The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution

Science, Год журнала: 2018, Номер 360(6392)

Опубликована: Апрель 26, 2018

Mapping the vertebrate developmental landscape As embryos develop, numerous cell types with distinct functions and morphologies arise from pluripotent cells. Three research groups have used single-cell RNA sequencing to analyze transcriptional changes accompanying development of (see Perspective by Harland). Wagner et al. sequenced transcriptomes more than 90,000 cells throughout zebrafish reveal how differentiate during axis patterning, germ layer formation, early organogenesis. Farrell profiled tens thousands embryonic applied a computational approach construct branching tree describing trajectories that lead 25 types. The revealed change their gene expression as they become specialized. Briggs examined whole frog embryos, spanning zygotic genome activation through organogenesis, map states differentiation across all lineages over time. These data approaches pave way for comprehensive reconstruction development. Science , this issue p. 981 eaar3131 eaar5780 ; see also 967

Язык: Английский

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Genenames.org: the HGNC and VGNC resources in 2019

Nucleic Acids Research, Год журнала: 2018, Номер 47(D1), С. D786 - D792

Опубликована: Окт. 4, 2018

The HUGO Gene Nomenclature Committee (HGNC) based at EMBL's European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. There are over 40 000 approved gene in our current database of which 19 for protein-coding Vertebrate (VGNC) was established 2016 assign standardized nomenclature line with vertebrate species that lack their own committees. VGNC initially assigned 15000 genes chimpanzee. We have extended this process other species, naming 14000 cow dog 13 horse date. Our HGNC website https://www.genenames.org has undergone a major design update, simplifying the homepage provide easy access search tools making site more mobile friendly. families pages now known as 'gene groups' increased number 1200, nearly half all named currently least one group. This article provides an overview online data resources, focusing on work last two years.

Язык: Английский

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3D genomics across the tree of life reveals condensin II as a determinant of architecture type

Science, Год журнала: 2021, Номер 372(6545), С. 984 - 989

Опубликована: Май 27, 2021

We investigated genome folding across the eukaryotic tree of life. find two types three-dimensional (3D) architectures at chromosome scale. Each type appears and disappears repeatedly during evolution. The architecture that an organism exhibits correlates with absence condensin II subunits. Moreover, depletion converts human to a state resembling seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together nucleoli, heterochromatin domains merge. propose physical model which lengthwise compaction chromosomes by mitosis determines chromosome-scale architecture, effects are retained subsequent interphase. This mechanism likely has been conserved since last common ancestor all eukaryotes.

Язык: Английский

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Collective durotaxis along a self-generated stiffness gradient in vivo

Nature, Год журнала: 2021, Номер 600(7890), С. 690 - 694

Опубликована: Дек. 8, 2021

Язык: Английский

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The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals

Nucleic Acids Research, Год журнала: 2020, Номер 49(D1), С. D831 - D847

Опубликована: Сен. 15, 2020

Abstract Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced by integrating data types (RNA-Seq, Affymetrix, situ hybridization, EST data). It based exclusively on curated healthy wild-type (e.g., no knock-out, treatment, disease), provide comparable reference of normal expression. Curation includes very large datasets such as GTEx (re-annotation samples ‘healthy’ or not) well many small ones. Data are integrated made between species thanks consistent annotation processing, calls presence/absence expression, along with scores. As result, capable detecting the conditions any single gene, accommodating type species. provides several tools for analyses, allowing, e.g., automated comparisons within retrieval prefered enrichment analyses sets genes. release 14.1 29 available at https://bgee.org/ through its Bioconductor R package BgeeDB.

Язык: Английский

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Xenbase: key features and resources of the Xenopus model organism knowledgebase

Genetics, Год журнала: 2023, Номер 224(1)

Опубликована: Фев. 9, 2023

Abstract Xenbase (https://www.xenbase.org/), the Xenopus model organism knowledgebase, is a web-accessible resource that integrates diverse genomic and biological data from research on laboratory frogs laevis tropicalis. The goal of to accelerate discovery empower research, enhance impact data, facilitate dissemination these data. also enhances value through high-quality curation, integration, providing bioinformatics tools optimized for experiments, linking human other organisms. plays an indispensable role in making interoperable accessible broader biomedical community accordance with FAIR principles. provides annotated updates organizations such as NCBI, UniProtKB, Ensembl, Gene Ontology consortium, most recently, Alliance Genomic Resources, common clearing house humans This article brief overview key recently added features Xenbase. New include processing high-throughput sequencing NCBI Expression Omnibus; curation anatomical, physiological, expression phenotypes newly created Phenotype Ontology; annotations; new anatomical drawings Normal Table development; integration latest v10.1 genome annotations. Finally, we highlight areas future development at continue support community.

Язык: Английский

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Spatiotemporal omics for biology and medicine

Cell, Год журнала: 2024, Номер 187(17), С. 4488 - 4519

Опубликована: Авг. 1, 2024

Язык: Английский

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Microsampling Capillary Electrophoresis Mass Spectrometry Enables Single-Cell Proteomics in Complex Tissues: Developing Cell Clones in Live Xenopus laevis and Zebrafish Embryos

Analytical Chemistry, Год журнала: 2019, Номер 91(7), С. 4797 - 4805

Опубликована: Март 3, 2019

Label-free single-cell proteomics by mass spectrometry (MS) is currently incompatible with complex tissues without requiring cell culturing, dissection, or tissue dissociation. We here report the first example of label-free MS-based directly in single cells live vertebrate embryos. Our approach integrates optically guided situ subcellular capillary microsampling, one-pot extraction-digestion collected proteins, peptide separation electrophoresis, ionization an ultrasensitive electrokinetically pumped nanoelectrospray, and detection high-resolution MS (Orbitrap). With a 700 zmol (420 000 copies) lower limit detection, this trace-sensitive technology confidently identified quantified ∼750-800 protein groups (<1% false-discovery rate) analyzing just ∼5 ng digest, viz. <0.05% total content from individual 16-cell Xenopus laevis (frog) embryo. After validating recovering animal-vegetal-pole proteomic asymmetry frog zygote, was applied to uncover reorganization as animal-dorsal (D11) embryo gave rise its neural-tissue-fated clone developing 32-, 64-, 128-cell stages. In addition enabling on smaller X. laevis, we also demonstrated be scalable zebrafish Microsampling raises exciting opportunities study developmental processes whole organisms at level building block life: cell.

Язык: Английский

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Fibroblast dedifferentiation as a determinant of successful regeneration

Developmental Cell, Год журнала: 2021, Номер 56(10), С. 1541 - 1551.e6

Опубликована: Май 1, 2021

Limb regeneration, while observed lifelong in salamanders, is restricted post-metamorphic Xenopus laevis frogs. Whether this loss due to systemic factors or an intrinsic incapability of cells form competent stem has been unclear. Here, we use genetic fate mapping establish that connective tissue (CT) the frog blastema, as case axolotls. Using heterochronic transplantation into limb bud and single-cell transcriptomic profiling, show axolotl CT dedifferentiate integrate lineages, including cartilage. In contrast, blastema do not fully re-express progenitor program, even when transplanted bud. Correspondingly, contribute extraskeletal CT, but developing Furthermore, using RNA-seq analysis find embryonic adult cartilage differentiation programs are molecularly distinct. This work defines restrictions dedifferentiation a limitation regeneration.

Язык: Английский

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Microglial trogocytosis and the complement system regulate axonal pruning in vivo

eLife, Год журнала: 2021, Номер 10

Опубликована: Март 11, 2021

Partial phagocytosis-called trogocytosis-of axons by microglia has been documented in ex vivo preparations but not directly observed vivo. The mechanisms that modulate microglial trogocytosis of and its function neural circuit development remain poorly understood. Here, we observe axon the developing Xenopus laevis retinotectal circuit. We show regulate pruning retinal ganglion cell are important for proper behavioral response to dark bright looming stimuli. Using bioinformatics, identify amphibian regulator complement activation 3, a homolog human CD46, as neuronally expressed synapse-associated inhibitory molecule inhibits axonal pruning. membrane-bound C3 fusion protein, demonstrate enhancing activity enhances Our results support model remodel via neurons can control this process through expression proteins.

Язык: Английский

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