Pattern formation articles within Nature Communications

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  • Article
    | Open Access

    Early stages of embryogenesis are known to depend on subcellular localization and transport of maternal mRNA, but systematic analyses have been hindered by a lack of methods for tracking of RNA. Here the authors combine spatially-resolved transcriptomics and single-cell RNA labeling to perform a spatio-temporal analysis of the transcriptome during early zebrafish development, revealing insights into this process.

    • Karoline Holler
    • , Anika Neuschulz
    •  & Jan Philipp Junker

  • Article
    | Open Access

    Mechanical forces, along with gene regulatory networks and cell-cell signalling, play an important role in the complex organization of tissues. Here the authors describe devices that actively apply mechanical force to developing neural tube, demonstrating that mechanical forces increase growth and enhance patterning.

    • Abdel Rahman Abdel Fattah
    • , Brian Daza
    •  & Adrian Ranga

  • Article
    | Open Access

    The skin of zebrafish is patterned by alternating blue stripes and yellow interstripes which arises from guanine crystal-containing cells called iridophores that reflect light. Here the authors track iridophores and see that they do not migrate between stripes and interstripes, but instead differentiate and proliferate in place based on their micro-environment.

    • Dvir Gur
    • , Emily J. Bain
    •  & David M. Parichy

  • Article
    | Open Access

    Morphogen gradients can be dynamic and transient yet give rise to stable cellular patterns. Here the authors show that a synthetic morphogen-induced mutual inhibition circuit produces stable boundaries when the spatial average of morphogens falls within the region of bistability.

    • Paul K. Grant
    • , Gregory Szep
    •  & Andrew Phillips

  • Article
    | Open Access

    The periodic organization of cells is typically associated with mechanisms based on intercellular signaling such as lateral inhibition and Turing patterning. Here the authors show that hair cells in the inner ear rearrange gradually into a checkerboard-like pattern through a tissue-wide shear motion that coordinates intercalation and delamination events.

    • Roie Cohen
    • , Liat Amir-Zilberstein
    •  & David Sprinzak

  • Article
    | Open Access

    Polycomb (PcG) and Trithorax (TrxG) group regulate several hundred target genes with important roles in development and disease. Here the authors combine experiment and theory to provide evidence that the Polycomb/Trithorax system has the potential for a rich repertoire of regulatory modes beyond simple epigenetic memory.

    • Jeannette Reinig
    • , Frank Ruge
    •  & Leonie Ringrose

  • Article
    | Open Access

    Stochastic pulsing of gene expression can generate phenotypic diversity in a genetically identical population of cells. Here, the authors show that stochastic pulsing in the expression of a sigma factor enables the formation of spatial patterns in a multicellular system, Bacillus subtilis bacterial biofilms.

    • Eugene Nadezhdin
    • , Niall Murphy
    •  & James C. W. Locke

  • Article
    | Open Access

    Vertebrate telencephalon formation requires Foxg-Fgf8 cross-regulation, but while ascidians express Foxg in the neural plate, they lack a telencephalon. Here the authors show that Foxg loss does not affect ascidian brain formation, indicating that telencephalon evolution required recruitment of Fgf downstream of Foxg.

    • Boqi Liu
    •  & Yutaka Satou

  • Article
    | Open Access

    Embryonic development produces different cell types in response to a small number of inductive signals. Here, the authors characterise how maternal factors modify chromatin to specify initial competence in Xenopus tropicalis, finding that the pioneering activity of the pluripotency factors Pou5f3 and Sox3 establishes competence for germ layer formation by remodelling chromatin before the onset of signalling.

    • George E. Gentsch
    • , Thomas Spruce
    •  & James C. Smith

  • 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

    The patterning of sensory bristles on the dorsal thorax of flies is regulated by two transcription factor families but the dynamics of this regulation is unclear. Here, the authors visualize seven E(spl)-HLH proteins, showing their regulated expression promotes mutual inhibition by Notch during notum patterning.

    • Lydie Couturier
    • , Khalil Mazouni
    •  & François Schweisguth

  • Article
    | Open Access

    How the cellular source of positional information compares across regenerative animals is unclear. Here, the authors find that planarian muscle, which harbours positional information, acts as a connective tissue by being a major site of matrisome gene expression and by maintaining tissue architecture.

    • Lauren E. Cote
    • , Eric Simental
    •  & Peter W. Reddien

  • Article
    | Open Access

    How heterogeneities arise in stem cell populations remains unclear. Here, Glen et al. find that in ESC colonies cell cycle asynchronies modulate gap junctions, causing variation in intracellular signalling molecule diffusion between cells, and ultimately in spatial heterogeneity in differentiation.

    • Chad M. Glen
    • , Todd C. McDevitt
    •  & Melissa L. Kemp

  • Article
    | Open Access

    Iridophores interact with other cells to give zebrafish their stripes, but what drives their form shifts is unknown. Here, modelling allows the authors to identify robust cues that may specify iridophore form and to find changes to these cues that likely account for altered patterns on related fish.

    • Alexandria Volkening
    •  & Björn Sandstede

  • Comment
    | Open Access

    Hox genes are known to regulate head-tail axis patterning but their molecular role in animals diverged from the bilaterian lineage is unclear. Here, Fabian Rentzsch and Thomas W. Holstein comment on a paper by Mark Martindale and colleagues on the functional role of two Hox genes in axial patterning of the sea anemone.

    • Fabian Rentzsch
    •  & Thomas W. Holstein

  • Article
    | Open Access

    Left-right (LR) axis specification is essential for embryonic patterning but a unifying mechanism across organisms has not been identified. Here, the authors show that Myosin1D, known to regulate Drosophila LR asymmetry, controls zebrafish LR Organizer function, and is therefore a conserved regulator of animal laterality.

    • Thomas Juan
    • , Charles Géminard
    •  & Maximilian Fürthauer

  • Perspective
    | Open Access

    What breaks symmetry in early mammalian embryonic development has been much questioned. Here, Magdalena Zernicka-Goetz and colleagues propose that compartmentalized intracellular reactions generate micro-scale inhomogeneity, which is amplified in the developing embryo, driving pattern formation.

    • Qi Chen
    • , Junchao Shi
    •  & Magdalena Zernicka-Goetz

  • Article
    | Open Access

    Biological self-organization uses hierarchical induction of gene expression but this has not been exploited by synthetic biology. Here the authors use an AND gate based on a split T7 RNA polymerase to organize programmed hierarchical patterning of gene expression across a bacterial population.

    • Christian R. Boehm
    • , Paul K. Grant
    •  & Jim Haseloff

  • Article
    | Open Access

    The neuroectoderm is patterned in a rostral-caudal axis in the embryo but how positional information is interpreted, is unclear. Here, the authors show that in mouse 3D embryonic stem cell cultures, there is self-patterning that depends on sequential activation of localised Fgf then Wnt signalling.

    • Nozomu Takata
    • , Eriko Sakakura
    •  & Yoshiki Sasai

  • Article
    | Open Access

    Planarian regenerative mechanisms suggest that muscle has an instructive role in patterning. Here, the authors show that muscle is also responsible for regenerative patterning information in an early-branching bilaterian, Hofstenia miamia, dating this back to the dawn of the Bilateria, over 550 million years ago.

    • Amelie A. Raz
    • , Mansi Srivastava
    •  & Peter W. Reddien

  • Article
    | Open Access

    Retinoic acid (RA) regulates the maintenance of somitogenesis symmetry. Here, the authors use a proteomic approach to identify a protein complex of Wdr5, Hdac1, Hdac2 that act together with RA and coactivator Rere/Atrophin2 and a histone methyltransferase Ehmt2 to regulate embryonic symmetry.

    • Gonçalo C. Vilhais-Neto
    • , Marjorie Fournier
    •  & Olivier Pourquié

  • Article
    | Open Access

    Organizers are regions in the embryo that induce cell fate and impart pattern on neighbouring regions. Here, the authors search for new organizers based on a common gene signature, and show that the Anterior Intestinal Portal endoderm induces cardiac identity, specifies ventricle and inhibits atrial character.

    • Claire Anderson
    • , Mohsin A. F. Khan
    •  & Claudio D. Stern

  • Article
    | Open Access

    The cornea is formed of cells that originate from the outer circle of stem cells and that move towards its centre. Here, the authors show that the movement pattern is self-organised, requiring no cues, and that stem cell leakage may account for the presence of stem cells at the centre of the cornea.

    • Erwin P. Lobo
    • , Naomi C. Delic
    •  & J. Guy Lyons

  • Article
    | Open Access

    It is unclear how the dorsal-ventral (DV) and anterior-posterior (AP) axes established in the gastrula affect tissues. Here, the authors show that in zebrafish kidney development, with regard to non-axial mesoderm, the classic DV axis corresponds to the AP axis, and is regulated by BMP and retinoic acid.

    • Richard W. Naylor
    • , Lauren Brilli Skvarca
    •  & Alan J. Davidson

  • Article
    | Open Access

    Patterning in the Drosophila eye is achieved by a series of signalling cascades over several cell distances. Here Gavish et al.model lateral inhibition in the developing eye to understand how developmental noise refines such patterning, identifying a novel activator required for buffering spatial variability.

    • Avishai Gavish
    • , Arkadi Shwartz
    •  & Naama Barkai

  • Article
    | Open Access

    Activation of the growth factor Trunk patterns the Drosophila embryonic termini but how this is regulated is unclear. Here, Johnson et al.report that Trunk is cleaved intracellularly by Furin proteases, and its extracellular accumulation is then mediated by the perforin-like protein Torso-like.

    • Travis K. Johnson
    • , Michelle A. Henstridge
    •  & Coral G. Warr

  • Article
    | Open Access

    Pigment pattern formation in zebrafish depends on the interactions between the pigment cells. Here the authors present a mathematical model based on mutual interaction of pigment cells in the absence of cell motion, revising the current model of the pattern formation that relies on reaction–diffusion Turing patterns.

    • D. Bullara
    •  & Y. De Decker

  • Article |

    Despite apparent morphological diversity, developmental interactions create predictable patterns of variation. Here the authors show that variation in the proportion of limbs, digits and somites and their response to artificial selection follow a rule that predicts the size of sequentially forming structures.

    • Nathan M. Young
    • , Benjamin Winslow
    •  & Kathryn Kavanagh

  • Article |

    Maternal molecular resources are invested in an egg so that different parts of the future embryo are specified and scaled in proportion to its size. Here the authors develop and experimentally test a model that evaluates the origins and limits of Bicoid morphogenetic gradient scaling in the fruit fly embryo.

    • Feng He
    • , Chuanxian Wei
    •  & Jun Ma

  • Article |

    In embryonic stem cells, extracellular signals are required to derepress developmental promoters to drive lineage specification, but the proteins involved in this process remain unknown. Here the authors show that the protein HEB directly associates with the Polycomb repressive complex 2 at genes involved in mesoderm and endoderm specification.

    • Se-Jin Yoon
    • , Joseph W. Foley
    •  & Julie C. Baker

  • Article |

    Haematopoietic stem/progenitor cells (HSPCs) transform from aortic endothelium into migratory cells that move through stroma and enter circulation to colonize haematopoietic tissues. Here the authors show that HSPCs' passage is facilitated by primitive macrophages that secrete extracellular matrix-degrading enzymes.

    • Jana Travnickova
    • , Vanessa Tran Chau
    •  & Karima Kissa

  • Article
    | Open Access

    The fibroblast growth factor (FGF) signalling pathway specifies the fate of pigmented cells in the ascidian Ciona intestinalis. Here, the authors obtain lineage-specific transcription profiles of pigment precursor cells and identify FGF downstream genes involved in central nervous system patterning, and the specification and differentiation of pigmented cells.

    • Claudia Racioppi
    • , Ashwani K. Kamal
    •  & Filomena Ristoratore

  • Article
    | Open Access

    The Drosophilahomologue of the vertebrate cell surface glycoprotein Cdon binds Hedgehog ligand and thereby prevents its diffusion. Here, the authors provide evidence for a similar mechanism during vertebrate optic vesicle patterning, where Cdon acts as a negative regulator of Hedgehog signalling to define the boundary between the optic stalk and the retina.

    • Marcos Julián Cardozo
    • , Luisa Sánchez-Arrones
    •  & Paola Bovolenta

  • Article
    | Open Access

    The morphogen, Bmp, regulates differentiation of cell fates along the ventral to dorsal axis during vertebrate embryonic development. Here, Xue et al. show that Bmp2b produced by the organizer during early gastrulation in zebrafish embryos has a role in the establishment of an appropriate Bmp morphogen activity gradient and the correct dorsoventral patterning of the embryos.

    • Yu Xue
    • , Xiudeng Zheng
    •  & Anming Meng

  • Article |

    Terminal patterning of the Drosophila embryo is thought to be regulated by local cleavage of the ubiquitous peptide hormone Trunk (Trk) controlled by the maternal gene torso-like (tsl)that is expressed only at embryo poles. Here, the authors show that cleavage of Trk is indeed required for patterning and can occur independently of Tsl.

    • Michelle A. Henstridge
    • , Travis K. Johnson
    •  & James C. Whisstock

  • Article |

    The histone demethylase Lsd1 regulates the balance between self-renewal and differentiation in human embryonic stem cells. Here, the authors show that the loss of Lsd1 in the trophectoderm of mouse embryos leads to premature differentiation of trophoblast stem cells, partially due to de-repression of the transcription factor Ovol2.

    • Dongmei Zhu
    • , Stefanie Hölz
    •  & Roland Schüle

  • Article |

    Bird wings resemble the digits on the hands of dinosaurs, but which digit positions gave rise to those seen in modern birds is still unclear. In this work, long-term fate maps of the chick wing polarizing region are presented, supporting fossil data that birds descended from theropods that had digits 1, 2 and 3.

    • Matthew Towers
    • , Jason Signolet
    •  & Cheryll Tickle

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