Continuous expression of reprogramming factors OSKM induces and maintains mouse pluripotency without specific growth factors and signaling inhibitors
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA725708 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14341114_1.fastq.gz | Fastqsanger.gz | |||
| SRR14341114_2.fastq.gz | Fastqsanger.gz | |||
| SRR14341115_1.fastq.gz | Fastqsanger.gz | |||
| SRR14341115_2.fastq.gz | Fastqsanger.gz | |||
| SRR14341116_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 36 |
Similar Datasets
Project description:Derivation and maintenance of pluripotent stem cells (PSCs) including embryonic stem cells(ESCs) and (iPSCs) usually requires optimization of complex culture media, which hinders the generation of PSCs from various species. Expression of Oct4, Sox2, Klf4 and c-Myc (OSKM) can reprogram somatic cells into iPSCs, even for species possessing no optimal culture condition. Here we explored whether expression of OSKM could induce and maintain pluripotency without specific growth factors and signaling inhibitors. Tet-On-OSKM/Oct4-GFP Mouse ESCs (mESCs) were derived from the embryos obtained after mating of Tet-On-OSKM mouse and Oct4-GFP mouse under the 2iL ( N2B27 plus MEK inhibitor PD0325901, GSK3β inhibitor ChIR99021, and leukemia inhibitory factor) condition. Tet-On-OSKM mouse was Gt(ROSA)26Sor tm1(rtTA*M2)Jae Col1a1 tm3(tetO-Pou5f1,-Sox2,-Klf4,-Myc)Jae/J(The Jackson Laboratory,011004), and Oct4-GFP mouse was B6;CBA-Tg(Pou5f1-EGFP)2Mnn/J (The Jackson Laboratory,004654).The culture medium of Tet-On-OSKM/Oct4-GFP mouse ESCs was switched from 2iL to N2B27 plus Doxycycline medium (OSKM medium), under which OSKM trangene was activated. These above cells switched from 2iL to OSKM medium were called OSKM-ESCs. Meanwhile 2iL-ESCs (continuely cultured in 2iL) served as the positive control group. 2iL-ESCs and OSKM-ESCs collected at selective days (d18, 25 and 38) after medium switch were collected for RNA-Seq. Moreover, Tet-On-OSKM mouse embryonic fibroblast (MEF) cells were reprogrammed under OSKM medium (N2B27 plus Doxycycline) and 2iL medium, respectively. The resulting OSKM-iPSCs were reprogrammed and cultured under OSKM medium.The 2iL-iPSCs were reprogrammed under 2iL plus Doxycycline medium and cultured under 2iL medium (without Doxycycline)once clones were picked up.RNA-Seq of these above samples was conducted to analyze gene expression. We found that via continuous expression of OSKM,OSKM-ESCs and OSKM-iPSCs propagated stably, expressed pluripotency marker genes, and formed three germ layers in teratomas. Importantly, OSKM-iPSCs could produce gene-modified animals through germline transmission.Transcriptional landscapes of OSKM-iPSCs resembled 2iL-ESCs, and were more similar to those of ESCs cultured in serum/LIF.
2021-08-24 | GSE173471 | GEO
Project description:Reprogramming cells from one fate to another, using transcription factors, generates cells for research and potential therapy, yet little is known about the initial engagement of reprogramming factors with the genome. We mapped the interactions between Oct4, Sox2, Klf4, and c-Myc (OSKM) and the human genome during the first 48 hours of cellular reprogramming to pluripotency. Unlike that reported in ES/iPS cells, we find extensive overlap in the initial binding of OSKM, demonstrating that the initial regulatory network differs markedly from that in pluripotency. OSK act as pioneer factors for c-Myc, and c-Myc enhances the engagement of OSK, including at many genes that are required for conversion to pluripotency. Distal enhancer sites in closed chromatin dominate the initial OSKM distribution. Hierarchical chromatin binding during reprogramming resembles that employed during development. Four chIP-seq data sets (Oct4, Sox2, Klf4, and c-Myc) are included, one lane per factor, no replicates. Also included is an input lane from the same conditions and two mock lentiviral controls (no exogenous OSKM factors) treated with Oct4 IP and c-Myc IP.
2012-11-16 | E-GEOD-36570 | biostudies-arrayexpress
Project description:Reprogramming cells from one fate to another, using transcription factors, generates cells for research and potential therapy, yet little is known about the initial engagement of reprogramming factors with the genome. We mapped the interactions between Oct4, Sox2, Klf4, and c-Myc (OSKM) and the human genome during the first 48 hours of cellular reprogramming to pluripotency. Unlike that reported in ES/iPS cells, we find extensive overlap in the initial binding of OSKM, demonstrating that the initial regulatory network differs markedly from that in pluripotency. OSK act as pioneer factors for c-Myc, and c-Myc enhances the engagement of OSK, including at many genes that are required for conversion to pluripotency. Distal enhancer sites in closed chromatin dominate the initial OSKM distribution. Hierarchical chromatin binding during reprogramming resembles that employed during development.
2012-11-16 | GSE36570 | GEO
Project description:ObjectivesDerivation and maintenance of pluripotent stem cells (PSCs) generally require optimized and complex culture media, which hinders the derivation of PSCs from various species. Expression of Oct4, Sox2, Klf4, and c-Myc (OSKM) can reprogram somatic cells into induced PSCs (iPSCs), even for species possessing no optimal culture condition. Herein, we explored whether expression of OSKM could induce and maintain pluripotency without PSC-specific growth factors and signaling inhibitors.MethodsThe culture medium of Tet-On-OSKM/Oct4-GFP mouse embryonic stem cells (ESCs) was switched from N2B27 with MEK inhibitor, GSK3β inhibitor, and leukemia inhibitory factor (LIF) (2iL) to N2B27 with doxycycline. Tet-On-OSKM mouse embryonic fibroblast (MEF) cells were reprogrammed in N2B27 with doxycycline. Cell proliferation was traced. Pluripotency was assessed by expression of ESC marker genes, teratoma, and chimera formation. RNA-Seq was conducted to analyze gene expression.ResultsVia continuous expression of OSKM, mouse ESCs (OSKM-ESCs) and the resulting iPSCs (OSKM-iPSCs) reprogrammed from MEF cells propagated stably, expressed pluripotency marker genes, and formed three germ layers in teratomas. Transcriptional landscapes of OSKM-iPSCs resembled those of ESCs cultured in 2iL and were more similar to those of ESCs cultured in serum/LIF. Furthermore, OSKM-iPSCs contributed to germline transmission.ConclusionsExpression of OSKM could induce and maintain mouse pluripotency without specific culturing factors. Importantly, OSKM-iPSCs could produce gene-modified animals through germline transmission, with potential applications in other species.
| S-EPMC8349648 | biostudies-literature
Project description:Ectopic expression of the transcription factors Oct4, Sox2, Klf4 and c-Myc (OSKM) can reprogram somatic cells into induced pluripotent stem cells (iPSCs). These iPSCs are highly similar to embryonic stem cells and can be used for regenerative medicine, drug screening and disease modelling. Despite recent advances, reprogramming is a slow and inefficient process. This suggests that there are several safeguarding mechanisms to counteract cell fate conversion. Cellular senescence is one of these barriers, which is mediated through activation of the tumour suppressors p53/p21CIP1, p15INK4b and p16INK4a. In this study, we have screened for shRNAs blunting reprogramming-induced senescence. To investigate the effects of OSKM expression on the transcriptome of human primary IMR90 fibroblasts, we performed RNA-sequencing (RNA-Seq). Cells were transduced with OSKM expression or control vector and RNA was extracted after 14 or 20 days. In addition, to study the transcriptome of cells bypassing OSKM-induced senescence due to p21 or mTOR depletion, we performed RNA-seq of cells transduced with OSKM and shRNA expressing vectors targeting p21 or mTOR for 14 or 20 days.
2018-02-09 | GSE94928 | GEO
Project description:Recent reports have proposed a new paradigm for obtaining mature somatic cell types from fibroblasts without going through a pluripotent state, by briefly expressing canonical iPSC reprogramming factors Oct4, Sox2, Klf4 and c-Myc (abbreviated as OSKM), in cells expanded in lineage differentiation promoting conditions. Here we apply genetic lineage tracing for endogenous Nanog, Oct4 and X chromosome reactivation during OSKM induced trans-differentiation, as these molecular events mark final stages for acquisition of induced pluripotency. Remarkably, the vast majority of reprogrammed cardiomyocytes or neural stem cells derived from mouse fibroblasts via OSKM mediated trans-differentiation were attained after transient acquisition of pluripotency, and followed by rapid differentiation. Our findings underscore a molecular and functional coupling between inducing pluripotency and obtaining “trans-differentiated” somatic cells via OSKM induction, and have implications on defining molecular trajectories assumed during different cell reprogramming methods. poly RNA-Seq was measured before, during and after conversion of mouse embryonic fibroblasts to neural stem cells using OSKM trans-differentiation method.
2015-04-30 | E-GEOD-67265 | biostudies-arrayexpress
Project description:Recent reports have proposed a new paradigm for obtaining mature somatic cell types from fibroblasts without going through a pluripotent state, by briefly expressing canonical iPSC reprogramming factors Oct4, Sox2, Klf4 and c-Myc (abbreviated as OSKM), in cells expanded in lineage differentiation promoting conditions. Here we apply genetic lineage tracing for endogenous Nanog, Oct4 and X chromosome reactivation during OSKM induced trans-differentiation, as these molecular events mark final stages for acquisition of induced pluripotency. Remarkably, the vast majority of reprogrammed cardiomyocytes or neural stem cells derived from mouse fibroblasts via OSKM mediated trans-differentiation were attained after transient acquisition of pluripotency, and followed by rapid differentiation. Our findings underscore a molecular and functional coupling between inducing pluripotency and obtaining “trans-differentiated” somatic cells via OSKM induction, and have implications on defining molecular trajectories assumed during different cell reprogramming methods. WGBS (Whole-Genome-Bisulfite-sequencing) were measured during conversion of mouse embryonic fibroblasts to neural stem cells using OSKM trans-differentiation method, as well as in mouse emrbyonic fibroblasts, and mouse ESCs.
2015-05-07 | E-GEOD-68601 | biostudies-arrayexpress
Project description:Recent reports have proposed a new paradigm for obtaining mature somatic cell types from fibroblasts without going through a pluripotent state, by briefly expressing canonical iPSC reprogramming factors Oct4, Sox2, Klf4 and c-Myc (abbreviated as OSKM), in cells expanded in lineage differentiation promoting conditions. Here we apply genetic lineage tracing for endogenous Nanog, Oct4 and X chromosome reactivation during OSKM induced trans-differentiation, as these molecular events mark final stages for acquisition of induced pluripotency. Remarkably, the vast majority of reprogrammed cardiomyocytes or neural stem cells derived from mouse fibroblasts via OSKM mediated trans-differentiation were attained after transient acquisition of pluripotency, and followed by rapid differentiation. Our findings underscore a molecular and functional coupling between inducing pluripotency and obtaining “trans-differentiated” somatic cells via OSKM induction, and have implications on defining molecular trajectories assumed during different cell reprogramming methods. poly RNA-Seq and Chromatin accesibility (ATAC-seq) were measured during conversion of mouse embryonic fibroblasts to neural stem cells using OSKM trans-differentiation method, as well as in mouse emrbyonic fibroblasts, iPSCs and mouse ESCs.
2015-04-30 | E-GEOD-67298 | biostudies-arrayexpress
Project description:Recent reports have proposed a new paradigm for obtaining mature somatic cell types from fibroblasts without going through a pluripotent state, by briefly expressing canonical iPSC reprogramming factors Oct4, Sox2, Klf4 and c-Myc (abbreviated as OSKM), in cells expanded in lineage differentiation promoting conditions. Here we apply genetic lineage tracing for endogenous Nanog, Oct4 and X chromosome reactivation during OSKM induced trans-differentiation, as these molecular events mark final stages for acquisition of induced pluripotency. Remarkably, the vast majority of reprogrammed cardiomyocytes or neural stem cells derived from mouse fibroblasts via OSKM mediated trans-differentiation were attained after transient acquisition of pluripotency, and followed by rapid differentiation. Our findings underscore a molecular and functional coupling between inducing pluripotency and obtaining “trans-differentiated” somatic cells via OSKM induction, and have implications on defining molecular trajectories assumed during different cell reprogramming methods.
2015-05-07 | GSE68601 | GEO
Project description:Recent reports have proposed a new paradigm for obtaining mature somatic cell types from fibroblasts without going through a pluripotent state, by briefly expressing canonical iPSC reprogramming factors Oct4, Sox2, Klf4 and c-Myc (abbreviated as OSKM), in cells expanded in lineage differentiation promoting conditions. Here we apply genetic lineage tracing for endogenous Nanog, Oct4 and X chromosome reactivation during OSKM induced trans-differentiation, as these molecular events mark final stages for acquisition of induced pluripotency. Remarkably, the vast majority of reprogrammed cardiomyocytes or neural stem cells derived from mouse fibroblasts via OSKM mediated trans-differentiation were attained after transient acquisition of pluripotency, and followed by rapid differentiation. Our findings underscore a molecular and functional coupling between inducing pluripotency and obtaining “trans-differentiated” somatic cells via OSKM induction, and have implications on defining molecular trajectories assumed during different cell reprogramming methods.
2015-04-30 | GSE67298 | GEO