C57BL/6 mouse embryo stem cells(mESC)-based transcription change in expression profile microarray with folate deficiency
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ABSTRACT:
PROVIDER: PRJNA511449 | ENA |
REPOSITORIES: ENA
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Project description:Different genes were chosen according to folate deficiency in the microarray. In the study here,C57BL/6C mESC with six consecutive generations under folate-deficiency was used to obtain whole genome-based expression microarray.
2018-12-22 | GSE124271 | GEO
Project description:Wnt signaling plays a major role in early neural development. An aberrant activation in Wnt/β-catenin pathway leads to defective anteroposterior patterning, resulting in neural tube closure defects (NTDs). Changes in folate metabolism may participate in early embryo fate determination. We report here that in C57BL/6C mouse embryonic stem cells (mESC), folate deficiency activates Wnt/β-catenin pathway by upregulating a chorion-specific transcription factor Gcm1. Specifically, folate deficiency promotes the formation of the Gcm1/β-catenin/T-cell factor (TCF4) complex to regulate the Wnt target gene transactivation through the Wnt-responsive elements. Moreover, the enhanced transcriptional activity of Gcm1 is found to be dependent on CREB binding protein. Lastly, in NTDs mouse models and low folate NTDs human brain samples, Gcm1 and Wnt/β-catenin target genes related to neural tube closure are specifically overexpressed. These results indicate that low folate promotes Wnt/β-catenin signaling via activating Gcm1, leading to aberrant vertebrate neural development
2018-12-27 | GSE124339 | GEO
Project description:Neural tube defects (NTDs) are one of the most severe congenital abnormalities. Maternal folate deficiency could impact the occurrence of NTDs. Histone H3 methyltransferase disruptor of telomeric silencing 1-like (DOT1L) expression was significantly downregulated, and low levels of H3K79me2 were found in the corresponding NTDs samples with their maternal serum folate under low levels. Using ChIP-seq assays, we found that a decrease of H3K79me2 downregulates the expression of Shh and Sufu in mouse embryonic stem cells (mESC) under folate deficiency. Our results indicate that abnormal Shh and Sufu genes expression reduced by aberrant Dot1l-mediated H3K79me2 levels could be the cause of NTDs occurrence.
2023-07-25 | GSE238081 | GEO
Project description:Folate deficiency promotes differentiation of vascular smooth muscle cells, but shifts the overall phenotype towards skeletal muscle
2020-01-22 | GSE125502 | GEO
Project description:Short-term folate deficiency has been linked to cognitive defects. Given folate’s role in regulating nucleotide synthesis and DNA and histone methylation, these changes are often linked to altered gene expression. We hypothesize that chronic folate deficiency will induce memory deficits that can be linked to tissue-specific changes in gene expression. This study placed mice on folic acid deficient or replete diets, containing either no source of folate or AIN-93G normal folic acid intake, beginning post-weaning and persisting through the end of adult life at 18 months. Cognitive outcomes were assessed using the novel object test for memory. Changes in hippocampal gene expression were examined by RNA microarray analysis and confirmed by qPCR. qPCR was also use to compare a subset of significant hippocampal genes to potential changes in liver and heart expression. Ontological categories were determined using GeneCodis for genes whose expression significantly changed in the deficient condition. Significantly enriched motifs in the deficient genes were examined using the HOMER bioinformatics analysis tool to identify transcription factors associated with changing genes. Folic acid deficient mice showed significant memory impairment (P<0.05) compared to replete counterparts beginning at 5 mo and persisting through 17 mo. These deficits were associated with 363 significantly downregulated and 101 significantly upregulated genes (P<0.05, fold change > 2) in the deficient condition. Of the 16 genes whose differential hippocampal expression was confirmed by qPCR, none were also differentially regulated in the heart, and only one was differentially regulated in the liver (P<0.05). Significant ontological categories for differential genes included nucleotide regulation, ion channel activity, and MAPK signaling. Two enriched motifs were identified and determined to be associated with MafB and Zfp410 binding sites. These genes and enriched motifs may represent targets for treatment or investigation of memory-related diseases.
2020-06-23 | GSE148126 | GEO
Project description:Transcriptome analysis of mouse embryonic stem cell lines derived from embryos cultured in optimal and suboptimal conditions compared to cell lines derived from control embryos. The use of assisted reproductive technologies (ART) such as in vitro fertilization (IVF) has resulted in the birth of more than 5 million children. While children conceived by these technologies are generally healthy, there is conflicting evidence suggesting an increase in adult-onset complications like glucose intolerance and high blood pressure in IVF children. Animal models indicate similar potential risks. It remains unclear what molecular mechanisms may be operating during in vitro culture to predispose the embryo to these diseases. One of the limitations faced by investigators is the paucity of the material in the preimplantation embryo to test for molecular analysis. To address this problem, we generated mouse embryonic stem cells (mESC) from blastocysts conceived after natural mating (mESCFB) or after IVF, using optimal (KSOM + 5% O2; mESCKAA) and suboptimal (Whitten’s Medium, + 20% O2, mESCWM) conditions.
2015-03-31 | GSE63821 | GEO
Project description:We demonstrate that expression of key markers of keratinocyte differentiation is suppressed by exposure to sodium arsenite. Folate deficiency exacerbates this effect. In addition, cancer-related cell movement genes, and growth and proliferation genes are altered. Several redox-sensitive transcription factors are implicated in mediating these gene expression changes due to arsenic treatment and folate deficiency. Experiment Overall Design: K6/ODC mice were maintained on either a folate deficient or folate sufficient diet and exposed to 0, 1, or 10 ppm sodium arsenite in the drinking water for 30 days. Total RNA was isolated from skin samples and gene expression analyzed using Affymetrix Mouse 430 2.0 GeneChips. Data from 24 samples, with four mice in each of the six treatment groups, were analyzed.
2008-06-16 | E-GEOD-8733 | biostudies-arrayexpress
Project description:Folate deficiency causes widespread DNA breakages and is responsible for neural tube defect (NTD). However, little is known about the implications and mechanisms of these DNA instability to NTD. Here, by performing high-throughput sequencing, we generate genome-wide epigenetic profiles and map the distribution of DNA double-strands breaks (DSBs) in folate-antagonist treated embryonic stem cells. We find that DSBs exhibit distinct preference in active promoters and inhibit the interaction between enhancers and promoters. We uncover DSBs affected CTCF binding as a causal link for the abnormal expression of NTD susceptible genes. Finally, we propose a two-ways model for screening NTD susceptible genes and verifying 7 candidate genes in NTD fetuses with low folate level. In summary, our work demonstrate that folate deficiency induced DSBs trigger the dysregulation of NTD susceptible genes through impacting epigenetic regulation.
2020-05-01 | GSE149627 | GEO
Project description:Transcriptome analysis of mouse embryonic stem cell lines derived from embryos cultured in optimal and suboptimal conditions compared to cell lines derived from control embryos. The use of assisted reproductive technologies (ART) such as in vitro fertilization (IVF) has resulted in the birth of more than 5 million children. While children conceived by these technologies are generally healthy, there is conflicting evidence suggesting an increase in adult-onset complications like glucose intolerance and high blood pressure in IVF children. Animal models indicate similar potential risks. It remains unclear what molecular mechanisms may be operating during in vitro culture to predispose the embryo to these diseases. One of the limitations faced by investigators is the paucity of the material in the preimplantation embryo to test for molecular analysis. To address this problem, we generated mouse embryonic stem cells (mESC) from blastocysts conceived after natural mating (mESCFB) or after IVF, using optimal (KSOM + 5% O2; mESCKAA) and suboptimal (Whitten’s Medium, + 20% O2, mESCWM) conditions. We analyzed three female cell lines per group for a total of nine mouse embryonic stem cells on Affymetrix MoGene 1.0 ST Arrays.
2015-03-31 | E-GEOD-63821 | biostudies-arrayexpress
Project description:We demonstrate that expression of key markers of keratinocyte differentiation is suppressed by exposure to sodium arsenite. Folate deficiency exacerbates this effect. In addition, cancer-related cell movement genes, and growth and proliferation genes are altered. Several redox-sensitive transcription factors are implicated in mediating these gene expression changes due to arsenic treatment and folate deficiency. Keywords: gene expression/microarray
2007-08-10 | GSE8733 | GEO