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author:("Shiota, kunin")
1.  RNA-Seq Analysis of Equine Conceptus Transcripts during Embryo Fixation and Capsule Disappearance 
PLoS ONE  2014;9(12):e114414.
Extensive studies have been conducted to characterize the unique phenomena of equine pregnancy. Most studies have focused on embryo transmigration when the embryo is covered with a mucin-like glycoprotein capsule and on the characterization of the chorionic girdle and chorionic gonadotropin (CG) secretion. However, the events preceding and following capsule disappearance have not been well studied. In this study, the mRNA expression in conceptus membranes at days 19, 21, and 25 (day 0 = day of ovulation) was analyzed by RNA-seq (SOLiD3), and transcript levels on these three days and day 13 were confirmed by real-time PCR. Of the 26,416 equine genes registered, 20,436 transcripts were aligned to sequences in the Ensembl database, from which 4,625 transcripts were registered in both Ensembl and the KEGG pathway. Each of the 4,625 transcripts was examined through KEGG pathway analysis, and 12 transcripts of integrins (ITGs) and collagens (COLs) were confirmed through real-time PCR. Our data indicated that extracellular matrix (ECM)-related mRNAs were highly expressed in day 19, 21, and 25 conceptus membranes. In combination with previous results, which confirmed a lack of laminin and fibronectin transcript expression in the endometrium, these observations suggest that in contrast to attachment through focal adhesion, conceptus chorionic membrane ECMs function as a scaffold-like structure to possibly maintain the shape of the conceptus and a separation between chorionic membranes and the uterine luminal epithelium.
PMCID: PMC4267804  PMID: 25514169
2.  DNA methylation profiles provide a viable index for porcine pluripotent stem cells 
Genesis (New York, N.y. : 2000)  2013;51(11):763-776.
Porcine induced pluripotent stem cells (iPSCs) provide useful information for translational research. The quality of iPSCs can be assessed by their ability to differentiate into various cell types after chimera formation. However, analysis of chimera formation in pigs is a labor-intensive and costly process, necessitating a simple evaluation method for porcine iPSCs. Our previous study identified mouse embryonic stem cell (ESC)-specific hypomethylated loci (EShypo-T-DMRs), and, in this study, 36 genes selected from these were used to evaluate porcine iPSC lines. Based on the methylation profiles of the 36 genes, the iPSC line, Porco Rosso-4, was found closest to mouse pluripotent stem cells among 5 porcine iPSCs. Moreover, Porco Rosso-4 more efficiently contributed to the inner cell mass (ICM) of blastocysts than the iPSC line showing the lowest reprogramming of the 36 genes (Porco Rosso-622-14), indicating that the DNA methylation profile correlates with efficiency of ICM contribution. Furthermore, factors known to enhance iPSC quality (serum-free medium with PD0325901 and CHIR99021) improved the methylation status at the 36 genes. Thus, the DNA methylation profile of these 36 genes is a viable index for evaluation of porcine iPSCs. genesis 51:763–776. © 2013 Wiley Periodicals, Inc.
PMCID: PMC4237151  PMID: 23913699
epigenetics; induced pluripotent stem cells; translational research
3.  Oocyte-specific linker histone H1foo is an epigenomic modulator that decondenses chromatin and impairs pluripotency 
Epigenetics  2012;7(9):1029-1036.
Mammalian oocytes contain the histone H1foo, a distinct member with low sequence similarity to other members in the H1 histone family. Oocyte-specific H1foo exists until the second embryonic cell stage. H1foo is essential for oocyte maturation in mice; however, the molecular function of this H1 subtype is unclear. To explore the function of H1foo, we generated embryonic stem (ES) cells ectopically expressing H1foo fused to an EGFP (H1foo-ES). Interestingly, ectopic expression of H1foo prevented normal differentiation into embryoid bodies (EBs). The EB preparations from H1foo-ES cells maintained the expression of pluripotent marker genes, including Nanog, Myc and Klf9, and prevented the shift of the DNA methylation profile. Because the short hairpin RNA-mediated knockdown of H1foo-EGFP recovered the differentiation ability, H1foo was involved in preventing differentiation. Furthermore, ChIP analysis revealed that H1foo-EGFP bound selectively to a set of hypomethylated genomic loci in H1foo-ES, clearly indicating that these loci were targets of H1foo. Finally, nuclease sensitivity assay suggested that H1foo made these target loci decondensed. We concluded that H1foo has an impact on the genome-wide, locus-specific epigenetic status.
PMCID: PMC3515012  PMID: 22868987
DNA methylation; histone H1; Oocyte-specific; nuclease-sensitivity; differentiation
4.  DNA methylation profile dynamics of tissue-dependent and differentially methylated regions during mouse brain development 
BMC Genomics  2013;14:82.
Tissues and their component cells have unique DNA methylation profiles comprising DNA methylation patterns of tissue-dependent and differentially methylated regions (T-DMRs). Previous studies reported that DNA methylation plays crucial roles in cell differentiation and development. Here, we investigated the genome-wide DNA methylation profiles of mouse neural progenitors derived from different developmental stages using HpyCH4IV, a methylation-sensitive restriction enzyme that recognizes ACGT residues, which are uniformly distributed across the genome.
Using a microarray-based genome-wide DNA methylation analysis system focusing on 8.5-kb regions around transcription start sites (TSSs), we analyzed the DNA methylation profiles of mouse neurospheres derived from telencephalons at embryonic days 11.5 (E11.5NSph) and 14.5 (E14.5NSph) and the adult brain (AdBr). We identified T-DMRs with different DNA methylation statuses between E11.5NSph and E14.5NSph at genes involved in neural development and/or associated with neurological disorders in humans, such as Dclk1, Nrcam, Nfia, and Ntng1. These T-DMRs were located not only within 2 kb but also distal (several kbs) from the TSSs, and those hypomethylated in E11.5NSph tended to be in CpG island (CGI-) associated genes. Most T-DMRs that were hypomethylated in neurospheres were also hypomethylated in the AdBr. Interestingly, among the T-DMRs hypomethylated in the progenitors, there were T-DMRs that were hypermethylated in the AdBr. Although certain genes, including Ntng1, had hypermethylated T-DMRs 5′ upstream, we identified hypomethylated T-DMRs in the AdBr, 3′ downstream from their TSSs. This observation could explain why Ntng1 was highly expressed in the AdBr despite upstream hypermethylation.
Mouse adult brain DNA methylation and gene expression profiles could be attributed to developmental dynamics of T-DMRs in neural-related genes.
PMCID: PMC3599493  PMID: 23387509
DNA methylation; Tissue-dependent and differentially methylated region; Neural progenitor cells
5.  DNA methylation profile of Aire-deficient mouse medullary thymic epithelial cells 
BMC Immunology  2012;13:58.
Medullary thymic epithelial cells (mTECs) are characterized by ectopic expression of self-antigens during the establishment of central tolerance. The autoimmune regulator (Aire), which is specifically expressed in mTECs, is responsible for the expression of a large repertoire of tissue-restricted antigens (TRAs) and plays a role in the development of mTECs. However, Aire-deficient mTECs still express TRAs. Moreover, a subset of mTECs, which are considered to be at a stage of terminal differentiation, exists in the Aire-deficient thymus. The phenotype of a specific cell type in a multicellular organism is governed by the epigenetic regulation system. DNA methylation modification is an important component of this system. Every cell or tissue type displays a DNA methylation profile, consisting of tissue-dependent and differentially methylated regions (T-DMRs), and this profile is involved in cell-type-specific genome usage. The aim of this study was to examine the DNA methylation profile of mTECs by using Aire-deficient mTECs as a model.
We identified the T-DMRs of mTECs (mTEC-T-DMRs) via genome-wide DNA methylation analysis of Aire−/− mTECs by comparison with the liver, brain, thymus, and embryonic stem cells. The hypomethylated mTEC-T-DMRs in Aire−/− mTECs were associated with mTEC-specific genes, including Aire, CD80, and Trp63, as well as other genes involved in the RANK signaling pathway. While these mTEC-T-DMRs were also hypomethylated in Aire+/+ mTECs, they were hypermethylated in control thymic stromal cells. We compared the pattern of DNA methylation levels at a total of 55 mTEC-T-DMRs and adjacent regions and found that the DNA methylation status was similar for Aire+/+ and Aire−/− mTECs but distinct from that of athymic cells and tissues.
These results indicate a unique DNA methylation profile that is independent of Aire in mTECs. This profile is distinct from other cell types in the thymic microenvironment and is indicated to be involved in the differentiation of the mTEC lineage.
PMCID: PMC3546423  PMID: 23116172
Medullary thymic epithelial cells; Aire; T-DMR
6.  DNA methylation status of nuclear-encoded mitochondrial genes underlies the tissue-dependent mitochondrial functions 
BMC Genomics  2010;11:481.
Mitochondria are semi-autonomous, semi-self-replicating organelles harboring their own DNA (mitochondrial DNA, mtDNA), and their dysregulation is involved in the development of various diseases. While mtDNA does not generally undergo epigenetic modifications, almost all mitochondrial proteins are encoded by nuclear DNA. However, the epigenetic regulation of nuclear-encoded mitochondrial genes (nuclear mt genes) has not been comprehensively analyzed.
We analyzed the DNA methylation status of 899 nuclear mt genes in the liver, brain, and heart tissues of mouse, and identified 636 nuclear mt genes carrying tissue-dependent and differentially methylated regions (T-DMRs). These nuclar mt genes are involved in various mitochondrial functions and they also include genes related to human diseases. T-DMRs regulate the expression of nuclear mt genes. Nuclear mt genes with tissue-specific hypomethylated T-DMRs were characterized by enrichment of the target genes of specific transcription factors such as FOXA2 in the liver, and CEBPA and STAT1 in the brain.
A substantial proportion of nuclear mt genes contained T-DMRs, and the DNA methylation status of numerous T-DMRs should underlie tissue-dependent mitochondrial functions.
PMCID: PMC2996977  PMID: 20723256
7.  BMP4 induction of trophoblast from mouse embryonic stem cells in defined culture conditions on laminin 
Because mouse embryonic stem cells (mESCs) do not contribute to the formation of extraembryonic placenta when they are injected into blastocysts, it is believed that mESCs do not differentiate into trophoblast whereas human embryonic stem cells (hESCs) can express trophoblast markers when exposed to bone morphogenetic protein 4 (BMP4) in vitro. To test whether mESCs have the potential to differentiate into trophoblast, we assessed the effect of BMP4 on mESCs in a defined monolayer culture condition. The expression of trophoblast-specific transcription factors such as Cdx2, Dlx3, Esx1, Gata3, Hand1, Mash2, and Plx1 was specifically upregulated in the BMP4-treated differentiated cells, and these cells expressed trophoblast markers. These results suggest that BMP4 treatment in defined culture conditions enabled mESCs to differentiate into trophoblast. This differentiation was inhibited by serum or leukemia inhibitory factor, which are generally used for mESC culture. In addition, we studied the mechanism underlying BMP4-directed mESC differentiation into trophoblast. Our results showed that BMP4 activates the Smad pathway in mESCs inducing Cdx2 expression, which plays a crucial role in trophoblast differentiation, through the binding of Smad protein to the Cdx2 genomic enhancer sequence. Our findings imply that there is a common molecular mechanism underlying hESC and mESC differentiation into trophoblast.
PMCID: PMC2862943  PMID: 20033790
BMP4; Smad; Cdx2; Trophoblast; Mouse embryonic stem cells
9.  Expression of the peroxisome proliferator activated receptor γ gene is repressed by DNA methylation in visceral adipose tissue of mouse models of diabetes 
BMC Biology  2009;7:38.
Adipose tissues serve not only as a store for energy in the form of lipid, but also as endocrine tissues that regulates metabolic activities of the organism by secreting various kinds of hormones. Peroxisome proliferator activated receptor γ (PPARγ) is a key regulator of adipocyte differentiation that induces the expression of adipocyte-specific genes in preadipocytes and mediates their differentiation into adipocytes. Furthermore, PPARγ has an important role to maintain the physiological function of mature adipocyte by controlling expressions of various genes properly. Therefore, any reduction in amount and activity of PPARγ is linked to the pathogenesis of metabolic syndrome.
In this study, we investigated the contribution of epigenetic transcriptional regulatory mechanisms, such as DNA methylation, to the expression of the PPARγ gene, and further evaluated the contribution of such epigenetic regulatory mechanisms to the pathogenesis of metabolic syndrome. In 3T3-L1 preadipocytes, the promoter of the PPARγ2 gene was hypermethylated, but was progressively demethylated upon induction of differentiation, which was accompanied by an increase of mRNA expression. Moreover, treatment of cells with 5'-aza-cytideine, an inhibitor of DNA methylation, increased expression of the PPARγ gene in a dose-dependent manner. Methylation in vitro of a PPARγ promoter-driven reporter construct also repressed the transcription of a downstream reporter gene. These results suggest that the expression of the PPARγ gene is inhibited by methylation of its promoter. We next compared the methylation status of the PPARγ promoters in adipocytes from wild-type (WT) mice with those from two diabetic mouse models: +Leprdb/+Leprdb and diet-induced obesity mice. Interestingly, we found increased methylation of the PPARγ promoter in visceral adipose tissues (VAT) of the mouse models of diabetes, compared to that observed in wild-type mice. We observed a concomitant decrease in the level of PPARγ mRNA in the diabetic mice compared to the WT mice.
We conclude that the expression of PPARγ gene is regulated by DNA methylation of its promoter region and propose that reduced expression of PPARγ owing to DNA methylation in adipocytes of the VAT may contribute to the pathogenesis of metabolic syndrome.
PMCID: PMC2715379  PMID: 19589179
10.  Transcription of mouse DNA methyltransferase 1 (Dnmt1) is regulated by both E2F-Rb-HDAC-dependent and -independent pathways 
Nucleic Acids Research  2003;31(12):3101-3113.
Abnormal expression of Dnmt1 in vivo induces cellular alterations such as transformation, and an increase in Dnmt1 mRNA plays a causal role in c-fos-, ras- and SV40 large T antigen-induced transformation of fibroblasts in vitro. Here, we have investigated the regulation of Dnmt1 transcription. We identified the promoter region and major transcription start sites of mouse Dnmt1 and found two important cis-elements within the core promoter region. One is an E2F binding site, and the other is a binding site for an as yet unidentified factor. Point mutations in the two cis-elements decreased promoter activity in both non-transformed and transformed cells. Thus, both sites play a critical role in regulation of Dnmt1 transcription in proliferating cells. Treatment with trichostatin A, a specific inhibitor of histone deacetylase, increased Dnmt1 promoter activity in G0/G1-arrested NIH 3T3 cells. Furthermore, the decrease in promoter activity induced by expression of E2F-1 and Rb was reversed by trichostatin A treatment of Saos-2 cells. Taken together, these data indicate that transcription of Dnmt1 is regulated in a complex fashion by E2F and other transcription factors through E2F-Rb-HDAC-dependent and -independent pathways. These findings suggest that Dnmt1 is a target gene of these pathways in cell proliferation, cell transformation and tumorigenesis.
PMCID: PMC162240  PMID: 12799438

Results 1-10 (10)