Human serpina3 modulates cortex expansion and folding
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA694137 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13509490.fastq.gz | Fastqsanger.gz | |||
| SRR13509491.fastq.gz | Fastqsanger.gz | |||
| SRR13509492.fastq.gz | Fastqsanger.gz | |||
| SRR13509493.fastq.gz | Fastqsanger.gz | |||
| SRR13509494.fastq.gz | Fastqsanger.gz |
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Project description:Purpose:To gain a deeper insight into how Serpina3 regulates neurogenesis and further controling cortex folding in mice brain, RNA-sequencing (RNA-seq) was performed to analyze the genome-wide changes by TCF20 deletion at E15. Methods: Total RNA was extracted from E15 telencephalic tissue of WT and serpina3 cKI mice. Then total RNA was quality controlled and quantified using an Agilent 2100 Bioanalyzer. After converting to cDNA and building library, high-throughput sequencing was performed using the Illumina HiSeq 2500 platform in Annoroad Genomics. Results: Approximately approximately one thousand transcripts showed differential expression between the WT and Serpina3 knock-in brain cortex, with a fold change ≥1.5 and p value <0.05. Gene ontology (GO) analysis showed that the up-regulated genes were enriched in the terms related to neurogenesis, neuronal specification, neural differentiation and secretion by cells. Up-regulated genes showed a significant enrichment of terms involved in up regulation of hypersensitivity and down regulation of inflammatory response. These results reflected the importance of serpina3 in cortical neurogenesis and cortex folding. Conclusions: We conclude that RNA-seq based transcriptome characterization would provide a framework for understanding how serpina3 contribute to brain cortical development.
2021-01-23 | GSE165345 | GEO
Project description:Evolution of the mammalian brain encompassed a remarkable increase in size of cerebral cortex, including tangential and radial expansion, but the mechanisms underlying these key parameters are still largely unknown. Here, we identified the novel DNA associated protein TRNP1 as a regulator of cerebral cortical expansion in both these dimensions. Gain and loss of function experiments in the mouse cerebral cortex in vivo demonstrate that high Trnp1 levels promote neural stem cell self-renewal and tangential expansion, while lower levels promote radial expansion resulting in a potent increase in the generation of intermediate progenitors and outer radial glial cells resulting in folding of the otherwise smooth murine cerebral cortex. Remarkably, TRNP1 expression levels exhibit regional differences also in the cerebral cortex of human fetuses anticipating radial or tangential expansion respectively. Thus, the dynamic regulation of TRNP1 is critical to regulate tangential and radial expansion of the cerebral cortex in mammals. We performed gene expression microarray analysis on embryonic mouse cerebral cortex derived from Trnp1 knockdown and control animals.
2013-04-26 | E-GEOD-40582 | biostudies-arrayexpress
Project description:Purpose: To better understand how Serpina3 modulate cortex enpansion and folding. We performed single cell sequencing to reveal the change of cell types in single cell level. Method: Single cell isolation was prepared from P0 telencephalic tissue of wild-type (WT) and serpina3f/+;Nestin-Cre mice. The fragmented cDNAs containing barcode and UMI sequences was built the library. Agilent 2100 Bioanalyzer was used to quality controlled and quantified. Single cell RNA-sequencing analysis was used by the Illumina platform in Annoroad Genomics. Results: Clustering and labeling of these cells visualized on a t-SNE plot between the wild-type (WT) and Serpina3f/+;Nestin-Cre mice brain cortex. Specific layer neurons were increased in Serpina3 knock in mice. Conclusions: Single cell RNA-seq data would provide an overall understanding how SERPINA3 gene contribute to generation of cortical expansion and folding in mice.
2021-01-26 | GSE165440 | GEO
Project description:Evolution of the mammalian brain encompassed a remarkable increase in size of cerebral cortex, including tangential and radial expansion, but the mechanisms underlying these key parameters are still largely unknown. Here, we identified the novel DNA associated protein TRNP1 as a regulator of cerebral cortical expansion in both these dimensions. Gain and loss of function experiments in the mouse cerebral cortex in vivo demonstrate that high Trnp1 levels promote neural stem cell self-renewal and tangential expansion, while lower levels promote radial expansion resulting in a potent increase in the generation of intermediate progenitors and outer radial glial cells resulting in folding of the otherwise smooth murine cerebral cortex. Remarkably, TRNP1 expression levels exhibit regional differences also in the cerebral cortex of human fetuses anticipating radial or tangential expansion respectively. Thus, the dynamic regulation of TRNP1 is critical to regulate tangential and radial expansion of the cerebral cortex in mammals.
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Project description:Gene regulatory landscape of cerebral cortex folding
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Project description:Our brains accommodate a largely folded cerebral cortex that associates to our advanced brain functions. Several theories have been proposed to explain the cortical folding process, reasoning the mechanical forces as neuronal tension in underlying layers, cellular expansion and glial progenitor’s diversity in the OSVZ; but the mechanistic insights and underlying genomics changes causing the appearance of cortical folds is still illusive. Importantly, no studies have attempted to comprehensively characterize the gene regulatory networks underlying cortical folding during development. Here, by using ferret as a model system, we have compared the transcriptomes of germinal layers between sulci and gyri, of different cortical areas and across two developmental stages (E30 & E34), to achieve a comprehensive understanding of the spatio-temporal dynamics of gene expression of cortical progenitors. Furthermore, we have also characterized the epigenetic landscape of germinal layers at E30 and E34, a critical period for their development, to correlate changes in chromatin at promoter and enhancer regions with the observed changes in gene expression. Our preliminary results indicate towards a clear transformational axis of gene regulation between germinal layers. By performing motif analysis of differentially expressed gene (DEGs), we reveal transcription factors which might have a critical role in determining cortical folding. The genes targeted by these factors belong to important pathways implicated in proliferation and neurogenesis. We highlight potential candidates in cortical folding through functional validation studies and acetylation (H3K27ac) levels for these genes correlate with their expression state. Importantly, these are critical for cell adhesion, migration and proliferation processes in-line with previous studies stating that proliferative divisions cause neocortical expansions. Our findings will have strong impact on the clinical interventions for neurological disorders relating to cortical malformation, while at the same time enhancing our understanding of molecular circuitry underlying gyrencephalic brain development and folding.
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Project description:The neocortex, the center for higher brain function, first emerged in mammals and has become massively expanded and folded in humans, constituting almost half the volume of the human brain. Primary microcephaly, a developmental disorder in which the brain is smaller than normal at birth, mainly results from there being fewer neurons in the neocortex because of defects in neural progenitor cells (NPCs). Outer radial glia (oRGs), NPCs that are abundant in gyrencephalic species but rare in lisencephalic species, are thought to play key roles in the expansion and folding of the neocortex. However, how oRGs expand, whether they are necessary for neocortical folding, and whether defects in oRGs cause microcephaly remain important questions in the study of brain development, evolution, and disease. Here, we show that oRG expansion in mice, ferrets, and human cerebral organoids requires cyclin-dependent kinase 6 (CDK6), the mutation of which causes primary microcephaly via an unknown mechanism. In a mouse model in which increased Hedgehog signaling expands oRGs and intermediate progenitor cells and induces neocortical folding, CDK6 loss selectively decreased oRGs and abolished neocortical folding. Remarkably, this function of CDK6 in oRG expansion did not require its kinase activity, was not shared by the highly similar CDK4 and CDK2, and was disrupted by the mutation causing microcephaly. Therefore, our results indicate that CDK6 is conserved to promote oRG expansion; that oRGs are necessary for neocortical folding; and that defects in oRG expansion may cause primary microcephaly.
2022-08-31 | GSE211990 | GEO
Project description:A massively expanded outer subventricular zone (OSVZ) in the primate and human has been proposed for generating majority of neocortical neurons, which consists of basally located radial glia cells. Previous studies with various strategies have tried to recognize genes specifically expressed in those cells; however, the molecular and cellular features of these cells still remain uncertain. By profiling gene expression across single cells isolated from cellular anatomy location and subtype sorting, we identified a primate-specific gene TMEM14B as a novel marker for basally located radial glia. Expression of TMEM14B induced dramatic increase in the number of radial glial and OSVZ region. Finally, we found that OSVZ progenitor’s extensive proliferative potential was up regulated through IQGAP1 phosphorylation and nuclear translocation, and remarkably, led to the gyrification in postnatal mouse. These results highlight that evolutionary expansion promoted by primate-specific genes enabling the evolutionary expansion and folding of the human neocortex.
2016-12-02 | GSE90734 | GEO
Project description:Purpose: To gain further insight into how FOXM1 causes generation of cortical expansion and folding in mice, single cell RNA-seq was used to analyze the cell type changes resulting from the cerebral cortices of P0 FOXM1 conditional knock in mice and littermate wild-type. Methods: Single cell isolation was prepared from P0 telencephalic tissue of wild-type (WT) and FOXM1f/+;Nestin-Cre mice. The fragmented cDNAs containing barcode and UMI sequences was built the library. Agilent 2100 Bioanalyzer was used to quality controlled and quantified. Single cell RNA-sequencing analysis was used by the Illumina HiSeq 2500 platform in Annoroad Genomics. Results: Clustering and labeling of these cells visualized on a t-SNE plot between the wild-type (WT) and FOXM1f/+;Nestin-Cre mice brain cortex. Conclusions: Single cell RNA-seq data would provide an overall understanding how FOXM1 gene contribute to generation of cortical expansion and folding in mice.
2020-02-26 | GSE145934 | GEO
Project description:Serpina3 modulates neuronal cell fate determination (scRNA sequencing)
| PRJNA694621 | ENA