Similar Datasets
Project description:MicroRNAs (miRNAs) regulate many neurodevelopmental events, including proliferation, neurogenesis, neuronal migration, and cell survival. Individual miRNAs interact with hundreds of mRNA transcripts, but the precise landscape of these interactions in the context of cell-type-specificity has not been determined. Here, we used multiple parallel approaches, including AGO2-HITS-CLIP, combined mRNA and miRNA single-cell profiling and bipartite network analysis, to reveal a non-uniformity of miRNA-mRNA interactions that supports both defined cell-type identities as well as their dynamic transitions during human brain development at stages of peak neurogenesis. miRNA-mRNA clusters dynamically exploit the redundancy of the miRNA target code to differentially cluster across transitions in brain development. Using cell-type-specific functional properties of miRNA-mRNA interactions, we identify the role of great ape-specific miR-2115 in regulating cortical progenitor cell proliferation by targeting a radial glia enriched gene, origin recognition complex subunit 4 (ORC4). Together, our study suggests that miRNAs contribute to cell identity by regulating the expression of cell-type-specific transcripts.
2018-11-21 | GSE107467 | GEO
Project description:MicroRNAs (miRNAs) regulate many neurodevelopmental events, including proliferation, neurogenesis, neuronal migration, and cell survival. Individual miRNAs interact with hundreds of mRNA transcripts, but the precise landscape of these interactions in the context of cell-type-specificity has not been determined. Here, we used multiple parallel approaches, including AGO2-HITS-CLIP, combined mRNA and miRNA single-cell profiling and bipartite network analysis, to reveal a non-uniformity of miRNA-mRNA interactions that supports both defined cell-type identities as well as their dynamic transitions during human brain development at stages of peak neurogenesis. miRNA-mRNA clusters dynamically exploit the redundancy of the miRNA target code to differentially cluster across transitions in brain development. Using cell-type-specific functional properties of miRNA-mRNA interactions, we identify the role of great ape-specific miR-2115 in regulating cortical progenitor cell proliferation by targeting a radial glia enriched gene, origin recognition complex subunit 4 (ORC4). Together, our study suggests that miRNAs contribute to cell identity by regulating the expression of cell-type-specific transcripts.
2018-11-21 | GSE107466 | GEO
Project description:Dynamic microRNA regulatory networks in establishing the Cellular specificity of developing human brains
| PRJNA420192 | ENA
Project description:Dynamic microRNA regulatory networks in establishing the Cellular specificity of developing human brains (miRNA-seq)
| PRJNA420199 | ENA
Project description:Dynamic microRNA regulatory networks in establishing the Cellular specificity of developing human brains (mRNA-seq)
| PRJNA420200 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2017-04-06 | GSE79046 | GEO
Project description:The regulation of gene expression in cells, including by microRNAs (miRNAs), is a dynamic process. Current methods for identifying miRNA targets by combining sequence and miRNA and mRNA expression data do not adequately use the temporal information and thus miss important miRNAs and their targets. We developed the MIRna Dynamic Regulatory Events Miner (mirDREM), a probabilistic modeling method that uses input-output hidden Markov models to reconstruct dynamic regulatory networks that explain how temporal gene expression is jointly regulated by miRNAs and transcription factors. We measured miRNA and mRNA expression for postnatal lung development in mice and used mirDREM to study the regulation of this process. The reconstructed dynamic network correctly identified known miRNAs and transcription factors. The method has also provided predictions about additional miRNAs regulating this process and the specific developmental phases they regulate, several of which were experimentally validated. Our analysis uncovered links between miRNAs involved in lung development and differentially expressed miRNAs in idiopathic pulmonary fibrosis patients, some of which we have experimentally validated using proliferation assays. These results indicate that some disease progression pathways in idiopathic pulmonary fibrosis may represent partial reversal of lung differentiation.
| S-EPMC3785769 | biostudies-literature
Project description:The oxytocin receptor (OTR) plays critical roles in social behavior development. Despite its significance, brain-wide quantitative understanding of OTR expression remains limited in postnatally developing brains. Here, we develop postnatal 3D template brains to register whole brain images with cellular resolution to systematically quantify OTR cell densities. We utilize fluorescent reporter mice (Otrvenus/+) and find that cortical regions show temporally and spatially heterogeneous patterns with transient postnatal OTR expression without cell death. Cortical OTR cells are largely glutamatergic neurons with the exception of cells in layer 6b. Subcortical regions show similar temporal regulation except the hypothalamus and two hypothalamic nuclei display sexually dimorphic OTR expression. Lack of OTR expression correlates with reduced dendritic spine densities in selected cortical regions of developing brains. Lastly, we create a website to visualize our high-resolution imaging data. In summary, our research provides a comprehensive resource for postnatal OTR expression in the mouse brain.
| S-EPMC7171089 | biostudies-literature
Project description:The mature eye lens contains a surface layer of epithelial cells called the lens epithelium that requires a functional mitochondrial population to maintain the homeostasis and transparency of the entire lens. The lens epithelium overlies a core of terminally differentiated fiber cells that must degrade their mitochondria to achieve lens transparency. These distinct mitochondrial populations make the lens a useful model system to identify those genes that regulate the balance between mitochondrial homeostasis and elimination. Here we used an RNA sequencing and bioinformatics approach to identify the transcript levels of all genes expressed by distinct regions of the lens epithelium and maturing fiber cells of the embryonic Gallus gallus (chicken) lens. Our analysis detected more than 15,000 unique transcripts expressed by the embryonic chicken lens. Of these, more than 3000 transcripts exhibited significant differences in expression between lens epithelial cells and fiber cells. Multiple transcripts coding for separate mitochondrial homeostatic and degradation mechanisms were identified to exhibit preferred patterns of expression in lens epithelial cells that require mitochondria relative to lens fiber cells that require mitochondrial elimination. These included differences in the expression levels of metabolic (DUT, PDK1, SNPH), autophagy (ATG3, ATG4B, BECN1, FYCO1, WIPI1), and mitophagy (BNIP3L/NIX, BNIP3, PARK2, p62/SQSTM1) transcripts between lens epithelial cells and lens fiber cells. These data provide a comprehensive window into all genes transcribed by the lens and those mitochondrial regulatory and degradation pathways that function to maintain mitochondrial populations in the lens epithelium and to eliminate mitochondria in maturing lens fiber cells.
| S-EPMC4132181 | biostudies-literature
Project description:The Dynamic Regulatory Events Miner (DREM) software reconstructs dynamic regulatory networks by integrating static protein-DNA interaction data with time series gene expression data. In recent years, several additional types of high-throughput time series data have been profiled when studying biological processes including time series miRNA expression, proteomics, epigenomics and single cell RNA-Seq. Combining all available time series and static datasets in a unified model remains an important challenge and goal. To address this challenge we have developed a new version of DREM termed interactive DREM (iDREM). iDREM provides support for all data types mentioned above and combines them with existing interaction data to reconstruct networks that can lead to novel hypotheses on the function and timing of regulators. Users can interactively visualize and query the resulting model. We showcase the functionality of the new tool by applying it to microglia developmental data from multiple labs.
| S-EPMC5868853 | biostudies-literature