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Moindrot B, Imaizumi Y, Feil R. Differential 3D genome architecture and imprinted gene expression: cause or consequence? Biochem Soc Trans 2024; 52:973-986. [PMID: 38775198 PMCID: PMC11346452 DOI: 10.1042/bst20230143] [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: 02/12/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 06/27/2024]
Abstract
Imprinted genes provide an attractive paradigm to unravel links between transcription and genome architecture. The parental allele-specific expression of these essential genes - which are clustered in chromosomal domains - is mediated by parental methylation imprints at key regulatory DNA sequences. Recent chromatin conformation capture (3C)-based studies show differential organization of topologically associating domains between the parental chromosomes at imprinted domains, in embryonic stem and differentiated cells. At several imprinted domains, differentially methylated regions show allelic binding of the insulator protein CTCF, and linked focal retention of cohesin, at the non-methylated allele only. This generates differential patterns of chromatin looping between the parental chromosomes, already in the early embryo, and thereby facilitates the allelic gene expression. Recent research evokes also the opposite scenario, in which allelic transcription contributes to the differential genome organization, similarly as reported for imprinted X chromosome inactivation. This may occur through epigenetic effects on CTCF binding, through structural effects of RNA Polymerase II, or through imprinted long non-coding RNAs that have chromatin repressive functions. The emerging picture is that epigenetically-controlled differential genome architecture precedes and facilitates imprinted gene expression during development, and that at some domains, conversely, the mono-allelic gene expression also influences genome architecture.
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Affiliation(s)
- Benoit Moindrot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Yui Imaizumi
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
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Matsuzaki H, Kimura M, Morihashi M, Tanimoto K. Imprinted DNA methylation of the H19 ICR is established and maintained in vivo in the absence of Kaiso. Epigenetics Chromatin 2024; 17:20. [PMID: 38840164 PMCID: PMC11151560 DOI: 10.1186/s13072-024-00544-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 05/23/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Paternal allele-specific DNA methylation of the imprinting control region (H19 ICR) controls genomic imprinting at the Igf2/H19 locus. We previously demonstrated that the mouse H19 ICR transgene acquires imprinted DNA methylation in preimplantation mouse embryos. This activity is also present in the endogenous H19 ICR and protects it from genome-wide reprogramming after fertilization. We also identified a 118-bp sequence within the H19 ICR that is responsible for post-fertilization imprinted methylation. Two mutations, one in the five RCTG motifs and the other a 36-bp deletion both in the 118-bp segment, caused complete and partial loss, respectively, of methylation following paternal transmission in each transgenic mouse. Interestingly, these mutations overlap with the binding site for the transcription factor Kaiso, which is reportedly involved in maintaining paternal methylation at the human H19 ICR (IC1) in cultured cells. In this study, we investigated if Kaiso regulates imprinted DNA methylation of the H19 ICR in vivo. RESULTS Neither Kaiso deletion nor mutation of Kaiso binding sites in the 118-bp region affected DNA methylation of the mouse H19 ICR transgene. The endogenous mouse H19 ICR was methylated in a wild-type manner in Kaiso-null mutant mice. Additionally, the human IC1 transgene acquired imprinted DNA methylation after fertilization in the absence of Kaiso. CONCLUSIONS Our results indicate that Kaiso is not essential for either post-fertilization imprinted DNA methylation of the transgenic H19 ICR in mouse or for methylation imprinting of the endogenous mouse H19 ICR.
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Affiliation(s)
- Hitomi Matsuzaki
- Institute of Life and Environmental Sciences, Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki, 305-8577, Japan.
| | - Minami Kimura
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Mizuki Morihashi
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Keiji Tanimoto
- Institute of Life and Environmental Sciences, Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki, 305-8577, Japan
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He Z, Zhang J, Chen Y, Ai C, Gong X, Xu D, Wang H. Transgenerational inheritance of adrenal steroidogenesis inhibition induced by prenatal dexamethasone exposure and its intrauterine mechanism. Cell Commun Signal 2023; 21:294. [PMID: 37853416 PMCID: PMC10585925 DOI: 10.1186/s12964-023-01303-0] [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: 06/21/2023] [Accepted: 08/30/2023] [Indexed: 10/20/2023] Open
Abstract
BACKGROUND Adrenal gland is the synthesis and secretion organ of glucocorticoid, which is crucial to fetal development and postnatal fate. Recently, we found that prenatal dexamethasone exposure (PDE) could cause adrenal dysfunction in offspring rats, but its multigenerational genetic effects and related mechanisms have not been reported. METHODS The PDE rat model was established, and female filial generation 1 (F1) rats mate with wild males to produce the F2, the same way for the F3. Three generation rats were sacrificed for the related detection. SW-13 cells were used to clarify the epigenetic molecular mechanism. RESULTS This study confirmed that PDE could activate fetal adrenal glucocorticoid receptor (GR). The activated GR, on the one hand, up-regulated Let-7b (in human cells) to inhibit steroidogenic acute regulatory protein (StAR) expression directly; on the other hand, down-regulated CCCTC binding factor (CTCF) and up-regulated DNA methyltransferase 3a/3b (Dnmt3a/3b), resulting in H19 hypermethylation and low expression. The decreased interaction of H19 and let-7 can further inhibit adrenal steroidogenesis. Additionally, oocytes transmitted the expression change of H19/let-7c axis to the next generation rats. Due to its genetic stability, F2 generation oocytes indirectly exposed to dexamethasone also inhibited H19 expression, which could be inherited to the F3 generation. CONCLUSIONS This cascade effect of CTCF/H19/Let-7c ultimately resulted in the transgenerational inheritance of adrenal steroidogenesis inhibition of PDE offspring. This study deepens the understanding of the intrauterine origin of adrenal developmental toxicity, and it will provide evidence for the systematic analysis of the transgenerational inheritance effect of acquired traits induced by PDE. Video Abstract.
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Affiliation(s)
- Zheng He
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, Hubei Province, China
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jinzhi Zhang
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, Hubei Province, China
| | - Yawen Chen
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, Hubei Province, China
| | - Can Ai
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, Hubei Province, China
| | - Xiaohan Gong
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, Hubei Province, China
| | - Dan Xu
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, Hubei Province, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disorder, Wuhan, 430071, China
| | - Hui Wang
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, Hubei Province, China.
- Hubei Provincial Key Laboratory of Developmentally Originated Disorder, Wuhan, 430071, China.
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Griazeva ED, Fedoseeva DM, Radion EI, Ershov PV, Meshkov IO, Semyanihina AV, Makarova AS, Makarov VV, Yudin VS, Keskinov AA, Kraevoy SA. Current Approaches to Epigenetic Therapy. EPIGENOMES 2023; 7:23. [PMID: 37873808 PMCID: PMC10594535 DOI: 10.3390/epigenomes7040023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/14/2023] [Accepted: 09/17/2023] [Indexed: 10/25/2023] Open
Abstract
Epigenetic therapy is a promising tool for the treatment of a wide range of diseases. Several fundamental epigenetic approaches have been proposed. Firstly, the use of small molecules as epigenetic effectors, as the most developed pharmacological method, has contributed to the introduction of a number of drugs into clinical practice. Secondly, various innovative epigenetic approaches based on dCas9 and the use of small non-coding RNAs as therapeutic agents are also under extensive research. In this review, we present the current state of research in the field of epigenetic therapy, considering the prospects for its application and possible limitations.
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Affiliation(s)
- Ekaterina D. Griazeva
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Pogodinskaya Str., 10, Building 1, Moscow 119121, Russia
| | - Daria M. Fedoseeva
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Pogodinskaya Str., 10, Building 1, Moscow 119121, Russia
| | - Elizaveta I. Radion
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Pogodinskaya Str., 10, Building 1, Moscow 119121, Russia
| | - Pavel V. Ershov
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Pogodinskaya Str., 10, Building 1, Moscow 119121, Russia
| | - Ivan O. Meshkov
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Pogodinskaya Str., 10, Building 1, Moscow 119121, Russia
| | - Alexandra V. Semyanihina
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Pogodinskaya Str., 10, Building 1, Moscow 119121, Russia
- Federal State Budgetary Institution “N.N. Blokhin National Medical Research Center of Oncology” of the Ministry of Health of the Russian Federation (N.N. Blokhin NMRCO), Kashirskoe Shosse, 24, Moscow 115478, Russia
- Federal State Budgetary Scientific Institution, Research Centre for Medical Genetics, Moskvorechye, 1, Moscow 115522, Russia
| | - Anna S. Makarova
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Pogodinskaya Str., 10, Building 1, Moscow 119121, Russia
| | - Valentin V. Makarov
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Pogodinskaya Str., 10, Building 1, Moscow 119121, Russia
| | - Vladimir S. Yudin
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Pogodinskaya Str., 10, Building 1, Moscow 119121, Russia
| | - Anton A. Keskinov
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Pogodinskaya Str., 10, Building 1, Moscow 119121, Russia
| | - Sergey A. Kraevoy
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Pogodinskaya Str., 10, Building 1, Moscow 119121, Russia
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Matsuzaki H, Takahashi T, Kuramochi D, Hirakawa K, Tanimoto K. Five nucleotides found in RCTG motifs are essential for post-fertilization methylation imprinting of the H19 ICR in YAC transgenic mice. Nucleic Acids Res 2023; 51:7236-7253. [PMID: 37334871 PMCID: PMC10415150 DOI: 10.1093/nar/gkad516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 06/02/2023] [Indexed: 06/21/2023] Open
Abstract
Genomic imprinting at the mouse Igf2/H19 locus is controlled by the H19 ICR, within which paternal allele-specific DNA methylation originating in sperm is maintained throughout development in offspring. We previously found that a 2.9 kb transgenic H19 ICR fragment in mice can be methylated de novo after fertilization only when paternally inherited, despite its unmethylated state in sperm. When the 118 bp sequence responsible for this methylation in transgenic mice was deleted from the endogenous H19 ICR, the methylation level of its paternal allele was significantly reduced after fertilization, suggesting the activity involving this 118 bp sequence is required for methylation maintenance at the endogenous locus. Here, we determined protein binding to the 118 bp sequence using an in vitro binding assay and inferred the binding motif to be RCTG by using a series of mutant competitors. Furthermore, we generated H19 ICR transgenic mice with a 5-bp substitution mutation that disrupts the RCTG motifs within the 118 bp sequence, and observed loss of methylation from the paternally inherited transgene. These results indicate that imprinted methylation of the H19 ICR established de novo during the post-fertilization period involves binding of specific factors to distinct sequence motifs within the 118 bp sequence.
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Affiliation(s)
- Hitomi Matsuzaki
- Faculty of Life and Environmental Sciences, Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Takuya Takahashi
- Graduate school of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Daichi Kuramochi
- Graduate school of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Katsuhiko Hirakawa
- Graduate school of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Keiji Tanimoto
- Faculty of Life and Environmental Sciences, Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
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Xiong L, Sun Y, Huang J, Ma P, Wang X, Wang J, Chen B, Chen J, Huang M, Huang S, Liu Y. Long Non-Coding RNA H19 Prevents Lens Fibrosis through Maintaining Lens Epithelial Cell Phenotypes. Cells 2022; 11:cells11162559. [PMID: 36010635 PMCID: PMC9406623 DOI: 10.3390/cells11162559] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 12/02/2022] Open
Abstract
The integrity of lens epithelial cells (LECs) lays the foundation for lens function and transparency. By contrast, epithelial-mesenchymal transition (EMT) of LECs leads to lens fibrosis, such as anterior subcapsular cataracts (ASC) and fibrotic forms of posterior capsule opacification (PCO). However, the underlying mechanisms remain unclear. Here, we aimed to explore the role of long non-coding RNA (lncRNA) H19 in regulating TGF-β2-induced EMT during lens fibrosis, revealing a novel lncRNA-based regulatory mechanism. In this work, we identified that lncRNA H19 was highly expressed in LECs, but downregulated by exposure to TGF-β2. In both human lens epithelial explants and SRA01/04 cells, knockdown of H19 aggravated TGF-β2-induced EMT, while overexpressing H19 partially reversed EMT and restored lens epithelial phenotypes. Semi-in vivo whole lens culture and H19 knockout mice demonstrated the indispensable role of H19 in sustaining lens clarity through maintaining LEC features. Bioinformatic analyses further implied a potential H19-centered regulatory mechanism via Smad-dependent pathways, confirmed by in vitro experiments. In conclusion, we uncovered a novel role of H19 in inhibiting TGF-β2-induced EMT of the lens by suppressing Smad-dependent signaling, providing potential therapeutic targets for treating lens fibrosis.
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Abstract
Diabetic nephropathy (DN), which is a common microvascular complication with a high incidence in diabetic patients, greatly increases the mortality of patients. With further study on DN, it is found that epigenetics plays a crucial role in the pathophysiological process of DN. Epigenetics has an important impact on the development of DN through a variety of mechanisms, and promotes the generation and maintenance of metabolic memory, thus ultimately leading to a poor prognosis. In this review we discuss the methylation of DNA, modification of histone, and regulation of non-coding RNA involved in the progress of cell dysfunction, inflammation and fibrosis in the kidney, which ultimately lead to the deterioration of DN.
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Matsuzaki H, Miyajima Y, Fukamizu A, Tanimoto K. Orientation of mouse H19 ICR affects imprinted H19 gene expression through promoter methylation-dependent and -independent mechanisms. Commun Biol 2021; 4:1410. [PMID: 34921234 PMCID: PMC8683476 DOI: 10.1038/s42003-021-02939-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 11/30/2021] [Indexed: 11/19/2022] Open
Abstract
The mouse Igf2/H19 locus is regulated by genomic imprinting, in which the paternally methylated H19 imprinting control region (ICR) plays a critical role in mono-allelic expression of the genes in the locus. Although the maternal allele-specific insulator activity of the H19 ICR in regulating imprinted Igf2 expression has been well established, the detailed mechanism by which the H19 ICR controls mono-allelic H19 gene expression has not been fully elucidated. In this study, we evaluated the effect of H19 ICR orientation on imprinting regulation in mutant mice in which the H19 ICR sequence was inverted at the endogenous locus. When the inverted-ICR allele was paternally inherited, the methylation level of the H19 promoter was decreased and the H19 gene was derepressed, suggesting that methylation of the H19 promoter is essential for complete repression of H19 gene expression. Unexpectedly, when the inverted allele was maternally inherited, the expression level of the H19 gene was lower than that of the WT allele, even though the H19 promoter remained fully hypomethylated. These observations suggested that the polarity of the H19 ICR is involved in controlling imprinted H19 gene expression on each parental allele, dependent or independent on DNA methylation of the H19 promoter.
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Affiliation(s)
- Hitomi Matsuzaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki, Japan.
| | - Yu Miyajima
- Graduate school of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Akiyoshi Fukamizu
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Keiji Tanimoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki, Japan
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He Z, Zhang J, Chen G, Cao J, Chen Y, Ai C, Wang H. H19/let-7 axis mediates caffeine exposure during pregnancy induced adrenal dysfunction and its multi-generation inheritance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 792:148440. [PMID: 34465058 DOI: 10.1016/j.scitotenv.2021.148440] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/01/2021] [Accepted: 06/09/2021] [Indexed: 06/13/2023]
Abstract
Previously, we systemically confirmed that prenatal caffeine exposure (PCE) could cause intrauterine growth retardation (IUGR) and adrenal steroid synthesis dysfunction in offspring rats. However, the multi-generation inheritance of adrenal dysfunction and its epigenetic mechanism has not been reported. In this study, the PCE rat model was established, part of the pregnant rats were executed on gestational day 20, while the others were delivered normally and the fetal rats were reared into adulthood. The PCE female rats of filial generation 1 (F1) were mated with wild males to produce F2 offspring, and the same way to produce F3 offspring. All the adult female rats of three generations were sacrificed for the related detection. Results showed that PCE could decrease fetal weight, increase IUGR rate, and elevate serum corticosterone level. Meanwhile, the expression of fetal adrenal GR, DNMT3a/3b, miRNA let-7c increased while those of CTCF, H19, and StAR decreased, and the total methylation rate of the H19 promoter region was enhanced. We used SW-13 cells to clarify the molecular mechanism and found that cortisol-induced in vitro changes of these indexes were consistent with those in vivo. We confirmed that high level of cortisol through activating GR, on the one hand, promoted let-7 expression and inhibited StAR expression; on the other hand, caused high methylation and low expression of H19 by down-regulating CTCF and up-regulating DNMT3a/3b, then enhanced let-7 inhibitory effect on StAR by "molecular sponge" effect. Finally, in vivo experiments showed that the adrenal steroid synthesis function and H19/let-7 axis presented the glucocorticoid-dependent changes in the adult female F1, F2, and F3. In conclusion, PCE can cause female adrenal dysfunction with matrilineal multi-generation inheritance, which is related to the programming alteration of the H19/let-7 axis. This study provides a novel perspective to explain the multi-generation inheritance of fetal-originated disease in IUGR offspring.
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Affiliation(s)
- Zheng He
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071, China; Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jinzhi Zhang
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071, China
| | - Guanghui Chen
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071, China
| | - Jiangang Cao
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071, China
| | - Yawen Chen
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071, China
| | - Can Ai
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071, China
| | - Hui Wang
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071, China; Hubei Provincial Key Laboratory of Developmentally Originated Disorder, Wuhan 430071, China.
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Huang TC, Chang KC, Chang JY, Tsai YS, Yang YJ, Chang WC, Mo CF, Yu PH, Chiang CT, Lin SP, Kuo PL. Variants in Maternal Effect Genes and Relaxed Imprinting Control in a Special Placental Mesenchymal Dysplasia Case with Mild Trophoblast Hyperplasia. Biomedicines 2021; 9:biomedicines9050544. [PMID: 34068021 PMCID: PMC8152467 DOI: 10.3390/biomedicines9050544] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/30/2021] [Accepted: 05/10/2021] [Indexed: 11/16/2022] Open
Abstract
Placental mesenchymal dysplasia (PMD) and partial hydatidiform mole (PHM) placentas share similar characteristics, such as placental overgrowth and grape-like placental tissues. Distinguishing PMD from PHM is critical because the former can result in normal birth, while the latter diagnosis will lead to artificial abortion. Aneuploidy and altered dosage of imprinted gene expression are implicated in the pathogenesis of PHM and also some of the PMD cases. Diandric triploidy is the main cause of PHM, whereas mosaic diploid androgenetic cells in the placental tissue have been associated with the formation of PMD. Here, we report a very special PMD case also presenting with trophoblast hyperplasia phenotype, which is a hallmark of PHM. This PMD placenta has a normal biparental diploid karyotype and is functionally sufficient to support normal fetal growth. We took advantage of this unique case to further dissected the potential common etiology between these two diseases. We show that the differentially methylated region (DMR) at NESP55, a secondary DMR residing in the GNAS locus, is significantly hypermethylated in the PMD placenta. Furthermore, we found heterozygous mutations in NLRP2 and homozygous variants in NLRP7 in the mother’s genome. NLRP2 and NLRP7 are known maternal effect genes, and their mutation in pregnant females affects fetal development. The variants/mutations in both genes have been associated with imprinting defects in mole formation and potentially contributed to the mild abnormal imprinting observed in this case. Finally, we identified heterozygous mutations in the X-linked ATRX gene, a known maternal–zygotic imprinting regulator in the patient. Overall, our study demonstrates that PMD and PHM may share overlapping etiologies with the defective/relaxed dosage control of imprinted genes, representing two extreme ends of a spectrum.
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Affiliation(s)
- Tien-Chi Huang
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan; (T.-C.H.); (J.-Y.C.); (W.-C.C.); (C.-F.M.)
| | - Kung-Chao Chang
- Department of Pathology, National Cheng Kung University Hospital, Tainan 704, Taiwan;
| | - Jen-Yun Chang
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan; (T.-C.H.); (J.-Y.C.); (W.-C.C.); (C.-F.M.)
| | - Yi-Shan Tsai
- Department of Radiology, National Cheng Kung University Hospital, Tainan 704, Taiwan;
| | - Yao-Jong Yang
- Department of Pediatrics, National Cheng Kung University Hospital, Tainan 704, Taiwan;
| | - Wei-Chun Chang
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan; (T.-C.H.); (J.-Y.C.); (W.-C.C.); (C.-F.M.)
| | - Chu-Fan Mo
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan; (T.-C.H.); (J.-Y.C.); (W.-C.C.); (C.-F.M.)
| | - Pei-Hsiu Yu
- Department of Obstetrics and Gynecology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan;
- Department of Obstetrics and Gynecology, Kuo General Hospital, Tainan 700, Taiwan
| | - Chun-Ting Chiang
- Department and Graduated Institute of Forensic Medicine, College of Medicine, National Taiwan University, Taipei 106, Taiwan;
| | - Shau-Ping Lin
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan; (T.-C.H.); (J.-Y.C.); (W.-C.C.); (C.-F.M.)
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei 106, Taiwan
- Center for Systems Biology, National Taiwan University, Taipei 106, Taiwan
- Correspondence: (S.-P.L.); (P.-L.K.)
| | - Pao-Lin Kuo
- Department of Obstetrics and Gynecology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan;
- Correspondence: (S.-P.L.); (P.-L.K.)
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Yang Z, Zhang T, Han S, Kusumanchi P, Huda N, Jiang Y, Liangpunsakul S. Long noncoding RNA H19 - a new player in the pathogenesis of liver diseases. Transl Res 2021; 230:139-150. [PMID: 33227504 PMCID: PMC9330166 DOI: 10.1016/j.trsl.2020.11.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 11/05/2020] [Accepted: 11/17/2020] [Indexed: 12/12/2022]
Abstract
The liver is a vital organ that controls glucose and lipid metabolism, hormone regulation, and bile secretion. Liver injury can occur from various insults such as viruses, metabolic diseases, and alcohol, which lead to acute and chronic liver diseases. Recent studies have demonstrated the implications of long noncoding RNAs (lncRNAs) in the pathogenesis of liver diseases. These newly discovered lncRNAs have various functions attributing to many cellular biological processes via distinct and diverse mechanisms. LncRNA H19, one of the first lncRNAs being identified, is highly expressed in fetal liver but not in adult normal liver. Its expression, however, is increased in liver diseases with various etiologies. In this review, we focused on the roles of H19 in the pathogenesis of liver diseases. This comprehensive review is aimed to provide useful perspectives and translational applications of H19 as a potential therapeutic target of liver diseases.
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Affiliation(s)
- Zhihong Yang
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana.
| | - Ting Zhang
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Sen Han
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Praveen Kusumanchi
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Nazmul Huda
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Yanchao Jiang
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Suthat Liangpunsakul
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana; Roudebush Veterans Administration Medical Center, Indianapolis, Indiana; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
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12
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Wang B, Suen CW, Ma H, Wang Y, Kong L, Qin D, Lee YWW, Li G. The Roles of H19 in Regulating Inflammation and Aging. Front Immunol 2020; 11:579687. [PMID: 33193379 PMCID: PMC7653221 DOI: 10.3389/fimmu.2020.579687] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/05/2020] [Indexed: 12/17/2022] Open
Abstract
Accumulating evidence suggests that long non-coding RNA H19 correlates with several aging processes. However, the role of H19 in aging remains unclear. Many studies have elucidated a close connection between H19 and inflammatory genes. Chronic systemic inflammation is an established factor associated with various diseases during aging. Thus, H19 might participate in the development of age-related diseases by interplay with inflammation and therefore provide a protective function against age-related diseases. We investigated the inflammatory gene network of H19 to understand its regulatory mechanisms. H19 usually controls gene expression by acting as a microRNA sponge, or through mir-675, or by leading various protein complexes to genes at the chromosome level. The regulatory gene network has been intensively studied, whereas the biogenesis of H19 remains largely unknown. This literature review found that the epithelial-mesenchymal transition (EMT) and an imprinting gene network (IGN) might link H19 with inflammation. Evidence indicates that EMT and IGN are also tightly controlled by environmental stress. We propose that H19 is a stress-induced long non-coding RNA. Because environmental stress is a recognized age-related factor, inflammation and H19 might serve as a therapeutic axis to fight against age-related diseases.
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Affiliation(s)
- Bin Wang
- The Chinese University of Hong Kong (CUHK)-Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GDL), Advanced Institute for Regenerative MedicineBioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.,Innovation Center for Translational Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chun Wai Suen
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Haibin Ma
- The Chinese University of Hong Kong (CUHK)-Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GDL), Advanced Institute for Regenerative MedicineBioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Yan Wang
- Innovation Center for Translational Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ling Kong
- The Chinese University of Hong Kong (CUHK)-Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GDL), Advanced Institute for Regenerative MedicineBioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Dajiang Qin
- The Chinese University of Hong Kong (CUHK)-Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GDL), Advanced Institute for Regenerative MedicineBioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.,Innovation Center for Translational Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuk Wai Wayne Lee
- Department of Orthopaedics & Traumatology, Stem Cells and Regenerative Medicine Laboratory, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China
| | - Gang Li
- The Chinese University of Hong Kong (CUHK)-Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GDL), Advanced Institute for Regenerative MedicineBioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.,Department of Orthopaedics & Traumatology, Stem Cells and Regenerative Medicine Laboratory, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China.,Ministry of Education Key Laboratory for Regenerative Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Innovation Center for Translational Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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13
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Xu W, Li H, Zhang M, Shi J, Wang Z. Locus-specific analysis of DNA methylation patterns in cloned and in vitro fertilized porcine embryos. J Reprod Dev 2020; 66:505-514. [PMID: 32908081 PMCID: PMC7768172 DOI: 10.1262/jrd.2019-076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Porcine somatic cell nuclear transfer (SCNT) is currently inefficient, as 1–3.95% of reconstructed embryos survive to term; inadequate or erroneous epigenetic
reprogramming of the specialized donor somatic nucleus could be a primary reason. Therefore, a locus-specific analysis of DNA methylation dynamics in
embryogenesis and the DNA methylation status of gametes and donor cells used for SCNT were conducted in the following developmentally important gene loci:
POU5F1, NANOG, SOX2, H19, IGF2, IGF2R,
XIST; and the retrotransposon LINE-1. There were significant epigenetic differences between the gametes and the somatic
donor cells. Three gamete-specific differentially methylated regions (DMRs) in POU5F1, XIST, and LINE-1 were
identified. A delayed demethylation process at POU5F1 and LINE-1 loci occurred after three successive cleavages, compared to
the in vitro fertilized (IVF) embryos. Although cloned embryos could undergo de-methylation and re-methylation dynamics at the DMRs of
imprinted genes (H19,IGF2R, and XIST), the re-methylation process was compromised, unlike in fertilized
embryos. LINE-1 loci are widely dispersed across the whole genome, and LINE-1 DMR might be a potential porcine nuclear
reprogramming epi-marker. Data from observations in our present and previous studies, and two published articles were pooled to produce a schematic diagram of
locus-specific, DNA methylation dynamics of cloned and IVF embryos during porcine early embryogenesis. This also indicated aberrant DNA methylation
reprogramming events, including inadequate DNA demethylation and insufficient re-methylation in cloned embryos. Further research should focus on mechanisms
underlying demethylation during the early cleavage of embryos and de novo DNA methylation at the blastocyst stage.
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Affiliation(s)
- Weihua Xu
- Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, College of Life Sciences, Longyan University, Longyan 364012, P. R. China.,Provincial Key Laboratory for Developmental Biology and Neurosciences, College of Life Sciences, Key Laboratory of Opto-Electronic Science and Technology for Medicine of Ministry of Education, Fujian Normal University, Fuzhou 350007, P. R. China
| | - Hongyi Li
- Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, College of Life Sciences, Longyan University, Longyan 364012, P. R. China
| | - Mao Zhang
- Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, College of Life Sciences, Longyan University, Longyan 364012, P. R. China
| | - Junsong Shi
- Guangdong Provincial Wen's Research Institute, Yunfu 527400, P. R. China
| | - Zhengchao Wang
- Provincial Key Laboratory for Developmental Biology and Neurosciences, College of Life Sciences, Key Laboratory of Opto-Electronic Science and Technology for Medicine of Ministry of Education, Fujian Normal University, Fuzhou 350007, P. R. China
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14
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Hori N, Kubo S, Sakasegawa T, Sakurai C, Hatsuzawa K. OCT3/4-binding sequence-dependent maintenance of the unmethylated state of CTCF-binding sequences with DNA demethylation and suppression of de novo DNA methylation in the H19 imprinted control region. Gene 2020; 743:144606. [DOI: 10.1016/j.gene.2020.144606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 11/25/2022]
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15
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Horii T, Morita S, Hino S, Kimura M, Hino Y, Kogo H, Nakao M, Hatada I. Successful generation of epigenetic disease model mice by targeted demethylation of the epigenome. Genome Biol 2020; 21:77. [PMID: 32234052 PMCID: PMC7110793 DOI: 10.1186/s13059-020-01991-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/08/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Epigenetic modifications, including DNA methylation, play an important role in gene silencing and genome stability. Consequently, epigenetic dysregulation can cause several diseases, such as cancer, obesity, diabetes, autism, and imprinting disorders. RESULTS We validate three methods for the generation of epigenome-edited mice using the dCas9-SunTag and single-chain variable fragment-TET1 catalytic domain. We generate model mice for Silver-Russell syndrome (SRS), an imprinting disorder, by target-specific DNA demethylation in the H19 differentially methylated region. Like SRS patients, these mice show H19 upregulation and Igf2 downregulation, leading to severe intrauterine and postnatal growth retardation. CONCLUSION This is the first report of an imprinting disease model animal generated by targeted demethylation of specific loci of the epigenome in fertilized eggs. Epigenome-edited animals are also useful for exploring the causative epimutations in epigenetic diseases.
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Affiliation(s)
- Takuro Horii
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, 3-39-15 Showa-machi, Maebashi, Gunma, 371-8512, Japan
| | - Sumiyo Morita
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, 3-39-15 Showa-machi, Maebashi, Gunma, 371-8512, Japan
| | - Shinjiro Hino
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Mika Kimura
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, 3-39-15 Showa-machi, Maebashi, Gunma, 371-8512, Japan
| | - Yuko Hino
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Hiroshi Kogo
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Izuho Hatada
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, 3-39-15 Showa-machi, Maebashi, Gunma, 371-8512, Japan.
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16
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Xiao Y, Liu R, Li X, Gurley EC, Hylemon PB, Lu Y, Zhou H, Cai W. Long Noncoding RNA H19 Contributes to Cholangiocyte Proliferation and Cholestatic Liver Fibrosis in Biliary Atresia. Hepatology 2019; 70:1658-1673. [PMID: 31063660 PMCID: PMC6819224 DOI: 10.1002/hep.30698] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/24/2019] [Indexed: 02/06/2023]
Abstract
Biliary atresia (BA) is a neonatal liver disease featuring cholestasis and severe liver fibrosis (LF). Despite advances in the development of surgical treatment, lacking an early diagnostic marker and intervention of LF invariably leads to death from end-stage liver disease in the early years of life. We previously reported that knockout of sphingosine 1-phosphate receptor 2 (S1PR2) protected mice from bile duct ligation (BDL)-induced cholangiocyte proliferation and LF. Our recent studies further showed that both hepatic and serum exosomal long noncoding RNA H19 (lncRNAH19) levels are correlated with cholestatic injury in multidrug resistance 2 knockout (Mdr2-/- ) mice. However, the role of lncRNAH19 in BA progression remains unclear. Here, we show that both hepatic and serum exosomal H19 levels are positively correlated with severity of fibrotic liver injuries in BA patients. H19 deficiency protects mice from BDL-induced cholangiocyte proliferation and LF by inhibiting bile-acid-induced expression and activation of S1PR2 and sphingosine kinase 2 (SphK2). Furthermore, H19 acts as a molecular sponge for members of the microRNA let-7 family, which results in up-regulation of high-mobility group AT-hook 2 (HMGA2), a known target of let-7 and enhancement of biliary proliferation. Conclusion: These results indicate that H19 plays a critical role in cholangiocyte proliferation and cholestatic liver injury in BA by regulating the S1PR2/SphK2 and let-7/HMGA2 axis. Serum exosomal H19 may represent a noninvasive diagnostic biomarker and potential therapeutic target for BA.
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Affiliation(s)
- Yongtao Xiao
- Department of Pediatric Surgery, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Institute of Pediatric Research, Shanghai, China
- Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China
| | - Runping Liu
- Department of Microbiology and Immunology and McGuire Veterans Affairs Medical Center, Virginia Commonwealth University, Richmond, VA
| | - Xiaojiaoyang Li
- Department of Microbiology and Immunology and McGuire Veterans Affairs Medical Center, Virginia Commonwealth University, Richmond, VA
| | - Emily C. Gurley
- Department of Microbiology and Immunology and McGuire Veterans Affairs Medical Center, Virginia Commonwealth University, Richmond, VA
| | - Phillip B. Hylemon
- Department of Microbiology and Immunology and McGuire Veterans Affairs Medical Center, Virginia Commonwealth University, Richmond, VA
| | - Ying Lu
- Department of Pediatric Surgery, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Institute of Pediatric Research, Shanghai, China
- Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China
| | - Huiping Zhou
- Department of Microbiology and Immunology and McGuire Veterans Affairs Medical Center, Virginia Commonwealth University, Richmond, VA
| | - Wei Cai
- Department of Pediatric Surgery, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Institute of Pediatric Research, Shanghai, China
- Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China
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17
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Abstract
Cellular heterogeneity, which was initially defined for tumor cells, is a fundamental property of all cellular systems, ranging from genetic diversity to cell-to-cell variation driven by stochastic molecular interactions involved all cellular processes. Different cells display substantial variation in gene expression and in response to environmental signaling even in an apparently homogeneous population of cells. Recent studies started to reveal the underlying mechanisms for cellular heterogeneity, particularly related to the states of chromatin. Accumulating evidence suggests that CTCF, an important factor regulating chromatin organization, plays a key role in the control of gene expression variation by stabilizing enhancer–promoter interaction.
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Affiliation(s)
- Gang Ren
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892 USA
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18
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Reynès C, Kister G, Rohmer M, Bouschet T, Varrault A, Dubois E, Rialle S, Journot L, Sabatier R. ISoLDE: a data-driven statistical method for the inference of allelic imbalance in datasets with reciprocal crosses. Bioinformatics 2019; 36:504-513. [PMID: 31350542 PMCID: PMC9883709 DOI: 10.1093/bioinformatics/btz564] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 07/08/2019] [Accepted: 07/22/2019] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Allelic imbalance (AI), i.e. the unequal expression of the alleles of the same gene in a single cell, affects a subset of genes in diploid organisms. One prominent example of AI is parental genomic imprinting, which results in parent-of-origin-dependent, mono-allelic expression of a limited number of genes in metatherian and eutherian mammals and in angiosperms. Currently available methods for identifying AI rely on data modeling and come with the associated limitations. RESULTS We have designed ISoLDE (Integrative Statistics of alleLe Dependent Expression), a novel nonparametric statistical method that takes into account both AI and the characteristics of RNA-seq data to infer allelic expression bias when at least two biological replicates are available for reciprocal crosses. ISoLDE learns the distribution of a specific test statistic from the data and calls genes 'allelically imbalanced', 'bi-allelically expressed' or 'undetermined'. Depending on the number of replicates, predefined thresholds or permutations are used to make calls. We benchmarked ISoLDE against published methods, and showed that ISoLDE compared favorably with respect to sensitivity, specificity and robustness to the number of replicates. Using ISoLDE on different RNA-seq datasets generated from hybrid mouse tissues, we did not discover novel imprinted genes (IGs), confirming the most conservative estimations of IG number. AVAILABILITY AND IMPLEMENTATION ISoLDE has been implemented as a Bioconductor package available at http://bioconductor.org/packages/ISoLDE/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Guilhem Kister
- Faculté de Pharmacie, Univ. Montpellier 34093 Montpellier, France
| | - Marine Rohmer
- Montpellier GenomiX, MGX, Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Tristan Bouschet
- Institut de Génomique Fonctionnelle, IGF, Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Annie Varrault
- Institut de Génomique Fonctionnelle, IGF, Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Emeric Dubois
- Montpellier GenomiX, MGX, Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Stéphanie Rialle
- Montpellier GenomiX, MGX, Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Laurent Journot
- Institut de Génomique Fonctionnelle, IGF, Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France,Montpellier GenomiX, MGX, Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France
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19
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Dang S, Ding D, Lu Y, Su Q, Lin T, Zhang X, Zhang H, Wang X, Tan H, Zhu Z, Li H. PM 2.5 exposure during pregnancy induces hypermethylation of estrogen receptor promoter region in rat uterus and declines offspring birth weights. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 243:851-861. [PMID: 30245447 DOI: 10.1016/j.envpol.2018.09.065] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 08/28/2018] [Accepted: 09/12/2018] [Indexed: 06/08/2023]
Abstract
Particulate matter 2.5 (PM2.5) exposures during pregnancy could lead to declined birth weight, intrauterine developmental restriction, and premature delivery, however, the underlying mechanisms are still not elucidated. There are few studies concerning the effects of PM2.5 exposure on maternal and child health in Xi'an (one of the cities with severe air pollution of PM2.5 in North China). Then, this study aimed to investigate the effect of PM2.5 exposure in Xi'an on the offspring birth weights and the possibly associated epigenetic mechanisms. We found the Low and High groups: the offspring with declined birth weights; the decreased mRNA and protein expression of the estrogen receptor (ERs) and eNOs in the uterus; the decreased endometria vascular diameter maximum (EVDM); the increased mRNA and protein expressions of the DNMT1 and 3b in the uterus; the elevated methylation levels of the CpG sites in the CpG island of ERα promoter region in the uterus. However, no differences were observed in the mRNA or protein expressions of ERβ and DNMT3a between the Clean and PM2.5 exposure groups, as well as endometriavascular density (EVD). Additionally, PM2.5 level was negatively correlated with the ERα protein expression, EVDM and offspring birth weight, as well as the methylation level of the CpG sites in the CpG island of ERα promoter region and the ERα protein expression in the uterus; whereas the ERα protein expression was positively correlated with the offspring birth weight, as well as PM2.5 level and the methylation level of the CpG sites in the CpG island of ERα promoter region in the uterus. Taken together, elevated methylation level of the CpG sites in the CpG island of ERα promoter region reduces ERα expression in the uterus, which could be one of the epigenetic mechanisms that pregnant PM2.5 exposure reduces the offspring birth weights.
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Affiliation(s)
- Shaokang Dang
- Division of Neonatology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Ding Ding
- Division of Neonatology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Yong Lu
- Department of Genetics, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Qian Su
- Division of Neonatology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Tianwei Lin
- Key Laboratory of Shaanxi Province Biomedicine, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710061, China
| | - Xiaoxiao Zhang
- Key Laboratory of Shaanxi Province Biomedicine, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710061, China
| | - Huiping Zhang
- Division of Neonatology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Xuebin Wang
- Department of Thermal Engineering, Energy and Power Engineering College of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Houzhang Tan
- Department of Thermal Engineering, Energy and Power Engineering College of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Zhongliang Zhu
- Key Laboratory of Shaanxi Province Biomedicine, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710061, China
| | - Hui Li
- Division of Neonatology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China.
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20
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Caldwell BA, Bartolomei MS. Mapping the diploid genome, one cell at a time. Nat Struct Mol Biol 2018; 25:994-995. [PMID: 30374084 DOI: 10.1038/s41594-018-0149-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Blake A Caldwell
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Marisa S Bartolomei
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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21
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Jeong H, Wu X, Smith B, Yi SV. Genomic Landscape of Methylation Islands in Hymenopteran Insects. Genome Biol Evol 2018; 10:2766-2776. [PMID: 30239702 PMCID: PMC6195173 DOI: 10.1093/gbe/evy203] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2018] [Indexed: 01/31/2023] Open
Abstract
Recent genome-wide DNA methylation analyses of insect genomes accentuate an intriguing contrast compared with those in mammals. In mammals, most CpGs are heavily methylated, with the exceptions of clusters of hypomethylated sites referred to as CpG islands. In contrast, DNA methylation in insects is localized to a small number of CpG sites. Here, we refer to clusters of methylated CpGs as “methylation islands (MIs),” and investigate their characteristics in seven hymenopteran insects with high-quality bisulfite sequencing data. Methylation islands were primarily located within gene bodies. They were significantly overrepresented in exon–intron boundaries, indicating their potential roles in splicing. Methylated CpGs within MIs exhibited stronger evolutionary conservation compared with those outside of MIs. Additionally, genes harboring MIs exhibited higher and more stable levels of gene expression compared with those that do not harbor MIs. The effects of MIs on evolutionary conservation and gene expression are independent and stronger than the effect of DNA methylation alone. These results indicate that MIs may be useful to gain additional insights into understanding the role of DNA methylation in gene expression and evolutionary conservation in invertebrate genomes.
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Affiliation(s)
- Hyeonsoo Jeong
- School of Biological Sciences, Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia
| | - Xin Wu
- School of Biological Sciences, Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia
| | - Brandon Smith
- School of Biological Sciences, Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia
| | - Soojin V Yi
- School of Biological Sciences, Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia
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22
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SanMiguel JM, Bartolomei MS. DNA methylation dynamics of genomic imprinting in mouse development. Biol Reprod 2018; 99:252-262. [PMID: 29462489 PMCID: PMC6044325 DOI: 10.1093/biolre/ioy036] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/31/2018] [Accepted: 02/07/2018] [Indexed: 01/05/2023] Open
Abstract
DNA methylation is an essential epigenetic mark crucial for normal mammalian development. This modification controls the expression of a unique class of genes, designated as imprinted, which are expressed monoallelically and in a parent-of-origin-specific manner. Proper parental allele-specific DNA methylation at imprinting control regions (ICRs) is necessary for appropriate imprinting. Processes that deregulate DNA methylation of imprinted loci cause disease in humans. DNA methylation patterns dramatically change during mammalian development: first, the majority of the genome, with the exception of ICRs, is demethylated after fertilization, and subsequently undergoes genome-wide de novo DNA methylation. Secondly, after primordial germ cells are specified in the embryo, another wave of demethylation occurs, with ICR demethylation occurring late in the process. Lastly, ICRs reacquire DNA methylation imprints in developing germ cells. We describe the past discoveries and current literature defining these crucial dynamics in relation to imprinted genes and the rest of the genome.
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Affiliation(s)
- Jennifer M SanMiguel
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marisa S Bartolomei
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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23
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Mai Q, Mai X, Huang X, Zhang D, Huang K, Zhou C. Imprinting Status in Two Human Parthenogenetic Embryonic Stem Cell Lines: Analysis of 63 Imprinted Gene Expression Levels in Undifferentiated and Early Differentiated Stages. Stem Cells Dev 2018; 27:430-439. [PMID: 29402175 DOI: 10.1089/scd.2017.0247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Human parthenogenetic embryonic stem cells (hPESCs) represent a source of histocompatible tissues for transplantation and carry two copies of the maternal genome, but lack the paternal genome. In this study, we selected 63 known human imprinted genes to investigate the imprinting status of hPESC. The expression level of these genes, including 27 maternally and 36 paternally imprinted were illustrated in hPESC and human embryonic stem cells (hESCs) derived from fertilized embryo lines. The expression activity changes of these genes were analyzed in undifferentiated and early differentiated hPESC lines. In addition, the methylation status of four differentially methylated regions (DMRs) of the imprinted genes was analyzed in undifferentiated and early differentiated hPESC and hESC lines. As a result, we found that all the maternally imprinted genes were expressed at similar levels in the undifferentiated hPESC lines and the hESC lines, except ZNF264 and ATP10A. Twenty-one analyzed paternal imprinted genes were expressed at the same level in two separated hPESC lines as well as compared with the hESC lines, whereas 15 other paternal imprinted genes were significantly downregulated or inactivated in hPESC lines as compared with the hESC line. During prolonged passage, the expression levels of the majority of imprinted genes remained stable in two hPESC lines. The four DMRs, including PEG3/ZIM2 (DMRs), SNURF/SNRPN DMRs, and KVDMR1 DMRs are highly methylated in the genes of two undifferentiated hPESCs and its embryonic bodies (EBs), whereas the genes of the undifferentiated hESCs and its EBs are half methylated. During the early differentiation stage, the imprinted genes showed the same expression trend and the expression levels of H19, IGF2, SLC22A2, SLC22A3/SLC22A18, and CPA4 were significantly upregulated in both hPESC lines. As conclusion, hPESCs show a substantial degree of epigenetic stability with respect to some imprinted genes.
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Affiliation(s)
- Qingyun Mai
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
| | - Xiuyun Mai
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China .,2 Reproductive Medical Center , Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Xin Huang
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
| | - Dan Zhang
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
| | - Kejun Huang
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
| | - Canquan Zhou
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
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Ying SY, Fang W, Lin SL. The miR-302-Mediated Induction of Pluripotent Stem Cells (iPSC): Multiple Synergistic Reprogramming Mechanisms. Methods Mol Biol 2018; 1733:283-304. [PMID: 29435941 DOI: 10.1007/978-1-4939-7601-0_23] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Pluripotency represents a unique feature of embryonic stem cells (ESCs). To generate ESC-like-induced pluripotent stem cells (iPSCs) derived from somatic cells, the cell genome needs to be reset and reprogrammed to express the ESC-specific transcriptome. Numerous studies have shown that genomic DNA demethylation is required for epigenetic reprogramming of somatic cell nuclei to form iPSCs; yet, the mechanism remains largely unclear. In ESCs, the reprogramming process goes through two critical stages: germline and zygotic demethylation, both of which erase genomic DNA methylation sites and hence allow for different gene expression patterns to be reset into a pluripotent state. Recently, miR-302, an ESC-specific microRNA (miRNA), was found to play an essential role in four aspects of this reprogramming mechanism-(1) initiating global genomic DNA demethylation, (2) activating ESC-specific gene expression, (3) inhibiting developmental signaling, and (4) preventing stem cell tumorigenicity. In this review, we will summarize miR-302 functions in all four reprogramming aspects and further discuss how these findings may improve the efficiency and safety of the current iPSC technology.
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Affiliation(s)
- Shao-Yao Ying
- Department of Integrative Anatomical Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - William Fang
- Department of Integrative Anatomical Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shi-Lung Lin
- Division of Regenerative Medicine, WJWU & LYNN (W&L) Institute for Stem Cell Research, Santa Fe Springs, CA, USA
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25
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Ward MA. An Interview with Dr Marisa Bartolomei. Biol Reprod 2017; 98:147-149. [PMID: 29228104 DOI: 10.1093/biolre/iox170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Monika A Ward
- Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii
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Kaneda M, Takahashi M, Yamanaka KI, Saito K, Taniguchi M, Akagi S, Watanabe S, Nagai T. Epigenetic analysis of bovine parthenogenetic embryonic fibroblasts. J Reprod Dev 2017; 63:365-375. [PMID: 28484201 PMCID: PMC5593088 DOI: 10.1262/jrd.2017-040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Although more than 100 imprinted genes have already been identified in the mouse and human genomes, little is known about genomic imprinting in cattle. For a better understanding of these genes in cattle, parthenogenetically activated bovine blastocysts were transferred to recipient cows to obtain parthenotes, and fibroblasts derived from a Day 40 (Day 0 being the day of parthenogenetic activation) parthenogenetic embryo (BpEFs) were successfully obtained. Bovine embryonic fibroblasts (BEFs) were also isolated from a normal fertilized embryo obtained from an artificially inseminated cow. The expression of imprinted genes was analyzed by RT-PCR. Paternally expressed genes (PEGs) in mouse (viz., IGF2, PEG3, ZAC1, NDN, DLK1, SGCE, and PEG10) were expressed in BEFs, but not in BpEFs, suggesting that these genes are also imprinted in cattle. However, other PEGs in mouse (viz., IMPACT, MAGEL2, SNRPN, and PEG1/MEST) were expressed in both BEFs and BpEFs. These genes may not be imprinted in BEFs. The expression of seven maternally expressed genes in mouse was also analyzed, and only CDKN1C was not expressed in BpEFs. The DNA methylation patterns of repetitive elements (Satellite I, Satellite II, alpha-satellite, and Art2) were not different between the BEFs and BpEFs; however, the differentially methylated region (DMR) of paternally methylated H19 was hypomethylated, whereas those of maternally methylated PEG3 and PEG10 were hypermethylated in BpEFs, as expected. The methylation of the SNRPN DMR was not different between the BEFs and BpEFs, in accordance with the SNRPN expression levels in both cell types. The XIST gene, which is essential for X chromosome inactivation in females, was expressed in BpEFs, whereas its DMR was half-methylated, suggesting that X chromosome inactivation is normal in these cells. Microarray analysis was also applied to identify novel PEGs that should be expressed only in BEFs but not in BpEFs. More than 300 PEG candidate genes, including IGF2, PEG3, and PEG10, were obtained. These results illustrate the epigenetic characteristic of bovine parthenogenetic embryos and contribute to the identification of novel imprinted genes in cattle.
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Affiliation(s)
- Masahiro Kaneda
- Division of Animal Life Science, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Masashi Takahashi
- Department of Animal Science, Graduate School of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan
| | | | - Koji Saito
- Kumamoto Prefectural Agriculture Research Center, Kumamoto 861-1113, Japan
| | - Masanori Taniguchi
- Kumamoto Prefectural Agriculture Research Center, Kumamoto 861-1113, Japan
| | - Satoshi Akagi
- Animal Breeding and Reproduction Research Division, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Ibaraki 305-0901, Japan
| | - Shinya Watanabe
- Animal Breeding and Reproduction Research Division, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Ibaraki 305-0901, Japan
| | - Takashi Nagai
- Headquarters, National Agriculture and Food Research Organization, Ibaraki 305-8517, Japan
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Dumasia K, Kumar A, Deshpande S, Balasinor NH. Estrogen signaling, through estrogen receptor β, regulates DNA methylation and its machinery in male germ line in adult rats. Epigenetics 2017; 12:476-483. [PMID: 28362134 DOI: 10.1080/15592294.2017.1309489] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Estrogen, through its receptors, regulates various aspects of spermatogenesis and male fertility. To understand the roles of estrogen receptors (ERα and ERβ) in male fertility, we have developed in vivo selective ER agonist administration models. Treatment of adult male rats with ERα or ERβ agonist for 60 d decreases fertility and litter size mainly due to increased pre- and post-implantation embryo loss. Since epigenetic mechanisms like DNA methylation play a crucial role in male fertility, we investigated the effects of the ER agonists on DNA methylation in spermatozoa. Treatment with ERβ agonist causes a significant decrease in DNA methylation both at the global level and at the H19 differentially methylated region (DMR). This could be due to decrease in DNA methyltransferases in the testis upon ERβ agonist treatment. The hypomethylation observed at the H19 DMR corroborates with aberrant expression of Igf2 and H19 imprinted genes in the resorbed embryos sired by ERβ agonist-treated males. Thus, our study demonstrates that ERβ regulates DNA methylation and methylating enzymes during adult rat spermatogenesis. Activation of estrogen signaling through ERβ could therefore cause DNA methylation defects leading to impaired male fertility. These results define a role for estrogen in epigenetic regulation of male germ line, suggesting that epigenetic insults by exposure to environmental estrogens could potentially affect male fertility.
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Affiliation(s)
- Kushaan Dumasia
- a Department of Neuroendocrinology , National Institute for Research in Reproductive Health (Indian Council of Medical Research) , Parel, Mumbai , India
| | - Anita Kumar
- a Department of Neuroendocrinology , National Institute for Research in Reproductive Health (Indian Council of Medical Research) , Parel, Mumbai , India
| | - Sharvari Deshpande
- a Department of Neuroendocrinology , National Institute for Research in Reproductive Health (Indian Council of Medical Research) , Parel, Mumbai , India
| | - Nafisa H Balasinor
- a Department of Neuroendocrinology , National Institute for Research in Reproductive Health (Indian Council of Medical Research) , Parel, Mumbai , India
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Gebert C, Rong Q, Jeong S, Iben J, Pfeifer K. H19ICR mediated transcriptional silencing does not require target promoter methylation. Biochem Biophys Res Commun 2016; 476:121-6. [PMID: 27178213 DOI: 10.1016/j.bbrc.2016.05.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 05/03/2016] [Indexed: 10/21/2022]
Abstract
Transcription of the reciprocally imprinted genes Insulin-like growth factor 2 (Igf2) and H19 is orchestrated by the 2.4-kb H19 Imprinting Control Region (H19ICR) located upstream of H19. Three known functions are associated with the H19ICR: (1) it is a germline differentially methylated region, (2) it is a transcriptional insulator, and (3) it is a transcriptional silencer. The molecular mechanisms of the DMR and insulator functions have been well characterized but the basis for the ICR's silencer function is less well understood. In order to study the role the H19ICR intrinsically plays in gene silencing, we transferred the 2.4-kb H19ICR to a heterologous non-imprinted location on chromosome 5, upstream of the alpha fetoprotein (Afp) promoter. Independent of its orientation, the 2.4-kb H19ICR silences transcription from the paternal Afp promoter. Thus silencing is a function intrinsic to this DNA element. Further, ICR mediated silencing is a developmental process that, unexpectedly, does not occur through DNA methylation at the target promoter.
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Affiliation(s)
- Claudia Gebert
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Qi Rong
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sangkyun Jeong
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - James Iben
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Karl Pfeifer
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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Ishida M. New developments in Silver-Russell syndrome and implications for clinical practice. Epigenomics 2016; 8:563-80. [PMID: 27066913 DOI: 10.2217/epi-2015-0010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Silver-Russell syndrome is a clinically and genetically heterogeneous disorder, characterized by prenatal and postnatal growth restriction, relative macrocephaly, body asymmetry and characteristic facial features. It is one of the imprinting disorders, which results as a consequence of aberrant imprinted gene expressions. Currently, maternal uniparental disomy of chromosome 7 accounts for approximately 10% of Silver-Russell syndrome cases, while ~50% of patients have hypomethylation at imprinting control region 1 at chromosome 11p15.5 locus, leaving ~40% of cases with unknown etiologies. This review aims to provide a comprehensive list of molecular defects in Silver-Russell syndrome reported to date and to highlight the importance of multiple-loci/tissue testing and trio (both parents and proband) screening. The epigenetic and phenotypic overlaps with other imprinting disorders will also be discussed.
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Affiliation(s)
- Miho Ishida
- University College London, Institute of Child Health, Genetics & Genomic Medicine programme, Genetics & Epigenetics in Health & Diseases Section, 30 Guilford Street, London, WC1N 1EH, UK
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30
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Sheaffer KL, Elliott EN, Kaestner KH. DNA Hypomethylation Contributes to Genomic Instability and Intestinal Cancer Initiation. Cancer Prev Res (Phila) 2016; 9:534-46. [PMID: 26883721 DOI: 10.1158/1940-6207.capr-15-0349] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 02/08/2016] [Indexed: 12/12/2022]
Abstract
Intestinal cancer is a heterogeneous disease driven by genetic mutations and epigenetic changes. Approximately 80% of sporadic colorectal cancers are initiated by mutation and inactivation of the adenomatous polyposis coli (APC) gene, which results in unrestrained intestinal epithelial growth and formation of adenomas. Aberrant DNA methylation promotes cancer progression by the inactivation of tumor suppressor genes via promoter methylation. In addition, global DNA hypomethylation is often seen before the formation of adenomas, suggesting that it contributes to neoplastic transformation. Previous studies employed mice with a hypomorphic mutation in DNA methyltransferase 1 (Dnmt1), which exhibited constitutive global DNA hypomethylation and decreased tumorigenesis in the Apc(Min/+) mouse model of intestinal cancer. However, the consequences of intestinal epithelial-specific acute hypomethylation during Apc(Min/+) tumor initiation have not been reported. Using temporally controlled intestinal epithelial-specific gene ablation, we show that total loss of Dnmt1 in the Apc(Min/+) mouse model of intestinal cancer causes accelerated adenoma initiation. Deletion of Dnmt1 precipitates an acute response characterized by hypomethylation of repetitive elements and genomic instability, which surprisingly is followed by remethylation with time. Two months post-Dnmt1 ablation, mice display increased macroadenoma load, consistent with a role for Dnmt1 and DNA methylation in maintaining genomic stability. These data suggest that DNA hypomethylation plays a previously unappreciated role in intestinal adenoma initiation. Cancer Prev Res; 9(7); 534-46. ©2016 AACRSee related article by Lee and Laird, p. 509.
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Affiliation(s)
- Karyn L Sheaffer
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ellen N Elliott
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Klaus H Kaestner
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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Ventura-Juncá P, Irarrázaval I, Rolle AJ, Gutiérrez JI, Moreno RD, Santos MJ. In vitro fertilization (IVF) in mammals: epigenetic and developmental alterations. Scientific and bioethical implications for IVF in humans. Biol Res 2015; 48:68. [PMID: 26683055 PMCID: PMC4684609 DOI: 10.1186/s40659-015-0059-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 11/30/2015] [Indexed: 01/06/2023] Open
Abstract
The advent of in vitro fertilization (IVF) in animals and humans implies an extraordinary change in the environment where the beginning of a new organism takes place. In mammals fertilization occurs in the maternal oviduct, where there are unique conditions for guaranteeing the encounter of the gametes and the first stages of development of the embryo and thus its future. During this period a major epigenetic reprogramming takes place that is crucial for the normal fate of the embryo. This epigenetic reprogramming is very vulnerable to changes in environmental conditions such as the ones implied in IVF, including in vitro culture, nutrition, light, temperature, oxygen tension, embryo-maternal signaling, and the general absence of protection against foreign elements that could affect the stability of this process. The objective of this review is to update the impact of the various conditions inherent in the use of IVF on the epigenetic profile and outcomes of mammalian embryos, including superovulation, IVF technique, embryo culture and manipulation and absence of embryo-maternal signaling. It also covers the possible transgenerational inheritance of the epigenetic alterations associated with assisted reproductive technologies (ART), including its phenotypic consequences as is in the case of the large offspring syndrome (LOS). Finally, the important scientific and bioethical implications of the results found in animals are discussed in terms of the ART in humans.
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Affiliation(s)
- Patricio Ventura-Juncá
- Bioethical Center and Department of Pediatrics, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile. .,Bioethics Center, Universidad Finis Terrae, Pedro de Valdivia 1509, Providencia, Región Metropolitana, 7501015, Santiago, Chile.
| | - Isabel Irarrázaval
- Bioethical Center and Department of Pediatrics, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - Augusto J Rolle
- Bioethical Center and Department of Pediatrics, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - Juan I Gutiérrez
- Bioethical Center and Department of Pediatrics, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - Ricardo D Moreno
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile. .,Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - Manuel J Santos
- Bioethical Center and Department of Pediatrics, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile. .,Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.
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Alexander KA, Wang X, Shibata M, Clark AG, García-García MJ. TRIM28 Controls Genomic Imprinting through Distinct Mechanisms during and after Early Genome-wide Reprogramming. Cell Rep 2015; 13:1194-1205. [PMID: 26527006 DOI: 10.1016/j.celrep.2015.09.078] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 09/08/2015] [Accepted: 09/25/2015] [Indexed: 01/08/2023] Open
Abstract
Genomic imprinting depends on the establishment and maintenance of DNA methylation at imprinting control regions. However, the mechanisms by which these heritable marks influence allele-specific expression are not fully understood. By analyzing maternal, zygotic, maternal-zygotic, and conditional Trim28 mutants, we found that the transcription factor TRIM28 controls genomic imprinting through distinct mechanisms at different developmental stages. During early genome-wide reprogramming, both maternal and zygotic TRIM28 are required for the maintenance of methylation at germline imprints. However, in conditional Trim28 mutants, Gtl2-imprinted gene expression was lost despite normal methylation levels at the germline IG-DMR. These results provide evidence that TRIM28 controls imprinting after early embryonic reprogramming through a mechanism other than the maintenance of germline imprints. Additionally, our finding that secondary imprints were hypomethylated in TRIM28 mutants uncovers a requirement of TRIM28 after genome-wide reprogramming for interpreting germline imprints and regulating DNA methylation at imprinted gene promoters.
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Affiliation(s)
- Katherine A Alexander
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Xu Wang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Maho Shibata
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - María J García-García
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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Elliott EN, Sheaffer KL, Schug J, Stappenbeck TS, Kaestner KH. Dnmt1 is essential to maintain progenitors in the perinatal intestinal epithelium. Development 2015; 142:2163-72. [PMID: 26023099 DOI: 10.1242/dev.117341] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 05/05/2015] [Indexed: 11/20/2022]
Abstract
The DNA methyltransferase Dnmt1 maintains DNA methylation patterns and genomic stability in several in vitro cell systems. Ablation of Dnmt1 in mouse embryos causes death at the post-gastrulation stage; however, the functions of Dnmt1 and DNA methylation in organogenesis remain unclear. Here, we report that Dnmt1 is crucial during perinatal intestinal development. Loss of Dnmt1 in intervillus progenitor cells causes global hypomethylation, DNA damage, premature differentiation, apoptosis and, consequently, loss of nascent villi. We further confirm the crucial role of Dnmt1 during crypt development using the in vitro organoid culture system, and illustrate a clear differential requirement for Dnmt1 in immature versus mature organoids. These results demonstrate an essential role for Dnmt1 in maintaining genomic stability during intestinal development and the establishment of intestinal crypts.
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Affiliation(s)
- Ellen N Elliott
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Karyn L Sheaffer
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan Schug
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Klaus H Kaestner
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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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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Tilghman SM. Twists and turns: a scientific journey. Annu Rev Cell Dev Biol 2014; 30:1-21. [PMID: 25288111 DOI: 10.1146/annurev-cellbio-100913-013512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this perspective I look back on the twists and turns that influenced the direction of my scientific career over the past 40 years. From my early ambition to be a chemist to my training in Philadelphia and Bethesda as a molecular biologist, I benefited enormously from generous and valuable mentoring. In my independent career in Philadelphia and Princeton, I was motivated by a keen interest in the changes in gene expression that direct the development of the mammalian embryo and inspired by the creativity and energy of my students, fellows, and research staff. After twelve years as President of Princeton University, I have happily returned to the faculty of the Department of Molecular Biology.
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Affiliation(s)
- Shirley M Tilghman
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544;
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Shin HS, Seo JH, Jeong SH, Park SW, Park Y, Son SW, Kim JS, Kang HG. Exposure of pregnant mice to chlorpyrifos-methyl alters embryonic H19 gene methylation patterns. ENVIRONMENTAL TOXICOLOGY 2014; 29:926-935. [PMID: 23125134 DOI: 10.1002/tox.21820] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 09/11/2012] [Accepted: 09/23/2012] [Indexed: 06/01/2023]
Abstract
The aim of this study was to identify whether chlorpyrifos methyl (CPM) exposure during pregnancy leads to changes in the methylation patterns of H19 gene. CPM 4, 20, 100 mg/kg bw/day was administered to 4 pregnant mice per group between 7 and 12 days post coitum (d.p.c.). Pregnant mice were killed at 13 d.p.c. The genomic methylation in primordial germ cells (PGCs) and fetal organs (the liver, intestine, and placenta) was examined. Four polymorphism sites in the H19 alleles of maternal (C57BL/6J) and paternal (CAST/Ei) alleles were identified at nucleotide position 1407, 1485, 1566, and 1654. The methylation patterns of 17 CpG sites were analyzed. The methylation level in male and female PGCs was not altered by CPM treatment in the maternal allele H19. The methylation level of the paternal H19 allele was altered in only male PGCs in response to the CPM treatment. The methylation level at a binding site for the transcriptional regulator CTCF2 was higher than that at the CTCF1 binding site in all CPM-treated groups. In the placenta, the aggregate methylation level of H19 was 56.89%in control group. But, those levels were ranged from 47.7% to 49.89% after treatment with increasing doses of CPM. H19 gene from the liver and intestine of 13 d.p.c. fetuses treated with CPM was hypomethylated as compared with controls, although H19 mRNA expression was unaltered. In the placenta, H19 expression was slightly increased in the CPM-treated group, although not significantly. IGF2 expression levels were not significantly changed in the placenta. In conclusion, CPM exposure during pregnancy alters the methylation status of the H19 gene in PGCs and embryonic tissues. We infer that these alterations are likely related to changes in DNA demethylase activity.
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Affiliation(s)
- Hyo-Sook Shin
- Toxicology & Residue Chemistry Division, Animal, Plant and Fisheries Quarantine and Inspection Agency, 175 Anyangro, Anyang-si, Gyeonggi-do 430-757, Republic of Korea
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Zhang HZ, Xia XY, Zhu F, Shen H, Song K, Shang ZJ. Correlation of deregulated like-acetylglucosaminyl transferase and aberrant α-dystroglycan expression with human tongue cancer metastasis. J Oral Maxillofac Surg 2014; 72:1106-18. [PMID: 24629698 DOI: 10.1016/j.joms.2013.12.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 12/20/2013] [Accepted: 12/26/2013] [Indexed: 11/16/2022]
Abstract
PURPOSE The present study examined the correlation of α-dystroglycan (α-DG) expression and like-acetylglucosaminyl transferase (LARGE) with metastasis of human tongue cancer. MATERIALS AND METHODS Fifty human tongue cancer tissues and 2 tongue squamous cell carcinoma cell lines (CAL27 and SCC4) were involved. Immunohistochemistry was used to detect the expression of α-DG and LARGE. Methylation-specific polymerase chain reaction was performed to assess the methylation status of the LARGE gene promoter. CAL27 and SCC4 cells were transfected with exogenous LARGE and treated with 5-aza-2'-deoxycytidine (Aza-dC), respectively. Glycol sites of α-DG were detected by western blotting. In addition, the laminin overlay assay, cell adhesion assay, and invasion assay were performed. RESULTS Immunohistochemical results showed that decreased expression of VIA4-1 and IIH6 (antibodies that recognize the glycol sites of α-DG) were correlated with the lymph node metastasis of tongue cancer (n = 50; P = .016 and .025, respectively). Decreased LARGE expression and hypermethylation of the LARGE gene promoter were correlated with lymph node metastasis and α-DG glycosylation in human tongue cancer (n = 50; P = .043 and .015 respectively). In addition, LARGE overexpression and Aza-dC treatment actively led to restoration of functional α-DG expression, elevation of laminin binding, and decrease of migratory ability in cancer cells. CONCLUSION The results suggested that absent α-DG expression and LARGE deregulation were closely associated with nodal metastasis of tongue cancer. Aberrant α-DG expression and glycosylation were attributed at least in part to the abnormal epigenetic modification of LARGE, especially the hypermethylation of its promoter.
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Affiliation(s)
- Han-Zhong Zhang
- PhD Student, State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine Ministry of Education, Wuhan University, Wuhan, China
| | - Xiao-Yan Xia
- PhD Student, State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine Ministry of Education, Wuhan University, Wuhan, China
| | - Fei Zhu
- PhD Student, State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine Ministry of Education, Wuhan University, Wuhan, China
| | - Hui Shen
- PhD Student, State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine Ministry of Education, Wuhan University, Wuhan, China
| | - Kai Song
- PhD Student, State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine Ministry of Education, Wuhan University, Wuhan, China
| | - Zheng-Jun Shang
- Professor, State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine Ministry of Education, Wuhan University, Wuhan, China; Department of Oral and Maxillofacial and Head and Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan, China.
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Song Q, Decato B, Hong EE, Zhou M, Fang F, Qu J, Garvin T, Kessler M, Zhou J, Smith AD. A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics. PLoS One 2013; 8:e81148. [PMID: 24324667 PMCID: PMC3855694 DOI: 10.1371/journal.pone.0081148] [Citation(s) in RCA: 256] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 10/18/2013] [Indexed: 12/11/2022] Open
Abstract
DNA methylation is implicated in a surprising diversity of regulatory, evolutionary processes and diseases in eukaryotes. The introduction of whole-genome bisulfite sequencing has enabled the study of DNA methylation at a single-base resolution, revealing many new aspects of DNA methylation and highlighting the usefulness of methylome data in understanding a variety of genomic phenomena. As the number of publicly available whole-genome bisulfite sequencing studies reaches into the hundreds, reliable and convenient tools for comparing and analyzing methylomes become increasingly important. We present MethPipe, a pipeline for both low and high-level methylome analysis, and MethBase, an accompanying database of annotated methylomes from the public domain. Together these resources enable researchers to extract interesting features from methylomes and compare them with those identified in public methylomes in our database.
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Affiliation(s)
- Qiang Song
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Benjamin Decato
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Elizabeth E. Hong
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Meng Zhou
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Fang Fang
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Jianghan Qu
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Tyler Garvin
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Michael Kessler
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Jun Zhou
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Andrew D. Smith
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
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Abstract
Imprinted gene expression--the biased expression of alleles dependent on their parent of origin--is an important type of epigenetic gene regulation in flowering plants and mammals. In plants, genes are imprinted primarily in the endosperm, the triploid placenta-like tissue that surrounds and nourishes the embryo during its development. Differential allelic expression is correlated with active DNA demethylation by DNA glycosylases and repressive targeting by the Polycomb group proteins. Imprinted gene expression is one consequence of a large-scale remodeling to the epigenome, primarily directed at transposable elements, that occurs in gametes and seeds. This remodeling could be important for maintaining the epigenome in the embryo as well as for establishing gene imprinting.
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Affiliation(s)
- Mary Gehring
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142;
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40
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Effects of DNMT1 and HDAC inhibitors on gene-specific methylation reprogramming during porcine somatic cell nuclear transfer. PLoS One 2013; 8:e64705. [PMID: 23741375 PMCID: PMC3669391 DOI: 10.1371/journal.pone.0064705] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 04/17/2013] [Indexed: 12/02/2022] Open
Abstract
Somatic cell nuclear transfer (SCNT) in mammalian cloning currently remains inefficient. Incomplete or erroneous epigenetic reprogramming of specialized donor somatic nuclear and resulting aberrant gene expression during development of cloned embryos is commonly believed as the main reason that causes the low efficiency of SCNT. Use of small molecular reprogramming modifiers to assist the somatic nucleus to mimic naturally occurring DNA methylation and chromatin remodeling in nucleus of fertilization-derived zygotes, has been widely attempted to improve cloning efficiency. However, impacts of these small modifiers on gene-specific methylation dynamics and their potential effects on methylation of imprinted gene have rarely been traced. Here, we attempted two relatively novel DNMT1 inhibitor (DNMTi) and histone deacetylase inhibitor (HDACi), scriptaid and RG108, and demonstrated their effects on dynamics of gene-specific DNA methylation and transcription of porcine SCNT embryos. We found that scriptaid and RG108 had synergetic effects on rescuing the disrupted methylation imprint of H19 during SCNT at least partially by repression over-expressed MBD3 in eight-cell cloned embryos. Furthermore, we firstly identified a differential methylation regions (DMRs) at 5′ flanking regions of XIST gene and found that scriptaid alone and its combination with RG108 modify the dynamics of both transcription and DNA methylation levels in cloned embryos, by different manners. Additionally, we found that scriptaid alone and its combination with RG108 can significantly promote the transcription of NANOG in cloned embryos and enhance their pre-implantation developmental capacity. Our results would contribute to uncovering the epigenetic reprogramming mechanisms underlying the effects of assisted small molecules on improvement of mammalian cloning efficiency.
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41
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Jacob KJ, Robinson WP, Lefebvre L. Beckwith-Wiedemann and Silver-Russell syndromes: opposite developmental imbalances in imprinted regulators of placental function and embryonic growth. Clin Genet 2013; 84:326-34. [PMID: 23495910 DOI: 10.1111/cge.12143] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 03/12/2013] [Accepted: 03/12/2013] [Indexed: 11/29/2022]
Abstract
Beckwith-Wiedemann syndrome (BWS) and Silver-Russell syndrome (SRS) are two congenital disorders with opposite outcomes on fetal growth, overgrowth and growth restriction, respectively. Although both disorders are heterogeneous, most cases of BWS and SRS are associated with opposite epigenetic or genetic abnormalities on 11p15.5 leading to opposite imbalances in the expression levels of imprinted genes. In this article, we review evidence implicating these genes in the developmental regulation of embryonic growth and placental function in mouse models. The emerging picture suggests that both SRS and BWS can be caused by the simultaneous and opposite deregulation of two groups of imprinted genes on 11p15.5. A detailed description of the phenotypic abnormalities associated with each syndrome must take into consideration the developmental functions of each gene involved.
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Affiliation(s)
- K J Jacob
- Department of Medical Genetics; Life Sciences Institute, Molecular Epigenetics Group, University of British Columbia, Vancouver, Canada
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42
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Hatanaka Y, Shimizu N, Nishikawa S, Tokoro M, Shin SW, Nishihara T, Amano T, Anzai M, Kato H, Mitani T, Hosoi Y, Kishigami S, Matsumoto K. GSE is a maternal factor involved in active DNA demethylation in zygotes. PLoS One 2013; 8:e60205. [PMID: 23560077 PMCID: PMC3613368 DOI: 10.1371/journal.pone.0060205] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 02/21/2013] [Indexed: 11/17/2022] Open
Abstract
After fertilization, the sperm and oocyte genomes undergo extensive epigenetic reprogramming to form a totipotent zygote. The dynamic epigenetic changes during early embryo development primarily involve DNA methylation and demethylation. We have previously identified Gse (gonad-specific expression gene) to be expressed specifically in germ cells and early embryos. Its encoded protein GSE is predominantly localized in the nuclei of cells from the zygote to blastocyst stages, suggesting possible roles in the epigenetic changes occurring during early embryo development. Here, we report the involvement of GSE in epigenetic reprogramming of the paternal genome during mouse zygote development. Preferential binding of GSE to the paternal chromatin was observed from pronuclear stage 2 (PN2) onward. A knockdown of GSE by antisense RNA in oocytes produced no apparent effect on the first and second cell cycles in preimplantation embryos, but caused a significant reduction in the loss of 5-methylcytosine (5mC) and the accumulation of 5-hydroxymethylcytosine (5hmC) in the paternal pronucleus. Furthermore, DNA methylation levels in CpG sites of LINE1 transposable elements, Lemd1, Nanog and the upstream regulatory region of the Oct4 (also known as Pou5f1) gene were clearly increased in GSE-knockdown zygotes at mid-pronuclear stages (PN3-4), but the imprinted H19-differential methylated region was not affected. Importantly, DNA immunoprecipitation of 5mC and 5hmC also indicates that knockdown of GSE in zygotes resulted in a significant reduction of the conversion of 5mC to 5hmC on LINE1. Therefore, our results suggest an important role of maternal GSE for mediating active DNA demethylation in the zygote.
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Affiliation(s)
- Yuki Hatanaka
- Division of Biological Science, Kinki University Graduate School of Biology-Oriented Science and Technology, Kinokawa, Wakayama, Japan
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Negrón-Pérez VM, Echevarría FD, Huffman SR, Rivera RM. Determination of Allelic Expression of H19 in Pre- and Peri-Implantation Mouse Embryos1. Biol Reprod 2013; 88:97. [DOI: 10.1095/biolreprod.112.105882] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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44
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Glier MB, Ngai YF, Sulistyoningrum DC, Aleliunas RE, Bottiglieri T, Devlin AM. Tissue-specific relationship of S-adenosylhomocysteine with allele-specific H19/Igf2 methylation and imprinting in mice with hyperhomocysteinemia. Epigenetics 2012; 8:44-53. [PMID: 23221482 DOI: 10.4161/epi.23063] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
DNA methylation is linked to homocysteine metabolism through the generation of S-adenosylmethionine (AdoMet) and S-Adenosylhomocysteine (AdoHcy). The ratio of AdoMet/AdoHcy is often considered an indicator of tissue methylation capacity. The goal of this study is to determine the relationship of tissue AdoMet and AdoHcy concentrations to allele-specific methylation and expression of genomically imprinted H19/Igf2. Expression of H19/Igf2 is regulated by a differentially methylated domain (DMD), with H19 paternally imprinted and Igf2 maternally imprinted. F1 hybrid C57BL/6J x Castaneous/EiJ (Cast) mice with (+/-), and without (+/+), heterozygous disruption of cystathionine-β-synthase (Cbs) were fed a control diet or a diet (called HH) to induce hyperhomocysteinemia and changes in tissue AdoMet and AdoHcy. F1 Cast x Cbs+/- mice fed the HH diet had significantly higher plasma total homocysteine concentrations, higher liver AdoHcy, and lower AdoMet/AdoHcy ratios and this was accompanied by lower liver maternal H19 DMD allele methylation, lower liver Igf2 mRNA levels, and loss of Igf2 maternal imprinting. In contrast, we found no significant differences in AdoMet and AdoHcy in brain between the diet groups but F1 Cast x Cbs+/- mice fed the HH diet had higher maternal H19 DMD methylation and lower H19 mRNA levels in brain. A significant negative relationship between AdoHcy and maternal H19 DMD allele methylation was found in liver but not in brain. These findings suggest the relationship of AdoMet and AdoHcy to gene-specific DNA methylation is tissue-specific and that changes in DNA methylation can occur without changes in AdoMet and AdoHcy.
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Affiliation(s)
- Melissa B Glier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Child & Family Research Institute, Vancouver, BC, Canada
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45
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Hori N, Yamane M, Kouno K, Sato K. Induction of DNA demethylation depending on two sets of Sox2 and adjacent Oct3/4 binding sites (Sox-Oct motifs) within the mouse H19/insulin-like growth factor 2 (Igf2) imprinted control region. J Biol Chem 2012; 287:44006-16. [PMID: 23115243 DOI: 10.1074/jbc.m112.424580] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
DNA demethylation is used to establish and maintain an unmethylated state. The molecular mechanisms to induce DNA demethylation at a particular genomic locus remain unclear. The mouse H19/insulin-like growth factor 2 (Igf2) imprinted control region (ICR) is a methylation state-sensitive insulator that regulates transcriptional activation of both genes. The unmethylated state of the ICR established in female germ cells is maintained during development, resisting the wave of genome-wide de novo methylation. We previously demonstrated that a DNA fragment (fragment b) derived from this ICR-induced DNA demethylation when it was transfected into undifferentiated mouse embryonal carcinoma cell lines. Moreover, two octamer motifs within fragment b were necessary to induce this DNA demethylation. Here, we demonstrated that both octamer motifs and their flanking sequences constitute Sox-Oct motifs (SO1 and SO2) and that the SO1 region, which requires at least four additional elements, including the SO2 region, contributes significantly to the induction of high-frequency DNA demethylation as a Sox-Oct motif. Moreover, RNAi-mediated inhibition of Oct3/4 expression in P19 cells resulted in a reduced DNA demethylation frequency of fragment b but not of the adenine phosphoribosyltransferase gene CpG island. The Sox motif of SO1 could function as a sensor for a hypermethylated state of the ICR to repress demethylation activity. These results indicate that Sox-Oct motifs in the ICR determine the cell type, DNA region, and allele specificity of DNA demethylation. We propose a link between the mechanisms for maintenance of the unmethylated state of the H19/Igf2 ICR and the undifferentiated cell-specific induction of DNA demethylation.
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Affiliation(s)
- Naohiro Hori
- Division of Molecular Biology, Faculty of Medicine, Department of Molecular and Cellular Biology, School of Life Sciences, Tottori University, Tottori 683-8503, Japan.
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46
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Kawahara M, Kono T. Roles of genes regulated by two paternally methylated imprinted regions on chromosomes 7 and 12 in mouse ontogeny. J Reprod Dev 2012; 58:175-9. [PMID: 22738900 DOI: 10.1262/jrd.2011-053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We studied the longevity of mice produced without sperm using the genomes of oocytes that are already committed to a germline cell lineage. The first sperm-free mouse "KAGUYA", which we term 'bi-maternal mouse', was born on 3 February, 2003. Bi-maternal embryos were generated using 2 sets of female genomes--one derived from fully grown oocytes from normal adults and the other from non-growing oocytes from newborn pups. These genomes were combined by nuclear transfer. We refined the technique for generating bi-maternal mice and found that genetic manipulations in only 2 regions--the imprinting centres of Igf2-H19 and Dlk1-Gtl2--on chromosomes 7 and 12 of the newborn pups allowed us to generate bi-maternal mice at a high rate. Studying bi-maternal conceptuses and mice provides further insight into the mechanisms by which paternally methylated imprinted genes regulate mammalian ontogenesis.
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Affiliation(s)
- Manabu Kawahara
- Laboratory of Animal Breeding and Reproduction, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.
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47
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Singh P, Lee DH, Szabó PE. More than insulator: multiple roles of CTCF at the H19-Igf2 imprinted domain. Front Genet 2012; 3:214. [PMID: 23087708 PMCID: PMC3471092 DOI: 10.3389/fgene.2012.00214] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 09/27/2012] [Indexed: 12/28/2022] Open
Abstract
CTCF (CCCTC-binding factor)-mediated insulation at the H19-Insulin-like growth factor 2 (Igf2) imprinted domain is a classic example for imprinted gene regulation. DNA methylation difference in the imprinting control region (ICR) is inherited from the gametes and subsequently determines parental allele-specific enhancer blocking and imprinted expression in the soma. Recent genetic studies showed that proper monoallelic enhancer blocking at the H19-Igf2 ICR is critical for development. Strict biallelic insulation at this locus causes perinatal lethality, whereas leaky biallelic insulation results in smaller size but no lethality. Apart from enhancer blocking, CTCF is also the master organizer of chromatin composition in the maternal allele along this imprinted domain, affecting not only histone tail covalent modifications but also those in the histone core. Additionally, CTCF binding in the soma protects the maternal allele from de novo DNA methylation. CTCF binding is not involved in the establishment of the gametic marks at the ICR, but it slightly delays de novo methylation in the maternally inherited ICR allele in prospermatogonia. This review focuses on the developmental and epigenetic consequences of CTCF binding at the H19-Igf2 ICR.
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Affiliation(s)
- Purnima Singh
- Department of Molecular and Cellular Biology, Beckman Research Institute Duarte, CA, USA
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48
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Shoshani O, Massalha H, Shani N, Kagan S, Ravid O, Madar S, Trakhtenbrot L, Leshkowitz D, Rechavi G, Zipori D. Polyploidization of murine mesenchymal cells is associated with suppression of the long noncoding RNA H19 and reduced tumorigenicity. Cancer Res 2012; 72:6403-13. [PMID: 23047867 DOI: 10.1158/0008-5472.can-12-1155] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Mesenchymal stromal cells (MSC) are used extensively in clinical trials; however, the possibility that MSCs have a potential for malignant transformation was raised. We examined the genomic stability versus the tumor-forming capacity of multiple mouse MSCs. Murine MSCs have been shown to be less stable and more prone to malignant transformation than their human counterparts. A large series of independently isolated MSC populations exhibited low tumorigenic potential under syngeneic conditions, which increased in immunocompromised animals. Unexpectedly, higher ploidy correlated with reduced tumor-forming capacity. Furthermore, in both cultured MSCs and primary hepatocytes, polyploidization was associated with a dramatic decrease in the expression of the long noncoding RNA H19. Direct knockdown of H19 expression in diploid cells resulted in acquisition of polyploid cell traits. Moreover, artificial tetraploidization of diploid cancer cells led to a reduction of H19 levels, as well as to an attenuation of the tumorigenic potential. Polyploidy might therefore serve as a protective mechanism aimed at reducing malignant transformation through the involvement of the H19 regulatory long noncoding RNA.
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Affiliation(s)
- Ofer Shoshani
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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49
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de Waal E, Yamazaki Y, Ingale P, Bartolomei MS, Yanagimachi R, McCarrey JR. Gonadotropin stimulation contributes to an increased incidence of epimutations in ICSI-derived mice. Hum Mol Genet 2012; 21:4460-72. [PMID: 22802074 DOI: 10.1093/hmg/dds287] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We previously demonstrated that intracytoplasmic sperm injection (ICSI), a type of assisted reproductive technology (ART), can induce epimutations and/or epimutant phenotypes in somatic tissues of adult mice produced by this method. In the present study, we compared the occurrence of epimutations in mice produced by natural conception, ICSI and somatic cell nuclear transfer. Surprisingly, we observed the highest frequency of epimutations in somatic tissues from ICSI-derived mice. We also observed a delay in reprogramming of the maternal allele of the imprinted H19 gene in spermatogonia from juvenile ICSI-derived male mice. These observations led us to hypothesize that the exposure of the maternal gametic genome to exogenous gonadotropins during the endocrine stimulation of folliculogenesis (superovulation) may contribute to the disruption of the normal epigenetic programming of imprinted loci in somatic tissues and/or epigenetic reprogramming in the germ line of ensuing offspring. To test this hypothesis, we uncoupled superovulation from ICSI by subjecting female mice to gonadotropin stimulation and then allowing them to produce offspring by natural mating. We found that mice produced in this way also exhibited epimutations and/or epimutant phenotypes in somatic tissues and delayed epigenetic reprogramming in spermatogenic cells, providing evidence that gonadotropin stimulation contributes to the induction of epimutations during ART procedures. Our results suggest that gonadotropin stimulation protocols used in conjunction with ART procedures should be optimized to minimize the occurrence of epimutations in offspring produced by these methods.
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Affiliation(s)
- Eric de Waal
- Department of Biology, University of Texas, San Antonio, TX 78249, USA
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50
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Fedoriw A, Mugford J, Magnuson T. Genomic imprinting and epigenetic control of development. Cold Spring Harb Perspect Biol 2012; 4:a008136. [PMID: 22687277 PMCID: PMC3385953 DOI: 10.1101/cshperspect.a008136] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Epigenetic mechanisms are extensively utilized during mammalian development. Specific patterns of gene expression are established during cell fate decisions, maintained as differentiation progresses, and often augmented as more specialized cell types are required. Much of what is known about these mechanisms comes from the study of two distinct epigenetic phenomena: genomic imprinting and X-chromosome inactivation. In the case of genomic imprinting, alleles are expressed in a parent-of-origin-dependent manner, whereas X-chromosome inactivation in females requires that only one X chromosome is active in each somatic nucleus. As model systems for epigenetic regulation, genomic imprinting and X-chromosome inactivation have identified and elucidated the numerous regulatory mechanisms that function throughout the genome during development.
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Affiliation(s)
- Andrew Fedoriw
- The University of North Carolina at Chapel Hill School of Medicine, Department of Genetics, Chapel Hill, North Carolina 27599, USA
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