المؤلفون: Hidenori Akutsu, Koichiro Nishino, Akihiro Umezawa, Yoshikazu Arai, Mayu Yamazaki-Inoue, Masashi Toyoda, Ken Takasawa

المصدر: Human Cell. 31:78-86

مصطلحات موضوعية: 0301 basic medicine, Homeobox protein NANOG, Cancer Research, Transcription, Genetic, Induced Pluripotent Stem Cells, Gene Expression, Biology, Stem cell marker, Epigenesis, Genetic, 03 medical and health sciences, Humans, Telomerase reverse transcriptase, Epigenetics, Induced pluripotent stem cell, Telomerase, Cells, Cultured, Cell Biology, DNA Methylation, Cellular Reprogramming, Cell biology, 030104 developmental biology, embryonic structures, DNA methylation, Cancer research, Stem cell, Reprogramming

الوصف: During reprogramming into human induced pluripotent stem cells (iPSCs), several stem cell marker genes are induced, such as OCT-4, NANOG, SALL4, and TERT. OCT-4, NANOG, and SALL4 gene expression can be regulated by DNA methylation. Their promoters become hypomethylated in iPSCs during reprogramming, leading to their induced expression. However, epigenetic regulation of the TERT gene remains unclear. In this study, we focused on epigenetic regulation of the human TERT gene and identified a differentially methylated region (DMR) at a distal region in the TERT promoter between human iPSCs and their parental somatic cells. Interestingly, the TERT-DMR was highly methylated in iPSCs, but low-level methylation was observed in their parental somatic cells. Region-specific, methylated-promoter assays showed that the methylated TERT-DMR up-regulated the promoter activity in iPSCs. In addition, Lamin B1 accumulated at the TERT-DMR in iPSCs, but not in their parent somatic cells. These results suggested that the TERT transcription was enhanced by DNA methylation at the TERT-DMR via binding to nuclear lamina during reprogramming. Our findings shed light on a new functional aspect of DNA methylation in gene expression.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f8aa0d08f3fa9c4452042a553317a751Test
https://doi.org/10.1007/s13577-017-0190-xTest

المؤلفون: Yuichi Hidaka, Daigo Yokoi, Shoichi Wakitani, Koichiro Nishino

المصدر: The Journal of Veterinary Medical Science

مصطلحات موضوعية: Male, musculoskeletal diseases, 0301 basic medicine, correlation analysis, Response element, Bone Marrow Cells, Core Binding Factor Alpha 1 Subunit, Biology, osteogenesis, 03 medical and health sciences, Dogs, Epigenetics of physical exercise, Species Specificity, stomatognathic system, Runx2, Transcription (biology), Animals, Promoter Regions, Genetic, Transcription factor, Cells, Cultured, DNA methylation, promoter, Osteoblasts, Full Paper, General Veterinary, musculoskeletal, neural, and ocular physiology, Cell Differentiation, Promoter, Methylation, musculoskeletal system, Molecular biology, Mice, Inbred C57BL, 030104 developmental biology, Differentially methylated regions, Gene Expression Regulation, embryonic structures, Anatomy

الوصف: Runt-related transcription factor 2 (Runx2) is essential for osteogenesis. This study aimes at identification of the genomic region differentially methylated in DNA for regulation of Runx2 expression. In the proximal promoter of mouse Runx2, DNA methylation was frequent at the region further than 3 kb relative to the transcription start site, in contrast to lower methylation status of the closer locus within 2 kb from the transcription start site. At the intermediate part, we identified a novel differentially methylated region in the Runx2 promoter region (Runx2-DMR): from -2.7 to -2.2 kb relative to the start site of Runx2 transcription in mice. In this region, the DNA methylation rate correlated negatively with Runx2 expression among mouse organs as well as among primary cultures of bone marrow from different dogs. Induction of mouse and dog mesenchymal-like cells into osteoblastic differentiation decreased the methylation rate of Runx2-DMR. Thus, in this study, we identified a novel genomic region in which DNA methylation status is related to Runx2 expression and detected demethylation of Runx2-DMR during osteoblastic differentiation in mouse and dog.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9955e2b11d79ce6c69fb546f0fc1e48dTest
https://doi.org/10.1292/jvms.16-0321Test

المؤلفون: Hatsune Makino, Akihiro Umezawa, Kunio Hirano, Hajime Okita, Shogo Nagata, Yoshitaka Miyagawa, Masato Nakagawa, Masashi Toyoda, Shinpei Yamaguchi, Shinya Yamanaka, Hidenori Akutsu, Nobutaka Kiyokawa, Koichiro Nishino, Takashi Tada

المصدر: Genes to Cells. 14:1395-1404

مصطلحات موضوعية: Male, Pluripotent Stem Cells, Homeobox protein NANOG, Cellular differentiation, Mice, Transgenic, Biology, Immunoenzyme Techniques, Kruppel-Like Factor 4, Mice, Genetics, Animals, Humans, Amnion, RNA, Messenger, Induced pluripotent stem cell, Embryonic Stem Cells, Yolk Sac, Chimera, Reverse Transcriptase Polymerase Chain Reaction, Gene Expression Profiling, Infant, Newborn, Teratoma, Gene Expression Regulation, Developmental, Cell Differentiation, Cell Biology, DNA Methylation, Cellular Reprogramming, Molecular biology, Embryonic stem cell, KLF4, embryonic structures, DNA methylation, Female, Stem cell, Reprogramming, Biomarkers

الوصف: Practical clinical applications for current induced pluripotent stem cell (iPSC) technologies are hindered by very low generation efficiencies. Here, we demonstrate that newborn human (h) and mouse (m) extra-embryonic amnion (AM) and yolk-sac (YS) cells, in which endogenous KLF4/Klf4, c-MYC/c-Myc and RONIN/Ronin are expressed, can be reprogrammed to hiPSCs and miPSCs with efficiencies for AM cells of 0.02% and 0.1%, respectively. Both hiPSC and miPSCs are indistinguishable from embryonic stem cells in colony morphology, expression of pluripotency markers, global gene expression profile, DNA methylation status of OCT4 and NANOG, teratoma formation and, in the case of miPSCs, generation of germline transmissible chimeric mice. As copious amounts of human AM cells can be collected without invasion, and stored long term by conventional means without requirement for in vitro culture, they represent an ideal source for cell banking and subsequent 'on demand' generation of hiPSCs for personal regenerative and pharmaceutical applications.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::27fb4cc8535a80736df1760dff065c0cTest
https://doi.org/10.1111/j.1365-2443.2009.01356.xTest

المؤلفون: Satoshi Tanaka, Naka Hattori, Kunio Shiota, Koichiro Nishino, Naoko Hattori, Yuko Imao, Jun Ohgane, Shintaro Yagi

المصدر: Genes to Cells. 12:387-396

مصطلحات موضوعية: Pluripotent Stem Cells, Homeobox protein NANOG, 5' Flanking Region, Cellular differentiation, Rex1, Biology, Decitabine, Hydroxamic Acids, Chromatin remodeling, Cell Line, Epigenesis, Genetic, Histones, Mice, Histone H3, Genetics, Animals, Promoter Regions, Genetic, Induced pluripotent stem cell, Embryonic Stem Cells, reproductive and urinary physiology, DNA Primers, Homeodomain Proteins, Base Sequence, Nanog Homeobox Protein, Acetylation, Cell Biology, DNA Methylation, Molecular biology, Trophoblasts, DNA-Binding Proteins, Mice, Inbred C57BL, embryonic structures, DNA methylation, Azacitidine, NIH 3T3 Cells, biological phenomena, cell phenomena, and immunity, Octamer Transcription Factor-3

الوصف: The Nanog and Oct-4 genes are essential for maintaining pluripotency of embryonic stem (ES) cells and early embryos. We previously reported that DNA methylation and chromatin remodeling underlie the cell type-specific mechanism of Oct-4 gene expression. In the present study, we found that there is a tissue-dependent and differentially methylated region (T-DMR) in the Nanog up-stream region. The T-DMR is hypomethylated in ES cells, but is heavily methylated in trophoblast stem (TS) cells and NIH/3T3 cells, in which the Nanog gene is repressed. Furthermore, in vitro methylation of T-DMR suppressed Nanog promoter activity in reporter assay. Chromatin immunoprecipitation assay revealed that histone H3 and H4 are highly acetylated, and H3 lysine (K) 4 is hypermethylated at the Nanog locus in ES cells. Conversely, histone deacetylation and H3-K4 demethylation occurred in TS cells. Importantly, in TS cells, hypermethylation of H3-K9 and -K27 is found only at the Nanog locus, not the Oct-4 locus, indicating that the combination of histone modifications associated with the Nanog gene is distinct from that of the Oct-4 gene. In conclusion, the Nanog gene is regulated by epigenetic mechanisms involving DNA methylation and histone modifications.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4736db39aaeeca5f37e550b421017b3bTest
https://doi.org/10.1111/j.1365-2443.2007.01058.xTest

المؤلفون: Akihiro Umezawa, Koichiro Nishino

المصدر: Stem Cells and Cancer Stem Cells, Volume 4 ISBN: 9789400728271

مصطلحات موضوعية: Cell type, Amnion, Cell, Biology, Embryonic stem cell, Cell biology, medicine.anatomical_structure, embryonic structures, DNA methylation, medicine, Epigenetics, Induced pluripotent stem cell, Reprogramming, reproductive and urinary physiology

الوصف: Epigenetic reprogramming is a critical event in the generation of induced pluripotent stem cells (iPSCs). Although the iPSCs from different sources are very similar to each other and to embryonic stem cells (ESCs), there are epigenetic differences in small fraction. iPSCs become epigenetically closer to each other with continuous passaging even though they have been derived from different cell types; human amnion, endometrium and menstrual blood cells. However, iPSCs exhibit distinct epigenetic distances from ESCs at early passages. Continuous passaging of the iPSCs diminishes the differences between iPSCs and ESCs via periodic aberrant hyper-methylation. This aberrant stochastic hyper-methylation and their convergence is a direct cause of the transgene-independent phases of iPS reprogramming. The number of passages for “convergence” of the aberrant hyper-methylation is dependent on the parental cell type. Interestingly, the amnion-derived-iPSCs show a more rapid decrease in the number of aberrant methylated sites during additional cultivation than endometrium-derived-iPSCs and menstrual blood cell-derived-iPSCs. Amnion cells offer additional benefits; they can be collected in a non-invasive manner and can be frozen and stored by conventional methods. Therefore, they are a strong candidate cell source for iPSC generation for clinical applications.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_________::4e3500970da5cad7aeda3d9946bbe82cTest
https://doi.org/10.1007/978-94-007-2828-8_6Test

المؤلفون: Hidenori Akutsu, Yoshihiro Fukawatase, Masashi Toyoda, Hironari Sakaguchi, Emi Chikazawa, Mayu Yamazaki-Inoue, Akihiro Umezawa, Koichiro Nishino

المصدر: PLoS Genetics
PLoS Genetics, Vol 7, Iss 5, p e1002085 (2011)

مصطلحات موضوعية: Epigenomics, Cancer Research, Microarrays, Cellular differentiation, Gene Expression, Epigenesis, Genetic, Chromosomes, Human, Transgenes, Induced pluripotent stem cell, Genetics (clinical), reproductive and urinary physiology, Stem Cells, Cell Differentiation, Methylation, Genomics, Immunohistochemistry, Cell biology, DNA methylation, embryonic structures, RNA, Long Noncoding, Epigenetics, DNA modification, Reprogramming, Research Article, Genetic Markers, Cell type, lcsh:QH426-470, Cell Potency, Induced Pluripotent Stem Cells, Biology, Cell Line, Genetics, Genome-Wide Association Studies, Humans, Gene Silencing, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Embryonic Stem Cells, Genome, Human, Proteins, Computational Biology, Human Genetics, DNA Methylation, Comparative Genomics, Molecular biology, Embryonic stem cell, lcsh:Genetics, Karyotyping, Genome Expression Analysis, Developmental Biology

الوصف: Epigenetic reprogramming is a critical event in the generation of induced pluripotent stem cells (iPSCs). Here, we determined the DNA methylation profiles of 22 human iPSC lines derived from five different cell types (human endometrium, placental artery endothelium, amnion, fetal lung fibroblast, and menstrual blood cell) and five human embryonic stem cell (ESC) lines, and we followed the aberrant methylation sites in iPSCs for up to 42 weeks. The iPSCs exhibited distinct epigenetic differences from ESCs, which were caused by aberrant methylation at early passages. Multiple appearances and then disappearances of random aberrant methylation were detected throughout iPSC reprogramming. Continuous passaging of the iPSCs diminished the differences between iPSCs and ESCs, implying that iPSCs lose the characteristics inherited from the parent cells and adapt to very closely resemble ESCs over time. Human iPSCs were gradually reprogrammed through the “convergence” of aberrant hyper-methylation events that continuously appeared in a de novo manner. This iPS reprogramming consisted of stochastic de novo methylation and selection/fixation of methylation in an environment suitable for ESCs. Taken together, random methylation and convergence are driving forces for long-term reprogramming of iPSCs to ESCs.
Author Summary iPSCs change to resemble ESCs via two phases: the transgene-dependent phase, in which the transcription factors act to transform somatic cells into pluripotent stem cells, and the transgene-independent phase, in which the transcription factors are silenced. In this study, we established human iPSCs derived from 5 different cell types by retroviral infection of the Yamanaka 4 factors, and we identified 8 novel epigenetic markers (SALL4, EPHA1, PTPN6, RAB25, GBP4, LYST, SP100, and UBE1L) by comprehensive DNA methylation analysis. The aberrant hyper-methylation in iPSCs occurred stochastically throughout the genome and decreased during the long-term iPSC reprogramming, suggesting that the aberrant stochastic hyper-methylation and their convergence are a direct cause of the transgene-independent phase of iPS reprogramming. These results favor the stochastic model of the Yamanaka model rather than the elite model. In addition, the stem cell–specific methylation states and the epigenetic difference between iPSCs and ESCs are useful indices for evaluating human iPSCs in therapeutic applications.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::15e8199c324e8efde60a4059f3c9e964Test
https://pubmed.ncbi.nlm.nih.gov/21637780Test

المؤلفون: Koichiro Nishino, Hajime Okita, Masakazu Machida, Taro Uyama, Yoshihiro Fukawatase, Masashi Toyoda, Yoshitaka Miyagawa, Akihiro Umezawa, Takuro Nakamura, Kenji Matsumoto, Hirohisa Saito, Hatsune Makino, Takashi Fujino, Nobutaka Kiyokawa, Yuichi Ishikawa, Hidenori Akutsu

المصدر: Experimental cell research. 315(16)

مصطلحات موضوعية: KOSR, Homeobox protein NANOG, Rex1, Cellular differentiation, Recombinant Fusion Proteins, Mice, SCID, Biology, Mesoderm, Mice, Mice, Inbred NOD, Morphogenesis, Animals, Humans, Cell Lineage, Induced pluripotent stem cell, Cells, Cultured, Oligonucleotide Array Sequence Analysis, Principal Component Analysis, Gene Expression Profiling, Teratoma, Gene Expression Regulation, Developmental, Cell Biology, Embryo, Mammalian, Molecular biology, Cell biology, P19 cell, Phenotype, Karyotyping, embryonic structures, Stem cell, RNA-Binding Protein EWS, Octamer Transcription Factor-3, Biomarkers, Adult stem cell

الوصف: POU5F1 (more commonly known as OCT4/3) is one of the stem cell markers, and affects direction of differentiation in embryonic stem cells. To investigate whether cells of mesenchymal origin acquire embryonic phenotypes, we generated human cells of mesodermal origin with overexpression of the chimeric OCT4/3 gene with physiological co-activator EWS (product of the EWSR1 gene), which is driven by the potent EWS promoter by translocation. The cells expressed embryonic stem cell genes such as NANOG, lost mesenchymal phenotypes, and exhibited embryonal stem cell-like alveolar structures when implanted into the subcutaneous tissue of immunodeficient mice. Hierarchical analysis by microchip analysis and cell surface analysis revealed that the cells are subcategorized into the group of human embryonic stem cells and embryonal carcinoma cells. These results imply that cells of mesenchymal origin can be traced back to cells of embryonic phenotype by the OCT4/3 gene in collaboration with the potent cis-regulatory element and the fused co-activator. The cells generated in this study with overexpression of chimeric OCT4/3 provide us with insight into cell plasticity involving OCT4/3 that is essential for embryonic cell maintenance, and the complexity required for changing cellular identity.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::236627bf456e432b38fdb8faf55f164fTest
https://pubmed.ncbi.nlm.nih.gov/19559696Test

المؤلفون: Masato Hiyama, Hiroyuki Imai, Koichiro Nishino, Kiyoshi Kano, Ken Takeshi Kusakabe, Shoichi Wakitani, Ken Takasawa, Wataru Fujii, Yasuo Kiso

المصدر: PLoS ONE
PLoS ONE, Vol 10, Iss 6, p e0130585 (2015)

مصطلحات موضوعية: lcsh:Medicine, Germ layer, Biology, Mice, Polyploid, Genes, Reporter, Animals, Epigenetics, lcsh:Science, Embryonic Stem Cells, Cell Proliferation, Genetics, Multidisciplinary, Tetraploid complementation assay, lcsh:R, fungi, food and beverages, Cell Differentiation, Embryo, DNA Methylation, Embryo, Mammalian, Embryonic stem cell, Cell biology, Tetraploidy, Blastocyst, embryonic structures, lcsh:Q, Female, Ploidy, Reprogramming, Germ Layers, Transcription Factors, Research Article

الوصف: Polyploid amphibians and fishes occur naturally in nature, while polyploid mammals do not. For example, tetraploid mouse embryos normally develop into blastocysts, but exhibit abnormalities and die soon after implantation. Thus, polyploidization is thought to be harmful during early mammalian development. However, the mechanisms through which polyploidization disrupts development are still poorly understood. In this study, we aimed to elucidate how genome duplication affects early mammalian development. To this end, we established tetraploid embryonic stem cells (TESCs) produced from the inner cell masses of tetraploid blastocysts using electrofusion of two-cell embryos in mice and studied the developmental potential of TESCs. We demonstrated that TESCs possessed essential pluripotency and differentiation potency to form teratomas, which differentiated into the three germ layers, including diploid embryonic stem cells. TESCs also contributed to the inner cell masses in aggregated chimeric blastocysts, despite the observation that tetraploid embryos fail in normal development soon after implantation in mice. In TESCs, stability after several passages, colony morphology, and alkaline phosphatase activity were similar to those of diploid ESCs. TESCs also exhibited sufficient expression and localization of pluripotent markers and retained the normal epigenetic status of relevant reprogramming factors. TESCs proliferated at a slower rate than ESCs, indicating that the difference in genomic dosage was responsible for the different growth rates. Thus, our findings suggested that mouse ESCs maintained intrinsic pluripotency and differentiation potential despite tetraploidization, providing insights into our understanding of developmental elimination in polyploid mammals.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cd0c35ff30da4889285f44be8342be60Test
https://doi.org/10.1371/journal.pone.0130585Test

المؤلفون: Kunio Shiota, Naoko Hattori, Yeoung Gyu Ko, Koichiro Nishino, Satoshi Tanaka, Yoshikazu Arai

المصدر: The Journal of biological chemistry. 280(10)

مصطلحات موضوعية: DNA (Cytosine-5-)-Methyltransferase 1, Transcription, Genetic, Embryonic Development, Biology, Biochemistry, DNA methyltransferase, Mice, Epigenetics of physical exercise, Pregnancy, Histone methylation, Animals, DNA (Cytosine-5-)-Methyltransferases, Molecular Biology, RNA-Directed DNA Methylation, Epigenomics, DNA Primers, Base Sequence, Gene Expression Regulation, Developmental, Cell Biology, Exons, DNA Methylation, Molecular biology, Isoenzymes, Differentially methylated regions, embryonic structures, DNA methylation, Oocytes, Female, 5' Untranslated Regions, Reprogramming

الوصف: Methylation of DNA is involved in tissue-specific gene control, and establishment of DNA methylation pattern in the genome is thought to be essential for embryonic development. Three isoforms of Dnmt1 (DNA methyltransferase 1) transcripts, Dnmt1s, Dnmt1o, and Dnmt1p, are produced by alternative usage of multiple first exons. Dnmt1s is expressed in somatic cells. Dnmt1p is found only in pachytene spermatocytes, whereas Dnmt1o is specific to oocytes and preimplantation embryos. Here we determined that there is a tissue-dependent differentially methylated region (T-DMR) in the 5' region of Dnmt1o but not in that of the Dnmt1s/1p. The methylation status of the Dnmt1o T-DMR was distinctively different in the oocyte from that in the sperm and adult somatic tissues and changed at each stage from fertilization to blastocyst stage, suggesting that active methylation and demethylation occur during preimplantation development. The T-DMR was highly methylated in somatic cells and embryonic stem cells. Analysis using Dnmt-deficient embryonic stem cell lines revealed that Dnmt1, Dnmt3a, and Dnmt3b are each partially responsible for maintenance of methylation of Dnmt1o T-DMR. In particular, there are compensatory and cooperative roles between Dnmt3a and Dnmt3b. Thus, the regulatory region of Dnmt1o, but not of Dnmt1s/1p, appeared to be a target of DNA methylation. The present study also suggested that the DNA methylation status of the gene region dynamically changes during embryogenesis independently of the change in the bulk DNA methylation status.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9e433097ab0644639d116fbbddf8434bTest
https://pubmed.ncbi.nlm.nih.gov/15634679Test

المؤلفون: Naoko Hattori, Kunio Shiota, Koichiro Nishino, Satoshi Tanaka

المصدر: The Journal of biological chemistry. 279(21)

مصطلحات موضوعية: Therapeutic gene modulation, Male, Time Factors, Biology, Y chromosome, Biochemistry, Mice, Genes, Reporter, parasitic diseases, Gene expression, Testis, Animals, Sulfites, Genes, sry, Gonads, Promoter Regions, Genetic, Molecular Biology, Gene, Regulation of gene expression, Models, Genetic, Reverse Transcriptase Polymerase Chain Reaction, Chromosome Mapping, Gene Expression Regulation, Developmental, Nuclear Proteins, Cell Differentiation, social sciences, Cell Biology, Methylation, DNA, Sequence Analysis, DNA, DNA Methylation, Molecular biology, Sex-Determining Region Y Protein, DNA-Binding Proteins, Kinetics, Testis determining factor, embryonic structures, DNA methylation, NIH 3T3 Cells, CpG Islands, geographic locations, Transcription Factors

الوصف: DNA methylation at CpG sequences is involved in tissue-specific and developmentally regulated gene expression. The Sry (sex-determining region on the Y chromosome) gene encodes a master protein for initiating testis differentiation in mammals, and its expression is restricted to gonadal somatic cells at 10.5-12.5 days post-coitum (dpc) in the mouse. We found that in vitro methylation of the 5'-flanking region of the Sry gene caused suppression of reporter activity, implying that Sry gene expression could be regulated by DNA methylation-mediated gene silencing. Bisulfite restriction mapping and sodium bisulfite sequencing revealed that the 5'-flanking region of the Sry gene was hypermethylated in the 8.5-dpc embryos in which the Sry gene was not expressed. Importantly, this region was specifically hypomethylated in the gonad at 11.5 dpc, while the hypermethylated status was maintained in tissues that do not express the Sry gene. We concluded that expression of the Sry gene is under the control of an epigenetic mechanism mediated by DNA methylation.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d82eb9ef4b609182af22d0eb3c9d4242Test
https://pubmed.ncbi.nlm.nih.gov/14978045Test