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Chromatin accessibility dynamics in a model of human forebrain development

ABSTRACT: Chromatin accessibility dynamics in a model of human forebrain development

PROVIDER: PRJNA549493 | ENA |

REPOSITORIES: ENA

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Chromatin accessibility dynamics in a model of human forebrain development

Project description:In this study, we used a forebrain 3D spheroid model to map chromatin accessibility and gene expression changes throughout a dense time course spanning 20 months of neuronal and glial maturation.

2020-01-23 | GSE132403 | GEO

Chromatin accessibility dynamics in a model of human forebrain development.

Project description: Not available

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Chromatin accessibility dynamics across C. elegans development and ageing

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Developmental dynamics of DNA accessibility during flower development [DNaseI-Seq]

Project description:Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programmes. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood. Here, we characterize the dynamic relationship of chromatin accessibility, gene expression and DNA-binding of two MADS-domain proteins during Arabidopsis flower development. The developmental dynamics of DNA-binding of APETALA1 and SEPALLATA3 is largely independent of chromatin accessibility, and our findings suggest that AP1 acts as M-bM-^@M-^Xpioneer factorM-bM-^@M-^Y that modulates chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes. Our data provide a primer to the idea that cellular differentiation in plants can be associated to dynamic changes in chromatin accessibility, as consequence of the action of master transcription factors. We used the AP1-GR system to conduct DNaseI hypersensitivity experiments at different stages of flower development. Samples were generated from tissue in which the AP1-GR protein was induced using a treatment of 1 uM DEX to the shoot apex. The material was collect before treatment and 2, 4 and 8 days after treatment. As control, naked DNA from wild-type inflorescences was used. Experiments were done in two biological replicates. The GSE47981 includes expression data that are complementary to the data in the GSE46986 and GSE46894.

2014-02-03 | E-GEOD-46894 | biostudies-arrayexpress

Chromatin accessibility dynamics and transcriptional regulation in Tetrahymena thermophila

Project description:Chromatin accessibility dynamics and their relationship to gene expression remain poorly understood in ciliated protozoa. Here, we investigate these dynamics in Tetrahymena thermophila by optimizing ATAC-seq to map chromatin accessibility across its transcriptionally active macronucleus during distinct life cycle stages. We demonstrate that chromatin accessibility at transcription start sites (TSSs) strongly correlates with gene expression levels. Intriguingly, partitioning ATAC-seq signals into nucleosome-free (NFR) and nucleosome-associated (NUC) regions revealed conserved TSS-proximal features: NFR signals peak upstream of TSSs, while phased +1 nucleosome arrays detected via NUC signals align with MNase-seq profiles. Temporal analysis uncovered stage-specific chromatin accessibility patterns, with global accessibility fluctuating dynamically across developmental phases. While most differentially accessible loci mirrored expression changes, subsets exhibited discordant regulation, suggesting context-specific chromatin-transcriptional coupling. Pharmacological inhibition of transcription using flavopiridol (FLV) triggered upstream chromatin compaction, elevated gene body accessibility, and enhanced nucleosome phasing, implicating transcription-coupled processes in shaping chromatin states. Cross-species comparisons of TSS-proximal accessibility across 13 eukaryotes revealed three conserved architectural modes (upstream-biased, symmetric, or upstream-restricted), with divergent spacing of +1 nucleosomes relative to TSSs. Our work establishes Tetrahymena as a model for studying chromatin dynamics in single-celled eukaryotes and provides evolutionary insights into the interplay between nucleosome organization, chromatin accessibility, and transcriptional regulation.

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Chromatin accessibility dynamics across C. elegans development and ageing [scap]

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Chromatin accessibility dynamics across C. elegans development and ageing [lcap]

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Chromatin Accessibility Dynamics during Chemical Induction of Pluripotency

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Chromatin accessibility dynamics of Chlamydia-infected epithelial cells

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Chromatin accessibility dynamics across C. elegans development and ageing [ChIP-seq]

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