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Distinct modes of cell competition shape mammalian tissue morphogenesis

ABSTRACT: Distinct modes of cell competition shape mammalian tissue morphogenesis

PROVIDER: PRJNA526869 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8720830_1.fastq.gz	Fastqsanger.gz
	SRR8720830_2.fastq.gz	Fastqsanger.gz
	SRR8720840_1.fastq.gz	Fastqsanger.gz
	SRR8720840_2.fastq.gz	Fastqsanger.gz
	SRR8720850_1.fastq.gz	Fastqsanger.gz

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Distinct modes of cell competition shape mammalian tissue morphogenesis

Project description:Cell competition (CC)—the sensing and elimination of less fit “loser” cells by neighbouring “winner” cells—was first described in Drosophila. Although proposed as a selection mechanism to optimize tissue and organ development, its evolutionary generality remains unclear. Here, by employing live-imaging, lineage-tracing, single cell transcriptomics and genetics, we unearth two intriguing CC mechanisms that sequentially shape and maintain stratified tissue architecture during mouse skin development. Early in embryonic epidermis, winner progenitors within the single-layered epithelium kill and clear neighbouring losers by engulfment. Upon stratification and skin barrier formation, the basal layer instead expels losers through a homeostatic upward flux of differentiating progeny. This CC switch is physiologically relevant, as when it is perturbed, so too is barrier formation. Our findings establish CC as a selective force to optimize function of a vertebrate tissue, but also illuminate how a tissue dynamically adjusts its CC strategies to preserve fitness as it encounters increased architectural complexity during morphogenesis.

2019-05-31 | GSE128241 | GEO

Distinct modes of cell competition shape mammalian tissue morphogenesis.

Project description:Cell competition-the sensing and elimination of less fit 'loser' cells by neighbouring 'winner' cells-was first described in Drosophila. Although cell competition has been proposed as a selection mechanism to optimize tissue and organ development, its evolutionary generality remains unclear. Here, by using live imaging, lineage tracing, single-cell transcriptomics and genetics, we identify two cell competition mechanisms that sequentially shape and maintain the architecture of stratified tissue during skin development in mice. In the single-layered epithelium of the early embryonic epidermis, winner progenitors kill and subsequently clear neighbouring loser cells by engulfment. Later, as the tissue begins to stratify, the basal layer instead expels losers through upward flux of differentiating progeny. This cell competition switch is physiologically relevant: when it is perturbed, so too is barrier formation. Our findings show that cell competition is a selective force that optimizes vertebrate tissue function, and illuminate how a tissue dynamically adjusts cell competition strategies to preserve fitness as its architectural complexity increases during morphogenesis.

| S-EPMC6638572 | biostudies-literature

Lactate-dependent Transcriptional Regulation Controls Mammalian Eye Morphogenesis

Project description:Lactate-dependent Transcriptional Regulation Controls Mammalian Eye Morphogenesis

| PRJNA837217 | ENA

Lactate-dependent Transcriptional Regulation Controls Mammalian Eye Morphogenesis [scRNA-seq]

Project description:Mammalian retinal metabolism favors aerobic glycolysis. However, the role of glycolytic metabolism in retinal morphogenesis remains unknown. We report that aerobic glycolysis is necessary for the early stages of retinal development. Taking advantage of an unbiased approach that combines the use of eye organoids and single-cell RNA sequencing, we identify specific glucose transporters and glycolytic genes in retinal progenitors. Next, we determine that the optic vesicle territory of mouse embryos displays elevated levels of glycolytic activity. At the functional level, we show that removal of Glucose transporter 1 and Lactate dehydrogenase A gene activity from developing retinal progenitors arrests eye morphogenesis. Surprisingly, we uncover that lactate-mediated upregulation of key eye-field transcription factors is controlled by the epigenetic modification of histone H3 acetylation through histone deacetylase activity. Our results identify an unexpected bioenergetic independent role of lactate as a signaling molecule necessary for mammalian eye morphogenesis.

2023-06-08 | GSE202758 | GEO

Lactate-dependent Transcriptional Regulation Controls Mammalian Eye Morphogenesis [RNA-seq]

2023-06-08 | GSE202757 | GEO

Lactate-dependent Transcriptional Regulation Controls Mammalian Eye Morphogenesis [H3K27ac ChIP-seq]

2023-06-08 | GSE224648 | GEO

Lactate-dependent Transcriptional Regulation Controls Mammalian Eye Morphogenesis [scRNA-seq]

Project description:Lactate-dependent Transcriptional Regulation Controls Mammalian Eye Morphogenesis [scRNA-seq]

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Lactate-dependent Transcriptional Regulation Controls Mammalian Eye Morphogenesis [RNA-seq]

Project description:Lactate-dependent Transcriptional Regulation Controls Mammalian Eye Morphogenesis [RNA-seq]

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Lactate-dependent Transcriptional Regulation Controls Mammalian Eye Morphogenesis [H3K27ac ChIP-seq]

Project description:Lactate-dependent Transcriptional Regulation Controls Mammalian Eye Morphogenesis [H3K27ac ChIP-seq]

| PRJNA932003 | ENA

Deconvolving the recognition of DNA shape from sequence

Project description:Binding of transcription factors to DNA is mediated by the recognition of the chemical signatures of the DNA bases and the three-dimensional shape of the DNA molecule. The direct contribution of DNA shape to DNA-binding specificity has been difficult to assess, as DNA shape is a consequence of its sequence. Here, we teased apart these two modes of recognition in the context of Hox-DNA binding. We made a series of mutations in Hox residues that, in a co-crystal structure, only recognize DNA shape, and tested the effect on DNA binding preferences using SELEX-seq. Analysis of shape features of selected sequences revealed that these residues are both necessary and sufficient for selection of sequences with distinct shape features. We used statistical machine learning to show that the accuracy of binding specificity predictions improves by adding shape features to a model that only depends on sequence. We conclude that shape readout is a direct and critical component of binding site selection by Hox proteins. Three rounds of SELEX were performed on a series of Hox mutants as described in Slattery et al, Cell, 2011 (PMID 22153072) and Riley et al, Methods in molecular Biology, 2014 (PMID 25151169). Briefly, His-tagged Scr and Antp mutant proteins were incubated with a randomized 16mer oligonucleotide library, and bound DNA was amplified and sequenced as described (PMID 22153072, PMID 25151169).

2015-01-21 | E-GEOD-65073 | biostudies-arrayexpress

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