Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide DNA methylation and expression profiling of MEFS and SKOM induced reprogramming cells after modulation of Cell cycle and Dnmt1 expression

ABSTRACT: Genome-wide DNA methylation and expression profiling of MEFS and SKOM induced reprogramming cells after modulation of Cell cycle and Dnmt1 expression

PROVIDER: PRJNA360927 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Expression Profiling of MEFs and SKOM induced reprogramming cells after modulation of Cell cycle and Dnmt1 expression

Project description:To generate association of DNA methylation level and gene expression profile, we applied RNA-sequencing on mouse embryonic fibroblasts (MEFs) after the modulation of cell cycle and Dnmt1 expression level. To characterize how these factors affect somatic reprogramming, samples of MEFs induced by Yamanaka factors (Sox2, Klf4, Oct4, cMyc) was also included. The cell cycle was accelerated by shRNA targeted to p53, and the expression of Dnmt1 was manipulated by either over expression or knock down.

2017-10-13 | GSE93416 | GEO

Genome-wide DNA methylation maps of mouse embryonic fibroblasts and reprogramming cells modulated by cell cycle and Dnmt1 expression

Project description:Dramatic change in DNA methylation patterns and levels both globally and/or locus-specifically is associated with the process of cell linage specification and somatic reprogramming. We found the expression of DNA methyltransferase 1 (Dnmt1) is tightly regulated by the features of cell cycle, which we referred as cell cycle-directed Dnmt1 expression adjustment. To further investigate how DNA methylation is affected by this mechanism, we applied reduced representation bisulphate sequencing (RRBS) to map genome-wide DNA methylation on mouse embryonic fibroblasts (MEFs). To characterize how this mechanism affects somatic reprogramming, samples of MEFs induced by Yamanaka factors (Sox2, Klf4, Oct4, cMyc) was included. The cell cycle was accelerated by shRNA targeted to p53, and the expression of Dnmt1 was manipulated genetically. We find 5mC level remains constant in regardless of cell proliferation rate, a result from the adjusted expression of Dnmt1. However, repressed expression of Dnmt1 in fast-proliferating cells results in global DNA demethylation. The patterns of DNA methylation and demethylation affected by this mechanism is sensitive to CpG densities. Generally, the results demonstrate cell cycle-directed Dnmt1 expression adjustment as an mechanism for the insurance of the stability of genomic 5mC inheritance.

2017-10-13 | GSE93058 | GEO

Reprogramming MEFs (mouse iPSCs)

Project description:Proteome of reprogramming mouse embryonic fibroblasts (MEFs) with or without Akt activation

2020-07-31 | PXD014856 | JPOST Repository

Genome-wide DNA methylation and expression profiling of MEFS and SKOM induced reprogramming cells after modulation of Cell cycle and Dnmt1 expression

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-10-13 | GSE93417 | GEO

Expression data in MEFs

Project description:Expression data in MEFs

| PRJNA448757 | ENA

ATM mediates pRB function to control DNMT1 protein stability and DNA methylation

Project description:The retinoblastoma tumor suppressor gene (RB) product has been implicated in epigenetic control of gene expression owing to its ability to physically bind to many of chromatin modifiers. However, the biological and clinical significance of this activity was not well elucidated. To address this, we performed genetic and epigenetic analyses in an Rb-deficient mouse thyroid C cell tumor model. Here we report that the genetic interaction of Rb and ATM regulates DNMT1 protein stability, and hence controls the DNA methylation status in the promoter of at least Ink4a, Shc2, FoxO6 and Noggin genes. Further, we demonstrate that inactivation of pRB promotes the Tip60 (acetyltransferase)-dependent ATM activation, allows activated ATM to physically bind to DNMT1 forming a complex with Tip60 and UHRF1 (E3 ligase), and consequently accelerates DNMT1 ubiquitination driven by Tip60-dependent acetylation. Our results indicate that inactivation of pRB pathway in coordination with aberration in DNA damage response leads to abnormal DNA methylation pattern by affecting the stability of DNMT1. 163; Rb-/-;ATM-/- MEFs, D4; DNMT1 knockdown from 163 cells and analysed at day 4, WT8S; 163 cells reconstituted with ATM expression vector

2013-05-31 | E-GEOD-47501 | biostudies-arrayexpress

RIPSEQ DNMT1 HL60

Project description:Identification of the all RNA species associated with DNMT1. Using a comparative genome-scale approach we identified and correlated the RNA species physically associated with DNMT1 and proximal to the annotated genes to the methylation status of the corresponding loci and expression levels of the respective genes. This comparative approach delineated the first -DNMT1 centered- 'epitranscriptome' map, a comprehensive map cross-referencing DNMT1-interacting transcripts to (i) DNA methylation and (ii) gene expression profile. Relationship between DNMT1-RNA interactions, DNA methylation and gene expression

2012-12-01 | E-GEOD-32162 | biostudies-arrayexpress

Global Transcriptional Analysis of Nuclear Reprogramming in the Transition from MEFs to iPSCs

Project description:Here, we focused on the intermediate stages of SCR by comparing the somatic cell line induced by OCT4, SOX2, and KLF4 (OSK) for 7 days with mouse embryonic fibroblasts (MEFs), iPSCs, and embryonic stem cells (ESCs). Transcriptional profiles of these four cell lines were analyzed by microarray, and we found that the transition process from day 7 to the formation of iPSCs is crucial for SCR and that the reverse expression patterns can provide more candidate markers to distinguish ESCs and somatic cells iPSC. Data confirmed that the viral infection results in defense innate immunity, DNA damage, and apoptosis in MEFs, which slows down cell proliferation and immortalization to inhibit SCR. Although SCR is initiated by OSK, the p53 signaling pathway can affect the transcriptional regulatory networks through cell cycle and genomic instability as a powerful core node. MEFs were derived from embryonic day 13.5 C57BL6 mice embryos. Cell line day7 is MEF induced by OCT4, SOX2, and KLF4 (OSK) for 7 days with mouse embryonic fibroblasts (MEFs), iPSCs, and embryonic stem cells (ESCs).

2012-10-01 | E-GEOD-37397 | biostudies-arrayexpress

DNMT1 KNOCKOUT IN MURINE LIVER (expression)

Project description:Gene expression analysis of liver after DNMT1 knock down. DNMT1 KO versus control livers at week 4, 8 and 20. 24 Samples analyzed

2016-04-01 | E-GEOD-67734 | biostudies-arrayexpress

DNMT1 KNOCKOUT IN MURINE LIVER (expression)

Project description:Gene expression analysis of liver after DNMT1 knock down. DNMT1 KO versus control livers at week 4, 8 and 20.

2016-04-01 | GSE67734 | GEO