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View article: Double stranded RNA sensing is silenced during early embryonic development
Double stranded RNA sensing is silenced during early embryonic development Open
The type I interferon response is inactive during early mammalian development and becomes functional only after gastrulation. As a result, the totipotent and pluripotent embryonic stages remain susceptible to pathogens, including viruses. …
View article: Methylome profiling of SetDB1 deficient ESCs reveals diverse epigenetic cross-talk during pluripotency
Methylome profiling of SetDB1 deficient ESCs reveals diverse epigenetic cross-talk during pluripotency Open
SetDB1 is best known as a chromatin modifier catalyzing H3K9me3. However, recent studies show that SetDB1 can promote H3K27me3-deposition and CTCF-binding, and potentially recruit de novo DNA methyltransferases. Given the tight connection …
View article: Stem cell culture conditions affect in vitro differentiation potential and mouse gastruloid formation
Stem cell culture conditions affect in vitro differentiation potential and mouse gastruloid formation Open
Aggregating low numbers of mouse embryonic stem cells (mESCs) and inducing Wnt signalling generates ‘gastruloids’, self-organising complex structures that display an anteroposterior organisation of cell types derived from all three germ la…
View article: Double stranded RNA sensing drives interferon silencing in early development
Double stranded RNA sensing drives interferon silencing in early development Open
In early mammalian development, the type I interferon (IFN) response is inactive, only becoming functional after gastrulation. As a result, the totipotent and pluripotent embryonic stages remain highly susceptible to pathogens, including v…
View article: PRC1 and PRC2 proximal interactome in mouse embryonic stem cells
PRC1 and PRC2 proximal interactome in mouse embryonic stem cells Open
Polycomb repressive complexes PRC1 and PRC2 control lineage-specific gene silencing during early embryogenesis. To better understand Polycomb biology, we profile the proximal interactome (proxeome) of multiple PRC1 and PRC2 subunits in mou…
View article: Multi-omics analysis reveals distinct gene regulatory mechanisms between primary and organoid-derived human hepatocytes
Multi-omics analysis reveals distinct gene regulatory mechanisms between primary and organoid-derived human hepatocytes Open
Hepatic organoid cultures are a powerful model to study liver development and diseases in vitro. However, hepatocyte-like cells differentiated from these organoids remain immature compared to primary human hepatocytes (PHHs), which are the…
View article: The exit of naïve pluripotency contains a lipid metabolism-induced checkpoint for genome integrity
The exit of naïve pluripotency contains a lipid metabolism-induced checkpoint for genome integrity Open
Pluripotent progenitors undergo dramatic cellular and biochemical transformations during peri-implantation development. These large-scale reprogramming events are fundamental for subsequent differentiation, but how they are integrated and …
View article: Integrative omics analysis reveals gene regulatory mechanisms distinguishing organoid-derived hepatocytes from primary human hepatocytes
Integrative omics analysis reveals gene regulatory mechanisms distinguishing organoid-derived hepatocytes from primary human hepatocytes Open
Background and Aims Hepatic organoid cultures are considered a powerful model system to study liver development and diseases in vitro . However, hepatocyte-like cells differentiated from such organoids remain immature compared to primary h…
View article: H3K27me3 at pericentromeric heterochromatin is a defining feature of the early mouse blastocyst
H3K27me3 at pericentromeric heterochromatin is a defining feature of the early mouse blastocyst Open
Early mouse development is characterized by structural and epigenetic changes while cells progress towards differentiation. At blastocyst stage, the segregation of the three primordial lineages is accompanied by establishment of differenti…
View article: Cholangiocyte organoids from human bile retain a local phenotype and can repopulate bile ducts in vitro
Cholangiocyte organoids from human bile retain a local phenotype and can repopulate bile ducts in vitro Open
The well‐established 3D organoid culture method enabled efficient expansion of cholangiocyte‐like cells from intrahepatic (IHBD) and extrahepatic bile duct (EHBD) tissue biopsies. The extensive expansion capacity of these organoids enables…
View article: A plug and play microfluidic platform for standardized sensitive low-input chromatin immunoprecipitation
A plug and play microfluidic platform for standardized sensitive low-input chromatin immunoprecipitation Open
Epigenetic profiling by chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become a powerful tool for genome-wide identification of regulatory elements, for defining transcriptional regulatory networks, and for screening f…
View article: STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells
STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells Open
Background Enhancers are distal regulators of gene expression that shape cell identity and control cell fate transitions. In mouse embryonic stem cells (mESCs), the pluripotency network is maintained by the function of a complex network of…
View article: Terminal keratinocyte differentiation in vitro is associated with a stable DNA methylome
Terminal keratinocyte differentiation in vitro is associated with a stable DNA methylome Open
The epidermal compartment of the skin is regenerated constantly by proliferation of epidermal keratinocytes. Differentiation of a subset of these keratinocytes allows the epidermis to retain its barrier properties. Regulation of keratinocy…
View article: A plug and play microfluidic platform for standardized sensitive low-input Chromatin Immunoprecipitation
A plug and play microfluidic platform for standardized sensitive low-input Chromatin Immunoprecipitation Open
Epigenetic profiling by ChIP-Seq has become a powerful tool for genome-wide identification of regulatory elements, for defining transcriptional regulatory networks and for screening for biomarkers. However, the ChIP-Seq protocol for low-in…
View article: Additional file 5 of STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells
Additional file 5 of STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells Open
Additional file 5: Table S4. Zic3 WT KO RNAseq.
View article: Additional file 2 of STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells
Additional file 2 of STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells Open
Additional file 2: Table S1. Public data.
View article: Additional file 4 of STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells
Additional file 4 of STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells Open
Additional file 4: Table S3. STARRseq 2iL SL ESCs.
View article: Additional file 6 of STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells
Additional file 6 of STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells Open
Additional file 6: Table S5 Trp53 WT KO RNAseq.
View article: Additional file 7 of STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells
Additional file 7 of STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells Open
Additional file 7: Table S6. Cistrome ChIPseq enrichment.