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YAP1 and QSER1 are Key Modulators of Embryonic Signaling Pathways in the Mammalian Epiblast [scRNA-seq]

ABSTRACT: YAP1 and QSER1 are Key Modulators of Embryonic Signaling Pathways in the Mammalian Epiblast [scRNA-seq]

PROVIDER: PRJNA1180567 | ENA |

REPOSITORIES: ENA

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YAP1 and QSER1 are Key Modulators of Embryonic Signaling Pathways in the Mammalian Epiblast [scRNA-seq]

Project description:The Hippo:YAP1 signaling pathway was long considered a master regulator of organ growth. However, recent evidence has challenged this view, showing that the loss of YAP1 does not prevent several organs from reaching their normal size. Hence, resolving the functions of YAP1 in the embryo has become a central question in the field. To shed light into this, we analyzed YAP1’s role in regulating pluripotency of the mammalian epiblast, using scRNAseq approaches. Conditional deletion of Yap1 in the mouse epiblast (Sox2-Cre) altered the expression of signaling and differentiation genes, including Nodal, Wnt3, Fgf8, and Nanog, without impairing cell proliferation. Instead, Yap1 loss led to hyperactivation of Nodal signaling and enhanced differentiation of the epiblast toward mesodermal fate. Furthermore, an unbiased screening in human pluripotent stem cells revealed that YAP1 transcriptionally cooperates with QSER1 protein, to regulate multiple WNT and NODAL signaling genes. Mechanistically, QSER1 represses lineage enhancers of signaling genes by counteracting RNA Polymerase II recruitment on YAP1-targets. Accordingly, QSER1 depletion, similar to YAP1, leads to hyperactive Nodal signaling in human 2D-gastruloids. Overall, our findings not only advance our understanding of YAP1’s role in early development but also open new avenues for exploring how the interplay with QSER1 could influence additional developmental processes.

2025-07-31 | GSE280804 | GEO

YAP1 and QSER1 are Key Modulators of Embryonic Signaling Pathways in the Mammalian Epiblast [ChIP-seq]

2025-07-31 | GSE280805 | GEO

YAP1 and QSER1 are Key Modulators of Embryonic Signaling Pathways in the Mammalian Epiblast [ChIP-seq]

Project description:YAP1 and QSER1 are Key Modulators of Embryonic Signaling Pathways in the Mammalian Epiblast [ChIP-seq]

| PRJNA1180568 | ENA

RNA Sequencing of H1 WT hESCs, H1 QSER1 KO hESCs, H1 TET1 KO hESCs, H1 QSER1/TET1 DKO hESCs, WT Day10 EBs, QSER1 KO Day10 EBs, TET1 KO Day10 EBs, QSER1/TET1 DKO Day10 EBs, WT PP1, QSER1 KO PP1, TET1 KO PP1, and QSER1/TET1 DKO PP1.

Project description:RNA Sequencing of H1 WT hESCs, H1 QSER1 KO hESCs, H1 TET1 KO hESCs, H1 QSER1/TET1 DKO hESCs, WT Day10 embryoid bodies (EBs), QSER1 KO Day10 EBs, TET1 KO Day10 EBs, QSER1/TET1 DKO Day10 EBs, WT pancreatic progenitors (PP1), QSER1 KO PP1, TET1 KO PP1, and QSER1/TET1 DKO PP1. DNA methylation is essential to mammalian development, and dysregulation can cause serious pathological conditions. Key enzymes responsible for deposition and removal of DNA methylation are known, but how they cooperate to tightly regulate the methylation landscape remains a central question. Utilizing a knockin DNA methylation reporter, we performed a genome-wide CRISPR/Cas screen in human embryonic stem cells to discover DNA methylation regulators. The top screen hit was an uncharacterized gene QSER1, which proved to be a key guardian of bivalent promoters and poised enhancers of developmental genes, especially those residing in DNA methylation valleys (or canyons). We further demonstrate cooperation of QSER1 and TET1 through genetic and biochemical interactions to inhibit DNMT3-mediated de novo methylation and safeguard developmental programs.

2021-03-19 | GSE169209 | GEO

Functional analysis QSER1

Project description:Functional analysis QSER1

| PRJNA747710 | ENA

Functional analysis QSER1

Project description:In this study, we found that QSER1 is a generic anti-apoptosis factor suppressing the p53 target apoptotic genes irrespective of p53 status.

2023-06-07 | GSE180299 | GEO

Methyl capture sequencing (Truseq Epic from Illumina) of H1 WT, H1 QSER1 KO, H1 TET1 KO, H1 DNMT3B KO, H1 QSER1 KOpm (passaged matched with DKOs), H1 QSER1/TET1 DKO, and H1 QSER1/DNMT3B DKO hESCs

Project description:DNA methylation is essential to mammalian development, and dysregulation can cause serious pathological conditions. Key enzymes responsible for deposition and removal of DNA methylation are known, but how they cooperate to tightly regulate the methylation landscape remains a central question. Utilizing a knockin DNA methylation reporter, we performed a genome-wide CRISPR/Cas screen in human embryonic stem cells to discover DNA methylation regulators. The top screen hit was an uncharacterized gene QSER1, which proved to be a key guardian of bivalent promoters and poised enhancers of developmental genes, especially those residing in DNA methylation valleys (or canyons). We further demonstrate cooperation of QSER1 and TET1 through genetic and biochemical interactions to inhibit DNMT3-mediated de novo methylation and safeguard developmental programs.

2021-03-19 | GSE169208 | GEO

Project description:RNA Sequencing of H1 WT hESCs, H1 QSER1 KO hESCs, H1 TET1 KO hESCs, H1 QSER1/TET1 DKO hESCs, WT Day10 EBs, QSER1 KO Day10 EBs, TET1 KO Day10 EBs, QSER1/TET1 DKO Day10 EBs, WT PP1, QSER1 KO PP1, TET1 KO PP1, and QSER1/TET1 DKO PP1.

| PRJNA715661 | ENA

Regulation of gene expression by YAP1

Project description:In order to define YAP1-specific gene expression patterns in gastric cancer, the constitutively active mutant YAP1 (YAP1-S127A) was over-expressed in MKN45 gastric cancer cells. Defined gene expression signature was later used to stratify gastric cancer patients according to the presence of the YAP1-activated signature. Three groups of samples are included: 1. Mock control; 2. Vector control; 3. YAP-S127A expression. Gene expression profiles of YAP-S127A mutant-expressing cells were compared to that of mock and vector control. Experiments were done in MKN45 gastric cancer cells.

2013-10-01 | E-GEOD-41387 | biostudies-arrayexpress

Methyl capture sequencing (Truseq Epic from Illumina) of H1 WT, H1 QSER1 KO, H1 TET1 KO, H1 DNMT3B KO, H1 QSER1 KOpm (passaged matched with DKOs), H1 QSER1/TET1 DKO, and H1 QSER1/DNMT3B DKO hESCs

Project description:Methyl capture sequencing (Truseq Epic from Illumina) of H1 WT, H1 QSER1 KO, H1 TET1 KO, H1 DNMT3B KO, H1 QSER1 KOpm (passaged matched with DKOs), H1 QSER1/TET1 DKO, and H1 QSER1/DNMT3B DKO hESCs

| PRJNA715660 | ENA

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