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Establish a rapid and efficient chemical reprogramming platform (RNA-Seq II)

ABSTRACT: Chemically reprogramming somatic cells to iPSCs is time-consuming and low-efficiency. Here, we discribe a rapid chemical reprogramming condition enabling generating iPSCs from MEFs in 12 days. To further investigate the mechemisms and draw an epigenetic maps during the rapid chemical reprogramming, we performed time-course RNA-seq, ATAC-seq, RRBS, CUT&Tag (H3K4me3, H3K18la, H3K9me3, H3K27me3 and H3K27ac) and scRNA-seq.

ORGANISM(S): Mus musculus

PROVIDER: GSE220554 | GEO | 2023/05/03

REPOSITORIES: GEO

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Establish a rapid and efficient chemical reprogramming platform (RRBS)

Project description:Chemically reprogramming somatic cells to iPSCs is time-consuming and low-efficiency. Here, we discribe a rapid chemical reprogramming condition enabling generating iPSCs from MEFs in 12 days. To further investigate the mechemisms and draw an epigenetic maps during the rapid chemical reprogramming, we performed time-course RNA-seq, ATAC-seq, RRBS and CUT&Tag (H3K4me3, H3K18la, H3K9me3, H3K27me3 and H3K27ac).

2023-05-03 | GSE188831 | GEO

Establish a rapid and efficient chemical reprogramming platform [scRNA-Seq]

Project description:Chemically reprogramming somatic cells to iPSCs is time-consuming and low-efficiency. Here, we discribe a rapid chemical reprogramming condition enabling generating iPSCs from MEFs in 12 days. To further investigate the mechemisms and draw an epigenetic maps during the rapid chemical reprogramming, we performed time-course RNA-seq, ATAC-seq, RRBS, CUT&Tag (H3K4me3, H3K18la, H3K9me3, H3K27me3 and H3K27ac) and scRNA-seq.

2023-05-03 | GSE218855 | GEO

Establish a rapid and efficient chemical reprogramming platform (ATAC-Seq)

2023-05-03 | GSE188824 | GEO

Establish a rapid and efficient chemical reprogramming platform (RNA-Seq)

2023-05-03 | GSE188830 | GEO

Establish a rapid and efficient chemical reprogramming platform (CUT&Tag)

2023-05-03 | GSE188826 | GEO

Dux promotes metabolism-lactylation-MET cascaded network during early iPSC reprogramming with Brg1 as the histone lactylation reader [Cut & Tag]

Project description:The process of reprogramming induced pluripotent stem cells (iPSCs) involves several crucial events, including the shutdown of somatic genes, the mesenchymal-epithelial transition (MET), activation of pluripotent genes, metabolic reprogramming, and epigenetic rewiring. These events intricately interact and influence each other, ultimately leading to the formation of iPSCs. However, the specific element that regulates the reprogramming network remains unclear. Dux, a factor known to promote totipotency during the transition from embryonic stem cells (ESCs) to 2C-like ESCs (2CLC), has not been extensively studied in the context of iPSC reprogramming. In this study, we demonstrate that the modification of H3K18la induced by Dux overexpression controls the metabolism-H3K18la-MET network, enhancing the efficiency of iPSC reprogramming through a metabolic switch and the recruitment of P300 via its C-terminal domain. Through the utilization of H3K18la regulators, we discover that H3K18la plays crucial roles in promoting MET. Furthermore, our proteomic analysis of H3K18la IP experiment uncover the specific recruitment of Brg1 during reprogramming, with both H3K18la and Brg1 being enriched on the promoters of genes associated with epithelial and pluripotency. In summary, our study has demonstrated the significant role of Dux-induced H3K18la in the early reprogramming process, highlighting its function as a potent trigger. Additionally, our research has revealed, for the first time, the binding of Brg1 to H3K18la, indicating its role as a reader of histone lactylation.

2024-03-01 | GSE251641 | GEO

Dux promotes metabolism-lactylation-MET cascaded network during early iPSC reprogramming with Brg1 as the histone lactylation reader [RNA-Seq]

2024-03-01 | GSE251640 | GEO

Coordination of engineered factors with TET1/2 promotes early stage epigenetic modification during somatic cell reprogramming

Project description:Somatic cell reprogramming towards induced pluripotent stem cells (iPSCs) holds great promise in future regenerative medicine, however, the reprogramming process mediated by the traditional defined factors (OSNK) is slow and extremely inefficient. Here we show that a combination of modified reprogramming factors (OySyNyK), in which the transactivation domain of the Yes-associated protein is fused to OCT4, SOX2 and NANOG respectively, could be used to establish a highly efficient and rapid reprogramming system for iPSC generation. We show that the efficiency of OySyNyK-induced iPSCs was up to 100-fold higher than that of induction by traditional OSNK. Moreover we show that the reprogramming by OySyNyK is very rapid (initiated at 24 h versus 5 d by OSNK). Compared with OSNK, we found that OySyNyK factors significantly increased the expression of Tet1/2 at the early stage, which will interact with OSNK factors, and co-occupy pluripotency loci in the genome for somatic cell reprogramming. Our studies not only establish a rapid and highly efficient iPSC reprogramming system, but also uncover a novel mechanism by which OSNK factors coordinate with TET proteins to regulate 5hmC-mediated epigenetic control, thereby promoting somatic cell reprogramming. We examined DNA hydroxymethylation progression of reprogramming intermediates. To this end, we profiled the genome-wide 5hmC distribution in MEFs, the reprogramming intermediates at different stages induced by either the OSNK or OySyNyK methods, and iPSCs using the chemical capture approach

2013-08-08 | E-GEOD-46202 | biostudies-arrayexpress

Resolving Cell Fate Decisions during Somatic Cell Reprogramming by Single-Cell RNA-seq

Project description:The use of Yamanaka factors or chemical compound converting mouse embryonic fibroblasts (MEFs) into induced pluripotent stem cells (iPSCs). However, these reprogramming processes are highly heterogeneous and remain poorly understood. Here we comprehensively profile the different stages of an optimized Oct4, Sox2, Klf4 and chemical-induced reprogramming at single-cell resolution.

2019-01-01 | GSE103221 | GEO

Reprogramming methods influence DNA methylation and expression patterns of mouse induced pluripotent stem cells [RNA-seq]

Project description:Induced pluripotent stem cells (iPSCs) can be derived from somatic cells through ectopic expression of transcriptional factors or chemical cocktails. Chemical reprogramming might be safe than transcriptional factors since there is no integration of exogenous genes. However, there is still little direct evidence to prove this hypothesis. In this study, we have performed whole genome profiling of the DNA methylomes of mouse chemical iPSCs (CiPSCs), transcriptional factors induced iPSCs (TF-iPSCs) and embryonic stem cells (ESCs). We find that the methylation levels of high-CpG-density promoters (HCPs) and intermediate- CpG-density promoters (ICPs) have no significant difference among them, but low-CpG-density promoters (LCP) and three retrotransposons (LINEs, LTRs and SINEs) show preference to different methylation levels. Surprisingly, CiPSCs are hypomethylated than TF-iPSCs and the major difference of methylation levels lies in the intergenic regions while two iPSCs lines are generally hypermethylated compared to ESCs. Moveover, we find the methylation states of imprinting control regions (ICRs) and the expression of imprinted genes of CiPSCs are more resemble ESCs than TF-iPSCs. Our data first provide the epigenetic states of chemical induced pluripotent stem cells and compare the difference of mouse CiPSCs, TF-iPSCs and ESCs. These observations might affect ongoing choices of reprogramming methods for disease modeling and give some guides for potential therapeutic applications.

2017-06-28 | GSE92983 | GEO

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