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      Combinatorial Smad2/3 Activities Downstream of Nodal Signaling Maintain Embryonic/Extra-Embryonic Cell Identities during Lineage Priming

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          Summary

          Epiblast cells in the early post-implantation stage mammalian embryo undergo a transition described as lineage priming before cell fate allocation, but signaling pathways acting upstream remain ill defined. Genetic studies demonstrate that Smad2/3 double-mutant mouse embryos die shortly after implantation. To learn more about the molecular disturbances underlying this abrupt failure, here we characterized Smad2/3-deficient embryonic stem cells (ESCs). We found that Smad2/3 double-knockout ESCs induced to form epiblast-like cells (EpiLCs) display changes in naive and primed pluripotency marker gene expression, associated with the disruption of Oct4-bound distal regulatory elements. In the absence of Smad2/3, we observed enhanced Bmp target gene expression and de-repression of extra-embryonic gene expression. Cell fate allocation into all three embryonic germ layers is disrupted. Collectively, these experiments demonstrate that combinatorial Smad2/3 functional activities are required to maintain distinct embryonic and/or extra-embryonic cell identity during lineage priming in the epiblast before gastrulation.

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          Highlights

          • Smad2/3 alters the transcriptome and activity of distal regulatory elements in EpiLCs

          • Smad2 prevents expression of extra-embryonic genes during priming and differentiation

          • Smad2/3 is essential for mesoderm and definitive endoderm cell fate allocation

          • Smad2/3 signaling balances Bmp signaling during neural precursor differentiation

          Abstract

          Using genetic ablation of Smad2/3 effectors downstream of Nodal signaling in mouse embryonic stem cells, Senft et al. show a requirement for Smad2/3 signaling to maintain embryonic/extra-embryonic cell identities during lineage priming before mesoderm and endoderm cell fate allocation and to balance Nodal/Bmp signaling during ectoderm differentiation.

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          Most cited references43

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          Reconstitution of the mouse germ cell specification pathway in culture by pluripotent stem cells.

          The generation of properly functioning gametes in vitro requires reconstitution of the multistepped pathway of germ cell development. We demonstrate here the generation of primordial germ cell-like cells (PGCLCs) in mice with robust capacity for spermatogenesis. PGCLCs were generated from embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) through epiblast-like cells (EpiLCs), a cellular state highly similar to pregastrulating epiblasts but distinct from epiblast stem cells (EpiSCs). Reflecting epiblast development, EpiLC induction from ESCs/iPSCs is a progressive process, and EpiLCs highly competent for the PGC fate are a transient entity. The global transcription profiles, epigenetic reprogramming, and cellular dynamics during PGCLC induction from EpiLCs meticulously capture those associated with PGC specification from the epiblasts. Furthermore, we identify Integrin-β3 and SSEA1 as markers that allow the isolation of PGCLCs with spermatogenic capacity from tumorigenic undifferentiated cells. Our findings provide a paradigm for the first step of in vitro gametogenesis. Copyright © 2011 Elsevier Inc. All rights reserved.
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            Master transcription factors determine cell-type-specific responses to TGF-β signaling.

            Transforming growth factor beta (TGF-β) signaling, mediated through the transcription factors Smad2 and Smad3 (Smad2/3), directs different responses in different cell types. Here we report that Smad3 co-occupies the genome with cell-type-specific master transcription factors. Thus, Smad3 occupies the genome with Oct4 in embryonic stem cells (ESCs), Myod1 in myotubes, and PU.1 in pro-B cells. We find that these master transcription factors are required for Smad3 occupancy and that TGF-β signaling largely affects the genes bound by the master transcription factors. Furthermore, we show that induction of Myod1 in nonmuscle cells is sufficient to redirect Smad3 to Myod1 sites. We conclude that cell-type-specific master transcription factors determine the genes bound by Smad2/3 and are thus responsible for orchestrating the cell-type-specific effects of TGF-β signaling. Copyright © 2011 Elsevier Inc. All rights reserved.
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              DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing

              Recent developments in next-generation sequencing have enabled whole-genome profiling of nucleosome organizations. Although several algorithms for inferring nucleosome position from a single experimental condition have been available, it remains a challenge to accurately define dynamic nucleosomes associated with environmental changes. Here, we report a comprehensive bioinformatics pipeline, DANPOS, explicitly designed for dynamic nucleosome analysis at single-nucleotide resolution. Using both simulated and real nucleosome data, we demonstrated that bias correction in preliminary data processing and optimal statistical testing significantly enhances the functional interpretation of dynamic nucleosomes. The single-nucleotide resolution analysis of DANPOS allows us to detect all three categories of nucleosome dynamics, such as position shift, fuzziness change, and occupancy change, using a uniform statistical framework. Pathway analysis indicates that each category is involved in distinct biological functions. We also analyzed the influence of sequencing depth and suggest that even 200-fold coverage is probably not enough to identify all the dynamic nucleosomes. Finally, based on nucleosome data from the human hematopoietic stem cells (HSCs) and mouse embryonic stem cells (ESCs), we demonstrated that DANPOS is also robust in defining functional dynamic nucleosomes, not only in promoters, but also in distal regulatory regions in the mammalian genome.
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                Author and article information

                Contributors
                Journal
                Cell Rep
                Cell Rep
                Cell Reports
                Cell Press
                2211-1247
                24 August 2018
                21 August 2018
                24 August 2018
                : 24
                : 8
                : 1977-1985.e7
                Affiliations
                [1 ]Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
                [2 ]Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
                Author notes
                []Corresponding author elizabeth.robertson@ 123456path.ox.ac.uk
                [3]

                Lead Contact

                Article
                S2211-1247(18)31195-1
                10.1016/j.celrep.2018.07.077
                6113931
                30134160
                47f0ac4b-d611-494c-b323-bf673e6db66a
                © 2018 The Author(s)

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

                History
                : 20 February 2018
                : 31 May 2018
                : 22 July 2018
                Categories
                Article

                Cell biology
                smad2,smad3,nodal signaling,bmp signaling,tgf-β signaling,embryonic stem cells,epiblast-like cells,lineage priming,extra-embryonic,cell fate allocation

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