Rattus norvegicus
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ABSTRACT:
PROVIDER: PRJNA684680 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We investigated the transcriptomic and epigenetic responses to a METH overdose in four regions of rat brain, including the nucleus accumbens, dentate gyrus, Ammon’s horn, and subventricular zone. We found that 24 hours after the METH overdose, 15.6% of genes changed expression and 27.6% of open-chromatin regions altered chromatin accessibility in all four rat brain regions. Interestingly, only a few of those differentially expressed genes (DEGs) and differentially accessible regions (DARs) were simultaneously affected. Among the four rat brain regions analyzed, 149 transcription factors (TFs) and 31 epigenetic factors were significantly affected by the METH overdose. The METH overdose also resulted in reversed regulation patterns of both gene and chromatin accessibility in the dentate gyrus and Ammon’s horn. About 70% of METH-induced chromatin accessibility alterations are highly enriched in neurological processes and shared conserved sequences to the human genome. Many of these conserved regions were active brain-specific enhancers and harbored the SNPs associated with human neurological functions and diseases. Our results indicate strong region-specific transcriptomic and epigenetic responses to a METH overdose in distinct rat brain regions. We describe the conservation of region-specific gene regulatory networks associated with a METH overdose. Overall, our study provides clues to a better understanding of the molecular responses to METH overdose in the human brain.
2023-07-20 | GSE199363 | GEO
Project description:We investigated the transcriptomic and epigenetic responses to a METH overdose in four regions of rat brain, including the nucleus accumbens, dentate gyrus, Ammon’s horn, and subventricular zone. We found that 24 hours after the METH overdose, 15.6% of genes changed expression and 27.6% of open-chromatin regions altered chromatin accessibility in all four rat brain regions. Interestingly, only a few of those differentially expressed genes (DEGs) and differentially accessible regions (DARs) were simultaneously affected. Among the four rat brain regions analyzed, 149 transcription factors (TFs) and 31 epigenetic factors were significantly affected by the METH overdose. The METH overdose also resulted in reversed regulation patterns of both gene and chromatin accessibility in the dentate gyrus and Ammon’s horn. About 70% of METH-induced chromatin accessibility alterations are highly enriched in neurological processes and shared conserved sequences to the human genome. Many of these conserved regions were active brain-specific enhancers and harbored the SNPs associated with human neurological functions and diseases. Our results indicate strong region-specific transcriptomic and epigenetic responses to a METH overdose in distinct rat brain regions. We describe the conservation of region-specific gene regulatory networks associated with a METH overdose. Overall, our study provides clues to a better understanding of the molecular responses to METH overdose in the human brain.
2023-07-20 | GSE199260 | GEO
Project description:Skeletal muscle accounts for the largest proportion of human body mass, on average, and is a key tissue in complex diseases and mobility. It is composed of several different cell and muscle fiber types. Here, we optimize single-nucleus ATAC-seq (snATAC-seq) to map skeletal muscle cell-specific chromatin accessibility landscapes in frozen human and rat samples, and single-nucleus RNA-seq (snRNA-seq) to map cell-specific transcriptomes in human. We additionally perform multi-omics profiling (gene expression and chromatin accessibility) on human and rat muscle samples.
| EGAS00001005730 | EGA
Project description:Gene expression differs between cell types and regions within complex tissues such as the developing brain. To discover regulatory elements underlying this specificity, we generated genome-wide maps of chromatin accessibility in nine anatomically-defined regions of the developing human telencephalon. Additionally, we defined the histone modification landscape of the prefrontal cortex and generated chromatin accessibility maps of its upper and deep layers. We predicted a subset of open chromatin regions (18%) that are most likely to be active enhancers, many of which are dynamic with 26% differing between early and late mid-gestation and 28% present in only one brain region. These predicted regulatory elements (pREs) are enriched proximal to genes with expression differences across developmental stages, regions, and cortical laminae; they harbor distinct sequence motifs that suggest potential upstream regulators. We leveraged this atlas to predict and validate novel regulatory elements of genes that control cortex laminar identity and genes associated with autism spectrum disorder (ASD). These include enhancers proximal to FEZF2 and BCL11A that were validated in mouse, and an enhancer of ASD gene SLC6A1 containing two functional de novo mutations in individuals with ASD whose enhancer function we validated via CRISPRa. These applications demonstrate the utility of this atlas for decoding neurodevelopmental gene regulation in health and disease.
2020-04-25 | GSE149268 | GEO
Project description:We analyzed differential methylation (via WGBS) between four distinct human brain regions (NAcc-nucleus accumbens, BA9-dorsolateral prefrontal cortex, BA24-anterior cingulate cortex, and HC-hippocampus) in both sorted nuclei and intact tissues. We isolated neuronal and non-neuronal (glial) nuclei from the same six individuals for each tissue via FACS using the neuronal marker, NeuN. Additionally, we performed WGBS from non-sorted tissues from these same brain regions in a total of 12 individuals (BA9 n = 9; BA24 n = 5; HC n = 6; NAcc n = 7). To complement our DNA methylation analyses, we measured gene expression (RNA-seq) and chromatin accessibility (ATAC-seq) in neuronal and non-neuronal nuclei from the nucleus accumbens and dorsolateral prefrontal cortex from six more individuals. We then performed an integrative analysis to understand how the epigenome contributes to brain region-specific function.
2018-12-17 | GSE96614 | GEO
Project description:We analyzed differential methylation (via WGBS) between four distinct human brain regions (NAcc-nucleus accumbens, BA9-dorsolateral prefrontal cortex, BA24-anterior cingulate cortex, and HC-hippocampus) in both sorted nuclei and intact tissues. We isolated neuronal and non-neuronal (glial) nuclei from the same six individuals for each tissue via FACS using the neuronal marker, NeuN. Additionally, we performed WGBS from non-sorted tissues from these same brain regions in a total of 12 individuals (BA9 n = 9; BA24 n = 5; HC n = 6; NAcc n = 7). To complement our DNA methylation analyses, we measured gene expression (RNA-seq) and chromatin accessibility (ATAC-seq) in neuronal and non-neuronal nuclei from the nucleus accumbens and dorsolateral prefrontal cortex from six more individuals. We then performed an integrative analysis to understand how the epigenome contributes to brain region-specific function.
2018-12-17 | GSE96613 | GEO
Project description:We analyzed differential methylation (via WGBS) between four distinct human brain regions (NAcc-nucleus accumbens, BA9-dorsolateral prefrontal cortex, BA24-anterior cingulate cortex, and HC-hippocampus) in both sorted nuclei and intact tissues. We isolated neuronal and non-neuronal (glial) nuclei from the same six individuals for each tissue via FACS using the neuronal marker, NeuN. Additionally, we performed WGBS from non-sorted tissues from these same brain regions in a total of 12 individuals (BA9 n = 9; BA24 n = 5; HC n = 6; NAcc n = 7). To complement our DNA methylation analyses, we measured gene expression (RNA-seq) and chromatin accessibility (ATAC-seq) in neuronal and non-neuronal nuclei from the nucleus accumbens and dorsolateral prefrontal cortex from six more individuals. We then performed an integrative analysis to understand how the epigenome contributes to brain region-specific function.
2018-12-17 | GSE96612 | GEO
Project description:Gene regulation in mammals involves a complex interplay between promoter and distal regulatory elements that function in concert to drive precise spatio-temporal gene expression programs. However, the dynamics of distal gene regulatory elements and its function in transcriptional reprogramming that underlies neurogenesis and neuronal activity remain largely unknown. Here we use a combinatorial analysis of genomewide datasets for chromatin accessibility (FAIRE-Seq) and enhancer mark H3K27ac to reveal a highly dynamic nature of chromatin accessibility during neurogenesis that gets restricted to certain genomic regions as neurons acquire a post-mitotic, terminally differentiated state. We further reveal that the distal open regions serve as target sites of distinct transcription factors that function in a stage-specific manner to contribute to the transcriptional program underlying neuronal commitment and maturation. A prolonged NMDA-driven neural activity results in epigenetic reprogramming at a large number of distal regulatory elements as well as dramatic reorganization of super-enhancers that in turn mediate critical transcriptional responses. Taken together, these findings reveal dynamics of distal regulatory landscape during neurogenesis and uncover novel regulatory elements that function in concert with epigenetic mechanisms and transcription factors to generate transcriptome underlying neuronal development and function. FAIRE-Seq and H3K27ac profiles for three stages on neuronal differentation viz. neuronal progenitors, day 1 neurons and day 10 neurons, were generated to understand the dynamics of accessible and ehancer chromatin landscape. Along with this we also generated RNASeq and H3K27ac profiles for day 10 neurons upon control and NMDA treatment.
2015-07-08 | E-GEOD-65713 | biostudies-arrayexpress
Project description:Suspended animation (e.g. hibernation, diapause) allows organisms to survive extreme environments. But the mechanisms underlying the evolution of suspended animation states are unknown. The African turquoise killifish has evolved diapause as a form of suspended development to survive the complete drought that occurs every summer. Here, we show that gene duplicates – paralogs – exhibit specialized expression in diapause compared to normal development in the African turquoise killifish. Surprisingly, paralogs with specialized expression in diapause are evolutionarily very ancient and are present even in vertebrates that do not exhibit diapause. To determine if evolution of diapause is due to the regulatory landscape rewiring at ancient paralogs, we assessed chromatin accessibility genome-wide in fish species with or without diapause. This analysis revealed an evolutionary recent increase in chromatin accessibility at very ancient paralogs in African turquoise killifish. The increase in chromatin accessibility is linked to the presence of new binding sites for transcription factors, likely due to de novo mutations and transposable element (TE) insertion. Interestingly, accessible chromatin regions in diapause are enriched for lipid metabolism genes, and our lipidomics studies uncover a striking difference in lipid species in African turquoise killifish diapause, which could be critical for long-term survival. Together, our results show that diapause likely originated by repurposing pre-existing gene programs via recent changes in the regulatory landscape. This work raises the possibility that suspended animation programs could be reactivated in other species for long-term preservation via transcription factor remodeling and suggests a mechanism for how complex adaptations evolve in nature.
2021-08-05 | ST001898 | MetabolomicsWorkbench