Mouse embryonic stem (ES) cells grown in serum exhibit greater heterogeneity in morphology and expression of pluripotency factors than ES cells cultured in defined medium with inhibitors of two kinases (Mek and GSK3), a condition known as "2i" postulated to establish a naive ground state. We show that the transcriptome and epigenome profiles of serum- and 2i-grown ES cells are distinct. 2i-treated cells exhibit lower expression of lineage-affiliated genes, reduced prevalence at promoters of the repressive histone modification H3K27me3, and fewer bivalent domains, which are thought to mark genes poised for either up- or downregulation. Nonetheless, serum- and 2i-grown ES cells have similar differentiation potential. Precocious transcription of developmental genes in 2i is restrained by RNA polymerase II promoter-proximal pausing. These findings suggest that transcriptional potentiation and a permissive chromatin context characterize the ground state and that exit from it may not require a metastable intermediate or multilineage priming.
BMP induction of Id proteins suppresses differentiation and sustains embryonic stem cell self-renewal in collaboration with STAT3
FGF stimulation of the Erk1/2 signalling cascade triggers transition of pluripotent embryonic stem cells from self-renewal to lineage commitment
Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells
Up-regulation of P-TEFb by the MEK1-extracellular signal-regulated kinase signaling pathway contributes to stimulated transcription elongation of immediate early genes in neuroendocrine cells
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology
Drosophila Kismet regulates histone H3 lysine 27 methylation and early elongation by RNA polymerase II
Dynamic equilibrium and heterogeneity of mouse pluripotent stem cells with distinct functional and epigenetic states
Eset partners with Oct4 to restrict extraembryonic trophoblast lineage potential in embryonic stem cells
Three inhibitors of FGF receptor, ERK, and GSK3 establishes germline-competent embryonic stem cells of C57BL/6N mouse strain with high efficiency and stability
Identification of a hormone-regulated dynamic nuclear actin network associated with estrogen receptor alpha in human breast cancer cell nuclei.
Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst
Human embryonic stem cells with biological and epigenetic characteristics similar to those of mouse ESCs
Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis
Functional heterogeneity of embryonic stem cells revealed through translational amplification of an early endodermal transcript
Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation
Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation
Phosphorylation of the PRC2 component Ezh2 is cell cycle-regulated and up-regulates its binding to ncRNA
Sequence-specific regulator Prdm14 safeguards mouse ESCs from entering extraembryonic endoderm fates
Inhibition of glycogen synthase kinase-3 alleviates Tcf3 repression of the pluripotency network and increases embryonic stem cell resistance to differentiation
Rapid and efficient reprogramming of somatic cells to induced pluripotent stem cells by retinoic acid receptor gamma and liver receptor homolog 1
Vitamin C facilitates pluripotent stem cell maintenance by promoting pluripotency gene transcription
PRDM14 ensures naive pluripotency through dual regulation of signaling and epigenetic pathways in mouse embryonic stem cells
Bivalent promoter marks and a latent enhancer may prime the leukaemia oncogene LMO1 for ectopic expression in T-cell leukaemia
PRMT5-mediated histone H4 arginine-3 symmetrical dimethylation marks chromatin at G + C-rich regions of the mouse genome
MYC/MAX control ERK signaling and pluripotency by regulation of dual-specificity phosphatases 2 and 7
The non-coding snRNA 7SK controls transcriptional termination, poising, and bidirectionality in embryonic stem cells
Single cell visualization of yeast gene expression shows correlation of epigenetic switching between multiple heterochromatic regions through multiple generations
A genome-wide RNAi screen reveals MAP kinase phosphatases as key ERK pathway regulators during embryonic stem cell differentiation
Global and stage specific patterns of Krüppel-associated-box zinc finger protein gene expression in murine early embryonic cells
Identification of a novel gene signature of ES cells self-renewal fluctuation through system-wide analysis
Striking similarity in the gene expression levels of individual Myc module members among ESCs, EpiSCs, and partial iPSCs
Efficient reprogramming of naïve-like induced pluripotent stem cells from porcine adipose-derived stem cells with a feeder-independent and serum-free system
Cell Cycle-Driven Heterogeneity: On the Road to Demystifying the Transitions between "Poised" and "Restricted" Pluripotent Cell States
High-throughput sequencing reveals the disruption of methylation of imprinted gene in induced pluripotent stem cells
The ability of inner-cell-mass cells to self-renew as embryonic stem cells is acquired following epiblast specification
FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells
Identification of Ccr4-not complex components as regulators of transition from partial to genuine induced pluripotent stem cells
Aneuploidy induces profound changes in gene expression, proliferation and tumorigenicity of human pluripotent stem cells
Stable methylation at promoters distinguishes epiblast stem cells from embryonic stem cells and the in vivo epiblasts
High-throughput single nucleotide variant discovery in E14 mouse embryonic stem cells provides a new reference genome assembly
β-catenin fluctuates in mouse ESCs and is essential for Nanog-mediated reprogramming of somatic cells to pluripotency
An epigenetic switch ensures transposon repression upon dynamic loss of DNA methylation in embryonic stem cells
Development of FGF2-dependent pluripotent stem cells showing naive state characteristics from murine preimplantation inner cell mass
Chicken embryonic stem cells and primordial germ cells display different heterochromatic histone marks than their mammalian counterparts
Serum-Based Culture Conditions Provoke Gene Expression Variability in Mouse Embryonic Stem Cells as Revealed by Single-Cell Analysis
Chromatin dynamics and the role of G9a in gene regulation and enhancer silencing during early mouse development
Calibrating ChIP-Seq with Nucleosomal Internal Standards to Measure Histone Modification Density Genome Wide
Transcriptome analysis of chicken ES, blastodermal and germ cells reveals that chick ES cells are equivalent to mouse ES cells rather than EpiSC
BMP-SMAD Signaling Regulates Lineage Priming, but Is Dispensable for Self-Renewal in Mouse Embryonic Stem Cells
FOXD3 Regulates Pluripotent Stem Cell Potential by Simultaneously Initiating and Repressing Enhancer Activity
Single cells get together: High-resolution approaches to study the dynamics of early mouse development
Dynamic Reorganization of Extremely Long-Range Promoter-Promoter Interactions between Two States of Pluripotency
Meeting report: 11th EMBL conference on transcription and chromatin - August 23-26, 2014 - Heidelberg, Germany
TGF-β-superfamily signaling regulates embryonic stem cell heterogeneity: self-renewal as a dynamic and regulated equilibrium
OCT4/SOX2-independent Nanog autorepression modulates heterogeneous Nanog gene expression in mouse ES cells
Polycomb determines responses to smad2/3 signaling in embryonic stem cell differentiation and in reprogramming
Ground State Conditions Induce Rapid Reorganization of Core Pluripotency Factor Binding before Global Epigenetic Reprogramming
Functional compensation between Myc and PI3K signaling supports self-renewal of embryonic stem cells
Comparative FAIRE-seq analysis reveals distinguishing features of the chromatin structure of ground state- and primed-pluripotent cells
Effects of Collective Histone State Dynamics on Epigenetic Landscape and Kinetics of Cell Reprogramming
Heterochromatin Protein 1β (HP1β) has distinct functions and distinct nuclear distribution in pluripotent versus differentiated cells
Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal
CHIR99021 promotes self-renewal of mouse embryonic stem cells by modulation of protein-encoding gene and long intergenic non-coding RNA expression
The impact of culture on epigenetic properties of pluripotent stem cells and pre-implantation embryos
Epigenomic comparison reveals activation of "seed" enhancers during transition from naive to primed pluripotency
Exit from pluripotency is gated by intracellular redistribution of the bHLH transcription factor Tfe3
Cdx2 efficiently induces trophoblast stem-like cells in naïve, but not primed, pluripotent stem cells
Targeting polycomb to pericentric heterochromatin in embryonic stem cells reveals a role for H2AK119u1 in PRC2 recruitment
Stem cells. m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation
Report on the 10th EMBL conference on transcription and chromatin: August 25-28, 2012 EMBL advanced training centre, Heidelberg, Germany
Peregrine: A rapid and unbiased method to produce strand-specific RNA-Seq libraries from small quantities of starting material
Dissecting mechanisms of mouse embryonic stem cells heterogeneity through a model-based analysis of transcription factor dynamics
Sexually dimorphic gene expression emerges with embryonic genome activation and is dynamic throughout development
Robust self-renewal of rat embryonic stem cells requires fine-tuning of glycogen synthase kinase-3 inhibition
Pausing of RNA polymerase II regulates mammalian developmental potential through control of signaling networks
Identifying division symmetry of mouse embryonic stem cells: negative impact of DNA methyltransferases on symmetric self-renewal
Primordial dwarfism gene maintains Lin28 expression to safeguard embryonic stem cells from premature differentiation
The two active X chromosomes in female ESCs block exit from the pluripotent state by modulating the ESC signaling network
NuRD suppresses pluripotency gene expression to promote transcriptional heterogeneity and lineage commitment
Stepwise differentiation of pluripotent stem cells into osteoblasts using four small molecules under serum-free and feeder-free conditions
Cell-cycle control of developmentally regulated transcription factors accounts for heterogeneity in human pluripotent cells
Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming
Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells
FGF signaling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency
Single-cell gene expression profiles define self-renewing, pluripotent, and lineage primed states of human pluripotent stem cells
Platform for induction and maintenance of transgene-free hiPSCs resembling ground state pluripotent stem cells
Erk1/2 activity promotes chromatin features and RNAPII phosphorylation at developmental promoters in mouse ESCs
Systematic identification of culture conditions for induction and maintenance of naive human pluripotency
Jun-Mediated Changes in Cell Adhesion Contribute to Mouse Embryonic Stem Cell Exit from Ground State Pluripotency
Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming
RISC-mediated control of selected chromatin regulators stabilizes ground state pluripotency of mouse embryonic stem cells
Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells
Loss of the Otx2-Binding Site in the Nanog Promoter Affects the Integrity of Embryonic Stem Cell Subtypes and Specification of Inner Cell Mass-Derived Epiblast
Live cell imaging of the nascent inactive X chromosome during the early differentiation process of naive ES cells towards epiblast stem cells
Culture adaptation alters transcriptional hierarchies among single human embryonic stem cells reflecting altered patterns of differentiation
Transcriptome analyses of inner cell mass and trophectoderm cells isolated by magnetic-activated cell sorting from bovine blastocysts using single cell RNA-seq
Embryonic Stem Cell Culture Conditions Support Distinct States Associated with Different Developmental Stages and Potency
Lineage-Specific Profiling Delineates the Emergence and Progression of Naive Pluripotency in Mammalian Embryogenesis
Heterogeneous lineage marker expression in naive embryonic stem cells is mostly due to spontaneous differentiation
Dzip3 regulates developmental genes in mouse embryonic stem cells by reorganizing 3D chromatin conformation
Dynamically reorganized chromatin is the key for the reprogramming of somatic cells to pluripotent cells
Membrane translocation of t-SNARE protein syntaxin-4 abrogates ground-state pluripotency in mouse embryonic stem cells
Chromatin states shape insertion profiles of the piggyBac, Tol2 and Sleeping Beauty transposons and murine leukemia virus
The epigenetic modifier ubiquitin-specific protease 22 (USP22) regulates embryonic stem cell differentiation via transcriptional repression of sex-determining region Y-box 2 (SOX2).
Disrupting Interactions Between β-Catenin and Activating TCFs Reconstitutes Ground State Pluripotency in Mouse Embryonic Stem Cells
Dnmt3b Prefers Germ Line Genes and Centromeric Regions: Lessons from the ICF Syndrome and Cancer and Implications for Diseases
OCT4 supports extended LIF-independent self-renewal and maintenance of transcriptional and epigenetic networks in embryonic stem cells
Simultaneous targeted inhibition of Sox2-Oct4 transcription factors using decoy oligodeoxynucleotides to repress stemness properties in mouse embryonic stem cells
The role of maternal-specific H3K9me3 modification in establishing imprinted X-chromosome inactivation and embryogenesis in mice
Pluripotency-associated miR-290/302 family of microRNAs promote the dismantling of naive pluripotency
Sex Differences in Early Embryogenesis: Inter-Chromosomal Regulation Sets the Stage for Sex-Biased Gene Networks: The dialogue between the sex chromosomes and autosomes imposes sexual identity soon after fertilization
Jmjd2c facilitates the assembly of essential enhancer-protein complexes at the onset of embryonic stem cell differentiation
Germ-line-competent embryonic stem cells of the Chinese Kunming mouse strain with long-term self-renewal ability
Mammalian embryo comparison identifies novel pluripotency genes associated with the naïve or primed state
A lncRNA fine tunes the dynamics of a cell state transition involving Lin28 , let-7 and de novo DNA methylation
Xist and Tsix Transcription Dynamics Is Regulated by the X-to-Autosome Ratio and Semistable Transcriptional States
The demethylase JMJD2C localizes to H3K4me3-positive transcription start sites and is dispensable for embryonic development
Histone H3 Lysine 36 Trimethylation Is Established over the Xist Promoter by Antisense Tsix Transcription and Contributes to Repressing Xist Expression
Long-Term Perfusion Culture of Monoclonal Embryonic Stem Cells in 3D Hydrogel Beads for Continuous Optical Analysis of Differentiation.
Allele-specific RNA-seq expression profiling of imprinted genes in mouse isogenic pluripotent states
Individual retrotransposon integrants are differentially controlled by KZFP/KAP1-dependent histone methylation, DNA methylation and TET-mediated hydroxymethylation in naïve embryonic stem cells
Non-invasive detection of DNA methylation states in carcinoma and pluripotent stem cells using Raman microspectroscopy and imaging
Negligible immunogenicity of terminally differentiated cells derived from induced pluripotent or embryonic stem cells
RNA polymerase II primes Polycomb-repressed developmental genes throughout terminal neuronal differentiation
The Hox proteins Ubx and AbdA collaborate with the transcription pausing factor M1BP to regulate gene transcription
Stat3 phosphorylation is required for embryonic stem cells ground state maintenance in 2i culture media
Activation of transcription factor circuity in 2i-induced ground state pluripotency is independent of repressive global epigenetic landscapes
Describing the Stem Cell Potency: The Various Methods of Functional Assessment and In silico Diagnostics
Role of transcription complexes in the formation of the basal methylation pattern in early development
PIXUL-ChIP: integrated high-throughput sample preparation and analytical platform for epigenetic studies
TERRA regulate the transcriptional landscape of pluripotent cells through TRF1-dependent recruitment of PRC2
Three-dimensional system enabling the maintenance and directed differentiation of pluripotent stem cells under defined conditions
Comparative analysis of naive, primed and ground state pluripotency in mouse embryonic stem cells originating from the same genetic background
Unbiased shRNA screening, using a combination of FACS and high-throughput sequencing, enables identification of novel modifiers of Polycomb silencing
Structural robustness of mammalian transcription factor networks reveals plasticity across development
Kmt2b conveys monovalent and bivalent H3K4me3 in mouse spermatogonial stem cells at germline and embryonic promoters
Hydrodynamic shear stress promotes epithelial-mesenchymal transition by downregulating ERK and GSK3β activities
E2F4 regulates transcriptional activation in mouse embryonic stem cells independently of the RB family
Vascular progenitors generated from tankyrase inhibitor-regulated naïve diabetic human iPSC potentiate efficient revascularization of ischemic retina.
Conversion between porcine naïve-like and primed ESCs and specific pluripotency marker identification.
Global hyperactivation of enhancers stabilizes human and mouse naive pluripotency through inhibition of CDK8/19 Mediator kinases.
β-Catenin safeguards the ground state of mousepluripotency by strengthening the robustness of the transcriptional apparatus
Prdm14 promotes germline fate and naive pluripotency by repressing FGF signalling and DNA methylation
The impact of microRNAs on transcriptional heterogeneity and gene co-expression across single embryonic stem cells
Contrasting epigenetic states of heterochromatin in the different types of mouse pluripotent stem cells
WNT Inhibition and Increased FGF Signaling Promotes Derivation of Less Heterogeneous Primed Human Embryonic Stem Cells, Compatible with Differentiation
Inhibition of MEK1/2 and GSK3 (2i system) affects blastocyst quality and early differentiation of porcine parthenotes
Untargeted histone profiling during naive conversion uncovers conserved modification markers between mouse and human
Machine Learning of Stem Cell Identities From Single-Cell Expression Data via Regulatory Network Archetypes
Bivalent promoter hypermethylation in cancer is linked to the H327me3/H3K4me3 ratio in embryonic stem cells.
Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding.
Netrin-1 promotes naive pluripotency through Neo1 and Unc5b co-regulation of Wnt and MAPK signalling.
Epithelial cadherin regulates transition between the naïve and primed pluripotent states in mouse embryonic stem cells
Inhibition of transforming growth factor β (TGF-β) signaling can substitute for Oct4 protein in reprogramming and maintain pluripotency.
An extended model for culture-dependent heterogenous gene expression and proliferation dynamics in mouse embryonic stem cells
STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells
In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states.
Derivation of stable embryonic stem cell-like, but transcriptionally heterogenous, induced pluripotent stem cells from non-permissive mouse strains.
DOT1L-controlled cell-fate determination and transcription elongation are independent of H3K79 methylation.
Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals
hnRNPLL controls pluripotency exit of embryonic stem cells by modulating alternative splicing of Tbx3 and Bptf.
In Vitro Derivation of Quiescent Mouse Embryonic Stem Cells Based on Distinct Mitochondrial Activity
Cell Signaling Coordinates Global PRC2 Recruitment and Developmental Gene Expression in Murine Embryonic Stem Cells
Unexpected low expression of porcine endogenous retroviruses (PERVs) in porcine expanded potential stem cells (EPSCs).
Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells
Pluripotent stem cell-derived models of neurological diseases reveal early transcriptional heterogeneity.
DNMTs Play an Important Role in Maintaining the Pluripotency of Leukemia Inhibitory Factor-Dependent Embryonic Stem Cells.
Widespread reorganisation of pluripotent factor binding and gene regulatory interactions between human pluripotent states.
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Cancer Epigenetics & Metabolism (Keystone)
Epigenetic changes are present and dysregulated in many cancers, including DNA methylation, non-coding RNA segments and post-translational protein modifications. The epigenetic changes may or may not provide advantages for the cancer cells. This feed focuses on the relationship between cell metabolism, epigenetics and tumor differentiation.