembourg, Belval L-4365, Luxembourg
| | - Jonathan D Turner
- Immune Endocrine Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health, Luxembourg.
| | - Archibold Mposhi
- Immune Endocrine Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health, Luxembourg
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2
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Zou LS, Cable DM, Barrera-Lopez IA, Zhao T, Murray E, Aryee MJ, Chen F, Irizarry RA. Detection of allele-specific expression in spatial transcriptomics with spASE. Genome Biol 2024; 25:180. [PMID: 38978101 PMCID: PMC11229351 DOI: 10.1186/s13059-024-03317-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 06/20/2024] [Indexed: 07/10/2024] Open
Abstract
Spatial transcriptomics technologies permit the study of the spatial distribution of RNA at near-single-cell resolution genome-wide. However, the feasibility of studying spatial allele-specific expression (ASE) from these data remains uncharacterized. Here, we introduce spASE, a computational framework for detecting and estimating spatial ASE. To tackle the challenges presented by cell type mixtures and a low signal to noise ratio, we implement a hierarchical model involving additive mixtures of spatial smoothing splines. We apply our method to allele-resolved Visium and Slide-seq from the mouse cerebellum and hippocampus and report new insight into the landscape of spatial and cell type-specific ASE therein.
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Affiliation(s)
- Luli S Zou
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Dylan M Cable
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, 02139, USA
| | | | - Tongtong Zhao
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Evan Murray
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Martin J Aryee
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Rafael A Irizarry
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
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3
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Rubin JB, Abou-Antoun T, Ippolito JE, Llaci L, Marquez CT, Wong JP, Yang L. Epigenetic developmental mechanisms underlying sex differences in cancer. J Clin Invest 2024; 134:e180071. [PMID: 38949020 PMCID: PMC11213507 DOI: 10.1172/jci180071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024] Open
Abstract
Cancer risk is modulated by hereditary and somatic mutations, exposures, age, sex, and gender. The mechanisms by which sex and gender work alone and in combination with other cancer risk factors remain underexplored. In general, cancers that occur in both the male and female sexes occur more commonly in XY compared with XX individuals, regardless of genetic ancestry, geographic location, and age. Moreover, XY individuals are less frequently cured of their cancers, highlighting the need for a greater understanding of sex and gender effects in oncology. This will be necessary for optimal laboratory and clinical cancer investigations. To that end, we review the epigenetics of sexual differentiation and its effect on cancer hallmark pathways throughout life. Specifically, we will touch on how sex differences in metabolism, immunity, pluripotency, and tumor suppressor functions are patterned through the epigenetic effects of imprinting, sex chromosome complement, X inactivation, genes escaping X inactivation, sex hormones, and life history.
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Affiliation(s)
| | | | - Joseph E. Ippolito
- Department of Radiology
- Department of Biochemistry and Molecular Biophysics
| | - Lorida Llaci
- Deartment of Genetics Washington University School of Medicine, St. Louis, Missouri, USA
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4
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Rohm D, Black JB, McCutcheon SR, Barrera A, Morone DJ, Nuttle X, de Esch CE, Tai DJ, Talkowski ME, Iglesias N, Gersbach CA. Activation of the imprinted Prader-Willi Syndrome locus by CRISPR-based epigenome editing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.03.583177. [PMID: 38496583 PMCID: PMC10942373 DOI: 10.1101/2024.03.03.583177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Epigenome editing with DNA-targeting technologies such as CRISPR-dCas9 can be used to dissect gene regulatory mechanisms and potentially treat associated disorders. For example, Prader-Willi Syndrome (PWS) is caused by loss of paternally expressed imprinted genes on chromosome 15q11.2-q13.3, although the maternal allele is intact but epigenetically silenced. Using CRISPR repression and activation screens in human induced pluripotent stem cells (iPSCs), we identified genomic elements that control expression of the PWS gene SNRPN from the paternal and maternal chromosomes. We showed that either targeted transcriptional activation or DNA demethylation can activate the silenced maternal SNRPN and downstream PWS transcripts. However, these two approaches function at unique regions, preferentially activating different transcript variants and involving distinct epigenetic reprogramming mechanisms. Remarkably, transient expression of the targeted demethylase leads to stable, long-term maternal SNRPN expression in PWS iPSCs. This work uncovers targeted epigenetic manipulations to reprogram a disease-associated imprinted locus and suggests possible therapeutic interventions.
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Affiliation(s)
- Dahlia Rohm
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Joshua B. Black
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Sean R. McCutcheon
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Alejandro Barrera
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27708, USA
| | - Daniel J. Morone
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Xander Nuttle
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Celine E. de Esch
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Derek J.C. Tai
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael E. Talkowski
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nahid Iglesias
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Charles A. Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
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5
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Zhang L, Han Z, He H, Zhang X, Zhang M, Li B, Wu Q. Meg8-DMR as the Secondary Regulatory Region Regulates the Expression of MicroRNAs While It Does Not Affect Embryonic Development in Mice. Genes (Basel) 2023; 14:1264. [PMID: 37372444 DOI: 10.3390/genes14061264] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Meg8-DMR is the first maternal methylated DMR to be discovered in the imprinted Dlk1-Dio3 domain. The deletion of Meg8-DMR enhances the migration and invasion of MLTC-1 depending on the CTCF binding sites. However, the biological function of Meg8-DMR during mouse development remains unknown. In this study, a CRISPR/Cas9 system was used to generate 434 bp genomic deletions of Meg8-DMR in mice. High-throughput and bioinformatics profiling revealed that Meg8-DMR is involved in the regulation of microRNA: when the deletion was inherited from the mother (Mat-KO), the expression of microRNA was unchanged. However, when the deletion occurred from the father (Pat-KO) and homozygous (Homo-KO), the expression was upregulated. Then, differentially expressed microRNAs (DEGs) were identified between WT with Pat-KO, Mat-KO, and Homo-KO, respectively. Subsequently, these DEGs were subjected to the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) term enrichment analysis to explore the functional roles of these genes. In total, 502, 128, and 165 DEGs were determined. GO analysis showed that these DEGs were mainly enriched in axonogenesis in Pat-KO and Home-KO, while forebrain development was enriched in Mat-KO. Finally, the methylation levels of IG-DMR, Gtl2-DMR, and Meg8-DMR, and the imprinting status of Dlk1, Gtl2, and Rian were not affected. These findings suggest that Meg8-DMR, as a secondary regulatory region, could regulate the expression of microRNAs while not affecting the normal embryonic development of mice.
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Affiliation(s)
- Liang Zhang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Zhengbin Han
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Hongjuan He
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Ximeijia Zhang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Mengyan Zhang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Boran Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Qiong Wu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China
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6
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Iwasaki Y, Aksu C, Reyes M, Ay B, He Q, Bastepe M. The long-range interaction between two GNAS imprinting control regions delineates pseudohypoparathyroidism type 1B pathogenesis. J Clin Invest 2023; 133:e167953. [PMID: 36853809 PMCID: PMC10104902 DOI: 10.1172/jci167953] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/21/2023] [Indexed: 03/01/2023] Open
Abstract
Genetic defects of GNAS, the imprinted gene encoding the stimulatory G protein α-subunit, are responsible for multiple diseases. Abnormal GNAS imprinting causes pseudohypoparathyroidism type 1B (PHP1B), a prototype of mammalian end-organ hormone resistance. Hypomethylation at the maternally methylated GNAS A/B region is the only shared defect in patients with PHP1B. In autosomal dominant (AD) PHP1B kindreds, A/B hypomethylation is associated with maternal microdeletions at either the GNAS NESP55 differentially methylated region or the STX16 gene located approximately 170 kb upstream. Functional evidence is meager regarding the causality of these microdeletions. Moreover, the mechanisms linking A/B methylation and the putative imprinting control regions (ICRs) NESP-ICR and STX16-ICR remain unknown. Here, we generated a human embryonic stem cell model of AD-PHP1B by introducing ICR deletions using CRISPR/Cas9. With this model, we showed that the NESP-ICR is required for methylation and transcriptional silencing of A/B on the maternal allele. We also found that the SXT16-ICR is a long-range enhancer of NESP55 transcription, which originates from the maternal NESP-ICR. Furthermore, we demonstrated that the STX16-ICR is an embryonic stage-specific enhancer enabled by the direct binding of pluripotency factors. Our findings uncover an essential GNAS imprinting control mechanism and advance the molecular understanding of PHP1B pathogenesis.
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Affiliation(s)
- Yorihiro Iwasaki
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Tazuke Kofukai Medical Research Institute, Kitano Hospital, Osaka, Japan
| | - Cagri Aksu
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Monica Reyes
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Birol Ay
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Qing He
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- The State Key Laboratory Breeding Base of Basic Science of Stomatology and Key Laboratory for Oral Biomedicine of the Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Murat Bastepe
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
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7
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Dong Y, Zhang C, Jin L, Li D, Chen W, Huo H, Li S.
PMM2
and
NARFL
are paternally imprinted genes in bovines. Anim Genet 2022; 53:592-598. [DOI: 10.1111/age.13247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 07/15/2022] [Accepted: 07/22/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Yanqiu Dong
- College of Life Science Agricultural University of Hebei Baoding Hebei China
| | - Cui Zhang
- College of Life Science Agricultural University of Hebei Baoding Hebei China
| | - Lanjie Jin
- College of Life Science Agricultural University of Hebei Baoding Hebei China
| | - Dongjie Li
- College of Bioscience and Bioengineering Hebei University of Science and Technology Shijiazhuang Hebei China
| | - Weina Chen
- Department of Traditional Chinese Medicine Hebei University Baoding Hebei China
| | - Haonan Huo
- College of Life Science Agricultural University of Hebei Baoding Hebei China
| | - Shijie Li
- College of Life Science Agricultural University of Hebei Baoding Hebei China
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8
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Fu J, Zhang L, Li D, Tian T, Wang X, Sun H, Ge A, Liu Y, Zhang X, Huang H, Meng S, Zhang D, Zhao L, Sun S, Zheng T, Jia C, Zhao Y, Pang D. DNA Methylation of Imprinted Genes KCNQ1, KCNQ1OT1, and PHLDA2 in Peripheral Blood Is Associated with the Risk of Breast Cancer. Cancers (Basel) 2022; 14:cancers14112652. [PMID: 35681632 PMCID: PMC9179312 DOI: 10.3390/cancers14112652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/23/2022] [Accepted: 05/25/2022] [Indexed: 02/01/2023] Open
Abstract
Methylation alterations of imprinted genes lead to loss of imprinting (LOI). Although studies have explored the mechanism of LOI in breast cancer (BC) development, the association between imprinted gene methylation in peripheral blood and BC risk is largely unknown. We utilized HumanMethylation450 data from TCGA and GEO (n = 1461) to identify the CpG sites of imprinted genes associated with BC risk. Furthermore, we conducted an independent case-control study (n = 1048) to validate DNA methylation of these CpG sites in peripheral blood and BC susceptibility. cg26709929, cg08446215, cg25306939, and cg16057921, which are located at KCNQ1, KCNQ1OT1, and PHLDA2, were discovered to be associated with BC risk. Subsequently, the association between cg26709929, cg26057921, and cg25306939 methylation and BC risk was validated in our inhouse dataset. All 22 CpG sites in the KCNQ1OT1 region were associated with BC risk. Individuals with a hypermethylated KCNQ1OT1 region (>0.474) had a lower BC risk (OR: 0.553, 95% CI: 0.397−0.769). Additionally, the methylation of the KCNQ1OT1 region was not significantly different among B cells, monocytes, and T cells, which was also observed at CpG sites in PHLDA2. In summary, the methylation of KCNQ1, KCNQ1OT1, and PHLDA2 was associated with BC risk, and KCNQ1OT1 methylation could be a potential biomarker for BC risk assessment.
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Affiliation(s)
- Jinming Fu
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, China; (J.F.); (L.Z.); (D.L.); (T.T.); (X.W.); (H.S.); (A.G.); (Y.L.); (H.H.); (S.M.); (D.Z.); (L.Z.); (S.S.); (T.Z.); (C.J.)
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou 221004, China
| | - Lei Zhang
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, China; (J.F.); (L.Z.); (D.L.); (T.T.); (X.W.); (H.S.); (A.G.); (Y.L.); (H.H.); (S.M.); (D.Z.); (L.Z.); (S.S.); (T.Z.); (C.J.)
| | - Dapeng Li
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, China; (J.F.); (L.Z.); (D.L.); (T.T.); (X.W.); (H.S.); (A.G.); (Y.L.); (H.H.); (S.M.); (D.Z.); (L.Z.); (S.S.); (T.Z.); (C.J.)
| | - Tian Tian
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, China; (J.F.); (L.Z.); (D.L.); (T.T.); (X.W.); (H.S.); (A.G.); (Y.L.); (H.H.); (S.M.); (D.Z.); (L.Z.); (S.S.); (T.Z.); (C.J.)
| | - Xuan Wang
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, China; (J.F.); (L.Z.); (D.L.); (T.T.); (X.W.); (H.S.); (A.G.); (Y.L.); (H.H.); (S.M.); (D.Z.); (L.Z.); (S.S.); (T.Z.); (C.J.)
| | - Hongru Sun
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, China; (J.F.); (L.Z.); (D.L.); (T.T.); (X.W.); (H.S.); (A.G.); (Y.L.); (H.H.); (S.M.); (D.Z.); (L.Z.); (S.S.); (T.Z.); (C.J.)
| | - Anqi Ge
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, China; (J.F.); (L.Z.); (D.L.); (T.T.); (X.W.); (H.S.); (A.G.); (Y.L.); (H.H.); (S.M.); (D.Z.); (L.Z.); (S.S.); (T.Z.); (C.J.)
| | - Yupeng Liu
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, China; (J.F.); (L.Z.); (D.L.); (T.T.); (X.W.); (H.S.); (A.G.); (Y.L.); (H.H.); (S.M.); (D.Z.); (L.Z.); (S.S.); (T.Z.); (C.J.)
| | - Xianyu Zhang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin 150081, China;
| | - Hao Huang
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, China; (J.F.); (L.Z.); (D.L.); (T.T.); (X.W.); (H.S.); (A.G.); (Y.L.); (H.H.); (S.M.); (D.Z.); (L.Z.); (S.S.); (T.Z.); (C.J.)
| | - Shuhan Meng
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, China; (J.F.); (L.Z.); (D.L.); (T.T.); (X.W.); (H.S.); (A.G.); (Y.L.); (H.H.); (S.M.); (D.Z.); (L.Z.); (S.S.); (T.Z.); (C.J.)
| | - Ding Zhang
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, China; (J.F.); (L.Z.); (D.L.); (T.T.); (X.W.); (H.S.); (A.G.); (Y.L.); (H.H.); (S.M.); (D.Z.); (L.Z.); (S.S.); (T.Z.); (C.J.)
| | - Liyuan Zhao
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, China; (J.F.); (L.Z.); (D.L.); (T.T.); (X.W.); (H.S.); (A.G.); (Y.L.); (H.H.); (S.M.); (D.Z.); (L.Z.); (S.S.); (T.Z.); (C.J.)
| | - Simin Sun
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, China; (J.F.); (L.Z.); (D.L.); (T.T.); (X.W.); (H.S.); (A.G.); (Y.L.); (H.H.); (S.M.); (D.Z.); (L.Z.); (S.S.); (T.Z.); (C.J.)
| | - Ting Zheng
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, China; (J.F.); (L.Z.); (D.L.); (T.T.); (X.W.); (H.S.); (A.G.); (Y.L.); (H.H.); (S.M.); (D.Z.); (L.Z.); (S.S.); (T.Z.); (C.J.)
| | - Chenyang Jia
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, China; (J.F.); (L.Z.); (D.L.); (T.T.); (X.W.); (H.S.); (A.G.); (Y.L.); (H.H.); (S.M.); (D.Z.); (L.Z.); (S.S.); (T.Z.); (C.J.)
| | - Yashuang Zhao
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, China; (J.F.); (L.Z.); (D.L.); (T.T.); (X.W.); (H.S.); (A.G.); (Y.L.); (H.H.); (S.M.); (D.Z.); (L.Z.); (S.S.); (T.Z.); (C.J.)
- Correspondence: (Y.Z.); (D.P.); Tel.: +86-451-8750-2823 (Y.Z.); +86-451-8750-2885 (D.P.)
| | - Da Pang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin 150081, China;
- Correspondence: (Y.Z.); (D.P.); Tel.: +86-451-8750-2823 (Y.Z.); +86-451-8750-2885 (D.P.)
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9
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Kobayashi EH, Shibata S, Oike A, Kobayashi N, Hamada H, Okae H, Arima T. Genomic imprinting in human placentation. Reprod Med Biol 2022; 21:e12490. [PMID: 36465588 PMCID: PMC9713850 DOI: 10.1002/rmb2.12490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/25/2022] [Accepted: 11/10/2022] [Indexed: 12/02/2022] Open
Abstract
Background Genomic imprinting (GI) is a mammalian-specific epigenetic phenomenon that has been implicated in the evolution of the placenta in mammals. Methods Embryo transfer procedures and trophoblast stem (TS) cells were used to re-examine mouse placenta-specific GI genes. For the analysis of human GI genes, cytotrophoblast cells isolated from human placental tissues were used. Using human TS cells, the biological roles of human GI genes were examined. Main findings (1) Many previously identified mouse GI genes were likely to be falsely identified due to contaminating maternal cells. (2) Human placenta-specific GI genes were comprehensively determined, highlighting incomplete erasure of germline DNA methylation in the human placenta. (3) Human TS cells retained normal GI patterns. (4) Complete hydatidiform mole-derived TS cells were characterized by aberrant GI and enhanced trophoblastic proliferation. The maternally expressed imprinted gene p57KIP2 may be responsible for the enhanced proliferation. (5) The primate-specific microRNA cluster on chromosome 19, which is a placenta-specific GI gene, is essential for self-renewal and differentiation of human TS cells. Conclusion Genomic imprinting plays diverse and important roles in human placentation. Experimental analyses using TS cells suggest that the GI maintenance is necessary for normal placental development in humans.
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Affiliation(s)
- Eri H. Kobayashi
- Department of Informative GeneticsTohoku University School of MedicineSendaiJapan
| | - Shun Shibata
- Department of Informative GeneticsTohoku University School of MedicineSendaiJapan
| | - Akira Oike
- Department of Informative GeneticsTohoku University School of MedicineSendaiJapan
| | - Norio Kobayashi
- Department of Informative GeneticsTohoku University School of MedicineSendaiJapan
| | - Hirotaka Hamada
- Department of Informative GeneticsTohoku University School of MedicineSendaiJapan
| | - Hiroaki Okae
- Department of Informative GeneticsTohoku University School of MedicineSendaiJapan
| | - Takahiro Arima
- Department of Informative GeneticsTohoku University School of MedicineSendaiJapan
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10
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Aykroyd BRL, Tunster SJ, Sferruzzi-Perri AN. Loss of imprinting of the Igf2-H19 ICR1 enhances placental endocrine capacity via sex-specific alterations in signalling pathways in the mouse. Development 2022; 149:dev199811. [PMID: 34982814 PMCID: PMC8783045 DOI: 10.1242/dev.199811] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 11/23/2021] [Indexed: 12/14/2022]
Abstract
Imprinting control region (ICR1) controls the expression of the Igf2 and H19 genes in a parent-of-origin specific manner. Appropriate expression of the Igf2-H19 locus is fundamental for normal fetal development, yet the importance of ICR1 in the placental production of hormones that promote maternal nutrient allocation to the fetus is unknown. To address this, we used a novel mouse model to selectively delete ICR1 in the endocrine junctional zone (Jz) of the mouse placenta (Jz-ΔICR1). The Jz-ΔICR1 mice exhibit increased Igf2 and decreased H19 expression specifically in the Jz. This was accompanied by an expansion of Jz endocrine cell types due to enhanced rates of proliferation and increased expression of pregnancy-specific glycoprotein 23 in the placenta of both fetal sexes. However, changes in the endocrine phenotype of the placenta were related to sexually-dimorphic alterations to the abundance of Igf2 receptors and downstream signalling pathways (Pi3k-Akt and Mapk). There was no effect of Jz-ΔICR1 on the expression of targets of the H19-embedded miR-675 or on fetal weight. Our results demonstrate that ICR1 controls placental endocrine capacity via sex-dependent changes in signalling.
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Affiliation(s)
| | | | - Amanda N. Sferruzzi-Perri
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
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11
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Qin C, Cheng Y, Shang X, Wang R, Wang R, Hao X, Li S, Wang Y, Li Y, Liu X, Shao J. Disturbance of the Dlk1-Dio3 imprinted domain may underlie placental Dio3 suppression and extracellular thyroid hormone disturbance in placenta-derived JEG-3 cells following decabromodiphenyl ether (BDE209) exposure. Toxicology 2021; 458:152837. [PMID: 34166751 DOI: 10.1016/j.tox.2021.152837] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/29/2021] [Accepted: 06/16/2021] [Indexed: 10/21/2022]
Abstract
Decabromodiphenyl ether (BDE209) has been widely used as a flame retardant in the past four decades, leading to human health consequences, especially neurological impairments. Our previous in vivo studies have suggested that developmental neurotoxicity in offspring may be the result of BDE209-induced placental type III iodothyronine deiodinase (Dio3) disturbance and consequent thyroid hormone (TH) instability. Dio3 is paternally imprinted gene, and its balanced expression is crucial in directing normal development and growth. In this study, we used placenta-derived cells to investigate how BDE209 affected Dio3 expression through interfering imprinting mechanisms in the delta-like homolog 1 (Dlk1)-Dio3 imprinted region. Gene chip analysis and RT-qPCR identified miR409-3p, miR410-5p, miR494-3p, miR668-3p and miR889-5p as potential candidates involved in Dio3 deregulation. The sodium bisulfite-clonal sequencing revealed the BDE209 affect methylation status of two differentially methylated regions (DMRs), intergenic-DMR (IG-DMR) and maternally expressed gene 3-DMR (MEG3-DMR). Our data indicate that placental Dio3 may be a potential molecular target for future study of BDE209 developmental toxicity. In particular, miRNAs, IG-DMR and MEG3-DMR in the Dlk1-Dio3 imprinted locus may be informative in directing studies in TH disturbance and developmental toxicity induced by in utero exposure to environmental persistent organic pollutants (POPs), and those candidate miRNAs may prove to be convenient and noninvasive biomarkers for future large-scale population studies.
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Affiliation(s)
- Chang Qin
- School of Public Health, Department of Occupational and Environmental Health Sciences, Dalian Medical University, Dalian, 116044, China
| | - Ying Cheng
- School of Public Health, Department of Occupational and Environmental Health Sciences, Dalian Medical University, Dalian, 116044, China; Zhongshan College of Dalian Medical University, Dalian, 116085, China
| | - Xiaona Shang
- School of Public Health, Department of Occupational and Environmental Health Sciences, Dalian Medical University, Dalian, 116044, China
| | - Ruijun Wang
- School of Public Health, Department of Occupational and Environmental Health Sciences, Dalian Medical University, Dalian, 116044, China
| | - Ruonan Wang
- School of Public Health, Department of Occupational and Environmental Health Sciences, Dalian Medical University, Dalian, 116044, China
| | - Xiaoji Hao
- School of Public Health, Department of Occupational and Environmental Health Sciences, Dalian Medical University, Dalian, 116044, China
| | - Sisi Li
- School of Public Health, Department of Occupational and Environmental Health Sciences, Dalian Medical University, Dalian, 116044, China
| | - Ye Wang
- School of Public Health, Department of Occupational and Environmental Health Sciences, Dalian Medical University, Dalian, 116044, China
| | - Yachen Li
- School of Public Health, Department of Occupational and Environmental Health Sciences, Dalian Medical University, Dalian, 116044, China
| | - Xiaohui Liu
- School of Public Health, Department of Occupational and Environmental Health Sciences, Dalian Medical University, Dalian, 116044, China.
| | - Jing Shao
- School of Public Health, Department of Occupational and Environmental Health Sciences, Dalian Medical University, Dalian, 116044, China; Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Diamond Bay Institute of Hematology, Second Hospital of Dalian Medical University, Dalian, Liaoning, 116027, China.
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12
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Ovarian Toxicity and Epigenetic Mechanisms of Phthalates and Their Metabolites. Curr Med Sci 2021; 41:236-249. [PMID: 33877540 DOI: 10.1007/s11596-021-2342-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 01/30/2021] [Indexed: 12/12/2022]
Abstract
Ovary plays an important role in the female reproductive system. The maintenance and regulation of ovarian function are affected by various physical and chemical factors. With the development of industrialization, environmental pollutants have caused great harm to public health. Phthalates, as a class of endocrine-disrupting chemicals (EDCs), are synthesized and used in large quantities as plasticizers due to their chemical properties. They are easily released into environment because of their noncovalent interactions with substances, causing human exposure and possibly impairing ovary. In recent years, more and more attention has been paid to the role of epigenetics in the occurrence and development of diseases. And it is urgent to study the role of methylation, gene imprinting, miRNA, and other epigenetic mechanisms in reproductive toxicology.
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13
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Bruscadin JJ, de Souza MM, de Oliveira KS, Rocha MIP, Afonso J, Cardoso TF, Zerlotini A, Coutinho LL, Niciura SCM, de Almeida Regitano LC. Muscle allele-specific expression QTLs may affect meat quality traits in Bos indicus. Sci Rep 2021; 11:7321. [PMID: 33795794 PMCID: PMC8016890 DOI: 10.1038/s41598-021-86782-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/17/2021] [Indexed: 02/01/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) located in transcript sequences showing allele-specific expression (ASE SNPs) were previously identified in the Longissimus thoracis muscle of a Nelore (Bos indicus) population consisting of 190 steers. Given that the allele-specific expression pattern may result from cis-regulatory SNPs, called allele-specific expression quantitative trait loci (aseQTLs), in this study, we searched for aseQTLs in a window of 1 Mb upstream and downstream from each ASE SNP. After this initial analysis, aiming to investigate variants with a potential regulatory role, we further screened our aseQTL data for sequence similarity with transcription factor binding sites and microRNA (miRNA) binding sites. These aseQTLs were overlapped with methylation data from reduced representation bisulfite sequencing (RRBS) obtained from 12 animals of the same population. We identified 1134 aseQTLs associated with 126 different ASE SNPs. For 215 aseQTLs, one allele potentially affected the affinity of a muscle-expressed transcription factor to its binding site. 162 aseQTLs were predicted to affect 149 miRNA binding sites, from which 114 miRNAs were expressed in muscle. Also, 16 aseQTLs were methylated in our population. Integration of aseQTL with GWAS data revealed enrichment for traits such as meat tenderness, ribeye area, and intramuscular fat . To our knowledge, this is the first report of aseQTLs identification in bovine muscle. Our findings indicate that various cis-regulatory and epigenetic mechanisms can affect multiple variants to modulate the allelic expression. Some of the potential regulatory variants described here were associated with the expression pattern of genes related to interesting phenotypes for livestock. Thus, these variants might be useful for the comprehension of the genetic control of these phenotypes.
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Affiliation(s)
- Jennifer Jessica Bruscadin
- grid.411247.50000 0001 2163 588XPost-Graduation Program of Evolutionary Genetics and Molecular Biology, Center of Biological Sciences and Health, Federal University of São Carlos, São Carlos, SP Brazil
| | - Marcela Maria de Souza
- grid.34421.300000 0004 1936 7312Post-Doctoral Fellow, Department of Animal Science, Iowa State University, Ames, IA USA
| | - Karina Santos de Oliveira
- grid.411247.50000 0001 2163 588XPost-Graduation Program of Evolutionary Genetics and Molecular Biology, Center of Biological Sciences and Health, Federal University of São Carlos, São Carlos, SP Brazil
| | - Marina Ibelli Pereira Rocha
- grid.411247.50000 0001 2163 588XPost-Graduation Program of Evolutionary Genetics and Molecular Biology, Center of Biological Sciences and Health, Federal University of São Carlos, São Carlos, SP Brazil
| | - Juliana Afonso
- grid.11899.380000 0004 1937 0722Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, SP Brazil
| | - Tainã Figueiredo Cardoso
- grid.460200.00000 0004 0541 873XEmbrapa Pecuária Sudeste, P. O. Box 339, São Carlos, SP 13564-230 Brazil
| | - Adhemar Zerlotini
- grid.460200.00000 0004 0541 873XEmbrapa Informática Agropecuária, Campinas, SP Brazil
| | - Luiz Lehmann Coutinho
- grid.11899.380000 0004 1937 0722Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, SP Brazil
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14
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Differences in Placental Imprinted Gene Expression across Preeclamptic and Non-Preeclamptic Pregnancies. Genes (Basel) 2020; 11:genes11101146. [PMID: 33003346 PMCID: PMC7601230 DOI: 10.3390/genes11101146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 11/16/2022] Open
Abstract
Preeclampsia is a multi-systemic syndrome that presents in approximately 5% of pregnancies worldwide and is associated with a range of subsequent postpartum and postnatal outcomes, including fetal growth restriction. As the placenta plays a critical role in the development of preeclampsia, surveying genomic features of the placenta, including expression of imprinted genes, may reveal molecular markers that can further refine subtypes to aid targeted disease management. In this study, we conducted a comprehensive survey of placental imprinted gene expression across early and late onset preeclampsia cases and preterm and term normotensive controls. Placentas were collected at delivery from women recruited at the Magee-Womens Hospital prenatal clinics, and expression levels were profiled across 109 imprinted genes. We observed downregulation of placental Mesoderm-specific transcript (MEST) and Necdin (NDN) gene expression levels (false discovery rate (FDR) < 0.05) among early onset preeclampsia cases compared to preterm controls. No differences in placental imprinted gene expression were observed between late onset preeclampsia cases and term controls. While few studies have linked NDN to pregnancy complications, reductions in MEST expression levels, as observed in our study, are consistently reported in the literature in relation to various pregnancy complications, including fetal growth restriction, suggesting a potential role for placental MEST expression as a biosensor of an adverse in utero environment.
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15
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Abstract
The mammalian genome experiences profound setting and resetting of epigenetic patterns during the life-course. This is understood best for DNA methylation: the specification of germ cells, gametogenesis, and early embryo development are characterised by phases of widespread erasure and rewriting of methylation. While mitigating against intergenerational transmission of epigenetic information, these processes must also ensure correct genomic imprinting that depends on faithful and long-term memory of gamete-derived methylation states in the next generation. This underscores the importance of understanding the mechanisms of methylation programming in the germline.
De novo methylation in the oocyte is of particular interest because of its intimate association with transcription, which results in a bimodal methylome unique amongst mammalian cells. Moreover, this methylation landscape is entirely set up in a non-dividing cell, making the oocyte a fascinating model system in which to explore mechanistic determinants of methylation. Here, we summarise current knowledge on the oocyte DNA methylome and how it is established, focussing on recent insights from knockout models in the mouse that explore the interplay between methylation and chromatin states. We also highlight some remaining paradoxes and enigmas, in particular the involvement of non-nuclear factors for correct
de novo methylation.
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Affiliation(s)
- Hannah Demond
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, UK.,Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
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16
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Yin Z, Zhang X, Li J, Jiao Y, Kong Q, Mu Y. Identification of Imprinted Genes and Their Differentially Methylated Regions in Porcine. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795419120135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Thiagalingam S. Epigenetic memory in development and disease: Unraveling the mechanism. Biochim Biophys Acta Rev Cancer 2020; 1873:188349. [PMID: 31982403 DOI: 10.1016/j.bbcan.2020.188349] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/22/2020] [Accepted: 01/22/2020] [Indexed: 01/14/2023]
Abstract
Epigenetic memory is an essential process of life that governs the inheritance of predestined functional characteristics of normal cells and the newly acquired properties of cells affected by cancer and other diseases from parental to progeny cells. Unraveling the molecular basis of epigenetic memory dictated by protein and RNA factors in conjunction with epigenetic marks that are erased and re-established during embryogenesis/development during the formation of somatic, stem and disease cells will have far reaching implications to our understanding of embryogenesis/development and various diseases including cancer. While there has been enormous progress made, there are still gaps in knowledge which includes, the identity of unique epigenetic memory factors (EMFs) and epigenome coding enzymes/co-factors/scaffolding proteins involved in the assembly of defined "epigenetic memorysomes" and the epigenome marks that constitute collections of gene specific epigenetic memories corresponding to specific cell types and physiological conditions. A better understanding of the molecular basis for epigenetic memory will play a central role in improving diagnostics and prognostics of disease states and aid the development of targeted therapeutics of complex diseases.
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Affiliation(s)
- Sam Thiagalingam
- Department of Medicine (Biomedical Genetics Section and Cancer Center), Department of Pathology & Laboratory Medicine, Department of Pharmacology & Experimental Therapeutics, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, United States of America.
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18
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Han Q, Bartels A, Cheng X, Meyer A, An YQC, Hsieh TF, Xiao W. Epigenetics Regulates Reproductive Development in Plants. PLANTS 2019; 8:plants8120564. [PMID: 31810261 PMCID: PMC6963493 DOI: 10.3390/plants8120564] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/23/2019] [Accepted: 11/27/2019] [Indexed: 12/20/2022]
Abstract
Seed, resulting from reproductive development, is the main nutrient source for human beings, and reproduction has been intensively studied through genetic, molecular, and epigenetic approaches. However, how different epigenetic pathways crosstalk and integrate to regulate seed development remains unknown. Here, we review the recent progress of epigenetic changes that affect chromatin structure, such as DNA methylation, polycomb group proteins, histone modifications, and small RNA pathways in regulating plant reproduction. In gametogenesis of flowering plants, epigenetics is dynamic between the companion cell and gametes. Cytosine DNA methylation occurs in CG, CHG, CHH contexts (H = A, C, or T) of genes and transposable elements, and undergoes dynamic changes during reproduction. Cytosine methylation in the CHH context increases significantly during embryogenesis, reaches the highest levels in mature embryos, and decreases as the seed germinates. Polycomb group proteins are important transcriptional regulators during seed development. Histone modifications and small RNA pathways add another layer of complexity in regulating seed development. In summary, multiple epigenetic pathways are pivotal in regulating seed development. It remains to be elucidated how these epigenetic pathways interplay to affect dynamic chromatin structure and control reproduction.
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Affiliation(s)
- Qiang Han
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
| | - Arthur Bartels
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
| | - Xi Cheng
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
| | - Angela Meyer
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Yong-Qiang Charles An
- US Department of Agriculture, Agricultural Research Service, Midwest Area, Plant Genetics Research Unit, Donald Danforth Plant Science Center, MO 63132, USA;
| | - Tzung-Fu Hsieh
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA;
- Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC 28081, USA
| | - Wenyan Xiao
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
- Correspondence: ; Tel.: +1-314-977-2547
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19
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Leng L, Sun J, Huang J, Gong F, Yang L, Zhang S, Yuan X, Fang F, Xu X, Luo Y, Bolund L, Peters BA, Lu G, Jiang T, Xu F, Lin G. Single-Cell Transcriptome Analysis of Uniparental Embryos Reveals Parent-of-Origin Effects on Human Preimplantation Development. Cell Stem Cell 2019; 25:697-712.e6. [DOI: 10.1016/j.stem.2019.09.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 06/27/2019] [Accepted: 09/03/2019] [Indexed: 11/16/2022]
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20
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Mitsiogianni M, Koutsidis G, Mavroudis N, Trafalis DT, Botaitis S, Franco R, Zoumpourlis V, Amery T, Galanis A, Pappa A, Panayiotidis MI. The Role of Isothiocyanates as Cancer Chemo-Preventive, Chemo-Therapeutic and Anti-Melanoma Agents. Antioxidants (Basel) 2019; 8:E106. [PMID: 31003534 PMCID: PMC6523696 DOI: 10.3390/antiox8040106] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 04/03/2019] [Accepted: 04/12/2019] [Indexed: 12/11/2022] Open
Abstract
Many studies have shown evidence in support of the beneficial effects of phytochemicals in preventing chronic diseases, including cancer. Among such phytochemicals, sulphur-containing compounds (e.g., isothiocyanates (ITCs)) have raised scientific interest by exerting unique chemo-preventive properties against cancer pathogenesis. ITCs are the major biologically active compounds capable of mediating the anticancer effect of cruciferous vegetables. Recently, many studies have shown that a higher intake of cruciferous vegetables is associated with reduced risk of developing various forms of cancers primarily due to a plurality of effects, including (i) metabolic activation and detoxification, (ii) inflammation, (iii) angiogenesis, (iv) metastasis and (v) regulation of the epigenetic machinery. In the context of human malignant melanoma, a number of studies suggest that ITCs can cause cell cycle growth arrest and also induce apoptosis in human malignant melanoma cells. On such basis, ITCs could serve as promising chemo-therapeutic agents that could be used in the clinical setting to potentiate the efficacy of existing therapies.
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Affiliation(s)
- Melina Mitsiogianni
- Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne NE1 8ST, UK.
| | - Georgios Koutsidis
- Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne NE1 8ST, UK.
| | - Nikos Mavroudis
- Department of Food and Nutritional Sciences, University of Reading, Reading RG6 6AP, UK.
| | - Dimitrios T Trafalis
- Laboratory of Pharmacology, Unit of Clinical Pharmacology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece.
| | - Sotiris Botaitis
- Second Department of Surgery, Democritus University of Thrace, 68100 Alexandroupolis, Greece.
| | - Rodrigo Franco
- Redox Biology Centre, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA.
| | - Vasilis Zoumpourlis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635 Athens, Greece.
| | - Tom Amery
- The Watrercress Company / The Wasabi Company, Waddock, Dorchester, Dorset DT2 8QY, UK.
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece.
| | - Aglaia Pappa
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece.
| | - Mihalis I Panayiotidis
- Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne NE1 8ST, UK.
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21
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Abstract
SummaryTRIM28/KAP1/TIF1β was identified as a universal transcriptional co-repressor and is critical for regulating post-fertilization methylation reprogramming in preimplantation embryos. In this study, three siRNAs (si647, si742, and si1153) were designed to target the TRIM28 mRNA sequence. After transfection of the mixture of the three siRNA (siMix) into bovine fibroblast cells, the most effective one for TRIM28 knockdown was selected. By injecting RNAi directed against TRIM28 mRNA, we found that TRIM28 knockdown in oocytes had the most effect on the H19 gene, in which differentially methylated region (DMR) methylation was almost completely absent at the 2-cell stage (1.4%), while control embryos showed 74% methylation. In addition, global H3K9me3 levels at the 2-cell stage were significantly higher in the in vitro fertilization (IVF) group than in the TRIM28 knockdown group (P<0.05). We further show that TRIM28 is highly expressed during oocyte maturation and reaches peak levels at the 2-cell stage. In contrast, at this stage, TRIM28 expression in somatic cell nuclear transfer (SCNT) embryos decreased significantly (P<0.05), suggesting that Trim28 transcripts are lost during SCNT. TRIM28 is required for the maintenance of methylation imprints in bovine preimplantation embryos, and the loss of TRIM28 during SCNT may contribute to the unfaithful maintenance of imprints in cloned embryos.
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22
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Abstract
Allele-specific expression arises when transcriptional activity at the different alleles of a gene differs considerably. Although extensive research has been carried out to detect and characterize this phenomenon, the landscape of allele-specific expression in cancer is still poorly understood. In this chapter, we describe a fast and reliable analysis pipeline to study allele-specific expression in cancer using next-generation sequencing data. The pipeline provides a gene-level analysis approach that exploits paired germline DNA and tumor RNA sequencing data and benefits from parallel computation resources when available.
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Affiliation(s)
- Alessandro Romanel
- Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy.
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23
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Shukla S, Penta D, Mondal P, Meeran SM. Epigenetics of Breast Cancer: Clinical Status of Epi-drugs and Phytochemicals. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1152:293-310. [PMID: 31456191 DOI: 10.1007/978-3-030-20301-6_16] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Epigenetics refers to alterations in gene expression due to differential histone modifications and DNA methylation at promoter sites of genes. Epigenetic alterations are reversible and are heritable during somatic cell division, but do not involve changes in nucleotide sequence. Epigenetic regulation plays a critical role in normal growth and embryonic development by controlling transcriptional activities of several genes. In last two decades, these modifications have been well recognized to be involved in tumor initiation and progression, which has motivated many investigators to incorporate this novel field in cancer drug development. Recently, growing number of epigenetic changes have been reported that are involved in the regulations of genes involved in breast tumor growth and metastasis. Drugs possessing epigenetic modulatory activities known as epi-drugs, mainly the inhibitors of histone deacetylases (HDACs) and DNA methyltransferases (DNMTs). Some of these drugs are undergoing different clinical trials for breast cancer treatment. Several phytochemicals such as green tea polyphenols, curcumin, genistein, resveratrol and sulforaphane have also been shown to alter epigenetic modifications in multiple cancer types including breast cancer. In this chapter, we summarize the role of epigenetic changes in breast cancer progression and metastasis. We have also discussed about various epigenetic modulators possessing chemopreventive and therapeutic efficacy against breast cancer with future perspectives.
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Affiliation(s)
- Samriddhi Shukla
- Department of Paediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Dhanamjai Penta
- Laboratory of Cancer Epigenetics, Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysore, India
| | - Priya Mondal
- Laboratory of Cancer Epigenetics, Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysore, India
| | - Syed Musthapa Meeran
- Laboratory of Cancer Epigenetics, Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysore, India.
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24
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Tunster SJ, Van de Pette M, Creeth HDJ, Lefebvre L, John RM. Fetal growth restriction in a genetic model of sporadic Beckwith-Wiedemann syndrome. Dis Model Mech 2018; 11:dmm.035832. [PMID: 30158284 PMCID: PMC6262809 DOI: 10.1242/dmm.035832] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/17/2018] [Indexed: 12/19/2022] Open
Abstract
Beckwith–Wiedemann syndrome (BWS) is a complex imprinting disorder involving fetal overgrowth and placentomegaly, and is associated with a variety of genetic and epigenetic mutations affecting the expression of imprinted genes on human chromosome 11p15.5. Most BWS cases are linked to loss of methylation at the imprint control region 2 (ICR2) within this domain, which in mice regulates the silencing of several maternally expressed imprinted genes. Modelling this disorder in mice is confounded by the unique embryonic requirement for Ascl2, which is imprinted in mice but not in humans. To overcome this issue, we generated a novel model combining a truncation of distal chromosome 7 allele (DelTel7) with transgenic rescue of Ascl2 expression. This novel model recapitulated placentomegaly associated with BWS, but did not lead to fetal overgrowth. Summary: A novel genetic mouse model of sporadic Beckwith–Wiedemann syndrome (BWS) recapitulates placentomegaly, but placental defects lead to late gestation fetal growth restriction, which contrasts with the fetal overgrowth characteristic of BWS in humans.
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Affiliation(s)
- Simon J Tunster
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | | | - Hugo D J Creeth
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Louis Lefebvre
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Rosalind M John
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
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Lou H, Le F, Hu M, Yang X, Li L, Wang L, Wang N, Gao H, Jin F. Aberrant DNA Methylation of IGF2-H19 Locus in Human Fetus and in Spermatozoa From Assisted Reproductive Technologies. Reprod Sci 2018; 26:997-1004. [PMID: 30270743 DOI: 10.1177/1933719118802052] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Given the higher risk of developing imprinting disorders in assisted reproductive technology (ART)-conceived children, we hypothesized that ART may affect DNA methylation of the insulin-like growth factor 2 (IGF2), H19, small nuclear ribonucleoprotein polypeptide N (SNRPN) differentially methylated regions (DMRs) at the fetal stage, which in turn may be associated with sperm abnormalities. A total of 4 patient groups were recruited, namely, multifetal reduction following in vitro fertilization (IVF)/ intracytoplasmic sperm injection (ICSI; n = 56), multifetal reduction following controlled ovarian hyperstimulation (COH; n = 42), male patients with normal semen parameters denoted as normozoospermia group (NZ) for IVF (n = 36), and male patients presenting with asthenozoospermia (OAZ) for ICSI (n = 38). The expression levels and the DNA methylation status of IGF2-H19 and SNRPN DMRs in the fetuses and the semen samples were evaluated by real-time quantitative polymerase chain reaction and pyrosequencing. In our results, the expression levels of H19 were significantly higher, whereas the methylation rates were lower in IVF-conceived fetuses compared to the control group (P < .05). Furthermore, higher methylation rates of IGF2 DMR2 and SNRPN DMR were detected both in IVF- and ICSI-conceived fetuses (P < .05). The data further indicated that the patients who presented with the majority of the CpG sites in the H19 DMR region that were lower methylated were those in the OAZ group. The results demonstrated that the epigenetic dysregulations of IGF2-H19 and SNRPN DMRs that were caused by ART were noted in the fetuses. Moreover, the present study suggested that epigenetic perturbations of the H19 DMR might be a key biomarker for spermatogenesis defects in humans.
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Affiliation(s)
- Hangying Lou
- 1 Center of Reproductive Medicine, School of Medicine, Zhejiang University, Hangzhou, China.,2 Key Laboratory of Reproductive Genetics, Ministry of Education, Hangzhou, China
| | - Fang Le
- 1 Center of Reproductive Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Minhao Hu
- 1 Center of Reproductive Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xinyun Yang
- 1 Center of Reproductive Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lejun Li
- 1 Center of Reproductive Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Liya Wang
- 1 Center of Reproductive Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Ning Wang
- 1 Center of Reproductive Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Huijuan Gao
- 1 Center of Reproductive Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Fan Jin
- 1 Center of Reproductive Medicine, School of Medicine, Zhejiang University, Hangzhou, China.,2 Key Laboratory of Reproductive Genetics, Ministry of Education, Hangzhou, China
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26
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Mitsiogianni M, Amery T, Franco R, Zoumpourlis V, Pappa A, Panayiotidis MI. From chemo-prevention to epigenetic regulation: The role of isothiocyanates in skin cancer prevention. Pharmacol Ther 2018; 190:187-201. [DOI: 10.1016/j.pharmthera.2018.06.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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27
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Gomez-Pinilla F, Yang X. System biology approach intersecting diet and cell metabolism with pathogenesis of brain disorders. Prog Neurobiol 2018; 169:76-90. [PMID: 30059718 PMCID: PMC6231047 DOI: 10.1016/j.pneurobio.2018.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 07/15/2018] [Indexed: 12/21/2022]
Abstract
The surge in meals high in calories has prompted an epidemic of metabolic disorders around the world such that the elevated incidence of obese and diabetic individuals is alarming. New research indicates that metabolic disorders pose a risk for neurological and psychiatric conditions including stroke, Alzheimer's disease, Huntington's disease, and depression, all of which have a metabolic component. These relationships are rooted to a dysfunctional interaction between molecular processes that regulate energy metabolism and synaptic plasticity. The strong adaptive force of dietary factors on shaping the brain during evolution can be manipulated to transform the interaction between cell bioenergetics and epigenome with the aptitude to promote long-lasting brain healthiness. A thorough understanding of the association between the broad action of nutrients and brain fitness requires high level data processing empowered with the capacity to integrate information from a multitude of molecular entities and pathways. Nutritional systems biology is emerging as a viable approach to elucidate the multiple molecular layers involved in information processing in cells, tissues, and organ systems in response to diet. Information about the wide range of cellular and molecular interactions elicited by foods on the brain and cognitive plasticity is crucial for the design of public health initiatives for curtailing the epidemic of metabolic and brain disorders.
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Affiliation(s)
- Fernando Gomez-Pinilla
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA; Department of Neurosurgery, UCLA Brain Injury Research Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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Hernandez A, Stohn JP. The Type 3 Deiodinase: Epigenetic Control of Brain Thyroid Hormone Action and Neurological Function. Int J Mol Sci 2018; 19:ijms19061804. [PMID: 29921775 PMCID: PMC6032375 DOI: 10.3390/ijms19061804] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/13/2018] [Accepted: 06/15/2018] [Indexed: 12/31/2022] Open
Abstract
Thyroid hormones (THs) influence multiple processes in the developing and adult central nervous system, and their local availability needs to be maintained at levels that are tailored to the requirements of their biological targets. The local complement of TH transporters, deiodinase enzymes, and receptors is critical to ensure specific levels of TH action in neural cells. The type 3 iodothyronine deiodinase (DIO3) inactivates THs and is highly present in the developing and adult brain, where it limits their availability and action. DIO3 deficiency in mice results in a host of neurodevelopmental and behavioral abnormalities, demonstrating the deleterious effects of TH excess, and revealing the critical role of DIO3 in the regulation of TH action in the brain. The fact the Dio3 is an imprinted gene and that its allelic expression pattern varies across brain regions and during development introduces an additional level of control to deliver specific levels of hormone action in the central nervous system (CNS). The sensitive epigenetic nature of the mechanisms controlling the genomic imprinting of Dio3 renders brain TH action particularly susceptible to disruption due to exogenous treatments and environmental exposures, with potential implications for the etiology of human neurodevelopmental disorders.
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Affiliation(s)
- Arturo Hernandez
- Center for Molecular Medicine, Maine Medical Center Research Institute, Maine Medical Center, Scarborough, ME 04074, USA.
- Graduate School for Biomedical Science and Engineering, University of Maine, Orono, ME 04469, USA.
- Department of Medicine, Tufts University School of Medicine, Boston, MA 02111, USA.
| | - J Patrizia Stohn
- Center for Molecular Medicine, Maine Medical Center Research Institute, Maine Medical Center, Scarborough, ME 04074, USA.
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Pearson BL, Ehninger D. Impact of paternal nutrition on epigenetic patterns. Epigenomics 2018; 10:115-117. [DOI: 10.2217/epi-2017-0134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Brandon L Pearson
- German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Str. 27, 53127 Bonn, Germany
| | - Dan Ehninger
- German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Str. 27, 53127 Bonn, Germany
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Imprinting defects at human 14q32 locus alters gene expression and is associated with the pathobiology of osteosarcoma. Oncotarget 2018; 7:21298-314. [PMID: 26802029 PMCID: PMC5008286 DOI: 10.18632/oncotarget.6965] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 11/25/2015] [Indexed: 11/25/2022] Open
Abstract
Osteosarcoma is the most common primary bone malignancy affecting children and adolescents. Although several genetic predisposing conditions have been associated with osteosarcoma, our understanding of its pathobiology is rather limited. Here we show that, first, an imprinting defect at human 14q32-locus is highly prevalent (87%) and specifically associated with osteosarcoma patients < 30 years of age. Second, the average demethylation at differentially methylated regions (DMRs) in the 14q32-locus varied significantly compared to genome-wide demethylation. Third, the 14q32-locus was enriched in both H3K4-me3 and H3K27-me3 histone modifications that affected expression of all imprinted genes and miRNAs in this region. Fourth, imprinting defects at 14q32 - DMRs are present in triad DNA samples from affected children and their biological parents. Finally, imprinting defects at 14q32-DMRs were also observed at higher frequencies in an Rb1/Trp53 mutation-induced osteosarcoma mouse model. Further analysis of normal and tumor tissues from a Sleeping Beauty mouse model of spontaneous osteosarcoma supported the notion that these imprinting defects may be a key factor in osteosarcoma pathobiology. In conclusion, we demonstrate that imprinting defects at the 14q32 locus significantly alter gene expression, may contribute to the pathogenesis of osteosarcoma, and could be predictive of survival outcomes.
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31
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Penta D, Somashekar BS, Meeran SM. Epigenetics of skin cancer: Interventions by selected bioactive phytochemicals. PHOTODERMATOLOGY PHOTOIMMUNOLOGY & PHOTOMEDICINE 2017; 34:42-49. [DOI: 10.1111/phpp.12353] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/26/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Dhanamjai Penta
- Laboratory of Cancer Epigenetics; Department of Biochemistry; CSIR-Central Food Technological Research Institute; Mysore India
| | - Bagganahalli S. Somashekar
- Laboratory of Cancer Epigenetics; Department of Biochemistry; CSIR-Central Food Technological Research Institute; Mysore India
| | - Syed Musthapa Meeran
- Laboratory of Cancer Epigenetics; Department of Biochemistry; CSIR-Central Food Technological Research Institute; Mysore India
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Hillman PR, Christian SGB, Doan R, Cohen ND, Konganti K, Douglas K, Wang X, Samollow PB, Dindot SV. Genomic imprinting does not reduce the dosage of UBE3A in neurons. Epigenetics Chromatin 2017; 10:27. [PMID: 28515788 PMCID: PMC5433054 DOI: 10.1186/s13072-017-0134-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/03/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The ubiquitin protein E3A ligase gene (UBE3A) gene is imprinted with maternal-specific expression in neurons and biallelically expressed in all other cell types. Both loss-of-function and gain-of-function mutations affecting the dosage of UBE3A are associated with several neurodevelopmental syndromes and psychological conditions, suggesting that UBE3A is dosage-sensitive in the brain. The observation that loss of imprinting increases the dosage of UBE3A in brain further suggests that inactivation of the paternal UBE3A allele evolved as a dosage-regulating mechanism. To test this hypothesis, we examined UBE3A transcript and protein levels among cells, tissues, and species with different imprinting states of UBE3A. RESULTS Overall, we found no correlation between the imprinting status and dosage of UBE3A. Importantly, we found that maternal Ube3a protein levels increase in step with decreasing paternal Ube3a protein levels during neurogenesis in mouse, fully compensating for loss of expression of the paternal Ube3a allele in neurons. CONCLUSIONS Based on our findings, we propose that imprinting of UBE3A does not function to reduce the dosage of UBE3A in neurons but rather to regulate some other, as yet unknown, aspect of gene expression or protein function.
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Affiliation(s)
- Paul R. Hillman
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77845 USA
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, TX 77845 USA
| | - Sarah G. B. Christian
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77845 USA
| | - Ryan Doan
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77845 USA
- Interdisciplinary Genetics Program, College of Agriculture and Life Sciences, Texas A&M University, College Station, TX 77845 USA
| | - Noah D. Cohen
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX USA
| | - Kranti Konganti
- Institute for Genome Science and Society, Texas A&M University, College Station, TX 77845 USA
| | - Kory Douglas
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX USA
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Xu Wang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853 USA
| | - Paul B. Samollow
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Scott V. Dindot
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77845 USA
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, TX 77845 USA
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, 4467 TAMU, College Station, TX 77843 USA
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Abstract
Epigenome editing aims for an introduction or removal of chromatin marks at a defined genomic region using artificial EpiEffectors resulting in a modulation of the activity of the targeted functional DNA elements. Rationally designed EpiEffectors consist of a targeting DNA-binding module (such as a zinc finger protein, TAL effector, or CRISPR/Cas complex) and usually, but not exclusively, a catalytic domain of a chromatin-modifying enzyme. Epigenome editing opens a completely new strategy for basic research of the central nervous system and causal treatment of psychiatric and neurological diseases, because rewriting of epigenetic information can lead to the direct and durable control of the expression of disease-associated genes. Here, we review current advances in the design of locus- and allele-specific DNA-binding modules, approaches for spatial, and temporal control of EpiEffectors and discuss some examples of existing and propose new potential therapeutic strategies based on epigenome editing for treatment of neurodegenerative and psychiatric diseases. These include the targeted silencing of disease-associated genes or activation of neuroprotective genes which may be applied in Alzheimer's and Parkinson's diseases or the control of addiction and depression. Moreover, we discuss allele-specific epigenome editing as novel therapeutic approach for imprinting disorders, Huntington's disease and Rett syndrome.
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O'Doherty AM, O'Shea LC, Sandra O, Lonergan P, Fair T, Forde N. Imprinted and DNA methyltransferase gene expression in the endometrium during the pre- and peri-implantation period in cattle. Reprod Fertil Dev 2017; 29:1729-1738. [DOI: 10.1071/rd16238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 08/24/2016] [Indexed: 12/14/2022] Open
Abstract
The endometrium plays a key role in providing an optimal environment for attachment of the preimplantation embryo during the early stages of pregnancy. Investigations over the past 2 decades have demonstrated that vital epigenetic processes occur in the embryo during the preimplantation stages of development. However, few studies have investigated the potential role of imprinted genes and their associated modulators, the DNA methyltransferases (DNMTs), in the bovine endometrium during the pre- and peri-implantation period. Therefore, in the present study we examined the expression profiles of the DNMT genes (3A, 3A2 and 3B) and a panel of the most comprehensively studied imprinted genes in the endometrium of cyclic and pregnant animals. Intercaruncular (Days 5, 7, 13, 16 and 20) and caruncular (Days 16 and 20) regions were analysed for gene expression changes, with protein analysis also performed for DNMT3A, DNMT3A2 and DNMT3B on Days 16 and 20. An overall effect of day was observed for expression of several of the imprinted genes. Tissue-dependent gene expression was detected for all genes at Day 20. Differences in DNMT protein abundance were mostly observed in the intercaruncular regions of pregnant heifers at Day 16 when DNMT3A, DNMT3A2 and DNMT3B were all lower when compared with cyclic controls. At Day 20, DNMT3A2 expression was lower in the pregnant caruncular samples compared with cyclic animals. This study provides evidence that epigenetic mechanisms in the endometrium may be involved with implantation of the embryo during the early stages of pregnancy in cattle.
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35
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Magnetic bead-liposome hybrids enable sensitive and portable detection of DNA methyltransferase activity using personal glucose meter. Biosens Bioelectron 2017; 87:537-544. [DOI: 10.1016/j.bios.2016.08.103] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/20/2016] [Accepted: 08/29/2016] [Indexed: 11/18/2022]
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36
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Schultz B, Yao X, Deng Y, Waner M, Spock C, Tom L, Persing J, Narayan D. A Common Polymorphism within the IGF2 Imprinting Control Region Is Associated with Parent of Origin Specific Effects in Infantile Hemangiomas. PLoS One 2015; 10:e0113168. [PMID: 26496499 PMCID: PMC4619854 DOI: 10.1371/journal.pone.0113168] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Accepted: 10/24/2014] [Indexed: 11/30/2022] Open
Abstract
Infantile hemangioma (IH) is the most common tumor of the pediatric age group, affecting up to 4% of newborns ranging from inconsequential blemishes, to highly aggressive tumors. Following well defined growth phases (proliferative, plateau involutional) IH usually regress into a fibro-fatty residuum. Despite the high prevalence of IH, little is known regarding the pathogenesis of disease. A reported six fold decrease in IGF2 expression (correlating with transformation of proliferative to involuted lesions) prompted us to study the IGF-2 axis further. We demonstrate that IGF2 expression in IH is strongly related to the expression of a cancer testes and suspected oncogene BORIS (paralog of CTCF), placing IH in the unique category of being the first known benign BORIS positive tumor. IGF2 expression was strongly and positively related to BORIS transcript expression. Furthermore, a stronger association was made when comparing BORIS levels against the expression of CTCF via either a percentage or difference between the two. A common C/T polymorphism at CTCF BS6 appeared to modify the correlation between CTCF/BORIS and IGF2 expression in a parent of origin specific manner. Moreover, these effects may have phenotypic consequences as tumor growth also correlates with the genotype at CTCF BS6. This may provide a framework for explaining the clinical variability seen in IH and suggests new insights regarding CTCF and BORIS related functionality in both normal and malignant states.
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Affiliation(s)
- Brent Schultz
- University of Washington, Division of Plastic Surgery, Seattle, WA, United States of America
| | - Xiaopan Yao
- Yale Center for Analytic Sciences at YSPH, New Haven, CT, United States of America
| | - Yanhong Deng
- Yale Center for Analytic Sciences at YSPH, New Haven, CT, United States of America
| | - Milton Waner
- Vascular Birthmark Institute, New York, NY, United States of America
| | | | - Laura Tom
- Division of Plastic Surgery, University of Washington, Seattle, WA, United States of America
| | - John Persing
- Yale Plastic and Reconstructive Surgery, New Haven, United States of America
| | - Deepak Narayan
- Yale Plastic and Reconstructive Surgery, New Haven, United States of America
- * E-mail:
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Tet-mediated imprinting erasure in H19 locus following reprogramming of spermatogonial stem cells to induced pluripotent stem cells. Sci Rep 2015; 5:13691. [PMID: 26328763 PMCID: PMC4556992 DOI: 10.1038/srep13691] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 08/03/2015] [Indexed: 12/12/2022] Open
Abstract
Selective methylation of CpG islands at imprinting control regions (ICR) determines the monoparental expression of a subset of genes. Currently, it is unclear whether artificial reprogramming induced by the expression of Yamanaka factors disrupts these marks and whether cell type of origin affects the dynamics of reprogramming. In this study, spermatogonial stem cells (SSC) that harbor paternalized imprinting marks, and fibroblasts were reprogrammed to iPSC (SSCiPSC and fiPSC). The SSCiPSC were able to form teratomas and generated chimeras with a higher skin chimerism than those derived from fiPSC. RNA-seq revealed extensive reprogramming at the transcriptional level with 8124 genes differentially expressed between SSC and SSCiPSC and only 490 between SSCiPSC and fiPSC. Likewise, reprogramming of SSC affected 26 of 41 imprinting gene clusters known in the mouse genome. A closer look at H19 ICR revealed complete erasure in SSCiPSC in contrast to fiPSC. Imprinting erasure in SSCiPSC was maintained even after in vivo differentiation into teratomas. Reprogramming of SSC from Tet1 and Tet2 double knockout mice however lacked demethylation of H19 ICR. These results suggest that imprinting erasure during reprogramming depends on the epigenetic landscape of the precursor cell and is mediated by TETs at the H19 locus.
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Wang M, Li D, Zhang M, Yang W, Cui Y, Li S. Methylation of KvDMR1 involved in regulating the imprinting of CDKN1C gene in cattle. Anim Genet 2015; 46:354-60. [PMID: 26059028 DOI: 10.1111/age.12297] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2015] [Indexed: 01/18/2023]
Abstract
The CDKN1C gene encodes a cyclin-dependent kinase inhibitor and is one of the key genes involved in the development of Beckwith-Wiedemann syndrome and cancer. In this study, using a direct sequencing approach based on a single nucleotide polymorphism (SNP) at genomic DNA and cDNA levels, we show that CDKN1C exhibits monoallelic expression in all seven studied organs (heart, liver, spleen, lung, kidney, muscle and subcutaneous fat) in cattle. To investigate how methylation regulates imprinting of CDKN1C in cattle, allele-specific methylation patterns in two putative differential methylation regions (DMRs), the CDKN1C DMR and KvDMR1, were analyzed in three tissues (liver, spleen and lung) using bisulfite sequencing PCR. Our results show that in the CDKN1C DMR both parental alleles were unmethylated in all three analyzed tissues. In contrast, KvDMR1 was differentially methylated between the two parental alleles in the same tissues. Statistical analysis showed that there is a significant difference in the methylation level between the two parental alleles (P < 0.01), confirming that this region is the DMR of KvDMR1 and that it may be correlated with CDKN1C imprinting.
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Affiliation(s)
- Mengnan Wang
- College of Life Science, Agricultural University of Hebei, Baoding, 071001, China
| | - Dongjie Li
- College of Life Science and Life Engineering, Science and Technology, University of Hebei, Shijiazhuang, 050018, China
| | - Mingyue Zhang
- College of Life Science, Agricultural University of Hebei, Baoding, 071001, China
| | - Wenzhi Yang
- College of Life Science, Agricultural University of Hebei, Baoding, 071001, China
| | - Yali Cui
- College of Life Science, Agricultural University of Hebei, Baoding, 071001, China
| | - Shijie Li
- College of Life Science, Agricultural University of Hebei, Baoding, 071001, China
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Thummuri D, Kumar S, Surapaneni SK, Tikoo K. Epigenetic regulation of protein tyrosine phosphatase PTPN12 in triple-negative breast cancer. Life Sci 2015; 130:73-80. [DOI: 10.1016/j.lfs.2015.03.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 03/09/2015] [Accepted: 03/12/2015] [Indexed: 10/23/2022]
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Neurodevelopmental Plasticity in Pre- and Postnatal Environmental Interactions: Implications for Psychiatric Disorders from an Evolutionary Perspective. Neural Plast 2015; 2015:291476. [PMID: 26060583 PMCID: PMC4427813 DOI: 10.1155/2015/291476] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 03/29/2015] [Accepted: 04/15/2015] [Indexed: 01/28/2023] Open
Abstract
Psychiatric disorders are disadvantageous behavioral phenotypes in humans. Accordingly, a recent epidemiological study has reported decreased fecundity in patients with psychiatric disorders, such as schizophrenia and autism spectrum disorders. Moreover, the fecundity of the relatives of these patients is not exceedingly higher compared to the fecundity of the relatives of normal subjects. Collectively, the prevalence of psychiatric disorders among humans is expected to decrease over generations. Nevertheless, in reality, the prevalence rates of psychiatric disorders in humans either have been constant over a long period of time or have even increased more recently. Several attempts to explain this fact have been made using biological mechanisms, such as de novo gene mutations or variants, although none of these explanations is fully comprehensive. Here, we propose a hypothesis towards understanding the biological mechanisms of psychiatric disorders from evolutionary perspectives. This hypothesis considers that behavioral phenotypes associated with psychiatric disorders might have emerged in the evolution of organisms as a neurodevelopmental adaptation against adverse environmental conditions associated with stress.
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41
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Jang H, Jang WG, Kim EJ, Do M, Oh KB, Hwang S, Shim H, Choo YK, Kwon DJ, Lee JW. Methylation and expression changes in imprinted genesH19andIgf2during serial somatic cell nuclear transfer using piglet fibroblasts. Anim Cells Syst (Seoul) 2015. [DOI: 10.1080/19768354.2014.995706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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Dppa3 expression is critical for generation of fully reprogrammed iPS cells and maintenance of Dlk1-Dio3 imprinting. Nat Commun 2015; 6:6008. [PMID: 25613421 PMCID: PMC4354275 DOI: 10.1038/ncomms7008] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 12/01/2014] [Indexed: 11/22/2022] Open
Abstract
Reprogramming of mouse somatic cells into induced pluripotent stem cells (iPSCs) often generates partially reprogrammed iPSCs (pre-iPSCs), low-grade chimera forming iPSCs (lg-iPSCs) and fully reprogrammed, high-grade chimera production competent iPSCs (hg-iPSCs). Lg-iPSC transcriptome analysis revealed misregulated Dlk1-Dio3 cluster gene expression and subsequently the imprinting defect at the Dlk1-Dio3 locus. Here, we show that germ-cell marker Dppa3 is present only in lg-iPSCs and hg-iPSCs, and that induction with exogenous Dppa3 enhances reprogramming kinetics, generating all hg-iPSCs, similar to vitamin C (Vc). Conversely, Dppa3-null fibroblasts show reprogramming block at pre-iPSCs state and Dlk1-Dio3 imprinting defect. At the molecular level, we show that Dppa3 is associated with Dlk1-Dio3 locus and identify that Dppa3 maintains imprinting by antagonizing Dnmt3a binding. Our results further show molecular parallels between Dppa3 and Vc in Dlk1-Dio3 imprinting maintenance and suggest that early activation of Dppa3 is one of the cascades through which Vc facilitates the generation of fully reprogrammed iPSCs. Reprogramming of mouse somatic cells into iPSCs often generates pre-iPSCs, low-grade iPSCs that show abnormal Dlk1-Dio3 imprinting, and fully reprogrammed, high-grade iPSCs. Here, the authors show that germ-cell marker Dppa3 enhances reprogramming kinetics, critical for the maintenance of Dlk1-Dio3 imprinting and generation of fully reprogrammed iPSCs.
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43
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Kharche SD, Goel AK, Jindal SK, Ranjan R, Rout PK, Agarwal SK, Goel P, Saraswat S, Vijh RK, Malakar D, Bag S, Sarkhel B, Bhanja SK. Development of parthenote following in vivo transfer of embryos in Capra hircus. In Vitro Cell Dev Biol Anim 2014; 50:893-8. [PMID: 25270684 DOI: 10.1007/s11626-014-9740-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 02/15/2014] [Indexed: 11/28/2022]
Abstract
The aim of this study is to generate parthenogenetic embryos from chemically activated in vitro matured caprine oocytes and to study the in vivo developmental potency of such embryos. The parthenogenetic embryos (2-8 and 16 cells to morula stage) were surgically transferred in 26 recipients. Pregnancy in recipients following embryo transfer was monitored by ultrasonography. The recipient aborted a foetus on day 34 post transfer. Sexing of parthenogenetic foetus showed a single band of amelogenin gene indicating female cell DNA. Microsatellite analysis revealed that the recipient has not contributed genetically to the parthenogenetic foetus confirming the identity of aborted foetus of parthenogenetic origin. The authors believe that this is the first authentic report on in vivo development of parthenogenetic foetus in Capra hircus.
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Affiliation(s)
- Suresh Dinkar Kharche
- Central Institute for Research on Goats, Makhdoom, PO Farah, 281122, Mathura, UP, India,
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44
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Meirelles FV, Bressan FF, Smith LC, Perecin F, Chiaratti MR, Ferraz JBS. Cytoplasmatic inheritance, epigenetics and reprogramming DNA as tools in animal breeding. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.05.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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45
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Zeng C, Peng W, Ding L, He L, Zhang Y, Fang D, Tang K. A preliminary study on epigenetic changes during boar spermatozoa cryopreservation. Cryobiology 2014; 69:119-27. [DOI: 10.1016/j.cryobiol.2014.06.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Revised: 05/23/2014] [Accepted: 06/18/2014] [Indexed: 02/05/2023]
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46
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Zhang K, Li D, Wang M, Wu G, Shi Y, Li S. The differential expression of alternatively spliced transcripts and imprinting status ofMEG9gene in cows. Anim Genet 2014; 45:660-4. [DOI: 10.1111/age.12195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Kun Zhang
- Department of Biochemistry and Molecular Biology; College of Life Science; Hebei Agriculture University; Baoding 071001 China
| | - Dongjie Li
- College of Life Science and Life Engineering; Hebei Science and Technology University; Shijiazhuang 050018 China
| | - Mengnan Wang
- Department of Biochemistry and Molecular Biology; College of Life Science; Hebei Agriculture University; Baoding 071001 China
| | - Guojiang Wu
- Department of Biochemistry and Molecular Biology; College of Life Science; Hebei Agriculture University; Baoding 071001 China
| | - Yunjiao Shi
- Department of Biochemistry and Molecular Biology; College of Life Science; Hebei Agriculture University; Baoding 071001 China
| | - Shijie Li
- Department of Biochemistry and Molecular Biology; College of Life Science; Hebei Agriculture University; Baoding 071001 China
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47
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Bechtel-Walz W, Huber TB. Chromatin dynamics in kidney development and function. Cell Tissue Res 2014; 356:601-8. [PMID: 24817101 DOI: 10.1007/s00441-014-1884-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 03/27/2014] [Indexed: 10/25/2022]
Abstract
Epigenetic mechanisms are fundamental key features of developing cells connecting developmental regulatory factors to chromatin modification. Changes in the environment during renal development can have long-lasting effects on the permanent tissue structure and the level of expression of important functional genes. These changes are believed to contribute to kidney disease occurrence and progression. Although the mechanisms of early patterning and cell fate have been well described for renal development, little is known about associated epigenetic modifications and their impact on how genes interact to specify the renal epithelial cells of nephrons and how this specification is relevant to maintaining normal renal function. A better understanding of the renal cell-specific epigenetic modifications and the interaction of different cell types to form this highly complex organ will not only help to better understand developmental defects and early loss of kidney function in children, but also help to understand and improve chronic disease progression, cell regeneration and renal aging.
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Affiliation(s)
- Wibke Bechtel-Walz
- Renal Division, University Hospital Freiburg, Breisacher Str. 66, 79106, Freiburg, Germany,
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48
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Variable allelic expression of imprinted genes in human pluripotent stem cells during differentiation into specialized cell types in vitro. Biochem Biophys Res Commun 2014; 446:493-8. [DOI: 10.1016/j.bbrc.2014.02.141] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 02/28/2014] [Indexed: 12/27/2022]
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49
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Skaar DA, Li Y, Bernal AJ, Hoyo C, Murphy SK, Jirtle RL. The human imprintome: regulatory mechanisms, methods of ascertainment, and roles in disease susceptibility. ILAR J 2014; 53:341-58. [PMID: 23744971 DOI: 10.1093/ilar.53.3-4.341] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Imprinted genes form a special subset of the genome, exhibiting monoallelic expression in a parent-of-origin-dependent fashion. This monoallelic expression is controlled by parental-specific epigenetic marks, which are established in gametogenesis and early embryonic development and are persistent in all somatic cells throughout life. We define this specific set of cis-acting epigenetic regulatory elements as the imprintome, a distinct and specially tasked subset of the epigenome. Imprintome elements contain DNA methylation and histone modifications that regulate monoallelic expression by affecting promoter accessibility, chromatin structure, and chromatin configuration. Understanding their regulation is critical because a significant proportion of human imprinted genes are implicated in complex diseases. Significant species variation in the repertoire of imprinted genes and their epigenetic regulation, however, will not allow model organisms solely to be used for this crucial purpose. Ultimately, only the human will suffice to accurately define the human imprintome.
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Affiliation(s)
- David A Skaar
- Department of Oncology, Duke University Medical Center, Durham, North Carolina, USA
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50
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Abstract
Deciphering the information encoded in the human genome is key for the further understanding of human biology, physiology and evolution. With the draft sequence of the human genome completed, elucidation of the epigenetic information layer of the human genome becomes accessible. Epigenetic mechanisms are mediated by either chemical modifications of the DNA itself or by modifications of proteins that are closely associated with DNA. Defects of the epigenetic regulation involved in processes such as imprinting, X chromosome inactivation, transcriptional control of genes, as well as mutations affecting DNA methylation enzymes, contribute fundamentally to the etiology of many human diseases. Headed by the Human Epigenome Consortium, the Human Epigenome Project is a joint effort by an international collaboration that aims to identify, catalog and interpret genome-wide DNA methylation patterns of all human genes in all major tissues. Methylation variable positions are thought to reflect gene activity, tissue type and disease state, and are useful epigenetic markers revealing the dynamic state of the genome. Like single nucleotide polymorphisms, methylation variable positions will greatly advance our ability to elucidate and diagnose the molecular basis of human diseases.
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Affiliation(s)
- Florian Eckhardt
- Epigenomics AG, Kleine Präsidentenstrasse 1, 10178 Berlin, Germany.
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