In vitro neuronal RNA-sequencing, in vivo cortical single nucleus RNA-sequencing, in vivo cortical ChIP-sequencing of H3K79me2 in models of DOT1L loss
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE279978 | GEO | 2025/11/13
REPOSITORIES: GEO
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Project description:In vitro neuronal RNA-sequencing, in vivo cortical single nucleus RNA-sequencing, in vivo cortical ChIP-sequencing of H3K79me2 in models of DOT1L loss
| PRJNA1175649 | ENA
Project description:During neuronal differentiation, the transcriptional profile and the epigenetic context of neural committed cells is subject to significant rearrangements, but a systematic quantification of global histone modification changes is still missing. Here, we show that H3K79me2 increases and H3K27ac decreases globally during in-vitro neuronal differentiation of murine embryonic stem cells. DOT1L mediates all three degrees of methylation of H3K79 and its enzymatic activity is critical to modulate cellular differentiation and reprogramming. In this context, we find that inhibition of DOT1L in neural progenitor cells biases the transcriptional state towards neuronal differentiation, resulting in transcriptional upregulation of genes marked with H3K27me3 on the promoter region. We further show that DOT1L inhibition affects accessibility of SOX2-bound enhancers and impairs SOX2 binding in neural progenitors. Our work provides evidence that DOT1L activity gates differentiation of progenitors by allowing SOX2-dependent transcription of stemness programs.
| S-EPMC7562744 | biostudies-literature
Project description:Epigenetic changes on DNA and chromatin are implicated in cell differentiation and organogenesis. For the heart, distinct histone methylation profiles were recently linked to stage-specific gene expression programs during cardiac differentiation in vitro. However, the enzymes catalyzing these modifications and the genes regulated by them remain poorly defined. We therefore decided to identify the epigenetic enzymes that are potentially involved in cardiomyogenesis by analyzing the expression profile of the 85 genes encoding the epigenetic-related proteins in mouse cardiomyocytes (CMs), and then study how they affect gene expression during differentiation and maturation of this cell type. We show here with gene expression screening of epigenetic enzymes that the highly expressed H3 methyltransferase disruptor of telomeric silencing 1-like (DOT1L) drives a transitional pattern of di-methylation on H3 lysine 79 (H3K79) in CMs at different stages of differentiation in vitro and in vivo. Through a genome-wide chromatin-immunoprecipitation DNA-sequencing approach, we found H3K79me2 enriched at genes expressed during cardiac differentiation. Moreover, knockdown of Dot1L affected the expression of H3K79me2-enriched genes. Our results demonstrate that histone methylation, and in particular DOT1L-mediated H3K79me2 modification, drives cardiomyogenesis through the definition of a specific transcriptional landscape.
| S-EPMC4986629 | biostudies-literature
Project description:The human brain has enormously complex cellular diversity and connectivities fundamental to our neural functions, yet difficulties in interrogating individual neurons has impeded understanding of the underlying transcriptional landscape. We developed a scalable approach to sequence and quantify RNA molecules in isolated neuronal nuclei from a postmortem brain, generating 3227 sets of single-neuron data from six distinct regions of the cerebral cortex. Using an iterative clustering and classification approach, we identified 16 neuronal subtypes that were further annotated on the basis of known markers and cortical cytoarchitecture. These data demonstrate a robust and scalable method for identifying and categorizing single nuclear transcriptomes, revealing shared genes sufficient to distinguish previously unknown and orthologous neuronal subtypes as well as regional identity and transcriptomic heterogeneity within the human brain.
| S-EPMC5038589 | biostudies-literature
Project description:The sympathetic nervous system regulates various visceral functions, including those of the heart, lungs, and digestive system, and maintains homeostasis. The prevertebral ganglia (PVG) in the peripheral nervous system serve as a vital relay station, transmitting efferent signals to visceral organs. The PVG receives innervation from intestinofugal afferent neurones (IFANs) that originate from the enteric plexus, as well as from spinal sensory nerves that innervate the enteric tract. While neural circuits comprising sensory and sympathetic nerves have been proposed, the exact diversity of the individual neurones in these circuits is still not well characterized in rats. In this study, we employed single-nuclei RNA-sequencing to characterize all the cell types present in the celiac ganglion (CG). We identified five distinct neural clusters, including celiac noradrenergic and celiac cholinergic neurones (CNA1-4, CACh). Among these, the CNA3 cluster expressed Tacr1 and Cckar, while the CACh cluster expressed Ramp1. Furthermore, we characterised Mki67-positive proliferating cells and found that they expressed genes associated with satellite glial cells (SGCs). Additionally, general resident and sympathetic SGCs with distinct SGC clusters were localised within the CG. Our data provide a valuable resource for investigating neural circuits within the PVG and for identifying target organs innervated by specific neuronal populations.
| S-EPMC11828872 | biostudies-literature
Project description:Epigenetic modification, including histone modification, precisely controls target gene expression. The posttranscriptional regulation of the innate signaling-triggered production of inflammatory cytokines and type I interferons has been fully elucidated, whereas the roles of histone modification alteration and epigenetic modifiers in regulating inflammatory responses need to be further explored. Di/tri-methylation modifications of histone 3 lysine 79 (H3K79me2/3) have been shown to be associated with gene transcriptional activation. Disruptor of telomeric silencing-1-like (Dot1l) is the only known exclusive H3K79 methyltransferase and regulates the proliferation and differentiation of tumor cells. However, the roles of Dot1l and Dot1l-mediated H3K79 methylation in innate immunity and inflammatory responses remain unclear. Here, we found that H3K79me2/3 modification levels at the Il6 and Ifnb1 promoters, as well as H3K79me2 modification at the Tnfα promoter, were increased in macrophages activated by Toll-like receptor (TLR) ligands or virus infection. The innate signals upregulated Dot1l expression in macrophages and THP1 cells. Dot1l silencing or a Dot1l inhibitor preferentially suppressed the production of IL-6 and interferon (IFN)-β but not of TNF-α in macrophages and THP1 cells triggered by TLR ligands or virus infection. Dot1l was recruited to the proximal promoter of the Il6 and Ifnb1 but not Tnfα gene and then mediated H3K79me2/3 modification at the Il6 and Ifnb1 promoters, consequently facilitating the transcription and expression of Il6 and Ifnb1. Thus, Dot1l-mediated selective H3K79me2/3 modifications at the Il6 and Ifnb1 promoters are required for the full activation of innate immune responses. This finding adds new insights into the epigenetic regulation of inflammatory responses and pathogenesis of autoimmune diseases.
| S-EPMC6952432 | biostudies-literature
Project description:To study whether acute inhibition of DOT1L induces global chromatin states alterations, we profile and compare the transcriptome, chromatin accessibility and epigenome (H3K4me3, H3K4me1, H3K27ac, H3K27me3, H3K36me3, H3K9me3, H3K79me2) of mESC and ES-derived NPC, treated with DMSO or EPZ5676.
2020-08-01 | GSE135318 | GEO
Project description:The superior colliculus (SC) is a sensorimotor structure in the midbrain that integrates input from multiple sensory modalities to initiate motor commands. It undergoes well-characterized steps of circuit assembly during development, rendering the mouse SC a popular model to study establishment of neural connectivity. Here we perform single-nucleus RNA-sequencing analysis of the mouse SC isolated at various developmental time points. Our study provides a transcriptomic landscape of the cell types that comprise the SC across murine development with particular emphasis on neuronal heterogeneity. We report a repertoire of genes differentially expressed across the different postnatal ages, many of which are known to regulate axon guidance and synapse formation. Using these data, we find that Pax7 expression is restricted to a subset of GABAergic neurons. Our data provide a valuable resource for interrogating the mechanisms of circuit development and identifying markers for manipulating specific SC neuronal populations and circuits.
| S-EPMC10592058 | biostudies-literature
Project description:ObjectiveTo explore the influence of SALL4 in cardiac fibroblasts on the progression of myocardial infarction.MethodsAnalysis of genes specifically expressed in myocardial infarction by bioinformatics methods; The impact of SALL4 on myocardial infarction was assessed using mouse ultrasound experiments and Masson staining; The effect of SALL4 on the expression levels of collagen-I and collagen-III in myocardial tissue was examined by immunohistochemical staining; The migration ability of cardiac fibroblasts was evaluated using a Transwell assay; The proliferative ability of cardiac fibroblasts was tested using a CCK-8 assay; The relative fluorescence intensity of α-SMA and CTGF in cardiac fibroblasts were checked through immunofluorescence staining experiment; The expression of SALL4, DOT1L, H3K79me2, P53, SHP2, YAP, nucleus-YAP, collagen-I, α-SMA, CTGF, and PAI-1 in myocardial tissues or cardiac fibroblasts was detected using western blot analysis.ResultsSALL4-specific high expression in myocardial infarction; SALL4 intensified the alterations in the heart structure of mice with myocardial infarction and worsened the fibrosis of myocardial infarction; SALL4 also promoted the expression of SALL4, DOT1L, H3K79me2, P53, SHP2, YAP, nucleus-YAP, collagen-I, collagen-III, α-SMA, CTGF, and PAI-1 in myocardial infarction tissues and cardiac fibroblasts; Subsequently, SALL4 could enhance the immunofluorescence intensity of α-SMA and CTGF; Moreover, SALL4 could promote the proliferation and migration of cardiac fibroblasts.ConclusionIn cardiac fibroblasts, SALL4 mediates the DOT1L/H3K79me2 signaling pathway to inhibit SHP2, which then promotes the YAP/TAZ signaling pathway, thereby facilitating the progression of myocardial infarction.
| S-EPMC11680873 | biostudies-literature
Project description:The liver plays an important role in xenobiotic metabolism and represents a primary target for toxic substances. Many different in vitro cell models have been developed in the past decades. In this study, we used RNA-sequencing (RNA-Seq) to analyze the following human in vitro liver cell models in comparison to human liver tissue: cancer-derived cell lines (HepG2, HepaRG 3D), induced pluripotent stem cell-derived hepatocyte-like cells (iPSC-HLCs), cancerous human liver-derived assays (hPCLiS, human precision cut liver slices), non-cancerous human liver-derived assays (PHH, primary human hepatocytes) and 3D liver microtissues. First, using CellNet, we analyzed whether these liver in vitro cell models were indeed classified as liver, based on their baseline expression profile and gene regulatory networks (GRN). More comprehensive analyses using non-differentially expressed genes (non-DEGs) and differential transcript usage (DTU) were applied to assess the coverage for important liver pathways. Through different analyses, we noticed that 3D liver microtissues exhibited a high similarity with in vivo liver, in terms of CellNet (C/T score: 0.98), non-DEGs (10,363) and pathway coverage (highest for 19 out of 20 liver specific pathways shown) at the beginning of the incubation period (0 h) followed by a decrease during long-term incubation for 168 and 336 h. PHH also showed a high degree of similarity with human liver tissue and allowed stable conditions for a short-term cultivation period of 24 h. Using the same metrics, HepG2 cells illustrated the lowest similarity (C/T: 0.51, non-DEGs: 5623, and pathways coverage: least for 7 out of 20) with human liver tissue. The HepG2 are widely used in hepatotoxicity studies, however, due to their lower similarity, they should be used with caution. HepaRG models, iPSC-HLCs, and hPCLiS ranged clearly behind microtissues and PHH but showed higher similarity to human liver tissue than HepG2 cells. In conclusion, this study offers a resource of RNA-Seq data of several biological replicates of human liver cell models in vitro compared to human liver tissue.
| S-EPMC7870774 | biostudies-literature