Oct4 regulates DNA methyltransferase 1 transcription by direct binding of the regulatory element
Cellular & Molecular Biology Letters volume 23, Article number: 39 (2018)
The transcription factor Oct4 plays a pivotal role in the pre-implantation development of the mouse embryo. DNA methyltransferase 1 (Dnmt1) maintains the changes in DNA methylation during mammalian early embryonic development. Little is known of the role of Oct4 in DNA methylation in mice. In this study, Kunming white mice were used as an animal model to reveal any correlation between DNA methylation and Oct4 during mammalian embryonic development.
The expressions of Dnmt1 and Oct4 were initially studied using real-time PCR. They exhibited different patterns during the pre-implantation stage. Moreover, by using a promoter assay and ChIP analysis, we found that the transcriptional activities of Dnmt1 in mouse NIH/3 T3 cells and CCE cells were regulated by Oct4 through direct binding to the − 554 to − 294 fragment of the upstream regulation element of Dnmt1. The downregulation of Dnmt1 expression and enzyme activity by mouse Oct4 were further confirmed by transfecting Oct4 siRNA into mouse CCE cells.
Our results indicate that Oct4 is involved in DNA methylation through the regulation of Dnmt1 transcription, especially during the early stages of mouse pre-implantation embryo development.
The transcription factors Oct4, Sox2, Klf4 and c-Myc (referred to as the OSKM factors or Yamanaka factors) are essential for mammalian embryo development, especially in the embryonic pre-implantation stage . A previous study found that the activities of these factors are essential for the self-renewal and pluripotency of mammalian embryonic stem cells (ESCs) and adult stem cells .
Recently, a novel type of stem cells called induced pluripotent stem (iPS) cells was successfully generated through retroviral introduction of the genes for the critically important OSKM factors. The highest efficiencies of induced pluripotency were achieved with combinations of all four factors .
Although little information is available on the molecular biology events that occur during embryonic pre-implantation and further development, there is sufficient evidence to indicate that these four factors have important functions in maintaining pluripotency and differentiation potential . However, many studies have found that adult mouse neural stem cells and human fetal neural stem cells can be directly reprogrammed to iPS cells through ectopic expression of Oct4 alone, suggesting that Oct4 is required and sufficient to reprogram mammalian somatic cells to pluripotency [4, 5].
Oct4 has been demonstrated to be a key transcription factor controlling pre-implantation development in the mouse embryo . Notably, Oct4 kinetics was identified as a predictive measure of developmental cell lineage patterning in the early mouse embryo . Furthermore, the specification of pluripotent cell identity requires the embryonic genome to express Oct4 during mouse development . In mouse blastocysts, Oct4 is required for the expression of multiple epiblast and primitive endoderm genes, and for the operation of multiple metabolic pathways essential for the continued growth of the pre-implantation embryo . These findings suggest that Oct4 has crucial roles in the early stages of development and differentiation, as evidenced elsewhere .
DNA methylation is an important epigenetic modification event during mouse embryonic development and in the processes of somatic cell reprogramming and gene silencing [10,11,12]. Dnmt1 is the major DNA methyltransferase responsible for methylating hemi-methylated cytosines in CpG sequences. It also acts as a maintenance methyltransferase that maintains genome-wide methylation patterns during genomic DNA replication [13, 14]. Many studies have shown that Dnmt1 plays a crucial role in normal mammalian development, and in cell proliferation and survival . Mutation of Dnmt1 results in extensive demethylation of the genome DNA, embryonic lethality, loss of imprinting, and alterations in X chromosome inactivation during mouse embryonic development, while the absence of Dnmt1 leads to the death of ES cells . Dnmt1 knockdown in germline cells leads to their immediate apoptosis .
During mouse oogenesis and pre-implantation development, Dnmt1 transcripts and protein were found to be expressed and proven to be responsible for the maintenance of methylation during pre-implantation stages other than the eight-cell embryo .
The expression of Oct4 and DNA methylation have been shown to be critical in the development of the mammalian pre-implantation embryo and in cell reprogramming . However, the results on the correlation between mouse Oct4 and Dnmt1 in these processes are still contradictory. Here, we used Kunming mice as a model to examine the expressions of Dnmt1 and Oct4 during the pre-implantation stage. The luciferase promoter assay and chromatin immunoprecipitation (ChIP) were performed to investigate the binding of Oct4 to the cis-regulation element of Dnmt1. RNAi of Oct4 in mouse CCE cells was also carried out to examine whether the expression level and enzyme activity of Dnmt1 was regulated by Oct4 in vitro. Our results are consistent with those in an earlier report . Thus, we have the reason to believe that Oct4 is involved in DNA methylation through regulation of the transcription of Dnmt1 and that this would also be true for human mesenchymal stem cells.
Mouse Dnmt1 and Oct4 expression in pre-implantation embryos from the zygote stage
Quantitative PCR results showed that the expression level of mouse Dnmt1 in the embryos increased from the zygote to the 4-cell stage and dramatically decreased from the 8-cell stage onwards (Fig. 1a), whereas the level of Oct4 increased steadily during the pre-implantation embryo stage (Fig. 1b).
Oct4 regulates mouse Dnmt1 gene transcription in vitro
Based on a prediction made using TFSEARCH and PROMO, a potential Oct4-binding site(TTTTGCAT/ATGCAAAA) was found in the − 475 to − 468 bp region relative to the transcription start site (TSS). To confirm the potential Oct4-binding site, four luciferase reporters were constructed and transfected in two different cell lines.
The results showed that the relative luciferase activities were higher in the groups that were co-transfected with Dnmt1-P1, 2 and 3 and Oct4 than in the separate control (Fig. 2a, b and e). Deletion of the upstream region from − 1228 to − 554 bp had no effect on the activation mediated by Oct4 (Fig. 2b and e), indicating that the first three constructs (Dnmt1-P1–1 through − 3) did not alter the Oct4 effect on the transcriptional activity of Dnmt1. By contrast, a decline in the relative luciferase activity in the shortest Dnmt1 promoter (-P1–4) was detected, indicating that the Oct4 positive regulatory element in the region between − 554 and − 294 bp relative to TSS could be lacking.
These findings are consistent with the results predicted using the web tools. As expected, mutation of this element to CCCCATGC remarkably decreased the promotor activity of Dnmt1 and the transcription activation efficiency of Oct4 (Fig. 2c and f). This result suggests that TTTTGCAT could be the possible binding site for Oct4 in the mouse Dnmt1 promoter region. Notably, co-transfection of Dnmt1-P1–3 and Oct4 increased luciferase activity in a dose-dependent manner (Fig. 2d and g).
Oct4 direct binding to the regulatory elements of mouse Dnmt1
Next, we examined whether Oct4 binds to the Dnmt1 promoter in vitro. The ESCAPE database was queried with the gene name Dnmt1 to conduct the enrichment analysis. As shown in Fig. 3a, CHIP_POU5F1–18,555,785 was markedly enriched (p = 2.167e-2). Additionally, to associate the Oct4-binding siteinformation in the Dnmt1 promoter, a high association score was obtained for Oct4 (0.955676) based on the relative distance to the TSS of Dnmt1, indicating that Dnmt1 is one of the potential target genes for Oct4 in human and mouse embryonic stem cells.
The ChIP assay was employed to investigate the binding affinity. The chromatin (from CCE cells) was immunoprecipitated with anti-RNA Pol II antibody (as a positive control), anti-IgG antibody (as a negative control), and a specific antibody against mouse Oct4. As shown in Fig. 3b and c, the anti-RNA Pol II and anti-Oct4 antibodies precipitated the proteins bound in vivo to the specific amplified sequence of the mouse Dnmt1 promoter in the region between − 554 and − 294 bp. Conversely, the non-specific IgG antibody failed to precipitate in vivo the proteins bound to this sequence, suggesting that mouse Oct4 has the potential to bind to the fragment of Dnmt1.
Dnmt1 expression was downregulated by Oct4 RNAi in CCE cells
We investigated whether the knockdown of Oct4 in CCE cells can decrease the mRNA level and enzyme activity of Dnmt1. To determine the transfection efficiency, 20 nM Red Fluorescent Oligo was transfected into CCE cells. As shown in Fig. 4a–c, the efficiency reached > 85%, indicating that these conditions could be used to perform the subsequent experiments. Notably, the morphology of CCE cells was obviously changed 48 h after transfection with the three siRNA of Oct4 (R1, R2, and R3; Fig. 4d–f), indicating that the self-renewal and undifferentiated state of the CCE cells were not maintained.
Real-time PCR and western blot were used to measure the mRNA and protein levels of Oct4 in the siRNA-transfected CCE cells. The Oct4 mRNA and protein levels in R1-, R2-, and R3-transfected groups dramatically decreased, while those in the control remained unchanged (Fig. 5a and b). The results show that both R2 and R3 reduced Oct4 mRNA by 95% of the level for the blank control at 48 h post-transfection. The protein levels of Oct4 were also obviously reduced in the R2- and R3-transfected groups (Fig. 5a and b).
A Dnmt1 assay was also performed to detect the enzyme activity of Dnmt1 in the transfected siRNA CCE cells. The value of the final OD (equal to the OD at 450 nm minus the OD at 655 nm) of the R2- and R3-transfected groups were 1.5 to 2 times lower than those of the negative control. The change rates and the amounts of Dnmt1 in the three siRNA CCE were approximately 60–80% of those of the negative control (Fig. 5c and d). These results indicate that the decline in Dnmt1 activity is dependent on the function of Oct4 in CCE cells.
Kunming white mice are widely used as model animals in China. The dynamic expression and cellular localization of Dnmt1 and Oct4 in pre-implantation embryos of other mouse strains have been reported [1, 21], but little is known about the mRNA expression pattern of Dnmt1 and Oct4 in pre-implantation embryos of the Kunming white mouse.
It is well known that epigenetic modification of the genome plays important roles in mouse early development. Many studies have shown that the global DNA methylation levels gradually decrease from 1-cell to 16-cell or morula stage embryos , but reaching their highest levels in blastocysts by activating the de novo methylation process on top of the normal maintenance methylation .
In this study, we found that Dnmt1 levels are inversely related to Oct4 mRNA levels during pre-implantation embryo stages. Our results show that the mRNA level of Dnmt1 before the 4-cell stage was relatively higher than that from the 8-cell stage onwards, further indicating that Dnmt1 is a maintenance methyltransferase in the pre-implantation period [14, 24]. The genomic re-methylation in the inner cell mass (ICM) and hypomethylated state in the trophectoderm of the blastocyst are achieved passively by decreasing the expression of Dnmt1 or caused by de novo methyltransferases (Dnmt3a and Dnmt3b) . This expression pattern of Dnmt1 also responds to the global DNA methylation levels during the mouse pre-implantation stage. Furthermore, while initially present as a maternal transcription factor in the oocyte , the Oct4 level is gradually raised by the embryo throughout the pre-implantation period and correlates with an undifferentiated phenotype. This indicates that Oct4 could function as a key player and construct gene regulation networks with other genes during mouse early development.
In a previous study, Oct4 was observed to be located in the ICM cells of blastocysts . It is worth noting that in the Kunming white mouse, the mRNA expression level of Oct4 increases with embryonic development and peaks during the blastocyst stage, as has also been reported in other mouse strains . Inspired by these previous and present data, we speculated that some correlation may exist between Oct4 and the transcription of Dnmt1.
Using bioinformatic analysis, an octamer motif was predicted in the region between − 475 and − 468 bp relative to TSS. Therefore, promoter analysis was performed to investigate whether Dnmt1 transcription is regulated by Oct4. Sequential deletion promoters of mouse Dnmt1 were isolated and cloned into luciferase reporter vectors, including a luciferase plasmid bearing a mutation in the − 475 to − 468 bp Oct4 binding motif. Using transfection assays, we found that no significant difference in the luciferase activities of mouse Dnmt1 among the Dnmt1 P-1 to P-3 groups when co-transfected with mouse Oct4, but significant differences were observed between those groups and the respective control treatments. On the other hand, the luciferase activity of Dnmt1 P-4 was obviously lower than those of Dnmt1 P-1 to − 3 groups, indicating that there is a cis-regulatory element of Oct4 in the mouse Dnmt1 promoter region (the region from − 554 to − 294 bp). Because of the endogenous high expression of Oct4 in CCE cells, we found that their luciferase basal activity was higher than that for NIH cells without overexpression of external Oct4 when co-transfected with mouse Dnmt1-P1 promoter. Meanwhile, the luciferase activity in CCE cells was lower than that for control cells (Dnmt1-Pwt promoter) when co-transfected with mouse Dnmt1-Pmu promoter, but there was no significant difference between Dnmt1-Pmu promoter-transfected groups with or without overexpression of external Oct4 (Additional file 1: Figure S1). These data indicate that mouse Dnmt1 gene expression might be regulated by Oct4 through direct binding to the promoter region of Dnmt1.
During MSC proliferation, Dnmt1 was upregulated by Oct4 through direct binding to its promoter, leading to decreased expression of p16 and p21 and the genes associated with their development and lineage differentiation . Breast cancer-associated gene1 (BRCA1) can bind to the DNMT1 promoter through a potential OCT1 site in both mouse and human cells . During cell transformation and tumorigenesis, mouse Dnmt1 transcription is regulated through both E2F-Rb-HDAC-dependent and -independent pathways . We employed the ChIP assay and sensitive two-color EMSA assay (Additional file 2: Figure S2) to confirm that the DNA fragment between − 554 and − 294 bp of Dnmt1 was directly bound by Oct4 in vitro. These results were consistent with those from other studies [30, 31].
Furthermore, in our study, silencing of Oct4 expression significantly reduced the expression and enzyme activity of Dnmt1 in CCE cells, while the overexpression of Oct4 obviously increased the amount of Dnmt1 in NCI-H157 cells (a line of human non-small cell lung cancer cells with a high endogenous Dnmt1mRNA level; Additional file 3: Figure S3).
These abovementioned previously reported findings, together with our data, reveal that Dnmt1 gene expression in vivo is regulated by Oct4. However, the DNA methylation status of the mouse Oct4 gene upstream region has been considered essential for its gene expression, i.e., the Oct4 enhancer/promoter region was hypomethylated in ES cells and the expression of Oct4 mRNA was detected in the Dnmt1n/n placenta but not in the wild-type placenta . In addition, aberrant Oct4 gene expression was identified in another examination . These results indicate that the maintenance of DNA methylation status by Dnmt1 in mice might be accompanied with a change in the expression level of Oct4 mRNA. Based on these results, we have reason to believe that DNA methylation catalyzed by Dnmt1 is modulated through Dnmt1 expression, which regulated by Oct4, whereas the spatial and temporal profiles of Oct4 are influenced through the DNA methylation status of its promoter and DNA methylation-mediated gene silencing.
Animals and collection of embryos
All animals were maintained with a photoperiod of 14 h light and 10 h dark at 20–25 °C for at least 2 weeks before use. Zygotes, 2-cell, 4-cell and 8-cell embryos, morulae, and blastocysts were collected for this study as described previously [33, 34]. All animal studies were approved by the Institutional Animal Care and Use Committee at Fuyang Teachers College in Anhui Province, China. This study was conducted in strict accordance with the recommendations in the 1988 Regulations on the Management of Laboratory Animals in China. The Kunming white mice that were used as a model in this examination were purchased from the Experimental Animal Center of Anhui Medical University (Certification of quality #34000200000077, 34,000,200,000,078).
RNA extraction and real-time PCR
Fifty embryos were used for each time point, and three replicates were performed for each stage. Total RNA extraction, cDNA synthesis from all the samples, and real-time PCR were conducted according to the manufacturer’s instructions as described previously . Gapdh was used as an internal control. The threshold cycle (Ct) was defined as the fractional cycle number by the method of global minimum. The ratio change in Oct4 and Dnmt1 relative to the Gapdh control gene was determined using the 2-△△Ct method . Data are expressed as the means ± SE for the three replicates.
A Kruskal-Wallis test, which was conducted with GraphPad Prism 5 software (GraphPad Software), was used to determine if there was a significant difference between the means (p < 0.05). All primers used for the study are listed in Additional file 4: Table S1.
The 1228-, 931-, 554- and 294-bp fragments of the 5′-flanking regions of the mouse Dnmt1 gene were generated via PCR and subcloned into the pGL3-Basic Vector (Promega Corp.) within the Mlu I and Hind III sites. The software Promoter 2.0 Prediction Server (http://diyhpl.us/~bryan/irc/protocol-online/protocol-cache/TFSEARCH.html) was used to predict the transcription start sites of mouse Dnmt1. Luciferase plasmid bearing a mutation in the − 475 to − 468 bp Oct4-binding motif was constructed via PCR-mediated mutagenesis using primers containing the mutations. The software TFSEARCH ver. 1.3. (http://diyhpl.us/~bryan/irc/protocol-online/protocol-cache/TFSEARCH.html) and PROMO searching tools (http://alggen.lsi.upc.es/) were employed to analyze all possible binding sites on the sense and antisense chains of the mouse Dnmt1 promoter. Mouse Oct4 were amplified and cloned into the pcDNA3.1 expression vector (Invitrogen) using gene-specific open reading frame (ORF) primers as described in our previous study . All inserted sequences were further confirmed via sequencing by Life Technologies Corporation.
Cell culture and luciferase assay
Using Lipofectamine 2000 (Invitrogen), mouse fibroblast cell line NIH/3 T3 cells were transfected with the following plasmids:
500 ng of normal or truncated constructs or mutants of the mouse Dnmt1 promoter, which were cloned into the pGL3-Basic luciferase reporter vector;
10, 50, 100, 200 or 500 ng of Oct4-pcDNA3.1 expression plasmid;
pRL-TK (Promega) at 100 ng/well.
Renilla luciferase from pRL-TK was employed as an internal control for transfection efficiency. Firefly luciferase and Renilla luciferase readings were obtained using the Dual-Luciferase Reporter Assay System (Promega) and GloMax 20/20 Luminometer (Promega). Cell culture, transient transfection and luciferase assays were performed as reported previously . For CCE mES cells, a mESC line derived from the 129/Sv mouse strain, donated by Professor Sijin Liu (Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences), was cultured and transfected with the same plasmids as the NTH/3 T3 cells using Effectene Transfection Reagent (Qiagen), as described previously [35, 36].
Chromatin immunoprecipitation (ChIP) assay
The online program ESCAPE (http://www.maayanlab.net/ESCAPE) and the GEO database with ID number GSE11431 were used to confirm whether Oct4 binds to the Dnmt1 promoter in vitro as described previously [30, 31]. ChIP assays were also performed with the Imprint Chromatin Immunoprecipitation Kit (Cat. No. CHP1, Sigma) according to the manufacturer’s instructions. Briefly, CCE cells were cross-linked in 1% formaldehyde at room temperature for 10 min. The isolated nuclei were lysed and followed by solubilization with shearing buffer containing a protease inhibitor cocktail (Sigma). The chromatin was then sonicated and immunoprecipitated. The antibodies used for ChIP studies were anti-RNA Pol II antibody, anti-IgG antibody (provided in the kit) and anti-Oct4 antibody (Abcam, ab19857). After reverse cross-linking and DNA purification, DNA from input (1:10 diluted) or immunoprecipitated samples was assayed via PCR, and the products were separated using 1.5% agarose gel electrophoresis. For quantitative ChIP analysis, real-time PCR was carried out with SYBR Green PCR Master Mix as described above.
The Δ Ct value in the results uses the following formula:
The percent input was derived with:
The primers used for ChIP analysis PCR reaction are shown in Additional file 4: Table S1.
RNA interference (RNAi) and transfection
Lipofectamine RNAiMAX (Invitrogen Life Technologies) was used to transfect the Stealth RNAi siRNA against Oct4 into CCE cells. The Stealth RNAi Negative Control Duplexes (Invitrogen Life Technologies) were used as a negative control. BLOCK-It Alexa Fluor Red Fluorescent Oligo (Invitrogen) was used to facilitate the assessment and optimize the delivery of double-stranded RNA oligonucleotides into the CCE cells. These siRNA sequences were submitted to a BLAST search to ensure that only the mouse Oct4 gene was targeted. The sequences of the three synthesized oligonucleotides were:
R1 sense 5’-CCAAUGCCGUGAAGUUGGAGAAGGU-3′ and anti-sense 5’-ACCUUCUCCAACUUCACGGCAUUGG-3′;
R2 sense, 5’-CCCGGAAGAGAAAGCGAACUAGCAU-3′ and anti-sense, 5’-AUGCUAGUUCGCUUUCUCUUCCGGG-3′;
R3 sense, 5’-CCAAUCAGCUUGGGCUAGAGAAGGA-3′ and anti-sense, 5’-UCCUUCUCUUAGCCCAAGCUGAUUGG-3′.
RNAi transfection was conducted according to the manufacturer’s instructions. Gene knockdown assays were performed after the complexes were added to the cells and incubated for 48 h at 37 °C in a CO2 incubator.
Gene knockdown and Dnmt1 assay
Real-time PCR and western blotting were conducted to investigate the mRNA and protein expression levels of mouse Oct4 and confirm whether Dnmt1 was downregulated. Total RNA extraction, cDNA synthesis, and real-time PCR were performed as described above. Total proteins were extracted from the RNAi-transfected CCE cells following the procedure detailed in the manual of the “NE-PER Nuclear and Cytoplasmic Extraction Reagents” (#78833, Thermo Fisher Scientific). The protein concentration was measured using a bicinchoninic acid assay on a NanoDrop 2000 spectrophotometer. Western blotting analysis was performed as described previously . The antibody against mouse Dnmt1 was purchased from Abcam (ab13537). For the Dnmt1 assay, the RNAi-transfected CCE cells were initially lysed with NE-PER Nuclear and Cytoplasmic Extraction Reagent, and the EpiQuik DNMT1 assay kit (Epigentek, P-3011) was used to detect the amount of Dnmt1 according to the manufacturer’s instructions and as described previously .
Our results demonstrate that Oct4 plays an important role in the transcription of Dnmt1 by direct binding to a specific site on the Dnmt1 promoter. The total amount of Dnmt1 in CCE cells is reduced by Oct4 as evidenced by the results of the knockdown assay. These findings might reveal a correlation between Oct4 and Dnmt1 during the stages of mouse pre-implantation embryo development and provide new insights into the mechanism of the early stages of mammalian embryonic development.
DNA (cytosine-5)-methyltransferase 1
Electrophoretic mobility shift assay
- ES cell:
Embryonic stem cell
Kruppel-like factor 4
Octamer-binding transcription factor 4
(sex determining region Y)-box 2
Li X, Kato Y, Tsunoda Y. Comparative analysis of development-related gene expression in mouse preimplantation embryos with different developmental potential. Mol Reprod Dev. 2005;72:152–60.
Kashyap V, Rezende NC, Scotland KB, Shaffer SM, Persson JL, Gudas LJ, Mongan NP. Regulation of stem cell pluripotency and differentiation involves a mutual regulatory circuit of the NANOG, OCT4, and SOX2 pluripotency transcription factors with polycomb repressive complexes and stem cell microRNAs. Stem Cells Dev. 2009;18:1093–108.
Takahashi K, Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 2006;126:663–76.
Kim JB, Greber B, Araúzo-Bravo MJ, Meyer J, Park KI, Zaehres H, Schöler HR. Direct reprogramming of human neural stem cells by OCT4. Nature. 2009;461:649–3.
Kim JB, Sebastiano V, Wu G, Araúzo-Bravo MJ, Sasse P, Gentile L, Ko K, Ruau D, Ehrich M, van den Boom D, Meyer J, Hübner K, Bernemann C, Ortmeier C, Zenke M, Fleischmann BK, Zaehres H, Schöler HR. Oct4-induced pluripotency in adult neural stem cells. Cell. 2009;136:411–9.
Plachta N, Bollenbach T, Pease S, Fraser SE, Pantazis P. Oct4 kinetics predict cell lineage patterning in the early mammalian embryo. Nat Cell Biol. 2011;13:117–23.
Tsai CC, Hung SC. Functional roles of pluripotency transcription factors in mesenchymal stem cells. Cell Cycle. 2012;11:3711–2.
Frum T, Halbisen MA, Wang C, Amiri H, Robson P, Ralston A. Oct4 cell-autonomously promotes primitive endoderm development in the mouse blastocyst. Dev Cell. 2013;25:610–22.
Jerabek S, Merino F, Schöler HR, Cojocaru V. OCT4: dynamic DNA binding pioneers stem cell pluripotency. Biochim Biophys Acta. 2014;1839:138–54.
Shi L, Wu J. Epigenetic regulation in mammalian preimplantation embryo development. Reprod Biol Endocrinol. 2009;7:59.
O'Doherty AM1, Magee DA, O'Shea LC, Forde N, Beltman ME, Mamo S, Fair T. DNA methylation dynamics at imprinted genes during bovine pre-implantation embryodevelopment. BMC Dev Biol. 2015;10(15):13.
Smith ZD, Meissner A. DNA methylation: roles in mammalian development. Nat Rev Genet. 2013;14:204–20.
Chen ZX, Riggs AD. DNA methylation and demethylation in mammals. J Biol Chem. 2011;286:18347–53.
Jurkowska RZ, Jurkowski TP, Jeltsch A. Structure and function of mammalian DNA methyltransferases. Chembiochem. 2011;12:206–22.
Tsumura A, Hayakawa T, Kumaki Y, Takebayashi S, Sakaue M, Matsuoka C, Shimotohno K, Ishikawa F, Li E, Ueda HR, Nakayama J, Okano M. Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b. Genes Cells. 2006;11:805–14.
Klose RJ, Bird AP. Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci. 2006;31:89–97.
Takashima S, Takehashi M, Lee J, Chuma S, Okano M, Hata K, Suetake I, Nakatsuji N, Miyoshi H, Tajima S, Tanaka Y, Toyokuni S, Sasaki H, Kanatsu-Shinohara M, Shinohara T. Abnormal DNA methyltransferase expression in mouse germline stem cells results in spermatogenic defects. Biol Reprod. 2009;81:155–64.
Hutnick LK, Huang X, Loo TC, Ma Z, Fan G. Repression of retrotransposal elements in mouse embryonic stem cells is primarily mediated by a DNA methylation-independent mechanism. J Biol Chem. 2010;285:21082–91.
Gu P, Xu X, Le Menuet D, Chung AC, Cooney AJ. Differential recruitment of methyl CpG-binding domain factors and DNA methyltransferases by the orphan receptor germ cell nuclear factor initiates the repression and silencing of Oct4. Stem Cells. 2011;29:1041–51.
Tsai CC, Su PF, Huang YF, Yew TL, Hung SC. Oct4 and Nanog directly regulate Dnmt1 to maintain self-renewal and undifferentiated state in mesenchymal stem cells. Mol Cell. 2012;47:169–82.
Hirasawa R, Chiba H, Kaneda M, Tajima S, Li E, Jaenisch R, Sasaki H. Maternal and zygotic Dnmt1 are necessary and sufficient for the maintenance of DNA methylation imprints during preimplantation development. Genes Dev. 2008;22:1607–16.
Yang X, Smith SL, Tian XC, Lewin HA, Renard JP, Wakayama T. Nuclear reprogramming of cloned embryos and its implications for therapeutic cloning. Nat Genet. 2007;39:295–302.
Saitou M, Kagiwada S, Kurimoto K. Epigenetic reprogramming in mouse pre-implantation development and primordial germ cells. Development. 2012;139:15–31.
Smith ZD, Chan MM, Mikkelsen TS, Gu H, Gnirke A, Regev A, Meissner A. A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature. 2012;484:339–44.
Nakanishi MO, Hayakawa K, Nakabayashi K, Hata K, Shiota K, Tanaka S. Trophoblast-specific DNA methylation occurs after the segregation of the trophectoderm and inner cell mass in the mouse periimplantation embryo. Epigenetics. 2012;7:173–82.
Ovitt CE, Schöler HR. The molecular biology of Oct4 in the early mouse embryo. Mol Hum Reprod. 1998;4:1021–31.
Ding J, Xu H, Faiola F, Ma'ayan A, Wang J. Oct4 links multiple epigenetic pathways to the pluripotency network. Cell Res. 2012;22:155–67.
Shukla V, Coumoul X, Lahusen T, Wang RH, Xu X, Vassilopoulos A, Xiao C, Lee MH, Man YG, Ouchi M, Ouchi T, Deng CX. BRCA1 affects global DNA methylation through regulation of DNMT1. Cell Res. 2010;20:1201–15.
Kimura H, Nakamura T, Ogawa T, Tanaka S, Shiota K. Transcription of mouse DNA methyltransferase 1 (Dnmt1) is regulated by both E2F-Rb-HDAC-dependent and -independent pathways. Nucleic Acids Res. 2003;31:3101–13.
Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, Loh YH, Yeo HC, Yeo ZX, Narang V, Govindarajan KR, Leong B, Shahab A, Ruan Y, Bourque G, Sung WK, Clarke ND, Wei CL, Ng HH. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell. 2008;133:1106–17.
Xu H, Baroukh C, Dannenfelser R, Chen EY, Tan CM, Kou Y, Kim YE, Lemischka IR, Ma'ayan A. ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells. Database (Oxford). 2013;2013:bat045.
Hattori N, Nishino K, Ko YG, Hattori N, Ohgane J, Tanaka S, Shiota K. Epigenetic control of mouse Oct4 gene expression in embryonic stem cells and trophoblast stem cells. J Biol Chem. 2004;279:17063–9.
Wu FR, Ding B, Qi B, Shang MB, Yang XX, Liu Y, Li WY. Sequence analysis, expression patterns and transcriptional regulation of mouse Ifrg15 during preimplantation embryonic development. Gene. 2012;507:119–24.
Wu FR, Liu Y, Shang MB, Yang XX, Ding B, Gao JG, Wang R, Li WY. Differences in H3K4 trimethylation in in vivo and in vitro fertilization mouse preimplantation embryos. Genet Mol Res. 2012;11:1099–108.
Chang TC, Liu CC, Hsing EW, Liang SM, Chi YH, Sung LY, Lin SP, Shen TL, Ko BS, Yen BL, Yet SF, Wu KK, Liou JY. 14-3-3σ regulates β-catenin-mediated mouse embryonic stem cell proliferation by sequestering GSK-3β. PLoS One. 2012;7:e40193.
Ko BS, Chang TC, Shyue SK, Chen YC, Liou JY. An efficient transfection method for mouse embryonic stem cells. Gene Ther. 2009;16:154–8.
Wu L, Wu F, Xie L, Wang D, Zhou L. Synergistic role of β-catenin1 and 2 in ovarian differentiation and maintenance of female pathway in Nile tilapia. Mol Cell Endocrinol. 2016;427:33–44.
Wu FR, Li DK, Su MM, Liu Y, Ding B, Wang R, Li WY. Oral administration of Schisandra chinensis extract suppresses Dnmt1 enzyme activity in Kunming mice ovaries. Genes Genomics. 2016;38:1121–8.
The authors wish to thank Professor Sijin Liu for providing the CCE cell lines. We are grateful to Professor Lixin Yang at Chinese Research Academy of Environment Sciences for comments on this manuscript.
This research was supported with grants from the National Natural Science Foundation of China (No. 31372273, 31501906), the Major Project of Discipline Construction in Anhui Province, and the Key Grant for the Key Projects of the Outstanding Young Talents in Colleges and Universities of Anhui Province (No. gxyqZD201619).
Availability of data and materials
Conclusions are based on data presented in the manuscript and the Additional file 1: Figure S1, Additional file 2: Figure S2, Additional file 3: Figure S3. Any additional data can be obtained directly from the corresponding authors.
Full name of ethical committee provided
All animal studies were approved by the Institutional Animal Care and Use Committee at Fuyang Teachers College in Anhui Province, China.
This study was conducted in strict accordance with the recommendations in the 1988 Regulations on the Management of Laboratory Animals in China. Kunming white mice that were used as a model were purchased from the Experimental Animal Center of Anhui Medical University (Certification of quality #34000200000077, 34,000,200,000,078).
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Figure S1. Promoter analysis of mouse Dnmt1 in NIH3T3 and CCE cells using the luciferase assay. A – The promoter activity of mouse Dnmt1 in NIH3T3 and CCE cells. Oct4-pcDNA3.1 (100 ng) plasmid was co-transfected with Dnmt1-P1 into NIH3T3 and CCE cells. B – The promoter activity of mouse Dnmt1-Pwt and -Pmu in CCE cells. Oct4-pcDNA3.1 (100 ng) plasmid was co-transfected with Dnmt1-Pwt and -Pmu into CCE cells. The total amount of the transfected plasmid, including the pRL-TK control vector (100 ng/well), was adjusted to 1.0 μg with pcDNA3.1 empty vectors. Firefly and Renilla luciferase activities were measured 48 h after the transfection. The relative luciferase activity was calculated by dividing the activity of firefly luciferase by the activity of Renilla luciferase. The data are presented as the means ± SD for triplicate transfections. (TIF 306 kb)
Figure S2. The results of the sensitive two-color EMSA assay showed direct binding of Oct4 to the mouse Dnmt1 promoter in vitro. A quantity of 20 ng of mouse Dnmt1 promoter (the region from − 554 to − 294 bp relative to TSS) was added to samples containing different amounts of Oct4 in 1 × binding buffer as described in the Methods section. The images were taken using an alpha gel imaging system. Lanes: (1) DL2000 markers; (2) 20 ng mouse Dnmt1 promoter; (3–9) 20 ng mouse Dnmt1 promoter interacting with increasing amounts (95, 190, 380, 570, 760, 950 and 1140 ng) of mouse Oct4 protein; (10, 11) 40 ng Oct4 protein without any mouse Dnmt1 promoter. A – Image of the EMSA gel stained with SYBR Green EMSA DNA stain to show DNA. B – The same gel stained with SYPRO Ruby EMSA protein stain to show the protein. (TIF 589 kb)
Figure S3. Dnmt1 assay results show the promoted amount of Dnmt1 in NCI-H157 cells when overexpressed with mouse Oct4. A – Illustrated standard curve generated with Dnmt1 Standard. B and C – The final OD (equal to the 450 nm OD minus the 655 nm OD) and the amount of Dnmt1 were enhanced in the Oct4+ group when compared with the control (Oct4− group). The results are presented as the means ± SD. The final values of (OD 450 nm – 650) from triplicate transfected samples were measured using a microplate reader. * and **Statistically significant difference of the comparisons with the negative control as determined with Student’s t-test at p < 0.05 and 0.01. (TIF 576 kb)
Table S1. List of primer sequences used in real-time PCR, promoter analyses and ChIP assay. (DOCX 12 kb)
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Wu, F., Wu, Q., Li, D. et al. Oct4 regulates DNA methyltransferase 1 transcription by direct binding of the regulatory element. Cell Mol Biol Lett 23, 39 (2018). https://doi.org/10.1186/s11658-018-0104-2