Single nuclei chromatin profiles of midbrain from genetically distinct mouse strains reveal cell identity transcription factors and cell type-specific gene regulatory variation
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PROVIDER: PRJEB53032 | ENA |
REPOSITORIES: ENA
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Project description:Here we report 20 658 single nuclei chromatin accessibility profiles of ventral midbrain cell types from two genetically diverse and commonly used mouse strains, C57BL6/J and A/J. In total we identify over 260 000 unique accessible sites. The distinct chromatin profiles are consistent with gene expression levels from single cell RNA-seq data and can distinguish ten midbrain cell types. Transcription factor (TF) binding motifs enriched at accessible regions controlling cell identity genes highlight the key TFs of each major cell type. The gene regulatory differences between the mouse strains manifest more on transcriptome than chromatin level.
2022-01-14 | E-MTAB-9225 | biostudies-arrayexpress
Project description:BackgroundCell types in ventral midbrain are involved in diseases with variable genetic susceptibility, such as Parkinson's disease and schizophrenia. Many genetic variants affect regulatory regions and alter gene expression in a cell-type-specific manner depending on the chromatin structure and accessibility.ResultsWe report 20,658 single-nuclei chromatin accessibility profiles of ventral midbrain from two genetically and phenotypically distinct mouse strains. We distinguish ten cell types based on chromatin profiles and analysis of accessible regions controlling cell identity genes highlights cell-type-specific key transcription factors. Regulatory variation segregating the mouse strains manifests more on transcriptome than chromatin level. However, cell-type-level data reveals changes not captured at tissue level. To discover the scope and cell-type specificity of cis-acting variation in midbrain gene expression, we identify putative regulatory variants and show them to be enriched at differentially expressed loci. Finally, we find TCF7L2 to mediate trans-acting variation selectively in midbrain neurons.ConclusionsOur data set provides an extensive resource to study gene regulation in mesencephalon and provides insights into control of cell identity in the midbrain and identifies cell-type-specific regulatory variation possibly underlying phenotypic and behavioural differences between mouse strains.
| S-EPMC8427957 | biostudies-literature
Project description:Single nucleus RNAseq of midbrain dopaminergic neuronal nuclei isolated by FACS
| PRJNA922521 | ENA
Project description:KDM5A is a chromatin remodeler disrupted in neurodevelopmental disease. To investigate the effect of losing KDM5A on the development of the hippocampus, we profiled hippocampi from wild type (WT) and Kdm5a -/- mice using single-nuclei RNA sequencing (snRNA-seq). We found that KDM5A regulates the development of specific subtypes of excitatory (CA1, CA2, CA3) and inhibitory (SST+, PVALB+) neurons, that loss of KDM5A leads to a more mature cellular identity in the hippocampus, and that KDM5A functions early in development to specify proper CA1 cell identity.
2023-09-01 | GSE235490 | GEO
Project description:Mutations in the SNCA gene cause autosomal dominant Parkinson’s disease (PD), with progressive loss of dopaminergic neurons in the substantia nigra, and accumulation of aggregates of α-synuclein. However, the sequence of molecular events that proceed from the SNCA mutation during development, to its end stage pathology is unknown. Utilising human induced pluripotent stem cells (hiPSCs) with SNCA mutations, we resolved the temporal sequence of pathophysiological events that occur during neuronal differentiation in order to discover the early, and likely causative, events in synucleinopathies. We adapted a small molecule-based protocol that generates highly enriched midbrain dopaminergic (mDA) neurons (>80%). We characterised their molecular identity using single-cell RNA sequencing and their functional identity through the synthesis and secretion of dopamine, the ability to generate action potentials, and form functional synapses and networks. RNA velocity analyses confirmed the developmental transcriptomic trajectory of midbrain neural precursors into different mDA neuronal clusters. To characterise the synucleinopathy, we adopted super-resolution methods to determine the number, size, and structure of aggregates in SNCA-mutant mDA neurons. By day 27 of differentiation, prior to maturation to mDA neurons of molecular and functional identity, we demonstrate the formation of small aggregates; specifically, β-sheet rich oligomeric aggregates, in SNCA-mutant midbrain immature neurons. The aggregation progresses over time to accumulate phosphorylated and fibrillar aggregates. When the midbrain neurons were functional, we observed impaired intracellular calcium signalling, evidenced with an increased basal calcium level and impairments in both cytosolic and mitochondrial calcium rearrangements. Once midbrain identity fully developed, SNCA-mutant neurons exhibited mitochondrial dysfunction, oxidative stress, lysosomal swelling as well as an upregulation of mitophagy and autophagy. In addition, SNCA-mutant neurons displayed pathophysiological excitability, revealed as a depolarised resting membrane potential, an increased input resistance, and impaired firing properties. Ultimately these multiple cellular stresses lead to an increase in cell death by day 62 post-differentiation. Our differentiation paradigm generates an efficient model for studying disease mechanisms in PD, and highlights that protein misfolding to generate intraneuronal oligomers is one of the earliest critical events driving disease in human neurons, rather than a late-stage hallmark of the disease.
2023-03-11 | PXD035500 | Pride
Project description:We optimised a new differentiation paradigm to produce midbrain dopaminergic neurons from hiPSCs. To characterise their identity, we performed scRNA-seq to investigate their gene expression and molecular identity.
2022-10-05 | GSE213569 | GEO
Project description:Embryonic stem (ES) cells were differentiated in culture to midbrain dopaminergic (mDA) progenitors and subjected to ChIP-seq analysis to resolve genome-wide binding sites of forkhead box protein A2 (Foxa2). Foxa2 was found to directly regulate multiple lineage pathways to specify midbrain dopaminergic and floor plate progenitor identity.
2012-07-01 | E-MTAB-1137 | biostudies-arrayexpress
Project description:Most neuronal types have a well-identified electrical phenotype. It is now admitted that a same phenotype can be produced using multiple biophysical solutions defined by ion channel expression levels. This argues that systems-level approaches are necessary to understand electrical phenotype genesis and stability. Midbrain dopaminergic (DA) neurons, although quite heterogeneous, exhibit a characteristic electrical phenotype. However, the quantitative genetic principles underlying this conserved phenotype remain unknown. Here we investigated the quantitative relationships between ion channels' gene expression levels in midbrain DA neurons using single-cell microfluidic qPCR. Using multivariate mutual information analysis to decipher high-dimensional statistical dependences, we unravel co-varying gene modules that link neurotransmitter identity and electrical phenotype. We also identify new segregating gene modules underlying the diversity of this neuronal population. We propose that the newly identified genetic coupling between neurotransmitter identity and ion channels may play a homeostatic role in maintaining the electrophysiological phenotype of midbrain DA neurons.
| S-EPMC6134142 | biostudies-other
Project description:Background: Precise spatiotemporal control of gene expression is essential for the establishment of correct cell numbers and identities during brain development. This process involves epigenetic control mechanisms, such as those mediated by the polycomb group protein Ezh2 that catalyzes trimethylation of histone H3K27 (H3K27me3) and thereby represses gene expression. Results: Here we show that Ezh2 plays a crucial role in development and maintenance of the midbrain. Conditional deletion of Ezh2 in the developing midbrain resulted in decreased neural progenitor proliferation, which is associated with derepression of cell cycle inhibitors and negative regulation of Wnt/beta-catenin signaling. Of note, Ezh2 ablation also promoted ectopic expression of a forebrain transcriptional program involving derepression of the forebrain determinants Foxg1 and Pax6. This was accompanied by reduced expression of midbrain markers, including Pax3 and Pax7, as a consequence of decreased Wnt/beta-catenin signaling. Conclusion: Ezh2 is required for appropriate brain growth and for maintenance of regional identity by H3K27me3-mediated gene repression and control of canonical Wnt signaling. After tissue isolation from dorsal midbrains of embryonic day (E) 10.5 embryos, total RNA was isolated with the RNAeasy kit (Qiagen) and RNase-Free DNase Set (79254, Qiagen) following the manufacturer's instructions. Isolated total RNA of E10.5 control (n=3, from 2 different litters) and Ezh2 cko (n=3, from 2 different litters) dorsal midbrains was used for microarray analysis performed at the Functional Genomics Center Zurich (FGCZ), Switzerland, using the Affymetrix A430 platform.
2015-11-09 | E-GEOD-74538 | biostudies-arrayexpress
Project description:In multicellular systems changes to the patterning of gene expression drive modifications in cell function and trait evolution. One striking example is found in more than sixty plant lineages where compartmentation of photosynthesis between cell types allowed evolution of the efficient C4 pathway from the ancestral C3 state. The molecular events enabling this transition are unclear. We used single nuclei sequencing to generate a cell level expression atlas for C3 rice and C4 sorghum during photomorphogenesis. In both species a conserved cistrome was identified for each cell type and initiation of photosynthesis gene expression was conditioned by cell identity. Photosynthesis genes switching expression from mesophyll in rice to bundle sheath in sorghum acquire hallmarks of bundle sheath identity. The sorghum bundle sheath has also acquired gene networks associated with C3 guard cells. We conclude C4 photosynthesis is based on rewiring in cis that exapts cell identity networks of C3 plants.
2023-12-05 | GSE248919 | GEO