Embryogenesis articles within Nature Communications

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  • Article
    | Open Access

    Zygotic genome activation in zebrafish relies on pluripotency transcription factors Pou5f3 and Sox19b. Here the authors investigate how these factors interact in vivo by analyzing the changes in chromatin state and time-resolved transcription in Pou5f3 and Sox19b single and double mutant embryos.

    • Meijiang Gao
    • , Marina Veil
    •  & Daria Onichtchouk

  • Article
    | Open Access

    How pluripotency transcription factors regulate the cellular architecture and energetics has remained largely unknown. Here the authors identify Lima1 as a key effector that mediates the pluripotency control of membrane dynamics and cellular metabolism.

    • Binyamin Duethorn
    • , Fabian Groll
    •  & Ivan Bedzhov

  • Article
    | Open Access

    Studying morphogen gradient formation and reception in mammalian development is challenging. Here, the authors show with human gastruloids that Nodal activity in live cells spreads via a relay mechanism with timing that is locally controlled by Lefty, which dictates mesoderm differentiation timing.

    • Lizhong Liu
    • , Anastasiia Nemashkalo
    •  & Aryeh Warmflash

  • Article
    | Open Access

    Synthetic embryo models have arisen as an approach to probe early development in vitro, facilitating the study of difficult to access stages. Here the authors present a simple system for generating embryo-like structures that resemble peri-implantation mouse embryos.

    • Jan Langkabel
    • , Arik Horne
    •  & Hubert Schorle

  • Article
    | Open Access

    Perturbations of the cardiopharyngeal mesoderm can lead to congenital defects in individuals with 22q11.2 deletion syndrome. Here the authors use single cell RNA-sequencing to identify a multilineage primed population within the mesoderm, marked by Tbx1, which has bipotent properties to form cardiac and branchiomeric muscle cells.

    • Hiroko Nomaru
    • , Yang Liu
    •  & Bernice E. Morrow

  • Article
    | Open Access

    The role of the transcriptional effector SMAD4 in vertebrate embryo development remains unresolved. Here the authors show that in the absence of Smad4, dorsal/ventral embryo patterning is disrupted due to the loss of BMP signaling, while Nodal signaling is maintained, but insufficient for optimal endoderm specification.

    • Luca Guglielmi
    • , Claire Heliot
    •  & Caroline S. Hill

  • Article
    | Open Access

    Activation of the zygotic genome is a critical transition during development, though the link to tissue-specific gene regulation remains unclear. Here the authors demonstrate distinct functions for Satb2 before and after zygotic genome activation, highlighting the temporal coordination of these roles.

    • Saurabh J. Pradhan
    • , Puli Chandramouli Reddy
    •  & Sanjeev Galande

  • Article
    | Open Access

    The mechanisms underlying how monozygotic (or identical) twins arise are yet to be determined. Here, the authors investigate this in an epigenome-wide association study, showing that monozygotic twinning has a characteristic DNA methylation signature in adult somatic tissues.

    • Jenny van Dongen
    • , Scott D. Gordon
    •  & Dorret I. Boomsma

  • Article
    | Open Access

    Human early development remains largely inaccessible, owing to technical and ethical limitations of working with natural embryos. Here the authors assess the extent to which human expanded pluripotent stem cells can specify distinct cell lineages and capture aspects of early human embryogenesis.

    • Berna Sozen
    • , Victoria Jorgensen
    •  & Magdalena Zernicka-Goetz

  • Article
    | Open Access

    The authors show that post-transcriptional regulation of the cilia-driven leftward flow target dand5 is central to symmetry breakage in frog, fish and mouse and is mediated by a 139 nt Bicc1 responsive element in the dand5 3′UTR, and they present evidence that Pkd2 regulates this Bicc1/dand5 module.

    • Markus Maerker
    • , Maike Getwan
    •  & Axel Schweickert

  • Article
    | Open Access

    Cells in the developing embryo interpret WNT signalling with context-dependence, but the mechanism decoding these cues is unclear. Here, the authors show that combinatorial TALE/HOX activity destabilizes nucleosomes at WNT-responsive regions to activate paraxial mesodermal genes.

    • Luca Mariani
    • , Xiaogang Guo
    •  & Elisabetta Ferretti

  • Comment
    | Open Access

    As it fulfills an irresistible need to understand our own origins, research on human development occupies a unique niche in scientific and medical research. In this Comment, we explore the progress in our understanding of human development over the past 10 years. The focus is on basic research, clinical applications, and ethical considerations.

    • Ali H. Brivanlou
    •  & Norbert Gleicher

  • Comment
    | Open Access

    In the next 10 years, the continued exploration of human embryology holds promise to revolutionize regenerative and reproductive medicine with important societal consequences. In this Comment we speculate on the evolution of recent advances made and describe emerging technologies for basic research, their potential clinical applications, and, importantly, the ethical frameworks in which they must be considered.

    • Ali H. Brivanlou
    • , Nicolas Rivron
    •  & Norbert Gleicher

  • Article
    | Open Access

    It remains unclear how spatial information controls endothelial cell identity and behavior in the developing heart. Here the authors perform single cell RNA sequencing at key developmental timepoints in mice to interrogate cellular contributions to coronary vessel patterning and maturation in the epicardium.

    • Pearl Quijada
    • , Michael A. Trembley
    •  & Eric M. Small

  • Article
    | Open Access

    Centrioles are ancient organelles with a conserved architecture and their rigidity is thought to restrict microtubule sliding. Here authors show that, in mammalian sperm, the atypical distal centriole and its surrounding atypical pericentriolar matrix form a dynamic basal complex that facilitates a cascade of internal sliding deformations, coupling tail beating with asymmetric head kinking.

    • Sushil Khanal
    • , Miguel Ricardo Leung
    •  & Tomer Avidor-Reiss

  • Article
    | Open Access

    Cytonemes are cellular projections known to transfer Wnt ligands between cells, but their regulation remains unclear. Here, the authors show that activation of the planar cell polarity protein Vangl2 generates long and branched cytonemes increasing paracrine Wnt/β-catenin signaling.

    • Lucy Brunt
    • , Gediminas Greicius
    •  & Steffen Scholpp

  • Article
    | Open Access

    During development, H3K27me3 is reallocated from large domains in preimplantation embryos to mark promoters of developmental genes. Here the authors show that the deubiquitinase Usp9x interacts with, deubiquitinates and stabilizes PRC2 and provide evidence that a Usp9x-PRC2 regulatory axis is critical at peri-implantation.

    • Trisha A. Macrae
    •  & Miguel Ramalho-Santos

  • Article
    | Open Access

    Erasure of DNA methylation from the parental genomes is critical to reset the methylome of differentiated gametes to pluripotent cells in the blastocyst. Here, the authors present a high-throughput single-cell method that enables strand-specific quantification of DNA methylation and identify distinct modes of DNA demethylation dynamics during early mammalian development.

    • Maya Sen
    • , Dylan Mooijman
    •  & Alexander van Oudenaarden

  • Article
    | Open Access

    In a newly fertilized egg, maternal and paternal chromosomes are enclosed in two separate pronuclei but the mechanisms in mammals for pronuclear movement are unclear. Here, the authors report that both F-actin and microtubule polymerization act in concern to drive inward movement of pronuclei towards the cell centre.

    • Kathleen Scheffler
    • , Julia Uraji
    •  & Melina Schuh

  • Article
    | Open Access

    The systematic characterization of C. elegans morphology during development has yet to be performed. Here, the authors produce a 3D atlas of C. elegans morphology from 17 embryos and 54 developmental stages, using an automated pipeline, CShaper (combining segmentation of fluorescently labeled membranes with automated cell lineage tracing).

    • Jianfeng Cao
    • , Guoye Guan
    •  & Hong Yan

  • Article
    | Open Access

    The paternal genome in mice undergoes widespread DNA methylation loss post-fertilization. Here, the authors apply allele-specific analysis of WGBS data to show that a number of genomic regions are simultaneously de novo methylated on the paternal genome dependent on maternal DNMT3A activity, which induces transcriptional silencing of this allele in the early embryo.

    • Julien Richard Albert
    • , Wan Kin Au Yeung
    •  & Matthew Lorincz

  • Article
    | Open Access

    Editor’s summary_NCOMMS-19-41732B The anterior pituitary gland controls body growth and reproduction but how early development is dynamically regulated is unclear. Here, the authors use scRNA-seq of human fetal pituitaries to identify different developmental routes and state transitions of five hormone-producing cell lineages, and a hybrid epithelial/mesenchymal state of pituitary stem cells.

    • Shu Zhang
    • , Yueli Cui
    •  & Jie Qiao

  • Article
    | Open Access

    How maternal RNA clearance is regulated in human preimplantation embryos is unclear. Here, the authors show there is a potential correlation between maternal mRNA decay defects and early developmental arrest from in vitro fertilized human embryos, suggesting that M-decay and Z-decay pathways may regulate such early development.

    • Qian-Qian Sha
    • , Wei Zheng
    •  & Heng-Yu Fan

  • Article
    | Open Access

    Preimplantation embryos undergo extensive transcriptomic and epigenomic remodeling. Here the authors assay open chromatin in bovine oocytes, embryos, and embryonic stem cells, and compare the transcriptomes and epigenomes of cattle, human and mouse embryos, revealing species-specific regulation of genome activation.

    • Michelle M. Halstead
    • , Xin Ma
    •  & Pablo J. Ross

  • Article
    | Open Access

    Polycomb repressive complex 2 (PRC2) methylates H3K27 and suppresses RNA polymerase II transcription by promoting a closed chromatin. Here the authors identify the transcription factor Ybx1 as an interactor that regulates the binding of PRC2 to chromatin and H3K27 methylation to promote the genetic programs underlying neural lineages and neural progenitor self-renewal–differentiation choices.

    • Myron K. Evans
    • , Yurika Matsui
    •  & Jamy C. Peng

  • Article
    | Open Access

    Aneuploidy, abnormal chromosome number, is a major cause of early pregnancy loss. Here the authors determine the extent of post-implantation development of human embryos with common aneuploidies in culture, finding developmental arrest of monosomy 21 embryos, and trophoblast hypo-proliferation in trisomy 16 embryos.

    • Marta N. Shahbazi
    • , Tianren Wang
    •  & Magdalena Zernicka-Goetz

  • Article
    | Open Access

    The MiDAC complex recruits class I histone deacetylases to chromatin but little is known about its precise structure and function. Here, the authors explore the role of MiDAC in the cell cycle and during mouse embryogenesis, and present cryoEM structures that provide insight into MiDAC’s mode of assembly.

    • Robert E. Turnbull
    • , Louise Fairall
    •  & John W. R. Schwabe

  • Article
    | Open Access

    The mechanisms behind the plasticity of embryos and how they deal with aneuploid cells are unclear. Here, the authors show that aneuploid cells in a mouse embryo are preferentially eliminated during pre- and peri-implantation development in a p53-dependent process involving both autophagy and apoptosis.

    • Shruti Singla
    • , Lisa K. Iwamoto-Stohl
    •  & Magdalena Zernicka-Goetz

  • Article
    | Open Access

    Many transcription factors regulate gene expression in a lineage- and process-specific manner, despite being expressed in several cell types. Here, the authors show that the Hox transcription factor Ubx has lineage-specific interactomes, which contribute to its cell context-dependent functions.

    • Julie Carnesecchi
    • , Gianluca Sigismondo
    •  & Ingrid Lohmann

  • Article
    | Open Access

    The BEN-solo proteins—including Insensitive (Insv), Elba1 and Elba2—function in both transcriptional repression and chromatin insulation. Here, the authors investigate the role of these proteins in Drosophila embryos, finding that ELBA and Insv function as general insulators and partition active chromatin to ensure proper gene activation in Drosophila.

    • Malin Ueberschär
    • , Huazhen Wang
    •  & Qi Dai

  • Article
    | Open Access

    How receptor localization affects morphogen gradient formation during embryonic development is unclear. Here, the authors study the relationship between the BMP gradient, receptor localization, and compartmentalized geometry in the early mouse embryo, using experimental data and computational simulation.

    • Zhechun Zhang
    • , Steven Zwick
    •  & Sharad Ramanathan

  • Article
    | Open Access

    The family of DNA methyltransferases (Dnmts) consists of four catalytically active enzymes that catalyze DNA methylation and also play a role as transcriptional regulators. Here the authors show that catalytically inactive Dnmt3b rescues a majority of methylation and expression changes in the absence of Dnmt3b during mouse embryonic development.

    • Pawel Nowialis
    • , Katarina Lopusna
    •  & Rene Opavsky

  • Article
    | Open Access

    Hox proteins are expressed in partially overlapping regions to inform development along the embryo’s head-tail axis. Here the authors analyse a cis regulatory module directly regulated by seven different Drosophila Hox proteins to uncover how different Hox class proteins differentially control its expression.

    • Carlos Sánchez-Higueras
    • , Chaitanya Rastogi
    •  & James C.-G. Hombría

  • Article
    | Open Access

    HSCs emerge from haemogenic endothelium (HE) in the dorsal aorta but whether these tissues share a common lineage is unclear. Here, the authors use a zebrafish runx1 reporter to show that HE maintains an arterial gene expression profile in the absence of Runx1, suggesting the aortic endothelium as a precursor of HE.

    • Florian Bonkhofer
    • , Rossella Rispoli
    •  & Roger Patient

  • Article
    | Open Access

    How the shape of the pre-implantation murine embryo changes dramatically upon implantation is unclear. Here, the authors use live imaging with a cdx2-GFP reporter line in combination with loss of function experiments to demonstrate that FGF signalling mediated trophectoderm morphogenesis orchestrates this process.

    • Neophytos Christodoulou
    • , Antonia Weberling
    •  & Magdalena Zernicka-Goetz

  • Article
    | Open Access

    Loss or over-expression of Grainyhead-like transcription factors (Grhl) prevents closure of the neural tube but the mechanism underlying this is unclear. Here, the authors show that Grhl2 regulates murine posterior-neuropore closure via changes in the identity and biomechanics of the non-neural, surface ectoderm cells.

    • Evanthia Nikolopoulou
    • , Caroline S. Hirst
    •  & Nicholas D. E. Greene

  • Article
    | Open Access

    Eukaryotic genomes are segregated into euchromatin and heterochromatin. Here the authors show that heterochromatin establishment during zebrafish embryo development is controlled by zygotic transcription of miR-430 and subsequent degradation of maternal transcripts encoding the chromatin remodeling protein Smarca2.

    • Kathrin Laue
    • , Srivarsha Rajshekar
    •  & Mary G. Goll

  • Article
    | Open Access

    The precise cellular patterning and decisions of early embryogenesis have been hard to mimic in vitro. Here, the authors culture murine embryonic and trophoblast stem cells together with extra-embryonic endoderm stem cells to form embryo-like structures (ETX-embryoids), which can initiate an implantation response.

    • Shaopeng Zhang
    • , Tianzhi Chen
    •  & Jianyong Han

  • Article
    | Open Access

    Early human embryonic development involves extensive changes in chromatin structure and transcriptional activity. Here the authors present LiCAT-seq, a method enabling simultaneous profiling of chromatin accessibility and gene expression with ultra-low input of cells and map chromatin accessibility and transcriptome landscapes for human pre-implantation embryos.

    • Longqi Liu
    • , Lizhi Leng
    •  & Ge Lin

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