ATACseq of CD34+ HPCs with viral overexpression of GATA3, TCF1 or BCL11B
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE151076 | GEO | 2020/07/29
REPOSITORIES: GEO
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Project description:The generation of TCRαβ and TCRγδ T cells proceeds through distinct developmental stages in which changing regulatory events control differentiation and lineage outcome. To clarify the underlying mechanisms, we employed RNAseq, ATACseq and ChIPmentation on well-defined thymocyte subsets that represent the continuum of human T cell development. The chromatin accessibility dynamics uncover stage-specific regulatory mechanisms and reveal that human T-lineage commitment is marked by the GATA3- and BCL11B-dependent closing of PU.1 sites. While the ß-selection checkpoint is marked by transcriptional changes and a temporary increase in H3K27me3 without modifications in open chromatin, emerging γδ T cells, that originate from common precursors as ß-selected cells, show dramatic changes in chromatin accessibility which results from strong TCR signaling. Furthermore, we unravel distinct chromatin landscapes between CD4 and CD8 αβ T cells that support their effector functions and reveal gene-specific regulatory mechanism that define mature T cells. This resource provides an important framework for studying gene regulatory mechanisms that drive human normal and malignant T cell development.
2020-07-29 | GSE151080 | GEO
Project description:The generation of TCRαβ and TCRγδ T cells proceeds through distinct developmental stages in which changing regulatory events control differentiation and lineage outcome. To clarify the underlying mechanisms, we employed RNAseq, ATACseq and ChIPmentation on well-defined thymocyte subsets that represent the continuum of human T cell development. The chromatin accessibility dynamics uncover stage-specific regulatory mechanisms and reveal that human T-lineage commitment is marked by the GATA3- and BCL11B-dependent closing of PU.1 sites. While the ß-selection checkpoint is marked by transcriptional changes and a temporary increase in H3K27me3 without modifications in open chromatin, emerging γδ T cells, that originate from common precursors as ß-selected cells, show dramatic changes in chromatin accessibility which results from strong TCR signaling. Furthermore, we unravel distinct chromatin landscapes between CD4 and CD8 αβ T cells that support their effector functions and reveal gene-specific regulatory mechanism that define mature T cells. This resource provides an important framework for studying gene regulatory mechanisms that drive human normal and malignant T cell development.
2020-07-29 | GSE151079 | GEO
Project description:The generation of TCRαβ and TCRγδ T cells proceeds through distinct developmental stages in which changing regulatory events control differentiation and lineage outcome. To clarify the underlying mechanisms, we employed RNAseq, ATACseq and ChIPmentation on well-defined thymocyte subsets that represent the continuum of human T cell development. The chromatin accessibility dynamics uncover stage-specific regulatory mechanisms and reveal that human T-lineage commitment is marked by the GATA3- and BCL11B-dependent closing of PU.1 sites. While the ß-selection checkpoint is marked by transcriptional changes and a temporary increase in H3K27me3 without modifications in open chromatin, emerging γδ T cells, that originate from common precursors as ß-selected cells, show dramatic changes in chromatin accessibility which results from strong TCR signaling. Furthermore, we unravel distinct chromatin landscapes between CD4 and CD8 αβ T cells that support their effector functions and reveal gene-specific regulatory mechanism that define mature T cells. This resource provides an important framework for studying gene regulatory mechanisms that drive human normal and malignant T cell development.
2020-07-29 | GSE151078 | GEO
Project description:The generation of TCRαβ and TCRγδ T cells proceeds through distinct developmental stages in which changing regulatory events control differentiation and lineage outcome. To clarify the underlying mechanisms, we employed RNAseq, ATACseq and ChIPmentation on well-defined thymocyte subsets that represent the continuum of human T cell development. The chromatin accessibility dynamics uncover stage-specific regulatory mechanisms and reveal that human T-lineage commitment is marked by the GATA3- and BCL11B-dependent closing of PU.1 sites. While the ß-selection checkpoint is marked by transcriptional changes and a temporary increase in H3K27me3 without modifications in open chromatin, emerging γδ T cells, that originate from common precursors as ß-selected cells, show dramatic changes in chromatin accessibility which results from strong TCR signaling. Furthermore, we unravel distinct chromatin landscapes between CD4 and CD8 αβ T cells that support their effector functions and reveal gene-specific regulatory mechanism that define mature T cells. This resource provides an important framework for studying gene regulatory mechanisms that drive human normal and malignant T cell development.
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2016-06-26 | E-GEOD-81274 | 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
Project description:Hereditary Leiomyomatosis and renal cell cancer is caused by fumarate hydratase loss of heterozygosity and subsequence accumulation of fumarate. Fumarate is known to activate the anti-oxidant response and is key for cellular survival. Fumarate succinates KEAP1 which releases NRF2 to activate the antioxidant response. The role of fumarate on the global regulatory chromatin landscape is less understood. Here, by integrating chromatin accessibility and histone ChIP-seq profiles, we identify complex transcription factor networks involved in the highly remodelled chromatin landscape of FH-deficient cells. We implicate FOXA2 in the maintenance of FH-deficient cells by regulating anti-oxidant response genes and subsequent metabolic output, independent of NRF2. These results identify new redox and amino acid metabolism regulators and provide new avenues for therapeutic intervention.
2022-06-01 | ST002199 | MetabolomicsWorkbench
Project description:Chronic lymphocytic leukemia (CLL) is characterized by substantial clinical heterogeneity, despite relatively few genetic alterations. To provide a basis for studying epigenome deregulation in CLL, we established genome-wide chromatin accessibility maps for 88 CLL samples from 55 patients using the ATAC-seq assay, and we also performed ChIPmentation and RNA-seq profiling for ten representative samples. Based on the resulting dataset, we devised and applied a bioinformatic method that links chromatin profiles to clinical annotations. Our analysis identified sample-specific variation on top of a shared core of CLL regulatory regions. IGHV mutation status – which distinguishes the two major subtypes of CLL – was accurately predicted by the chromatin profiles, and gene regulatory networks inferred for IGHV-mutated vs. IGHV-unmutated samples identified characteristic differences between these two disease subtypes. In summary, we found widespread heterogeneity in the CLL chromatin landscape, established a community resource for studying epigenome deregulation in leukemia, and demonstrated the feasibility of chromatin accessibility mapping in cancer cohorts and clinical research.
2016-06-26 | GSE81274 | GEO
Project description:Chromatin accessibility is a hallmark of active regulatory function in the genome and variation of chromatin accessibility across individuals has been shown to contribute to complex traits and disease susceptibility. However, the mechanisms responsible for chromatin variation among different individuals and how this variation contributes to phenotypic diversity remain poorly understood. We examined chromatin accessibility variation in liver tissue from seven strains of adult mice that have phenotypic diversity in response to a high-fat/high-sucrose diet. Remarkably, nearly 40% of the loci with the greatest degree of chromatin variability across the strains are associated with transposable elements (TEs), with evolutionarily younger TEs being particularly enriched for regions of chromatin variation. We found that evolutionary younger and older TEs have differential chromatin accessibility profiles and are enriched for binding sites of different transcription factors, indicating the role of TEs in the evolution of regulatory networks in the liver. We also demonstrate that TE polymorphisms and epigenetic regulation of TEs contribute to regulatory variation across different strains through providing binding sites for liver transcription factors. Intriguingly, variable chromatin loci that are associated with liver metabolism are primarily TE-associated. We demonstrate that TEs contribute to regulatory variation in liver and have downstream effects on metabolism. Our data reveal TEs as a novel and important contributor to regulatory and phenotypic variation in the liver and suggest that regulatory variation at TEs is a major contributor to phenotypic variation in populations. Examination of chromatin accessibility with FAIRE-seq in livers of male mice (A/J, AKR/J, BALB/cJ, C57BL/6J, C3H/HeJ, CBA/J, DBA/2J, BXH2/TyJ, and BXH19/TyJ) fed a high-fat, high-sucrose diet.
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