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      Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos

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          Summary

          The major and essential objective of pre-implantation development is to establish embryonic and extra-embryonic cell fates. To address when and how this fundamental process is initiated in mammals, we characterize transcriptomes of all individual cells throughout mouse pre-implantation development. This identifies targets of master pluripotency regulators Oct4 and Sox2 as being highly heterogeneously expressed between blastomeres of the 4-cell embryo, with Sox21 showing one of the most heterogeneous expression profiles. Live-cell tracking demonstrates that cells with decreased Sox21 yield more extra-embryonic than pluripotent progeny. Consistently, decreasing Sox21 results in premature upregulation of the differentiation regulator Cdx2, suggesting that Sox21 helps safeguard pluripotency. Furthermore, Sox21 is elevated following increased expression of the histone H3R26-methylase CARM1 and is lowered following CARM1 inhibition, indicating the importance of epigenetic regulation. Therefore, our results indicate that heterogeneous gene expression, as early as the 4-cell stage, initiates cell-fate decisions by modulating the balance of pluripotency and differentiation.

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          Highlights

          • Oct4 and Sox2 targets such as Sox21 are highly heterogeneous in the 4-cell embryo

          • Depleting Sox21 levels leads to upregulation of Cdx2 and extra-embryonic fate

          • Sox21 expression responds to the histone H3R26 methyltransferase CARM1

          • Heterogeneous gene expression initiates cell-fate decisions at the 4-cell stage

          Abstract

          Heterogeneous gene expression in 4-cell stage in mouse embryos contributes to cell-fate decisions, with lower levels of Sox21 promoting extra-embryonic fate over pluripotency.

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          Most cited references36

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          Accounting for technical noise in single-cell RNA-seq experiments.

          Single-cell RNA-seq can yield valuable insights about the variability within a population of seemingly homogeneous cells. We developed a quantitative statistical method to distinguish true biological variability from the high levels of technical noise in single-cell experiments. Our approach quantifies the statistical significance of observed cell-to-cell variability in expression strength on a gene-by-gene basis. We validate our approach using two independent data sets from Arabidopsis thaliana and Mus musculus.
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            Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing.

            Mammalian pre-implantation development is a complex process involving dramatic changes in the transcriptional architecture. We report here a comprehensive analysis of transcriptome dynamics from oocyte to morula in both human and mouse embryos, using single-cell RNA sequencing. Based on single-nucleotide variants in human blastomere messenger RNAs and paternal-specific single-nucleotide polymorphisms, we identify novel stage-specific monoallelic expression patterns for a significant portion of polymorphic gene transcripts (25 to 53%). By weighted gene co-expression network analysis, we find that each developmental stage can be delineated concisely by a small number of functional modules of co-expressed genes. This result indicates a sequential order of transcriptional changes in pathways of cell cycle, gene regulation, translation and metabolism, acting in a step-wise fashion from cleavage to morula. Cross-species comparisons with mouse pre-implantation embryos reveal that the majority of human stage-specific modules (7 out of 9) are notably preserved, but developmental specificity and timing differ between human and mouse. Furthermore, we identify conserved key members (or hub genes) of the human and mouse networks. These genes represent novel candidates that are likely to be key in driving mammalian pre-implantation development. Together, the results provide a valuable resource to dissect gene regulatory mechanisms underlying progressive development of early mammalian embryos.
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              Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst.

              Three distinct cell types are present within the 64-cell stage mouse blastocyst. We have investigated cellular development up to this stage using single-cell expression analysis of more than 500 cells. The 48 genes analyzed were selected in part based on a whole-embryo analysis of more than 800 transcription factors. We show that in the morula, blastomeres coexpress transcription factors specific to different lineages, but by the 64-cell stage three cell types can be clearly distinguished according to their quantitative expression profiles. We identify Id2 and Sox2 as the earliest markers of outer and inner cells, respectively. This is followed by an inverse correlation in expression for the receptor-ligand pair Fgfr2/Fgf4 in the early inner cell mass. Position and signaling events appear to precede the maturation of the transcriptional program. These results illustrate the power of single-cell expression analysis to provide insight into developmental mechanisms. The technique should be widely applicable to other biological systems. Copyright 2010 Elsevier Inc. All rights reserved.
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                Author and article information

                Contributors
                Journal
                Cell
                Cell
                Cell
                Cell Press
                0092-8674
                1097-4172
                24 March 2016
                24 March 2016
                : 165
                : 1
                : 61-74
                Affiliations
                [1 ]Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
                [2 ]European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
                [3 ]Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
                [4 ]Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
                [5 ]Cancer Research UK-Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, UK
                Author notes
                []Corresponding author marioni@ 123456ebi.ac.uk
                [∗∗ ]Corresponding author mz205@ 123456cam.ac.uk
                [6]

                Co-first author

                Article
                S0092-8674(16)30061-7
                10.1016/j.cell.2016.01.047
                4819611
                27015307
                792981ef-cbab-41fa-bda2-80c4e2701f0c
                © 2016 The Authors

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

                History
                : 9 June 2015
                : 10 November 2015
                : 22 January 2016
                Categories
                Article

                Cell biology
                Cell biology

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