Unique regulation of cis-regulatory elements facilitates reacquisition of pluripotency [ChIP-seq]
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE117203 | GEO | 2019/09/19
REPOSITORIES: GEO
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Project description:Ectopic expression of selected transcription factors enables reprogramming of somatic cells to pluripotency. Despite steady progress in the field the exact molecular mechanisms that coordinate this remarkable transition remain still largely elusive. To better understand the final steps during the acquisition of pluripotency, we optimized an experimental system where cells exit pluripotency and then are systematically challenged to reacquire pluripotency. Using this approach we identify a transient period of deterministic reprogramming during which cells exposed to ectopic transcription factors, but not serum/LIF alone, revert to pluripotency with near 100% efficiency before approaching somatic kinetics (1-2 weeks) and efficiencies (1-2%). Investigation of the transient phase reveals unique molecular dynamics that point to a set of cis-regulatory elements that appear central to facilitating reprogramming. Interestingly, these regions retain an epigenetic signature during in vitro and in vivo differentiation and may act as primary targets of ectopically induced factors during somatic cell reprogramming.
2019-09-19 | GSE117204 | GEO
Project description:Ectopic expression of selected transcription factors enables reprogramming of somatic cells to pluripotency. Despite steady progress in the field the exact molecular mechanisms that coordinate this remarkable transition remain still largely elusive. To better understand the final steps during the acquisition of pluripotency, we optimized an experimental system where cells exit pluripotency and then are systematically challenged to reacquire pluripotency. Using this approach we identify a transient period of deterministic reprogramming during which cells exposed to ectopic transcription factors, but not serum/LIF alone, revert to pluripotency with near 100% efficiency before approaching somatic kinetics (1-2 weeks) and efficiencies (1-2%). Investigation of the transient phase reveals unique molecular dynamics that point to a set of cis-regulatory elements that appear central to facilitating reprogramming. Interestingly, these regions retain an epigenetic signature during in vitro and in vivo differentiation and may act as primary targets of ectopically induced factors during somatic cell reprogramming.
2019-09-19 | GSE117202 | GEO
Project description:Ageing is the gradual decline in organismal fitness that occurs over time leading to tissue dysfunction and disease. At the cellular level, ageing is associated with reduced function, altered gene expression and a perturbed epigenome. Somatic cell reprogramming, the process of converting somatic cells to induced pluripotent stem cells (iPSCs), can reverse these age-associated changes. However, during iPSC reprogramming somatic cell identity is lost, and can be difficult to reacquire as re-differentiated iPSCs often resemble foetal rather than mature adult cells. Recent work has demonstrated that the epigenome is already rejuvenated by the maturation phase of reprogramming, which suggests full iPSC reprogramming is not required to reverse ageing of somatic cells. Here we have developed the first “maturation phase transient reprogramming” (MPTR) method, where reprogramming factors are expressed until this rejuvenation point followed by withdrawal of their induction. Using dermal fibroblasts from middle age donors, we found that cells reacquire their fibroblast identity following MPTR, possibly as a result of persisting epigenetic memory at enhancers. Excitingly, our method substantially rejuvenated multiple cellular attributes including the transcriptome, which was rejuvenated by around 30 years as measured by a novel transcriptome clock. The epigenome, including H3K9me3 histone methylation levels and the DNA methylation ageing clock, was rejuvenated to a similar extent. MPTR fibroblasts produced youthful levels of collagen proteins, suggesting functional rejuvenation. Overall, our work demonstrates that it is possible to separate rejuvenation from pluripotency reprogramming, which should facilitate the discovery of novel anti-ageing genes and therapies.
2022-04-19 | GSE165177 | GEO
Project description:Ageing is the gradual decline in organismal fitness that occurs over time leading to tissue dysfunction and disease. At the cellular level, ageing is associated with reduced function, altered gene expression and a perturbed epigenome. Somatic cell reprogramming, the process of converting somatic cells to induced pluripotent stem cells (iPSCs), can reverse these age-associated changes. However, during iPSC reprogramming somatic cell identity is lost, and can be difficult to reacquire as re-differentiated iPSCs often resemble foetal rather than mature adult cells. Recent work has demonstrated that the epigenome is already rejuvenated by the maturation phase of reprogramming, which suggests full iPSC reprogramming is not required to reverse ageing of somatic cells. Here we have developed the first “maturation phase transient reprogramming” (MPTR) method, where reprogramming factors are expressed until this rejuvenation point followed by withdrawal of their induction. Using dermal fibroblasts from middle age donors, we found that cells reacquire their fibroblast identity following MPTR, possibly as a result of persisting epigenetic memory at enhancers. Excitingly, our method substantially rejuvenated multiple cellular attributes including the transcriptome, which was rejuvenated by around 30 years as measured by a novel transcriptome clock. The epigenome, including H3K9me3 histone methylation levels and the DNA methylation ageing clock, was rejuvenated to a similar extent. MPTR fibroblasts produced youthful levels of collagen proteins, suggesting functional rejuvenation. Overall, our work demonstrates that it is possible to separate rejuvenation from pluripotency reprogramming, which should facilitate the discovery of novel anti-ageing genes and therapies.
2022-04-19 | GSE165176 | GEO
Project description:Ageing is the gradual decline in organismal fitness that occurs over time leading to tissue dysfunction and disease. At the cellular level, ageing is associated with reduced function, altered gene expression and a perturbed epigenome. Somatic cell reprogramming, the process of converting somatic cells to induced pluripotent stem cells (iPSCs), can reverse these age-associated changes. However, during iPSC reprogramming somatic cell identity is lost, and can be difficult to reacquire as re-differentiated iPSCs often resemble foetal rather than mature adult cells. Recent work has demonstrated that the epigenome is already rejuvenated by the maturation phase of reprogramming, which suggests full iPSC reprogramming is not required to reverse ageing of somatic cells. Here we have developed the first “maturation phase transient reprogramming” (MPTR) method, where reprogramming factors are expressed until this rejuvenation point followed by withdrawal of their induction. Using dermal fibroblasts from middle age donors, we found that cells reacquire their fibroblast identity following MPTR, possibly as a result of persisting epigenetic memory at enhancers. Excitingly, our method substantially rejuvenated multiple cellular attributes including the transcriptome, which was rejuvenated by around 30 years as measured by a novel transcriptome clock. The epigenome, including H3K9me3 histone methylation levels and the DNA methylation ageing clock, was rejuvenated to a similar extent. MPTR fibroblasts produced youthful levels of collagen proteins, suggesting functional rejuvenation. Overall, our work demonstrates that it is possible to separate rejuvenation from pluripotency reprogramming, which should facilitate the discovery of novel anti-ageing genes and therapies.
2022-04-19 | GSE165179 | GEO
Project description:Ageing is the gradual decline in organismal fitness that occurs over time leading to tissue dysfunction and disease. At the cellular level, ageing is associated with reduced function, altered gene expression and a perturbed epigenome. Somatic cell reprogramming, the process of converting somatic cells to induced pluripotent stem cells (iPSCs), can reverse these age-associated changes. However, during iPSC reprogramming somatic cell identity is lost, and can be difficult to reacquire as re-differentiated iPSCs often resemble foetal rather than mature adult cells. Recent work has demonstrated that the epigenome is already rejuvenated by the maturation phase of reprogramming, which suggests full iPSC reprogramming is not required to reverse ageing of somatic cells. Here we have developed the first “maturation phase transient reprogramming” (MPTR) method, where reprogramming factors are expressed until this rejuvenation point followed by withdrawal of their induction. Using dermal fibroblasts from middle age donors, we found that cells reacquire their fibroblast identity following MPTR, possibly as a result of persisting epigenetic memory at enhancers. Excitingly, our method substantially rejuvenated multiple cellular attributes including the transcriptome, which was rejuvenated by around 30 years as measured by a novel transcriptome clock. The epigenome, including H3K9me3 histone methylation levels and the DNA methylation ageing clock, was rejuvenated to a similar extent. MPTR fibroblasts produced youthful levels of collagen proteins, suggesting functional rejuvenation. Overall, our work demonstrates that it is possible to separate rejuvenation from pluripotency reprogramming, which should facilitate the discovery of novel anti-ageing genes and therapies.
2022-04-19 | GSE165178 | GEO
Project description:Somatic cell reprogramming into pluripotent stem cells (iPSC) through the forced expression of defined factors induces changes in genome architecture reflective of the embryonic stem cell state. However, only a small minority of cells typically transition to pluripotency, which has limited our understanding of what defines cells that successfully reprogram. Here, we characterize the changes that occur across the DNA regulatory landscape during reprogramming by time-course profiling of isolated sub-populations of reprogramming intermediates poised to become iPSC. Widespread reconfiguration of chromatin states and transcription factor occupancy occurs early during reprogramming, and cells that fail to reprogram partially retain regulatory elements active in their somatic cell state. A second wave of reconfiguration occurs just prior to cells achieving pluripotency, where a majority of early changes revert to the somatic cell state and many of the changes that define the pluripotent state become established. Our comprehensive characterization of the molecular changes that occur during reprogramming broaden our understanding of the reprogramming process by providing crucial insights into iPSC generation, and shed light on how transcription factors in general access and change the chromatin during cell fate transitions.
2017-12-06 | GSE101905 | GEO
Project description:Spermatogonial stem cells (SSCs) can spontaneously dedifferentiate into embryonic stem cell (ESC)-like cells, which are designated as multipotent SSCs (mSSCs), without ectopic expression of reprogramming factors. SSCs express key OSKM reprogramming factors at some levels, and do not require ectopic expression of any gene for the acquisition of pluripotency during reprogramming to mSSCs. Therefore, we reasoned that additional factors are required to regulate SSC reprogramming. In this study, we first compared the expression of reprogramming signature genes among somatic cells, iPSC, SSCs, mSSCs, and partially reprogramed cells, and found that they appear to have similar pluripotency states, whereas their transcriptional program differs. We developed a systems biology approach to prioritise genes for pluripotency regulatory factors by integrating transcriptome and interactome data on the genome-wide functional network. Then, we performed a series of systematic gene prioritisation steps and identified 53 candidates, which included some known reprogramming factors. We experimentally validated one particular candidate, Positive cofactor 4 (Pc4), which was expressed in PSCs and yielded a positive RNA interference (RNAi) response in an Oct4 reporter assay. We demonstrated that Pc4 enhanced the efficiency of OSKM-mediated reprogramming by promoting the transcriptional activity of key pluripotency factors, and by regulating the expression of many protein- and miRNA-encoding genes involved in reprogramming and somatic cell-specific genes. Pc4-overexpressing mESC lines were established by Venus (YFP)-expressing lentiviral transfection. The mESCs were split at a density of 2 ´ 104 cells onto fresh MEF feeder cells seeded into a 6 well dish (containing mESC growth medium) with virus particles, and 25 μg/ml polybrene (Sigma Aldrich) was added. After 24 h, the medium was replaced with fresh growth medium. After 4 days later, mESC colonies expressing YFP were picked and replated. Three different Pc4-overexpressing mESC lines were established.
2015-10-30 | E-GEOD-74149 | biostudies-arrayexpress
Project description:Pluripotency can be induced in somatic cells by ectopic expression of defined transcription factors, however the identity of epigenetic regulators driving the progression of cellular reprogramming requires further investigation. Here we uncover a non-redundant role for the JmjC-domain-containing protein histone H3 methylated Lys 27 (H3K27) demethylase Utx, as a critical regulator for the induction, but not for the maintenance, of primed and naM-CM-/ve pluripotency in mice and in humans. Utx depletion results in aberrant H3K27me3 repressive chromatin demethylation dynamics, which subsequently hampers the reactivation of pluripotency promoting genes during reprogramming. Remarkably, Utx deficient primordial germ cells (PGCs) display a cell autonomous aberrant epigenetic reprogramming in vivo during their embryonic maturation, resulting in the lack of functional contribution to the germ-line lineage. Samples include UTX+/Y (WT) and UTX-/Y (KO) cells from mouse ES cells and mouse embryonic fibroblast (MEF) before and after DOX induction (initiating reprogramming by OSKM factors). One sample is OSKM-induced Nanog-/- fibroblasts.
2012-05-29 | E-GEOD-35775 | biostudies-arrayexpress