DNA methylation dynamics studies with MethylRO mouse
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE57024 | GEO | 2014/04/24
SECONDARY ACCESSION(S): PRJNA245230
REPOSITORIES: GEO
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Project description:We studied the effects of chemical exposure on global DNA methylation by using mCherry-methyl-CpG-binding domain (MBD)-nls human induced pluripotent stem cells (iPSCs). According to the fluorescent MBD parameters, we divided the effects of 135 chemical on global DNA methylation into 3 categories; reduction (hypomethylation), increase (hypermethylation) and little/no effect. We performed DNA methylome assay to examine the effects of 6 epigenotoxic chemicals on genome-wide DNA methylation patterns in human iPSCs. Our results indicated that hypermethylation agents increased DNA methylation and downregulated the expression of genes involved in cell cycle or development.
2021-07-23 | GSE180453 | GEO
Project description:We studied the effects of chemical exposure on global DNA methylation by using mCherry-MBD-nls human iPS cells. By using 135 chemical library, we could devide the effects of global DNA methylation into 3 categories; reduction (hypomethylation), increase (hypermethylation) and little/no effect. We further performed both genome-wide DNA methylation and stemness-related gene expression (100 genes) analyses, and results indicated that hypermethylation agents increased DNA methylation and downregulated the expression of genes involved in cell cycle or development.
2023-04-01 | GSE228658 | GEO
Project description:We studied the effects of chemical exposure on global DNA methylation by using mCherry-methyl-CpG-binding domain (MBD)-nls human induced pluripotent stem cells (iPSCs). According to the fluorescent MBD parameters, we divided the effects of 135 chemical on global DNA methylation into 3 categories; reduction (hypomethylation), increase (hypermethylation) and little/no effect. We performed RNA-seq analysis to examine the effects of chemicals on the expression of 100 stemness-related genes. In this series of experiment, we selected 5 compounds for genome-wide analyses. Etoposide, propyl gallate, and biotin were selected as representative chemicals of hypermethylation agents. Theophylline and bisphenol A were selected as representative chemicals of hypomethylation agents and undefined-epigenetic agents, respectively. Our results indicated that hypermethylation agents increased DNA methylation and downregulated the expression of genes involved in cell cycle or development.
2021-07-23 | GSE180452 | GEO
Project description:ATF6 is a key regulator of the unfolded protein response. Through use of zebrafish and cultured cells we demonstrate that ATF6 drives fatty liver disease by interaction with fatty acid synthase (FASN). Total small RNA from livers of 5 dpf larval zebrafish were collected: 2 batches of Tg(fabp10:nls-mCherry) control larvae, 2 batches of ethanol-treated Tg(fabp10:nls-mCherry) larvae, and 1 batch of Tg(fabp10:nAtf6-cherry; cmlc2:GFP). Each batch was purified for preparation of high-throughput sequencing libraries.
2014-05-01 | E-GEOD-56498 | biostudies-arrayexpress
Project description:The objective of this study was to test how restoration of mitochondrial respiration using AOX affects the development of cardiac ischemia-reperfusion (IR) injuries in C57BL/ 6J mice. AOX transgenic mice have Ciona intestinalis AOX coding sequence knocked into the Rosa26 locus with AOX expression controlled by a CAG promoter as described elsewhere (Szibor et al. (2017) Dis Model Mech 10: 163–171). Consequences of 45 min of cardiac ischemia were studied 3 and 9 weeks after reperfusion in both wild-type and AOX litter mates.
2020-01-30 | PXD014061 | Pride
Project description:UHRF1 is an essential regulator of DNA methylation that is highly expressed in many cancers. Using transgenic zebrafish, cultured cells and human tumors, we demonstrate that UHRF1 is an oncogene. RNAseq was used to assess the variation in gene expression between control and experimental samples. Total small RNA from 2 batches of Tg(fabp10:has.UHRF1-GFP)High and age matched Tg(fabp10:nls-mCherry) control 5 dpf zebrafish livers was purified for preparation of high-throughput sequencing libraries.
2013-11-22 | E-GEOD-52605 | biostudies-arrayexpress
Project description:The goal of this study is to compare gene expression levels in the livers of larval Tg(fabp10:nls-mcherry) exposed to 1 mM inorganic arsenic from 4-120 hpf to the unexposed siblings. Samples were collected from Tg(fabp10:nls-mcherry) zebrafish larvae that were derived from incrossed parents of the same strain. The background of transgenic lines were typically from mixed outcrosses of the transgenics to AB, TAB5, and TAB14 strains when regenerating the lines as the working stocks aged. All samples were collected at approximately 120 hpf - natural spawning at 8:30-9:00AM EST on day zero, samples were collected at 8-10AM EST on day 5.
2017-11-12 | GSE104953 | GEO
Project description:Purpose: The E3 ubiquitin ligase Parkin is a well-characterized regulator of mitochondrial autophagy (mitophagy); however, it is becoming increasingly appreciated to perform additional roles in various compartments of the cell. Our laboratory confirmed the presence of Parkin in the nucleus of various tissues (biochemical fractionations) and cell types (immunofluorescent imaging). Hypoxia-induced nuclear translocation of Parkin occured independent of the mitophagy regulator PINK1, and Parkinson's disease-associated mutants were restricted from the nuclueus. Accordingly, we inserted a nuclear localization sequence (NLS) at the n-terminus of Parkin and overexpressed both NLS Parkin and the wild-type protein in HeLa cells cultured at normoxia and hypoxia. Next-generation RNA-sequencing (RNA-seq) was used to determine the effect of nuclear Parkin on cellular transcription. Methods: mCherry-tagged NLS and wild-type Parkin were overexpressed in HeLa cells. Differential expression analyses were performed on Parkin vs. mCherry control cells and NLS Parkin vs. mCherry control cells at normoxia and following 12hr of hypoxia (n=3/group/condition). Paired-end sequencing was performed using the HiSeq4000. FastQC v0.11.3 was used for quality control, Trimmomatic v0.36 was used to trim reads which were aligned to the human genome (GRCh37.p13) using the STAR aligner v2.5.3a. Read quantification was performed with RSEM v 1.3.0 and the Gencode release 19. The R BioConductor packages edgeR and limma were used to implement the limma-voom method for differential expression analysis. Results: During normoxia, Parkin had no effect on basal transcription; however, overexpression of NLS Parkin was associated with 168 differentially expressed genes (DEGs: fold-change </= 1.5, FDR < 0.05) relative to mCherry control cells. Following hypoxia, the transcriptome associated with the overexpression of wild-type Parkin more closely resembled that of NLS Parkin. Along these lines, Parkin overexpression during hypoxia coincided with a total of 158 DEGs, 37% of which were shared with NLS Parkin. Overlapping and shared DEGs among Parkin and NLS Parkin were implicated in cellular metabolism, HIF1 signaling and survival. Our follow up co-immunoprecipitation and real-time quantitative PCR studies demonstrated that Parkin interacts with the Estrogen Related Receptor Alpha (ERRa) to promote the induction of its downstream target genes. Conclusions: Nuclear translocation of Parkin is a novel means by which this cytoprotective protein contributes to cellular homeostasis and especially critical during hypoxia.
2019-11-06 | GSE139989 | GEO
Project description:To investigate Keratin 19 (KRT19) expression dynamics in pancreatic development, we established a human pluripotent stem cell (PSC)-based KRT19-mCherry reporter system in various genetic backgrounds to monitor KRT19 expression from ist endogenous gene locus. A genuine differentiation protocol to generate mature pancreatic duct-like organoids (PDLO) was applied. While KRT19/mCherry expression became evident at early endoderm stage, mCherry signal was present in nearly all cells at pancreatic endoderm (PE) and pancreatic progenitor (PP) stage. Interestingly, despite homogenous KRT19 expression, the mCherry positivity dropped to 50% after ductal maturation, indicating a permanent switch from biallelic to monoallelic expression. DNA methylation profiling separated the distinct differentiation intermediates with site specific DNA methylation patterns occuring at the KRT19 locus during ductal maturation. Accordingly, the monoallelic switch was partially reverted upon treatment with a DNA-methyltransferase inhibitor.
2023-06-08 | GSE234345 | GEO
