Genomes and Genes
mouse embryonic stem cells
Summary: PLURIPOTENT STEM CELLS derived from the BLASTOCYST INNER CELL MASS of day 3.5 mouse embryos.
- Wang M, Tang L, Liu D, Ying Q, Ye S. The transcription factor Gbx2 induces expression of Kruppel-like factor 4 to maintain and induce naïve pluripotency of embryonic stem cells. J Biol Chem. 2017;292:17121-17128 pubmed publisher..These findings expand our understanding of the pluripotency control network and may inform the development of culture conditions for improved ESC maintenance and differentiation. ..
- Semba Y, Harada A, Maehara K, Oki S, Meno C, Ueda J, et al. Chd2 regulates chromatin for proper gene expression toward differentiation in mouse embryonic stem cells. Nucleic Acids Res. 2017;45:8758-8772 pubmed publisher..These results suggest that Chd2 is essential in preventing suppressive chromatin formation for developmentally regulated genes and determines subsequent effects on developmental processes in the undifferentiated state. ..
- Díaz Díaz C, Fernandez de Manuel L, Jimenez Carretero D, Montoya M, Claveria C, Torres M. Pluripotency Surveillance by Myc-Driven Competitive Elimination of Differentiating Cells. Dev Cell. 2017;42:585-599.e4 pubmed publisher..In the mouse embryo, cell competition promotes pluripotency maintenance by elimination of primed lineages before gastrulation. The mechanism described here is relevant to mammalian embryo development and induced pluripotency. ..
- Lee C, Peng S, Shen L, Lee C, Du T, Kang M, et al. The Role of N-?-acetyltransferase 10 Protein in DNA Methylation and Genomic Imprinting. Mol Cell. 2017;68:89-103.e7 pubmed publisher..Our study thus links Naa10p mutation-associated Ogden syndrome to defective DNA methylation and genomic imprinting. ..
- Aldiri I, Xu B, Wang L, Chen X, Hiler D, Griffiths L, et al. The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis. Neuron. 2017;94:550-568.e10 pubmed publisher..The epigenome of retinoblastomas was more similar to that of the normal retina than that of retina-derived iPSCs, and we identified retina-specific epigenetic memory. ..
- Zhou F, Xie F, Jin K, Zhang Z, Clerici M, Gao R, et al. USP4 inhibits SMAD4 monoubiquitination and promotes activin and BMP signaling. EMBO J. 2017;36:1623-1639 pubmed publisher..An increase in monoubiquitinated SMAD4 in USP4-depleted mouse embryonic stem cells (mESCs) decreased both the BMP- and activin-induced changes in the embryonic stem cell fate...
- Tani H, Takeshita J, Aoki H, Nakamura K, Abe R, Toyoda A, et al. Identification of RNA biomarkers for chemical safety screening in mouse embryonic stem cells using RNA deep sequencing analysis. PLoS ONE. 2017;12:e0182032 pubmed publisher..We used undifferentiated mouse embryonic stem cells (mESCs) as a simplified cell-based toxicity assay...
- Donato V, Bonora M, Simoneschi D, Sartini D, Kudo Y, Saraf A, et al. The TDH-GCN5L1-Fbxo15-KBP axis limits mitochondrial biogenesis in mouse embryonic stem cells. Nat Cell Biol. 2017;19:341-351 pubmed publisherSelf-renewing naive mouse embryonic stem cells (mESCs) contain few mitochondria, which increase in number and volume at the onset of differentiation. KBP (encoded by Kif1bp) is an interactor of the mitochondrial-associated kinesin Kif1B?...
- Stevens T, Lando D, Basu S, Atkinson L, Cao Y, Lee S, et al. 3D structures of individual mammalian genomes studied by single-cell Hi-C. Nature. 2017;544:59-64 pubmed publisher..By studying genes regulated by pluripotency factor and nucleosome remodelling deacetylase (NuRD), we illustrate how the determination of single-cell genome structure provides a new approach for investigating biological processes. ..
- Beagrie R, Scialdone A, Schueler M, Kraemer D, Chotalia M, Xie S, et al. Complex multi-enhancer contacts captured by genome architecture mapping. Nature. 2017;543:519-524 pubmed publisher..We apply GAM to mouse embryonic stem cells and identify enrichment for specific interactions between active genes and enhancers across very large ..
- Aherrahrou R, Aherrahrou Z, Schunkert H, Erdmann J. Coronary artery disease associated gene Phactr1 modulates severity of vascular calcification in vitro. Biochem Biophys Res Commun. 2017;491:396-402 pubmed publisher..Taken together, we demonstrated that PHACTR1 gene expression increases with the progression of calcification and that regulation of PHACTR1 in SMCs modulates the severity of vascular calcification. ..
- Wang Y, Fan C, Zheng Y, Li C. Dynamic chromatin accessibility modeled by Markov process of randomly-moving molecules in the 3D genome. Nucleic Acids Res. 2017;45:e85 pubmed publisher..We conclude that SSD is a novel and better measure of dynamic chromatin activity and accessibility. ..
- Maddalena L, Selim S, Fonseca J, Messner H, McGowan S, Stuart J. Hydrogen peroxide production is affected by oxygen levels in mammalian cell culture. Biochem Biophys Res Commun. 2017;493:246-251 pubmed publisher..Together, these observations indicate the importance, and difficulty, of regulating oxygen levels experienced by cells in culture. ..
- Ha M, Hong S. Gene-regulatory interactions in embryonic stem cells represent cell-type specific gene regulatory programs. Nucleic Acids Res. 2017;45:10428-10435 pubmed publisher..Our new approach expands our understanding of the differential gene regulatory information in developments encoded in regulatory networks of ESCs...
- Ukai H, Kiyonari H, Ueda H. Production of knock-in mice in a single generation from embryonic stem cells. Nat Protoc. 2017;12:2513-2530 pubmed publisher..In this report, we describe the basic technologies and protocols for this procedure, and discuss the current challenges for next-generation mammalian genetics in organism-level systems biology studies...
- Afouda B, Lynch A, de Paiva Alves E, Hoppler S. Genome-wide transcriptomics analysis identifies sox7 and sox18 as specifically regulated by gata4 in cardiomyogenesis. Dev Biol. 2018;434:108-120 pubmed publisher..In order to test for conservation in mammalian cardiomyogenesis, we confirmed in mouse embryonic stem cells (ESCs) undergoing cardiomyogenesis that knockdown of Gata4 leads to reduced Sox7 (and Sox18) expression ..
- Waisman A, Vázquez Echegaray C, Solari C, Cosentino M, Martyn I, Deglincerti A, et al. Inhibition of Cell Division and DNA Replication Impair Mouse-Naïve Pluripotency Exit. J Mol Biol. 2017;429:2802-2815 pubmed publisher..act as "windows of opportunity" for changes in cell identity, we established synchronized cultures of mouse embryonic stem cells as they exit the ground state of pluripotency...
- Oh J, Kim G, Kim S, Lee S. Antofine, a natural phenanthroindolizidine alkaloid, suppresses angiogenesis via regulation of AKT/mTOR and AMPK pathway in endothelial cells and endothelial progenitor cells derived from mouse embryonic stem cells. Food Chem Toxicol. 2017;107:201-207 pubmed publisher..The underlying mechanism of anti-angiogenic activity of antofine was, in part, associated with the modulation of AKT/mTOR and AMP-activated protein kinase (AMPK) signaling in VEGF-stimulated HUVECs. ..
- Neri F, Rapelli S, Krepelova A, Incarnato D, Parlato C, Basile G, et al. Intragenic DNA methylation prevents spurious transcription initiation. Nature. 2017;543:72-77 pubmed publisher..Here we show that, in mouse embryonic stem cells, Dnmt3b-dependent intragenic DNA methylation protects the gene body from spurious RNA polymerase II ..
- Chumarina M, Azevedo C, Bigarreau J, Vignon C, Kim K, Li J, et al. Derivation of mouse embryonic stem cell lines from tyrosine hydroxylase reporter mice crossed with a human SNCA transgenic mouse model of Parkinson's disease. Stem Cell Res. 2017;19:17-20 pubmed publisher..These mESC lines can help to study the impact of human aSYN expression in neurons and oligodendrocytes, and also trace GFP-expressing midbrain neurons. ..
- Wei M, Li S, Yang Z, Zheng W, Le W. Gold nanoparticles enhance the differentiation of embryonic stem cells into dopaminergic neurons via mTOR/p70S6K pathway. Nanomedicine (Lond). 2017;12:1305-1317 pubmed publisherThis study aimed to investigate the effect of gold nanoparticles (AuNPs) on differentiation of mouse embryonic stem cells (ESCs) into dopaminergic (DA) neurons and explore the possible underlying molecular mechanisms...
- Lee B, Lee J, Shen W, Rhee C, Chung H, Kim J. Fbxl19 recruitment to CpG islands is required for Rnf20-mediated H2B mono-ubiquitination. Nucleic Acids Res. 2017;45:7151-7166 pubmed publisher..Altogether, our results demonstrate that Fbxl19 recruitment to CpG islands is required for Rnf20-mediated H2B mono-ubiquitination. ..
- Wongpaiboonwattana W, Stavridis M. Neural differentiation of mouse embryonic stem cells in serum-free monolayer culture. J Vis Exp. 2015;:e52823 pubmed publisherThe ability to differentiate mouse embryonic stem cells (ESC) to neural progenitors allows the study of the mechanisms controlling neural specification as well as the generation of mature neural cell types for further study...
- Ebeid M, Sripal P, Pecka J, Beisel K, Kwan K, Soukup G. Transcriptome-wide comparison of the impact of Atoh1 and miR-183 family on pluripotent stem cells and multipotent otic progenitor cells. PLoS ONE. 2017;12:e0180855 pubmed publisher..family and/or Atoh1 that was used to transfect two different developmental cell models: pluripotent mouse embryonic stem cells (mESCs) and immortalized multipotent otic progenitor (iMOP) cells representing an advanced developmental ..
- Wang A, Juan A, Ko K, Tsai P, Zare H, Dell Orso S, et al. The Elongation Factor Spt6 Maintains ESC Pluripotency by Controlling Super-Enhancers and Counteracting Polycomb Proteins. Mol Cell. 2017;68:398-413.e6 pubmed publisher..Thus, in addition to serving as a histone chaperone and transcription elongation factor, Spt6 counteracts repression by opposing H3K27me3 deposition at critical genomic regulatory regions. ..
- Kazemier H, Paeschke K, Lansdorp P. Guanine quadruplex monoclonal antibody 1H6 cross-reacts with restrained thymidine-rich single stranded DNA. Nucleic Acids Res. 2017;45:5913-5919 pubmed publisher..Cross-reactivity of 1H6 to immobilized single stranded T-rich DNA next to its previously reported specificity for bona fide G4 structures needs to be taken into account in the interpretation of 1H6 binding to (sub-) cellular structures. ..
- Zhang P, Rausch C, Hastert F, Boneva B, Filatova A, Patil S, et al. Methyl-CpG binding domain protein 1 regulates localization and activity of Tet1 in a CXXC3 domain-dependent manner. Nucleic Acids Res. 2017;45:7118-7136 pubmed publisher..Our study provides new insights on how cytosine modifications, their modifiers and readers cross-regulate themselves. ..
- Matsuda K, Mikami T, Oki S, Iida H, Andrabi M, Boss J, et al. ChIP-seq analysis of genomic binding regions of five major transcription factors highlights a central role for ZIC2 in the mouse epiblast stem cell gene regulatory network. Development. 2017;144:1948-1958 pubmed publisher..3) The binding sites for SOX2 and POU5F1 in mouse embryonic stem cells (ESCs) and EpiSCs are divergent, reflecting the shift in the major acting TFs from SOX2/POU5F1 in ESCs ..
- Havrilak J, Melton K, Shannon J. Endothelial cells are not required for specification of respiratory progenitors. Dev Biol. 2017;427:93-105 pubmed publisher..5 Flk-/- embryos is likely due to developmental delay resulting from the insufficient delivery of oxygen, nutrients, and other factors in the absence of a vasculature. ..
- Miyauchi H, Ohta H, Nagaoka S, Nakaki F, Sasaki K, Hayashi K, et al. Bone morphogenetic protein and retinoic acid synergistically specify female germ-cell fate in mice. EMBO J. 2017;36:3100-3119 pubmed publisher..Our findings represent a framework for a comprehensive delineation of the sex-determination pathway in mammalian germ cells, including humans. ..
- Shradhanjali A, Riehl B, Lee J, Ha L, Lim J. Enhanced cardiomyogenic induction of mouse pluripotent cells by cyclic mechanical stretch. Biochem Biophys Res Commun. 2017;488:590-595 pubmed publisher..Combined data suggest that stretch loading may serve as a potent trigger to induce functional CM development in both beating dynamics and genomic development, which is still a challenge for myocardial regenerative medicine. ..
- Nagano T, Lubling Y, Várnai C, Dudley C, Leung W, Baran Y, et al. Cell-cycle dynamics of chromosomal organization at single-cell resolution. Nature. 2017;547:61-67 pubmed publisher..Our single-cell data therefore allow re-interpretation of chromosome conformation maps through the prism of the cell cycle. ..