Development

  • Article
    | Open Access

    Short open reading frames (smORFs) of less than 100 codons exist in the thousands in metazoan genomes, mostly with yet unknown functions. Here the authors show how a smORF conserved from flies to vertebrates produces a secreted peptide that enhances the diffusion of the cell signalling protein Wingless.

    • Emile G. Magny
    • , Ana Isabel Platero
    •  & Juan Pablo Couso
  • Article
    | Open Access

    Nail-patella syndrome (NPS) is characterized by nail dysplasia, absent/hypoplastic patellae, chronic kidney disease, and glaucoma and can be caused by haploinsufficiency of LMX1B; however, not all patients harbor pathogenic LMX1B mutations. Here the authors show that loss-of-function variations in upstream enhancer sequences are responsible for a limb specific form of human NPS.

    • Endika Haro
    • , Florence Petit
    •  & Kerby C. Oberg
  • Article
    | Open Access

    CTCF is as an architectural protein involved in 3D genome folding; however its contribution to animal development has not been well characterized. Here the authors show that CTCF is not only pivotal for 3D chromatin structure and enhancer-promoter interactions in zebrafish, but it is also essential for controlling the expression of thousands of genes during development.

    • Martin Franke
    • , Elisa De la Calle-Mustienes
    •  & José L. Gómez-Skarmeta
  • Article
    | Open Access

    Intricate color patterns are a defining aspect of morphological diversity in the Felidae. Here the authors apply morphological and single-cell gene expression analysis to fetal skin of domestic cats to identify when, where, and how, during fetal development, felid color patterns are established.

    • Christopher B. Kaelin
    • , Kelly A. McGowan
    •  & Gregory S. Barsh
  • Article
    | Open Access

    The development of the coronal suture remains incompletely understood. Here the authors perform scRNA-seq and expression validation to uncover the cellular diversity within the murine embryonic coronal suture, thus revealing possible mechanisms for its loss in craniosynostosis.

    • D’Juan T. Farmer
    • , Hana Mlcochova
    •  & Stephen R. F. Twigg
  • Article
    | Open Access

    Poised enhancers (PEs) in embryonic stem cells have accessible chromatin, are bound by repressive Polycomb Group proteins, and interact with their targets prior to activation. However, whether this is recapitulated in vivo is unknown. Here the authors show PEs display these features in mouse embryos, are prevalent across vertebrates, and are required for developmental gene expression.

    • Giuliano Crispatzu
    • , Rizwan Rehimi
    •  & Alvaro Rada-Iglesias
  • Article
    | Open Access

    How the genetic background modifies the expression of mutations is a key question that is addressed in this study in the context of seam cell development in Caenorhabditis elegans isolates. One amino acid deletion in a conserved heat shock protein is sufficient to shape phenotype expressivity upon mutation of a GATA transcription factor.

    • Sneha L. Koneru
    • , Mark Hintze
    •  & Michalis Barkoulas
  • Article
    | Open Access

    How the developing skin epidermis is transformed from a simple single-layered epithelium to a complex and stratified barrier is still an open question. Here, the authors provide a model based on high proliferation and delamination of the keratinocyte progenitors that support the stratification process.

    • Mareike Damen
    • , Lisa Wirtz
    •  & Hisham Bazzi
  • Article
    | Open Access

    Sensory hair cells develop an asymmetric architecture to restrict stimulus detection to a single axis. Here the authors identify GPR156 as directing a 180-degree reversal in hair cell orientation through Gαi, downstream of EMX2 in the mouse inner ear and zebrafish lateral line.

    • Katie S. Kindt
    • , Anil Akturk
    •  & Basile Tarchini
  • Article
    | Open Access

    How transcription factors regulate cell fates in native tissues is unclear. Here, the authors report that differential chromatin binding of NKX2-1 determines opposing alveolar cell fates in the murine lung, showing loss of YAP/TAZ directs NKX2-1 to alternative binding sites leading to cell fate conversion.

    • Danielle R. Little
    • , Anne M. Lynch
    •  & Jichao Chen
  • Article
    | Open Access

    Acheiropodia is associated with homozygous deletions in the LMBR1 gene around ZRS, an enhancer regulating SHH during limb development, but how these deletions lead to this phenotype is unknown. Here the authors use whole-genome sequencing, ChIP-seq, 4C-seq and DNA FISH to show that alterations in CTCF motifs are responsible via altered enhancer–promoter interactions.

    • Aki Ushiki
    • , Yichi Zhang
    •  & Nadav Ahituv
  • Article
    | Open Access

    Drosophila m6A writer complex regulates alternative splicing of the Sex-lethal gene. Here the authors show that a potential E3 ligase Hakai interacts with the fly m6A writer complex and that m6A level is reduced in Hakai mutant flies.

    • Yanhua Wang
    • , Lifeng Zhang
    •  & Dong Yan
  • Article
    | Open Access

    Immune cells are known to aggravate the inflammatory impact of Duchene muscular dystrophy. Here, the authors describe impaired thymic development and suggest thymic involution in this model of disease is linked to disease acceleration due to impaired immunological tolerance.

    • Andrea Farini
    • , Clementina Sitzia
    •  & Yvan Torrente
  • Article
    | Open Access

    The SWI/SNF complex BAF and the histone H3K4 methyltransferase MLL4 (KMT2D) play critical roles in enhancer activation, however the interplay between them has remained unclear. Here the authors show that BAF and MLL4 are interdependent in promoting enhancer activation by lineage-determining transcription factors during adipogenesis.

    • Young-Kwon Park
    • , Ji-Eun Lee
    •  & Kai Ge
  • Article
    | Open Access

    Sex chromosome gene content and expression is unusual. Here the authors use single cell RNA-Seq on Drosophila larvae to demonstrate that the single X and pair of 4th chromosomes are specifically inactivated in primary spermatocytes, while genes on the single Y chromosome become maximally active in primary spermatocytes.

    • Sharvani Mahadevaraju
    • , Justin M. Fear
    •  & Brian Oliver
  • Article
    | Open Access

    Animals respond to hypoxic stress by adjusting metabolic processes to balance survival and reproduction. Here the authors identify the transcription factor PQM-1 as a metabolic regulator that balances hypoxic lipid and carbohydrate metabolism in C. elegans to limit somatic integrity and promote progeny survival.

    • Thomas Heimbucher
    • , Julian Hog
    •  & Coleen T. Murphy
  • 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

    Asparaginyl-tRNA synthetase1 (NARS1) is required for protein synthesis. Here, the authors identify biallelic NARS1 mutations in individuals with microcephaly and neurodevelopmental delay. Cortical brain organoid modeling recapitulates microcephaly characteristics and scRNA-seq reveals a role for NARS1 in radial glial cell proliferation.

    • Lu Wang
    • , Zhen Li
    •  & Joseph G. Gleeson
  • Article
    | Open Access

    XPO5 mediates nuclear export of miRNA hairpin precursors (pre-miRNAs) through a RanGTP-dependent binding. Here the authors employ HITS-CLIP and biochemical analysis and show that XPO5 binds and promotes nuclear processing of clustered pri-miRNAs, with extensive double-stranded regions, independently of RanGTP.

    • Jingjing Wang
    • , Jerome E. Lee
    •  & Rui Yi
  • Article
    | Open Access

    How hormonal signaling in the mammary epithelium controls the surrounding extracellular matrix is unclear. Here, the authors show that a secreted protease, Adamts18, induced by upstream estrogen-progesterone activated Wnt4 in myoepithelial cells, remodels the basement membrane and contributes to mammary epithelial stemness.

    • Dalya Ataca
    • , Patrick Aouad
    •  & Cathrin Brisken
  • Article
    | Open Access

    Although micro(mi)RNA-based post-transcriptional regulatory mechanisms have been implicated in the assembly and modulation of synaptic connections, few miRNAs have been identified that control synapse formation. Here, authors performed an unbiased screen for novel regulators of synapse morphogenesis at the Drosophila larval neuromuscular junction and discovered that miR-34 inhibits Nrx-IV to influence active zone formation, whereas, postsynaptic miR-34 inhibits Hts to regulate the initiation of bouton formation from presynaptic terminals.

    • Elizabeth M. McNeill
    • , Chloe Warinner
    •  & David Van Vactor
  • Article
    | Open Access

    Congenital scoliosis is a complex genetic disorder characterized by vertebral malformation. Here, the authors demonstrate that loss of dstyk leads to scoliosis in zebrafish due to dysregulated biogenesis of notochord vacuoles and that DSTYK is required for lysosome biogenesis through mTORC1 regulation.

    • Xianding Sun
    • , Yang Zhou
    •  & Lin Chen
  • Article
    | Open Access

    The adult mammalian inner ear cells cannot regenerate nor proliferate. Here, the authors show that co-activation of Myc and NOTCH pathways can stimulate proliferation of inner ear sensory epithelial cells, which can be induced to become hair cell-like cells in vitro and in vivo.

    • Yilai Shu
    • , Wenyan Li
    •  & Zheng-Yi Chen
  • Article
    | Open Access

    Mapping transcription factors (TFs) occupancy is essential for understanding transcriptional programs. Here the authors use biotinylated knockin alleles of key cardiac TFs (GATA4, NKX2-5, MEF2A, MEF2C, SRF, TBX5, TEAD1) to map their genome-wide occupancy in the fetal and adult mouse heart, providing insight into the cardiac transcriptional regulatory network.

    • Brynn N. Akerberg
    • , Fei Gu
    •  & William T. Pu
  • Article
    | Open Access

    The molecular role of ciliary Polycystin-2 (PC2) in cyst formation and polycystic kidney disease (ADKPD) is unclear. Here, the authors identify a PC2 mutant lacking ciliary localisation but with active Ca2+ channel function in mice, that is sufficient to generate an ADPKD phenotype.

    • Rebecca V. Walker
    • , Jennifer L. Keynton
    •  & Dominic P. Norris
  • Article
    | Open Access

    Polycomb Repressive Complex 2 (PRC2) plays critical roles in transcriptional silencing during development. Here the authors identify EZHIP as a cofactor of PRC2 expressed predominantly in the gonads, finding that EZHIP limits the enzymatic activity of PRC2 in germ cells in mice.

    • Roberta Ragazzini
    • , Raquel Pérez-Palacios
    •  & Raphaël Margueron
  • Article
    | Open Access

    Meiotic DSB formation, repair and recombination occur in a continuum of substages termed leptonema, zygonema, pachynema, and diplonema. Here, authors develop a method for isolating pure sub-populations of nuclei that allows for detailed study of meiotic substages.

    • Kwan-Wood Gabriel Lam
    • , Kevin Brick
    •  & R. Daniel Camerini-Otero
  • Article
    | Open Access

    Pioneer transcription factor Pax7 specifies melanotrope cells, which then allows for the binding of Tpit transcription factor. Here, authors find that while binding of heterochromatin targeting by Pax7 is independent of Tpit, Pax7-dependent chromatin opening requires Tpit.

    • Alexandre Mayran
    • , Kevin Sochodolsky
    •  & Jacques Drouin
  • Article
    | Open Access

    Prior evidence suggested mesenchymal stromal cells (MSCs) required for skeletal formation, maintenance, and repair arise postnatally. Here, the authors show that Hoxa11 lineage-marked cells give rise to all skeletal lineages from embryogenesis through adulthood and are upstream progenitors of LepR- and Osx-lineage MSCs

    • Kyriel M. Pineault
    • , Jane Y. Song
    •  & Deneen M. Wellik
  • Article
    | Open Access

    Why and how mutations in genes encoding BAF complex components lead to distinct disease entitites remains unresolved. In this study, authors establish the first Smarcb1 mutant mouse model with multiple brain abnormalities recapitulating human Coffin–Siris syndrome and show that one prominent midline abnormality, corpus callosum agenesis, is due to midline glia aberrations.

    • Alina Filatova
    • , Linda K. Rey
    •  & Ulrike A. Nuber
  • Article
    | Open Access

    The transcriptional signature of embryonic lethality has not been defined. Here, the authors, as part of the Deciphering the Mechanisms of Developmental Disorders programme, define genes causing murine embryonic lethality around E9.5 and identify developmental delay transcriptional signatures.

    • John E. Collins
    • , Richard J. White
    •  & Elisabeth M. Busch-Nentwich
  • Article
    | Open Access

    Our limited understanding of the hybrid sterility (HS) mechanism in Asian–African rice hybrids hampers utilization of the interspecific heterosis for rice production. Here, the authors identify S1-mediated HS-related tripartite gamete killer-protector system, and explore their evolutionary relationship.

    • Yongyao Xie
    • , Jintao Tang
    •  & Letian Chen
  • Article
    | Open Access

    The hypoxia response pathway couples oxygen availability to physiological adaptations. Using the model system Drosophila melanogaster, here the authors show that hypoxia inhibits TORC1 signalling and increases lipid levels in the larval fat body and that these effects are required for development to adulthood.

    • Byoungchun Lee
    • , Elizabeth C. Barretto
    •  & Savraj S. Grewal
  • Article
    | Open Access

    Cerebral Cavernous Malformations (CCM) are often caused by mutations in CCM1/KRIT1. Here, Chapman et al. elegantly show that the CCM complex promotes apoptosis by regulating zinc homeostasis and storage via a conserved mechanism that likely generates the pathological defects observed in CCM.

    • Eric M. Chapman
    • , Benjamin Lant
    •  & W. Brent Derry
  • Article
    | Open Access

    The process of alveologenesis is incompletely understood, partly due to the lack of applicable real-time imaging methods. Here the authors describe the process of alveologenesis and the behaviour of epithelial cells in real-time, using widefield microscopy and image deconvolution in precision-cut lung slices, revealing the dominant role of epithelial cell migration.

    • Khondoker M. Akram
    • , Laura L. Yates
    •  & Charlotte H. Dean
  • Article
    | Open Access

    Examples of overdominance are usually explained by deleterious effects in homozygotes. Here, Kellenberger et al. describe a case of overdominance in the floral color of the Alpine orchid Gymnadenia rhellicani apparently maintained by pollinator preferences without deleterious effects in homozygotes.

    • Roman T. Kellenberger
    • , Kelsey J. R. P. Byers
    •  & Philipp M. Schlüter
  • Article
    | Open Access

    Biogenesis and function of miRNAs in somatic cells is well characterized, but their role in the germline has not been established. Here the authors identify and characterize Drosha independent and dependent miRNAs during C. elegans oogenesis, revealing their roles in meiotic progression and oocyte development.

    • Amanda L. Minogue
    • , Michael R. Tackett
    •  & Swathi Arur
  • Article
    | Open Access

    The BAF complex is a multi-subunit chromatin remodeling complex that plays important roles in transcription regulation. Here the authors provide evidence that BRD9 and GLTSCR1/BICRA or its paralog GLTSCR1-like/BICRAL define a non-canonical BAF complex that regulates naive pluripotency in mouse embryonic stem cells.

    • Jovylyn Gatchalian
    • , Shivani Malik
    •  & Diana C. Hargreaves
  • Article
    | Open Access

    During early embryogenesis, critical cardiac specification events occur. Here the authors isolate cardiac progenitor cells from early zebrafish embryos and characterize accessible chromatin regions specific to this cell population, finding that many of these regions overlap with conserved non-coding elements that are ortholgous to accessible chromatin regions in human.

    • Xuefei Yuan
    • , Mengyi Song
    •  & Michael D. Wilson