Distinct modes of SMAD2 chromatin binding and remodeling shape the transcriptional response to Nodal/Activin signaling
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE77488 | GEO | 2016/12/31
SECONDARY ACCESSION(S): PRJNA310622
REPOSITORIES: GEO
Similar Datasets
Project description:NODAL/Activin signaling orchestrates key processes during embryonic development via SMAD2. How SMAD2 activates programs of gene expression that are modulated over time however, is not known. Here we delineate the sequence of events that occur from SMAD2 binding to transcriptional activation, and the mechanisms underlying them. NODAL/Activin signaling induces dramatic chromatin landscape changes, and a dynamic transcriptional network regulated by SMAD2, acting via multiple mechanisms. Crucially we have discovered two modes of SMAD2 binding. SMAD2 can bind pre-acetylated nucleosome-depleted sites. However, it also binds to unacetylated, closed chromatin, independently of pioneer factors, where it induces nucleosome displacement and histone acetylation. For a subset of genes, this requires SMARCA4. We find that long term modulation of the transcriptional responses requires continued NODAL/Activin signaling. Thus SMAD2 binding does not linearly equate with transcriptional kinetics, and our data suggest that SMAD2 recruits multiple co-factors during sustained signaling to shape the downstream transcriptional program.
| S-EPMC5305219 | biostudies-literature
Project description:During development, key processes are orchestrated by Nodal/Activin signaling via SMAD2. Interplay between the SMADs, co-factors and chromatin determines cell-type specific responses, but the sequence of events underpinning SMAD2-mediated transcription is unknown. We performed RNA-and ChIP-sequencing for SMAD2, RNA Polymerase II and various histone modifications in different signaling states. Integration of these data reveals a dynamic transcriptional network downstream of Nodal/Activin signaling regulated by SMAD2 acting via multiple mechanisms. Upon ligand stimulation, SMAD2 can bind to pre-acetylated nucleosome-depleted sites, but also to unacetylated closed chromatin, where it induces nucleosome displacement and histone acetylation. Importantly, SMAD2 binding is highly dynamic and does not directly correlate with the transcriptional kinetics of target genes. Moreover, we show that SMAD2 initiates transcription by inducing RNA Polymerase II recruitment. We therefore define new paradigms for SMAD2-dependent transcription and provide a framework to understand how cells correctly execute gene expression programs in response to Nodal/Activin signaling.
2016-12-31 | GSE77454 | GEO
Project description:During development, key processes are orchestrated by Nodal/Activin signaling via SMAD2. Interplay between the SMADs, co-factors and chromatin determines cell-type specific responses, but the sequence of events underpinning SMAD2-mediated transcription is unknown. We performed RNA-and ChIP-sequencing for SMAD2, RNA Polymerase II and various histone modifications in different signaling states. Integration of these data reveals a dynamic transcriptional network downstream of Nodal/Activin signaling regulated by SMAD2 acting via multiple mechanisms. Upon ligand stimulation, SMAD2 can bind to pre-acetylated nucleosome-depleted sites, but also to unacetylated closed chromatin, where it induces nucleosome displacement and histone acetylation. Importantly, SMAD2 binding is highly dynamic and does not directly correlate with the transcriptional kinetics of target genes. Moreover, we show that SMAD2 initiates transcription by inducing RNA Polymerase II recruitment. We therefore define new paradigms for SMAD2-dependent transcription and provide a framework to understand how cells correctly execute gene expression programs in response to Nodal/Activin signaling.
2016-12-31 | GSE76742 | GEO
Project description:Distinct modes of SMAD2 chromatin binding and remodeling shape the transcriptional response to Nodal/Activin signaling
| PRJNA310622 | ENA
Project description:Nodal and Activin are morphogens of the TGFbeta superfamily of signaling molecules that direct differential cell fate decisions in a dose- and distance-dependent manner. During early embryonic development the Nodal/Activin pathway is responsible for the specification of mesoderm, endoderm, node, and mesendoderm. In contradiction to this drive towards cellular differentiation, the pathway also plays important roles in the maintenance of self-renewal and pluripotency in embryonic and epiblast stem cells. The molecular basis behind stem cell interpretation of Nodal/Activin signaling gradients and the undertaking of disparate cell fate decisions remains poorly understood. Here, we show that any perturbation of endogenous signaling levels in mouse embryonic stem cells leads to their exit from self-renewal towards divergent differentiation programs. Increasing Nodal signals above basal levels by direct stimulation with Activin promotes differentiation towards the mesendodermal lineages while repression of signaling with the specific Nodal/Activin receptor inhibitor SB431542 induces trophectodermal differentiation. To address how quantitative Nodal/Activin signals are translated qualitatively into distinct cell fates decisions, we performed chromatin immunoprecipitation of phospho-Smad2, the primary downstream transcriptional factor of the Nodal/Activin pathway, followed by massively parallel sequencing, and show that phospho-Smad2 binds to and regulates distinct subsets of target genes in a dose-dependent manner. Crucially, Nodal/Activin signaling directly controls the Oct4 master regulator of pluripotency by graded phospho-Smad2 binding in the promoter region. Hence stem cells interpret and carry out differential Nodal/Activin signaling instructions via a corresponding gradient of Smad2 phosphorylation that selectively titrates self-renewal against alternative differentiation programs by direct regulation of distinct target gene subsets and Oct4 expression.
| S-EPMC3121749 | biostudies-literature
Project description:In this experiment patterns of chromatin accessibility were compared in P19 mouse embryonic teratoma cells treated with either the Nodal/Activin singalling inhibitor SB-431542, or with Activin for 1hr (acute signalling) and 8 hr (prolonged signalling), or left untreated (chronic signalling)
2022-04-10 | GSE178315 | GEO
Project description:Nodal and Activin are morphogens of the TGFbeta superfamily of signaling molecules that direct differential cell fate decisions in a dose- and distance-dependent manner. During early embryonic development the Nodal/Activin pathway is responsible for the specification of mesoderm, endoderm, node and mesendoderm. In contradiction to this drive towards cellular differentiation, the pathway also plays important roles in the maintenance of self-renewal and pluripotency in embryonic and epiblast stem cells. The molecular basis behind stem cell interpretation of Nodal/Activin signaling gradients and the undertaking of disparate cell fate decisions remains poorly understood. Here, we show that any perturbation of endogenous signaling levels in mouse ES cells leads to their exit from self renewal towards divergent differentiation programs. Increasing Nodal signals above basal levels by direct stimulation with Activin promotes differentiation towards the mesendodermal lineages while repression of signaling with the specific Nodal/Activin receptor inhibitor SB431542 induces trophectodermal differentiation. To address how quantitative Nodal/Activin signals are translated qualitatively into distinct cell fates decisions, we performed chromatin immunoprecipitation of phospho-Smad2 the primary downstream transcriptional factor of the Nodal/Activin pathway followed by massively parallel sequencing and show that phospho-Smad2 binds to and regulates distinct subsets of target genes in a dose-dependent manner. Crucially, Nodal/Activin signaling directly controls the Oct4 master regulator of pluripotency by graded phospho-Smad2 binding in the promoter region. Hence stem cells interpret and carry out differential Nodal/Activin signaling instructions via a corresponding gradient of Smad2 phosphorylation that selectively titrates self-renewal against alternative differentiation programs by direct regulation of distinct target gene subsets and Oct4 expression. Four biological replicates consisting of 4 different passages of E14TG2a ES cells at P20, P21, P23 and P24
2011-06-30 | E-GEOD-23239 | biostudies-arrayexpress
Project description:The Nodal/Activin morphogens are secreted signaling molecules that form concentration gradients during early embryogenesis providing stem cells with positional information and differentiation instructions important for embryonic patterning. The molecular basis driving stem cell interpretation of signaling gradients and the undertaking of distinct cell fate decisions remains poorly understood. We show that perturbation of endogenous Nodal/Activin signaling in ES cells leads to exit from self renewal towards mesendodermal differentiation at high signaling and trophectoderm induction during low signaling. ChIP-seq of Phospho-Smad2, the downstream transcription factor of the Nodal/Activin pathway reveals binding to distinct subsets of target genes in a dose dependent manner including the promoter region of the Oct4 master regulator of stemness. Consequently, both Oct4 mRNA and protein levels are directly driven by graded Nodal/Activin signaling. Hence stem cells interpret and carry out differential Nodal/Activin signaling instructions via a corresponding gradient of Smad2 phosphorylation that selectively titers self renewal against alternative differentiation programs. 3 pSmad2 ChIP samples corresponding to ES cells pretreated for 6 hours in 10uM SB followed by 18 hours in 25ng/ml Activin, 1/5000 DMSO and 10uM SB in 20% KSR media. Controls include the corresponding input DNA for each treatment.
2011-01-31 | E-GEOD-23581 | biostudies-arrayexpress
Project description:Nodal and Activin are morphogens of the TGFbeta superfamily of signaling molecules that direct differential cell fate decisions in a dose- and distance-dependent manner. During early embryonic development the Nodal/Activin pathway is responsible for the specification of mesoderm, endoderm, node and mesendoderm. In contradiction to this drive towards cellular differentiation, the pathway also plays important roles in the maintenance of self-renewal and pluripotency in embryonic and epiblast stem cells. The molecular basis behind stem cell interpretation of Nodal/Activin signaling gradients and the undertaking of disparate cell fate decisions remains poorly understood. Here, we show that any perturbation of endogenous signaling levels in mouse ES cells leads to their exit from self renewal towards divergent differentiation programs. Increasing Nodal signals above basal levels by direct stimulation with Activin promotes differentiation towards the mesendodermal lineages while repression of signaling with the specific Nodal/Activin receptor inhibitor SB431542 induces trophectodermal differentiation. To address how quantitative Nodal/Activin signals are translated qualitatively into distinct cell fates decisions, we performed chromatin immunoprecipitation of phospho-Smad2 the primary downstream transcriptional factor of the Nodal/Activin pathway followed by massively parallel sequencing and show that phospho-Smad2 binds to and regulates distinct subsets of target genes in a dose-dependent manner. Crucially, Nodal/Activin signaling directly controls the Oct4 master regulator of pluripotency by graded phospho-Smad2 binding in the promoter region. Hence stem cells interpret and carry out differential Nodal/Activin signaling instructions via a corresponding gradient of Smad2 phosphorylation that selectively titrates self-renewal against alternative differentiation programs by direct regulation of distinct target gene subsets and Oct4 expression.
2011-06-30 | GSE23239 | GEO
Project description:The Nodal/Activin morphogens are secreted signaling molecules that form concentration gradients during early embryogenesis providing stem cells with positional information and differentiation instructions important for embryonic patterning. The molecular basis driving stem cell interpretation of signaling gradients and the undertaking of distinct cell fate decisions remains poorly understood. We show that perturbation of endogenous Nodal/Activin signaling in ES cells leads to exit from self renewal towards mesendodermal differentiation at high signaling and trophectoderm induction during low signaling. ChIP-seq of Phospho-Smad2, the downstream transcription factor of the Nodal/Activin pathway reveals binding to distinct subsets of target genes in a dose dependent manner including the promoter region of the Oct4 master regulator of stemness. Consequently, both Oct4 mRNA and protein levels are directly driven by graded Nodal/Activin signaling. Hence stem cells interpret and carry out differential Nodal/Activin signaling instructions via a corresponding gradient of Smad2 phosphorylation that selectively titers self renewal against alternative differentiation programs.
2011-01-31 | GSE23581 | GEO