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Regional Differences in Progenitor Consumption Dynamics Shape Brain Growth during Development

ABSTRACT: Regional Differences in Progenitor Consumption Dynamics Shape Brain Growth during Development

PROVIDER: PRJNA1008340 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25736700.fastq.gz	Fastqsanger.gz
	SRR25736701.fastq.gz	Fastqsanger.gz
	SRR25736702.fastq.gz	Fastqsanger.gz
	SRR25736703.fastq.gz	Fastqsanger.gz
	SRR25736704.fastq.gz	Fastqsanger.gz

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Regional Differences in Progenitor Consumption Dynamics Shape Brain Growth during Development

Project description:The structure of vertebrate brains emerges from a shared template where three primary regions — the hindbrain, midbrain, and forebrain — develop during embryogenesis to establish the circuits responsible for distinct functions. While the molecular mechanisms underlying the segmentation of the neural tube into these regions are relatively well understood, how their relative expansion is regulated during embryogenesis remains largely unknown. To address this question, we first generated a single-cell resolution atlas of birthdate across the entire mouse brain (https://www.neurobirth.org), which we next leveraged to identify brain-region-specific neurogenic patterns and investigate underlying molecular mechanisms. We show that in brain regions that expand, such as the neocortex, neurogenesis is sustained (sustained neurogenic regions), while it is limited to the first few days of brain development in hindbrain regions that are comparatively less developed (transient neurogenic regions). We demonstrate that sustained cortical neurogenesis is made possible by a progressive lengthening of the cell cycle and associated lower levels of consumptive divisions in apical progenitors (AP), which preserve the progenitor pool for longer periods. Finally, using single-cell RNA sequencing of AP across the developing brain, we identify spatio-temporal molecular determinants of AP cycling behavior and demonstrate a critical role for the mitochondrial membrane protein Fam210b in regulating region-specific cycling properties. These results identify a parsimonious mechanism to regulate neuronal production in different parts of the brain, in which the time window during which neurons are generated appears to be a critical determinant of a region’s expansion during development and evolution.

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Regional differences in mRNA and lncRNA expression patterns in the non-failing human heart

Project description:Background: Although chamber specialization is critical for proper cardiac function, a comprehensive, genome-wide analysis of the cardiac transcriptome, including identification of regional differences in mRNA and lncRNA expression patterns for the four chambers and interventricular septum of the non-failing human heart, has not been performed. Methods and Results: mRNA and long noncoding RNA (lncRNA) transcriptional profiling of the left (LA) and right (RA) atria, left (LV) and right (RV) ventricles, and the interventricular septum (IVS) of non-failing human hearts (N=8) was performed by deep sequencing. Analysis of the mRNA and lncRNA expression profiles revealed that the different regions of the heart are distinct. Differential expression analysis of paired tissue samples identified 5,747 mRNAs and 2,794 lncRNAs with chamber-enriched expression patterns. The largest differences in mRNA and lncRNA expression were evident between atria and ventricular samples, including regional differences in ~20% of all cardiac expressed mRNA and lncRNA transcripts. Regional differences in mRNA and lncRNA expression were also evident, although to a lesser extent, between the LA and RA, and between the LV, RV and IVS. Gene ontology classification of differentially expressed gene sets revealed regional differences in chamber specialization, including differences in signaling, metabolism, and muscle contraction. Sex differences in mRNA and lncRNA gene expression profiles were also identified between male and female LA and RA samples. Conclusions: There are marked regional differences in the mRNA and lncRNA expression profiles in non-failing adult human heart, and are associated with chamber specialization.

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Regulatory element copy number differences shape primate expression profiles

Project description:Regulatory element copy number differences shape primate expression profiles

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Differential gene expression in mouse retina related to regional differences in vulnerability to hyperoxia

Project description:Purpose: In the C57BL/6J mouse retina, hyperoxia-induced degeneration of photoreceptors shows strong regional variation, beginning at a locus ~0.5mm inferior to the optic disc. To identify gene expression differences that might underlie this variability in vulnerability, we have used microarray techniques to describe regional (superior-inferior) variations in gene expression in the retina. Methods: Young adult C57BL/6J mice raised in dim cyclic illumination (12h 5lux, 12h darkness) were exposed to hyperoxia (75% oxygen for 2w). Retinas were collected from hyperoxia-exposed and control animals without fixation, and divided into superior and inferior halves. RNA was extracted from each sample, purified and hybridised to mouse 1.0 ST arrays (Affymetrix). The consistency of the microarray results was assessed with quantitative PCR for selected genes. Expression data were analysed to identify genes and ncRNAs whose differential expression between superior and inferior retina could be associated with relative vulnerability to hyperoxia.

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Regional Analysis of The Brain Transcriptome In Mice Bred For High And Low Methamphetamine Consumption

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