Identification of MRG15 as barrier to somatic reprogramming
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1083950 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28230006_1.fastq.gz | Fastqsanger.gz | |||
| SRR28230006_2.fastq.gz | Fastqsanger.gz | |||
| SRR28230007_1.fastq.gz | Fastqsanger.gz | |||
| SRR28230007_2.fastq.gz | Fastqsanger.gz | |||
| SRR28230008_1.fastq.gz | Fastqsanger.gz |
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Project description:Epigenetic reprogramming requires depletion of 4 factors ; Oct4, Sox2, Klf-4 and c-Myc. We have 4 groups of samples. 2 group is collected as fibroblasts and it is referred as Day Zero. The other groups are collected at the sixth day of epigenetic reprogramming referred as Day Six. Day 18 of epigenetic reprogramming, %5- 15 of cell population transformed into pluripotent stem cells. At day six this percentage is lower.Our previous studies have showed that inhibition of H3K36me3 mark thusleading to H3K36me2 mark on chromatin) significantly increased reprogramming efficiency. A CRISPR Knock-Out Library was built to identify which of the H3K36me3 mark reader protein can phenocopy absence of K36me3 loss in terms of reprogramming efficiency. MRG15 Knock Out has showed the most similar increase in reprogramming as loss of K36me3 mark. It has been reported that MRG15 is responsible from alternative splicing of some genes. Our hypothesis is; in the presence of H3K36me3 mark MRG15 can bind this mark on chromatin and recruit proteins related to alternative splicing ( eg. PTBP1)and regulate alternative splicing.
2025-01-01 | GSE260899 | GEO
Project description:Mammalian oocytes can reprogram somatic cells into totipotent state, which allows animal cloning through somatic cell nuclear transfer (SCNT). However, the great majority of SCNT embryos fail to develop to term due to poorly defined reprogramming defects. Here we demonstrate that histone H3 lysine 9 trimethylation (H3K9me3) in donor nuclei is a major epigenetic barrier that prevents efficient nuclear reprogramming in mouse oocytes. Comparative transcriptome analysis of early embryos revealed reprogramming resistant regions (RRRs) where transcriptional activation at 2-cell embryos is inhibited by SCNT compared to in vitro fertilization (IVF). RRRs significantly overlap with H3K9me3 enrichment in donor somatic cells. Importantly, removal of the H3K9me3 by ectopic expression of an H3K9me3 demethylase Kdm4d in recipient oocytes not only reactivates most RRRs, but also greatly improves development of SCNT embryos. Furthermore, the use of Suv39h1/2-depleted somatic nuclei as donors also greatly improves the development of SCNT embryos. Our study thus reveals H3K9me3 as an epigenetic barrier in SCNT-mediated reprogramming and provides a feasible method for improving mammalian cloning efficiency.
2014-11-07 | GSE59073 | GEO
Project description:Abstract: Chromatin-regulating factors safeguard cell identities by suppressing ectopic gene expression thereby imposing barriers for transcription factor-induced reprogramming of cell fates. Identifying factors opposing the induction of ectopic cell fates is important to better understand developmental differentiation processes and may improve cellular reprogramming for therapeutic approaches. Reprogramming barriers have previously been studied mostly in tissue cultures. Hence, knowledge about chromatin regulators acting as reprogramming barriers in vivo needs improvement. We therefore made use of the nematode C. elegans as an in vivo gene discovery tool and interrogated its chromatin-regulating factors for being involved in protecting germ cells against reprogramming to neurons by performing automated RNAi screening. We identified the conserved chromodomain factor MRG-1 (MRG15 in humans) as a barrier for converting germ cells into neurons and characterized its protein-protein and genome interactions using IP-MS and ChIP-seq in wild-type animals versus mutants lacking the germline. We found that MRG-1 associates predominantly with genes carrying active histone modifications but it also cooperates with the histone H3K9 methyltransferase SET-26 in order to prevent conversion of germ cells into neurons. Conserved chromatin regulators such as MRG-1 potentially have similar functions in higher organisms as shown previously for the histone chaperone LIN-53 (CAF-1p48/RBBP7). LIN-53 was initially identified as a barrier of C. elegans germ cell reprogramming and was later shown to also block reprogramming in mammals. Such remarkable conservation of reprogramming barriers illustrates that understanding cell fate protection in C. elegans could help to improve the generation of new cell types for therapeutic approaches in humans.
2019-02-21 | GSE110969 | GEO
Project description:Uncovering novel factors in induced pluripotent stem cells is of great significance for understanding the molecular mechanisms of cell fate determination and advancing somatic cell reprogramming technology. The applicant has, for the first time, discovered that overexpressing RORA significantly enhances somatic cell reprogramming, suggesting that RORA may be one of the key factors in this process. This project aims to investigate the molecular mechanisms by which RORA promotes reprogramming and, based on these findings, establish a more efficient somatic cell reprogramming system. This research is expected to reveal new reprogramming factors and develop a more efficient somatic cell reprogramming system, thereby providing new insights and perspectives for understanding the molecular mechanisms of somatic cell reprogramming and cell fate transition.
2025-09-25 | PXD068806 |
Project description:Epigenetic regulators have important roles during embryonic development as well as somatic cell reprogramming. We previously showed that inhibition of DOT1L, the histone H3 lysine 79 methyltransferase, increases the efficiency of reprogramming via regulation of lineage specific genes. However, the role of DOT1L-interacting proteins in reprogramming remains unknown. In this study, DOT1L interactors were identified using the BioID method in which a promiscuous BirA ligase (BirA*) was employed to biotinylate DOT1L-proximal proteins. The resulting interaction candidates were investigated for their effects on reprogramming. Candidate genes were knocked-down in human fibroblasts via shRNAs followed by reprogramming. Our results indicated that knock-down of AF10 (MLLT10), significantly increased the iPSC generation efficiency, suggesting that it acts as a barrier to reprogramming similar to DOT1L. This finding was verified by CRISPR/Cas9 mediated knockout of AF10. Overexpression of AF10 reversed the effect of AF10 knockout and decreased reprogramming efficiency. To determine how AF10 silencing changes the gene expression, RNA-sequencing was performed on human fibroblasts undergoing reprogramming. AF10 suppression resulted in downregulation of fibroblast-specific genes and accelerated the activation of pluripotency-related genes. Our analysis also demonstrated that silencing of AF10 results in gene expression changes similar to DOT1L inhibition during reprogramming. Taken together, this study uncovered AF10 as a novel barrier to reprogramming and contributed to our understanding of epigenetic mechanisms that maintain cell identity.
2020-11-09 | GSE161043 | GEO
Project description:DOT1L-interacting protein AF10 (MLLT10) is a barrier to somatic cell reprogramming
| PRJNA675353 | ENA
Project description:Automated RNAi screening reveals MRG-1/MRG15 as a barrier for germline to neuron reprogramming in C. elegans
| PRJNA435423 | ENA
Project description:Ash1 is a classic Trithorax group protein possessing an H3K36-specific histone methyltransferase activity. Ash1 plays a critical role in antagonizing Polycomb silencing and its loss-of-function mutations lead to inactivation of certain Hox genes and homeotic transformation. Here, we report the purification of Ash1 complex with the identification of two novel subunits, Mrg15 and Nurf55. Interestingly, Mrg15 stimulates the enzymatic activity of Ash1 in vitro, and such stimulation is independent of the chromo domain of Mrg15. In vivo, Mrg15 is recruited by Ash1 to their common target genes and Mrg15 is essential for the proper deposition of H3K36me2 at these regions.
2017-10-04 | GSE93100 | GEO
Project description:Somatic cells can be directly reprogrammed to pluripotency by exogenous expression of transcription factors, classically Oct4, Sox2, Klf4 and c-Myc. While distinct types of somatic cells can be reprogramed with varying efficiencies and by different modified reprogramming protocols, induced pluripotent stem cell (iPSC) induction remains inefficient and stochastic where a fraction of the cells converts into iPSCs. The nature of rate limiting barrier(s) preventing majority of cells to convert into iPSCs remains elusive. Here we show that neutralizing Mbd3, a core member of the Mbd3/NURD co-repressor and chromatin-remodeling complex, results in deterministic and synchronized reprogramming of multiple differentiated cell types to pluripotency. 100% of Mbd3 depleted mouse and human somatic cells convert into iPSCs after seven days of reprogramming factor induction. Our findings delineate a critical pathway blocking the reestablishment of pluripotency, and offer a novel platform for future dissection of epigenetic dynamics leading to iPSC formation at high resolution. Samples include Mbd3+/+, Mbd3flox/- and Mbd3-/- cells from mouse ES cells and mouse embryonic fibroblast (MEF) before and after DOX induction (initiating reprogramming by OSKM factors).
2013-09-12 | E-GEOD-45352 | biostudies-arrayexpress
Project description:Somatic cells can be directly reprogrammed to pluripotency by exogenous expression of transcription factors, classically Oct4, Sox2, Klf4 and c-Myc. While distinct types of somatic cells can be reprogramed with varying efficiencies and by different modified reprogramming protocols, induced pluripotent stem cell (iPSC) induction remains inefficient and stochastic where a fraction of the cells converts into iPSCs. The nature of rate limiting barrier(s) preventing majority of cells to convert into iPSCs remains elusive. Here we show that neutralizing Mbd3, a core member of the Mbd3/NURD co-repressor and chromatin-remodeling complex, results in deterministic and synchronized reprogramming of multiple differentiated cell types to pluripotency. 100% of Mbd3 depleted mouse and human somatic cells convert into iPSCs after seven days of reprogramming factor induction. Our findings delineate a critical pathway blocking the reestablishment of pluripotency, and offer a novel platform for future dissection of epigenetic dynamics leading to iPSC formation at high resolution. Samples include Mbd3+/+, Mbd3flox/- and Mbd3-/- cells from mouse ES cells and mouse embryonic fibroblast (MEF) before and after DOX induction (initiating reprogramming by OSKM factors). Two histone modifications are given: H3K4me3, H3K27me3. In addition binding data of Mbd3 and Mi2B in various stages.
2013-09-12 | E-GEOD-49766 | biostudies-arrayexpress