Project description:Compared to that of other mammals, human cortical neurons exhibit higher dendritic complexity and synaptic density, and the maturation process is much protracted. However, the molecular mechanism governing these specific features is unclear. Here, we report that the hominoid-specific gene TBC1D3, a core duplicon in the human genome, promotes dendritic arborization and maintains the slow pace of synaptogenesis. Furthermore, to gain insights into the mechanism by which the TBC1D3-MICAL1-ATRX complex determines the slow pace of spinogenesis, we conducted chromatin immunoprecipitation sequencing (ChIP-seq) experiment using an ATRX antibody targeting the C-terminal region in cultured mouse cortical neurons.
Project description:Compared to that of other mammals, human cortical neurons exhibit higher dendritic complexity and synaptic density, and the maturation process is much protracted. However, the molecular mechanism governing these specific features is unclear. Here, we report that the hominoid-specific gene TBC1D3, a core duplicon in the human genome, promotes dendritic arborization and maintains the slow pace of synaptogenesis. Furthermore, to gain insights into the mechanism by which the TBC1D3-MICAL1-ATRX complex determines the slow pace of spinogenesis, we conducted chromatin immunoprecipitation sequencing (ChIP-seq) experiment using an ATRX antibody targeting the C-terminal region in cultured mouse cortical neurons.
Project description:The use of gene expression signatures to classify compounds, identify efficacy or toxicity, and differentiate close analogs relies on the sensitivity of the method to identify modulated genes. We used a novel ligation-based targeted whole transcriptome expression profiling assay, TempO-Seq®, to determine whether previously unreported compound-responsive genes could be identified and incorporated into a broad but specific compound signature. TempO-Seq exhibits 99.6% specificity, single cell sensitivity, and excellent correlation with fold differences measured by RNA-Seq (R2 = 0.9) for 20,629 targets. Unlike many expression assays, TempO-Seq does not require RNA purification, cDNA synthesis, or capture of targeted RNA, and lacks a 3′ end bias. To investigate the sensitivity of the TempO-Seq assay to identify significantly modulated compound-responsive genes, we derived whole transcriptome profiles from MCF-7 cells treated with the histone deacetylase inhibitor Trichostatin A (TSA) and identified more than 9,000 differentially expressed genes. The TSA profile for MCF-7 cells overlapped those for HL-60 and PC-3 cells in the Connectivity Map (cMAP) database, suggesting a common TSA-specific expression profile independent of baseline gene expression. A 43-gene cell-independent TSA signature was extracted from cMAP and confirmed in TempO-Seq MCF-7 data. Additional genes that were not previously reported to be TSA responsive in the cMAP database were also identified. TSA treatment of 5 cell types revealed 1,136 differentially expressed genes in common, including 785 genes not previously reported to be TSA responsive. We conclude that TSA induces a specific expression signature that is consistent across widely different cell types, that this signature contains genes not previously associated with TSA responses, and that TempO-Seq provides the sensitive differential expression detection needed to define such compound-specific, cell-independent, changes in expression.
Project description:The postsynaptic density (PSD) is a protein condensate composed of ~1,000 proteins beneath the postsynaptic membrane of excitatory synapses. The number, shape, and plasticity of synapses are altered during development. However, the dynamics of synaptic protein composition across development have not been fully understood. Here we show alterations of PSD protein composition in mouse and primate brains during development. Proteins involved in synapse regulation are enriched in the differentially expressed (288 decreased and 267 increased) proteins on mouse PSD after a 2-week-old, which may be involved in changes of synaptic signal transduction. We find that the changes in PSD protein abundance in mouse brains correlate with gene expression levels in postnatal mice and perinatal primates. Proteome analysis of PSD from developing common marmosets (Callithrix jacchus) shows that the changes of PSD composition in mouse brain after 2-week-old occur in the marmoset brain mainly during the neonatal period and continue until adulthood. We also describe the changes of PSD proteome at the late developmental stage of marmoset, which may be involved in synaptic pruning observed in primate brains. The maturation of PSD composition is likely defective in autism spectrum disorder (ASD). Our results provide a comprehensive architecture of the remodeling of PSD composition across development, which may explain the molecular basics of synapse maturation and the pathology of psychiatric disorders, such as ASD.
Project description:Comparison of luminal and basal breast cancer cells under acute normoxia and hypoxia. Cells were plated in 96-well plates and incubated 24 hrs under normoxia or hypoxia after which the wells were washed once with cold PBS and lysed using TempO-Seq lysis buffer for 15 min at room temperature. Samples were stored at −80 °C before shipping to BioClavis for whole genome TempO-Seq analysis. For normoxia (NX) 21% oxygen was used and for hypoxia (HX) 1%oxygen was used. Each condition has 3 biological replicates.
Project description:Comparison of luminal and basal breast cancer cells under chronic normoxia and hypoxia. Cells were plated in 96-well plates and incubated 5 days under normoxia or hypoxia after which the wells were washed once with cold PBS and lysed using TempO-Seq lysis buffer for 15 min at room temperature. Samples were stored at −80 °C before shipping to BioClavis for whole genome TempO-Seq analysis. For normoxia (NX) 21% oxygen was used and for hypoxia (HX) 1%oxygen was used. Each condition has 3 biological replicates.
Project description:Using the TempO-Seq rat S1500+ platform we performed gene expression analysis of using 63 purified RNA samples from the livers of rats exposed to controls or chemicals that fall into one of five modes of action (MOAs): constitutive androstane receptor/pregnane X receptor (CAR/PXR) activation, aryl hydrocarbon receptor (AhR) activation, peroxisome proliferator-activated receptor-alpha (PPARA) activation, cytotoxicity or DNA damage. The TempO-Seq data generated was used to compare to gene expression data acquired from the same samples run on Affymetrix microarays (GEO: GSE47875) and Illumina RNA-Seq (GEO: GSE55347, SRA:SRP039021).