Similar Datasets
Project description:The experiment was designed to investigate the regulatory landscape of H3K27me3, a histone methylation form, in the hippocampal neurons upon lead exposure. It reveals that the targeting pathways were altered and migrated throughout the genome, indicating that H3K27me3's sophisticated alterations are responsible for lead-led impairment of hippocampal neurons. Besides, the causes leading to its adaptive changes were figured out.
2018-11-17 | E-MTAB-6837 | biostudies-arrayexpress
Project description:Transcriptome profiling of rat primary hippocampal neurons when the dyslexia candidate gene DCDC2 is overexpressed using transient transfections.<br><br>Additional processed data files and their associated custom CDF are available on the FTP site for this experiment.
2011-03-01 | E-MTAB-518 | biostudies-arrayexpress
Project description:Proper assembly of complex neural circuits requires the coordinated action of a limited set of axon guidance molecules, including plexins. To probe the extracellular vicinity of PlxnA2 in primary hippocampal neurons, we used in this work antibody directed proximity biotinylation and identified candidate co-receptors.
2026-03-16 | PXD060323 | Pride
Project description:To understand how cells communicate with each other, it is essential to define the cellular secretome, a collection of proteins including soluble secreted, unconventionally secreted and proteolytically-shed proteins. Quantitative methodologies to decipher the secretome are challenging, due to the requirement of large cell numbers and abundant serum proteins that interfere with the detection of low-abundant cellular secretome proteins. Here, we have use the highe perfomance secretome-protein-enrichment-with-click-sugars method (hiSPECS) for glyco-secretome analysis. We applied this method to investigate differences of hippocampal and cortical murine neurons. Additionally, we have inhibited the Alzheimer related protease BACE1 to identify potential substrates in the secretome of hippocampal neurons.
2020-09-25 | PXD020503 | Pride
Project description:Neurons express Phactr1 at high level (Allen et al., 2004), and Phactr1 mutations are associated with morphological and functional developmental defects in cortical neurons (Hamada et al., 2018). To identify targets of the Phactr1/PP1 phosphatase holoenzyme, we cultured hippocampal and cortical neurons from wildtype and Phactr1-null animals, treated them either with Latrunculin B or Cytochalasin D to inhibit or activate formation of the Phactr1/PP1 complex (Wiezlak et al., 2012), and analysed phosphorylation profiles using TMT phosphoproteomics. Among over 9000 phosphorylation sites quantified, we found numerous phosphorylation sites that differed significantly in their response to these stimuli in wildtype as opposed to Phactr1-null neurons.
2020-10-28 | PXD019882 | Pride
Project description:A central hallmark of brain aging is the alteration of neuronal functions in the hippocampus, leading to a progressive decline in learning and memory. Multiple reports have shown the importance of blood-borne factors in inter-tissue communication for the maintenance of cognitive fitness and proper regulation of neuronal homeostasis throughout life. Among these blood-borne factors, we identified Osteocalcin (OCN), a bone-derived hormone. OCN induces autophagy machinery in hippocampal neurons which is essential for activity-dependent synaptic plasticity. However, the way in which blood-borne factors like OCN communicate with neurons, including their regulatory mechanisms, remains largely elusive. Here, we show the importance of a core primary cilium (PC)-proteins/autophagy machinery axis in hippocampal neurons that mediate the effects of the pro-youthful blood factor OCN on neuronal homeostasis and cognitive fitness. We found that OCN’s receptor, GPR158, is present at the PC of hippocampal neurons and mediates the regulation of autophagy machinery by OCN. During aging, PC-core proteins are reduced in hippocampal neurons and associated with neuronal PC morphological abnormalities. Restoring their levels is sufficient to improve neuronal autophagy and cognitive impairments in aged mice. Mechanistically, we found that OCN promotes neuronal autophagy in the hippocampus by the induction of PC-dependent cAMP response element-binding protein (CREB) signaling pathway. Altogether, this study proposes a novel paradigm for blood factor-neuron communication dependent on a neuronal PC/autophagy axis by identifying a novel regulatory pathway fostering cognitive fitness and providing the foundation for autophagy-based therapeutic strategies to treat age-related cognitive dysfunction.
2024-11-07 | PXD056975 | Pride
Project description:Proteomics of hippocampal tissues in PS19 and wildtype mice with PKD1 deletion
2026-02-11 | PXD074329 |
Project description:To investigate the possible roles on mitotic/microtubule-related genes during hippocampal neuron differentiation, we dissected E18.5 mouse embryonic hippocampi, cultured neurons in vitro and collected total RNA samples from different timepoints of differentiation.
2018-06-03 | GSE113680 | GEO
Project description:BackgroundThe ability to deposit histone H3K27-trimethyl (me3) marks is essential for transcriptional repression by Polycomb Repressive Complex 2 (PRC2). This is largely attributed to Polycomb repressive complex 1 (PRC1), whose recruitment is H3K27me3-dependent. Yet it is unclear how H3K27me3 contributes to transcription regulation independently of PRC1.ResultsTo address this question, we identified H3K27me3-binding proteins in the unicellular eukaryote Paramecium where PRC2 targets transposable elements (TEs) and PRC1 is absent. We show that the chromodomain protein Firefly is a H3K27me3 reader in vitro and accumulates onto TEs in a H3K27me3-dependent manner. We also identify Firefly interactors: Sleepy, a coiled-coil containing protein and TfIIs4, a transcription elongation factor. We show that Firefly, Sleepy and TfIIs4 are jointly required in vivo for correct H3K27me3 accumulation and nascent transcription at TEs.ConclusionsThis positive feedback loop to enrich H3K27me3 at TEs is analogous to self-reinforcing loops leading to H3K9 methylation at repeats in fungi, plants and animals. Our work reveals a unique association between H3K27me3 readers and active transcription.
2026-03-03 | PXD065449 | Pride
Project description:We report genome-wide binding targets of REF6, a H3K27me3 demethylase and also high-throughput profiling of histone modifications of H3K27me3 in Arabidopsis flowers. Using chromatin-immunoprecipitation followed by high-throughput sequencing, we mapped thousands of binding targets of REF6 in flowers and in addition, we used a second fixative, DSG to capture more indirect targets of REF6. In order to investigate the function of indirect binding of REF6 represented H3K27me3 demethylase, the binding targets of DNA binding domain deleted REF6 were identified in the triple mutant background in which REF6 and its two homologs were mutated. Meanwhile, the H3K27me3 marked regions in both wild type and triple mutant flowers were defined. By analyzing the differentially enriched H3K27me3 region and REF6 binding profile, we found that REF6 functions to determine the boundary of H3K27me3 regions. Comparison of binding profiles of REF6 in flowers and in seedlings (ref) revealed a tissue-specific binding manner. More importantly, we found that the indirect binding of REF6 is mediated by trans factors and this indirect binding is crucial for REF6 function, especially in reproductive organs in Arabidopsis. Our results provide novel molecular insights into REF6 functions.
2018-07-09 | GSE106942 | GEO