Neural Stem Cells Direct Axon Guidance via their Radial Fiber Scaffold
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ABSTRACT:
PROVIDER: PRJNA639825 | ENA |
REPOSITORIES: ENA
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Project description:During the development of the Drosophila central nervous system the process of midline crossing is orchestrated by a number of guidance receptors and ligands. Many key axon guidance molecules have been identified in both invertebrates and vertebrates, but the transcriptional regulation of growth cone guidance remains largely unknown. One open question is whether transcriptional regulation plays a role in midline crossing, or if local translation can account for the necessary fine tuning of protein levels. To investigate this issue, we conducted a genome wide analysis of transcription in Drosophila embryos using wild type and a number of well-characterized Drosophila guidance mutants and transgenics. We also analyzed a publicly available microarray time course of Drosophila embryonic development with an axon guidance focus. Using hopach, a novel clustering method which is well suited to microarray data analysis, we identified groups of genes with similar expression patterns across guidance mutants and transgenics. We then systematically characterized the resulting clusters with respect to their relevance to axon guidance using two complementary controlled vocabularies: the Gene Ontology (GO) and anatomical annotations of the Atlas of Pattern of Gene Expression (APoGE) in situ hybridization database. The analysis indicates that regulation of gene expression does play a role in the process of axon guidance in Drosophila. We also find a strong link between axon guidance and hemocyte migration, a result that agrees with mounting evidence that axon guidance molecules are co-opted in vertebrate vascularization. Cell cyclin activity in the context of axon guidance is also suggested from our array data. RNA and protein patterns of cell cyclin in axon guidance mutants and transgenics support this possible link. This study provides important insights into the regulation of axon guidance in vivo and suggests that transcription does play a role in control of axon guidance. Keywords: Mutant Analysis
2006-12-14 | GSE6515 | GEO
Project description:To determine the genes regulated by Fezf2 during neocortical development, we performed RNA-seq on Fezf2 +/+; Emx1-cre (Fezf2 wildtype) and Fezf2 fl/+; Emx1-Cre (Fezf2 Knockout) neocortices isolated from the P0 mice. After RNA isolation from the dissected tissue the samples were processed for library preperation using Illumina Poly-A RNA kit. Fezf2 can reprogram the upper layer neocortical neurons to form corticospinal tract. To understand the key transcriptomic changes driven by Fezf2 that drive this reprogramming, we performed in RNA-seq on the cells over-expressing Fezf2 and Gfp or Gfp. At E15.5, in utero electroporations targeting cortical plate, were performed in pregnant mice with Fezf2 and Gfp plasmids or with Gfp plasmid alone, which was used as control. At P3, the Gfp positive cells were FAC sorted from Fezf2 and Gfp, or Gfp cortices and processed for library preparations using NUGEN Ovation® V2 system. Libraries were sequenced using Illumina 2000 platform to generate 75bp single reads. At least 10 million uniquely mapped reads were obtained for each sample. To determine the genes directly regulated by FEZF2, we performed the ChIP-Seq on N2A cells that were transfected to over express FEZF2 using pCAG- Fezf2-V5 and pCAG-V5. After 48 hr, of transfection, cells were fixed and processed for ChIP seq. Libraries were prepared using Illumina TruSeq ChIP Libary Preparation Kit.
2020-12-05 | GSE152611 | GEO
Project description: Not available
| S-EPMC7529949 | biostudies-literature
Project description:During the development of the Drosophila central nervous system the process of midline crossing is orchestrated by a number of guidance receptors and ligands. Many key axon guidance molecules have been identified in both invertebrates and vertebrates, but the transcriptional regulation of growth cone guidance remains largely unknown. One open question is whether transcriptional regulation plays a role in midline crossing, or if local translation can account for the necessary fine tuning of protein levels. To investigate this issue, we conducted a genome wide analysis of transcription in Drosophila embryos using wild type and a number of well-characterized Drosophila guidance mutants and transgenics. We also analyzed a publicly available microarray time course of Drosophila embryonic development with an axon guidance focus. Using hopach, a novel clustering method which is well suited to microarray data analysis, we identified groups of genes with similar expression patterns across guidance mutants and transgenics. We then systematically characterized the resulting clusters with respect to their relevance to axon guidance using two complementary controlled vocabularies: the Gene Ontology (GO) and anatomical annotations of the Atlas of Pattern of Gene Expression (APoGE) in situ hybridization database. The analysis indicates that regulation of gene expression does play a role in the process of axon guidance in Drosophila. We also find a strong link between axon guidance and hemocyte migration, a result that agrees with mounting evidence that axon guidance molecules are co-opted in vertebrate vascularization. Cell cyclin activity in the context of axon guidance is also suggested from our array data. RNA and protein patterns of cell cyclin in axon guidance mutants and transgenics support this possible link. This study provides important insights into the regulation of axon guidance in vivo and suggests that transcription does play a role in control of axon guidance. Experiment Overall Design: Several mutants and transgenics were analyzed, totalizing 17 distinct conditions. Individual descriptions are included in each microarray. For each condition there are 3 or 4 replicates. The file's name indicates the replicates, e.g., comm.a reflects the replicate a of mutant commissureless. The experiment design covers a range of mutants and transgenics of key axon guidance mutans, in different dosages. The protocol was the standard Affymetrix protocol.
2008-06-15 | E-GEOD-6515 | biostudies-arrayexpress
Project description:We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified, suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting.
2018-02-19 | GSE103692 | GEO
Project description:Defective axon guidance links H3K4 deregulation to neurodevelopment disorder
| PRJNA601754 | ENA
Project description:Ten-eleven translocation (Tet) is an important gene in neurodevelopment, but how Tet regulates brain development is still under study. Mutations in human TET proteins have been found in individuals with neurodevelopmental disorders. Here we report a new function of Tet in regulating Drosophila early brain development. We found that mutation on the Tet DNA-binding domain (TetAXXC) resulted in axon guidance defects in the mushroom body (MB). Tet is required in early brain development during the outgrowth of MB β axons. Transcriptomic study of TetAXXC mutant and wild-type pupal brains shows that glutamine synthetase 2 (Gs2), a key enzyme in glutamatergic signaling, is the most significantly down-regulated gene in the Tet mutant brains. RNAi knockdown or CRISPR/Cas9 mutagenesis of Gs2 recapitulates the TetAXXC phenotype. Surprisingly, Tet and Gs2 act in the insulin-producing cells (IPCs) to control MB axon guidance, and overexpression of Gs2 in the IPCs rescue the axonal defects of TetAXXC. Treating TetAXXC with the metabotropic glutamate receptor antagonist MPEP can also rescue the phenotype confirming Tet function in regulating glutamatergic signaling. TetAXXC and the Drosophila homolog of Fragile X Messenger Ribonucleoprotein protein mutant (Fmr13) have similar mushroom body axonal defects and reduction in Gs2 transcription, and, importantly, overexpression of Gs2 in the IPCs of Fmr1 mutants also rescues the axonal defects. Our studies reveal a new function of Tet in regulating axon guidance in the brain via glutamatergic signaling and suggest overlapping functions between Tet and Fmr1.
2024-04-20 | GSE231534 | GEO
Project description:Using the highly sensitive miRNA array, we screened 40 microRNAs abundant in the olfactory bulb and we explored the functions of these miRNAs in the olfactory bulb by Gene Ontology and Kyoto Encyclopedia of Genes annotation. The enrichment results indicated that these miRNAs mainly participated in the axon guidance process. Furthermore, the quantitative real-time polymerase chain reaction, immunohistochemistry, and dual luciferase reporter assay results showed that miR-30c is a specific regulator of semaphorin-3A, which will give new insights in disclosing the mechanism of functional maintenance and sexual-specific differentiation of the olfactory bulb. In this study, three samples from steady-state mice were used to acquire the miRNA expression profiling and the function of the abudant miRNAs in the olfactory bulb were analyzed by bioinformatic methods.Finally, miR-30c was experimentally validated to be a regulator of semaphorin-3A, an important axon guidance cue in the nervous system.
2014-08-27 | E-GEOD-55463 | biostudies-arrayexpress
Project description:The chromodomain helicase binding protein 4 (CHD4) is an ATP-dependent chromatin remodeler—De-novo pathogenic variants of CHD4 cause Sifrim-Hitz-Weiss syndrome (SIHIWES). Patients with SIHIWES show delayed development, intellectual disability, facial dysmorphism, and hearing loss. Many cochlear cell types, including spiral ganglion neurons (SGNs), express CHD4. SGNs are the primary afferent neurons that convey sound information from the cochlea, but the function of CHD4 in SGNs is unknown. We employed the Neurog1(Ngn1) CreERT2 Chd4 conditional knockout animals to delete Chd4 in SGNs. SGNs are classified as type I and type II neurons. SGNs lacking CHD4 showed abnormal fasciculation of type I neurons along with improper pathfinding of type II fibers. CHD4 binding to chromatin from immortalized multipotent otic progenitor-derived neurons was used to identify candidate target genes in SGNs. Gene ontology analysis of CHD4 target genes revealed cellular processes involved in axon guidance, axonal fasciculation, and ephrin receptor signaling pathway. We validated increased Epha4 transcripts in SGNs from Chd4 conditional knockout cochleae. The results suggest that CHD4 attenuates the transcription of axon guidance genes to form the stereotypic pattern of SGN peripheral projections. The results implicate how epigenetic changes affect circuit wiring by modulating axon guidance molecule expression and provide insights into neurodevelopmental diseases.
2024-02-26 | GSE250033 | GEO
Project description:Recently, genome-wide molecular analyses have identified an altered axon guidance SLIT-ROBO signaling pathway in Pancreatic ductal adenocarcinoma (PDAC). To examine whether ROBO3 signaling is involved in the transcriptional determination of basal-like PDAC-subtype specification and functions, we performed RNA-seq analysis following ROBO3 silencing in the basal-like cell line PANC1.
2022-07-31 | E-MTAB-11476 | biostudies-arrayexpress