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Klf5 confers embryonic and extra-embryonic bi-potential cell fate in early blastomeres and embryonic stem cells

ABSTRACT: Klf5 confers embryonic and extra-embryonic bi-potential cell fate in early blastomeres and embryonic stem cells

PROVIDER: PRJNA771686 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16356305.fastq.gz	Fastqsanger.gz
	SRR16356306.fastq.gz	Fastqsanger.gz
	SRR16356307.fastq.gz	Fastqsanger.gz
	SRR16356308.fastq.gz	Fastqsanger.gz
	SRR16356309_1.fastq.gz	Fastqsanger.gz

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Klf5 confers embryonic and extra-embryonic bi-potential cell fate in early blastomeres and embryonic stem cells

Project description:Klf5 confers embryonic and extra-embryonic bi-potential cell fate in early blastomeres and embryonic stem cells

| PRJNA564308 | ENA

Klf5 confers embryonic and extra-embryonic bi-potential cell fate in early blastomeres and embryonic stem cells

Project description:This study examines the transcriptomes of embryonic stem cells following overexpression of Klf5. Additionally, this study examines the transcripomes of single embryos either treated with scramble siRNA or siRNA targeting Klf5.

2021-10-20 | GSE186005 | GEO

Klf5 confers embryonic and extra-embryonic bi-potential cell fate in early blastomeres and embryonic stem cells

Project description:This study determines the genome-wide binding profile of a V5-tagged KLF5 transription factor exogenously expressed in mouse embryonic stem cells.

2021-09-22 | GSE137036 | GEO

Derivation of porcine extra-embryonic endoderm cell lines reveals distinct signaling pathway and multipotency states

Project description:We detected the gene expression differences between porcine extra-embryonic endoderm cells and naïve like and primed porcine ESCs. Gene expression of porcine extra-embryonic endoderm cells was distinct with porcine naïve like and primed embryonic stem cells. Pearson correlation analysis confirmed that porcine naïve like and primed ESCs have stronger correlation than the correlation between either pXEN cells and porcine naïve like ESCs or primed ESCs. Porcine extra-embryonic endoderm cells have a distinct identity, clustering neither with porcine naïve like ESCs nor with primed ESCs. We confirmed that porcine extra-embryonic endoderm cells lack the expression of key pluripotency genes, such as Sox2, Pou5f1 and Klf4, but they expressed other pluripotency genes, such as Sall4, Lin28a and Klf5. Furthermore, porcine extra-embryonic endoderm cells robustly express Gata4, Gata6 and Sox17 as well as genes encoding ExEn-associated cell surface proteins or basement membrane components Pdgfra, Col4a2, Lama1, Lamb1, Sparc, Ihh, Hnf4a and Dab2, which is in contrast to porcine naïve like ESCs that express these genes at a low level or lack expression altogether

2021-12-01 | GSE183270 | GEO

Klf5 functions as a multi-lineage reprogramming transcription factor

Project description:The transcription factor Klf5 is indispensable for both embryonic (redundantly with Klf4) and extra-embryonic development during pre-implantation, yet its role in re-establishing these different fates in vitro remains largely unexplored. Here, we demonstrate that in the absence of WNT signaling activation at the beginning, ectopic expression of Klf5 in post-implantation epiblast stem cells (EpiSCs) not only induces naïve pluripotency, but also exclusively drives reprogramming into trophoblast stem cells (TSCs) and primordial germ cells (PGCs) by directly reactivating key lineage-specific determinants. Single-cell transcriptome analysis reveals distinct reprogramming trajectories toward these three fates, alongside a non-reprogramming trajectory that driven by Klf5-mediated BMP signaling activation. Moreover, endogenous Klf5 is crucial for establishing TSC and PGC fates from embryonic stem cells driven by other inducers. Our findings highlight Klf5’s multipotent reprogramming capacity and its pivotal role in early TSC and PGC fate specification, offering new insights into its versatile functions during embryonic development.

2025-06-01 | GSE281941 | GEO

Transcription Factor Co-Expression Mediates Lineage Priming for Embryonic and Extra-Embryonic Differentiation [CUT&RUN]

Project description:In early mammalian development, cleavage stage blastomeres and cells of the inner cell mass (ICM) of the blastocyst co-express embryonic and extra-embryonic transcriptional determinants. Using a double protein-based reporter we identify embryonic stem cells (ESC) that co-express the extra-embryonic factor GATA6 alongside the embryonic factor SOX2 in specific conditions. Based on single cell transcriptomics we find these population resemble unsegregated ICM, exhibiting enhanced differentiation potential for endoderm while maintaining epiblast competence and suggesting they represent an ideal model to determine how GATA6 and SOX2 influence each other's DNA binding. To relate this binding to future fate, we describe a complete enhancer set in both ESCs and naïve extraembryonic endoderm stem cells and ask whether SOX2 and GATA6 recognize these elements in ICM-like ESC sub-population. Both factors support cooperative recognition in these lineages, with GATA6 bound alongside SOX2 on a fraction of pluripotency enhancers and SOX2 alongside GATA6 more extensively on endoderm enhancers. Our findings suggest that cooperative binding between these antagonistic factors both supports self-renewal and prepares progenitor cells for later differentiation

2023-12-05 | GSE227886 | GEO

Dynamic proteomic profiling of extra-embryonic endoderm differentiation in mouse embryonic stem cells

Project description:During mammalian pre-implantation development, the cells of the blastocyst’s inner cell mass differentiate into the epiblast and primitive endoderm lineages, which give rise to the fetus and extra-embryonic tissues, respectively. Extra-embryonic endoderm differentiation can be modeled in vitro by induced expression of GATA transcription factors in mouse embryonic stem cells. Here we use this GATA-inducible system to quantitatively monitor the dynamics of global proteomic changes during the early stages of this differentiation event and also investigate the fully differentiated phenotype, as represented by embryo-derived extra-embryonic endoderm (XEN) cells. Using mass spectrometry-based quantitative proteomic profiling with multivariate data analysis tools, we reproducibly quantified 2,336 proteins across three biological replicates and have identified clusters of proteins characterized by distinct, dynamic temporal abundance profiles. We first used this approach to highlight novel marker candidates of the pluripotent state and extra-embryonic endoderm differentiation. Through functional annotation enrichment analysis, we have shown that the downregulation of chromatin-modifying enzymes, the re-organization of membrane trafficking machinery and the breakdown of cell-cell adhesion are successive steps of the extra-embryonic differentiation process. Thus, applying a range of sophisticated clustering approaches to a time-resolved proteomic dataset has allowed the elucidation of complex biological processes which characterize stem cell differentiation and could establish a general paradigm for the investigation of these processes.

2015-06-13 | PXD001901 | Pride

Identifying targets of Klf2, Klf4, Klf5 and p53 in mouse embryonic stem cells

Project description:This SuperSeries is composed of the following subset Series: GSE9774: Klf2, Klf4, Klf5 and p53 in mouse embryonic stem cells GSE9775: To identify the target genes of Klf2, Klf4 and Klf5 in mouse embryonic stem cells. Keywords: SuperSeries Refer to individual Series

2010-06-25 | E-GEOD-9535 | biostudies-arrayexpress

KLF5 co-immunoprecipitation mass spectrometry

Project description:Lineage plasticity is a hallmark of pancreatic ductal adenocarcinoma (PDAC) and contributes to tumor heterogeneity and therapeutic resistance. Here, we identify KLF5 as a dynamic master regulator of epithelial lineage identity in PDAC, with dichotomous roles in promoting either classical or basal-like transcriptional programs. Through unbiased proteomic and genetic screens, we uncover the AAA+ ATPases RUVBL1 and RUVBL2 as essential coactivators of KLF5 across both lineage states. We demonstrate that ATP hydrolysis by RUVBL1/2 is required for the stable interaction with an intrinsically disordered region of KLF5, enabling its recruitment to lineage-specific enhancers and driving transcriptional regulation of identity-defining genes. Notably, small-molecule inhibitors of RUVBL1/2 ATPase activity, which have anti-PDAC activity in vivo, suppress KLF5-dependent transcription. These findings define a previously unrecognized mechanism of ATP hydrolysis-dependent transcriptional coactivation by AAA+ ATPases and highlight a potential therapeutic strategy for modulating aberrant lineage programs in cancer. This project contains files relative to a Co-IP MS with KLF5-MBP as bait.

2025-08-21 | PXD066112 | Pride

Single-cell mRNA sequencing of embryonic and extra-embryonic mesoderm and extra-embryonic structures in mouse embryo during gastrulation.

Project description:Single-cell mRNA sequencing of embryonic and extra-embryonic mesoderm and extra-embryonic structures in mouse embryo during gastrulation.

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