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94 results for “chromatin condensation”
Multiscale Bayesian Simulations Reveal Functional Chromatin Condensation of Gene Loci
<p>Chromatin, the complex assembly of DNA and associated proteins, plays a pivotal role in orchestrating various genomic functions. To aid our understanding of the principles underlying chromatin organization, we introduce Hi-C metainference, a Bayesian approach that integrates Hi-C contact frequencies into multiscale prior models of chromatin. This approach combines both bottom-up (the physics-based prior) and top-down (the data-driven posterior) strategies to characterize the 3D organization of a target genomic locus. We first demonstrate the capability of this method to accurately reconstruct the structural ensemble and the dynamics of a system from contact information. We then apply the approach to investigate the Sox2, Pou5f1, and Nanog loci of mouse embryonic stem cells using a bottom-up chromatin model at 1kb resolution. We observe that the studied loci are conformationally heterogeneous and organized as crumpled globules, favoring contacts between distant enhancers and promoters. Using nucleosome-resolution simulations, we then reveal how the Nanog gene is functionally organized across the multiple scales of chromatin. At the local level, we identify diverse tetranucleosome folding motifs with a characteristic distribution along the genome, predominantly open at cis-regulatory elements and compact in between. At the larger scale, we find that enhancer-promoter contacts are driven by the transient condensation of chromatin into compact domains stabilized by extensive inter-nucleosome interactions. Overall, this work highlights the condensed, but dynamic nature of chromatin in vivo, contributing to a deeper understanding of gene structure-function relationships.</p>
Data from: In diverse conditions intrinsic chromatin condensate have liquid-like material properties
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Data from: Multi-scale structure of chromatin condensates explains phase separation and material properties
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Data from: Cryo-electron tomography reveals the multiplex anatomy of condensed native chromatin and its unfolding by histone citrullination
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Data from: Nucleolar sub-compartments in motion during rRNA synthesis inhibition: contraction of nucleolar condensed chromatin and gathering of fibrillar centers are concomitant
The nucleolus produces the large polycistronic transcript (47S precursor) containing the 18S, 5.8S and 28S rRNA sequences and hosts most of the nuclear steps of pre-rRNA processing. Among numerous components it contains condensed chromatin and active rRNA genes which adopt a more accessible conformation. For this reason, it is a paradigm of chromosome territory organization. Active rRNA genes are clustered within several fibrillar centers (FCs), in which they are maintained in an open configuration by Upstream Binding Factor (UBF) molecules. Here, we used the reproducible reorganization of nucleolar components induced by the inhibition of rRNA synthesis by Actinomycin D (AMD) to address the steps of the spatiotemporal reorganization of FCs and nucleolar condensed chromatin. To reach that goal, we used two complementary approaches: i) time-lapse confocal imaging of cells expressing one or several GFP-tagged proteins (fibrillarin, UBF, histone H2B) and ii) ultrastructural identification of nucleolar components involved in the reorganization. Data obtained by time lapse confocal microscopy were analyzed through detailed 3D imaging. This allowed us to demonstrate that AMD treatment induces no fusion and no change in the relative position of the different nucleoli contained in one nucleus. In contrast, for each nucleolus, we observed step by step gathering and fusion of both FCs and nucleolar condensed chromatin. To analyze the reorganization of FCs and condensed chromatin at a higher resolution, we performed correlative light and electron microscopy electron microscopy (CLEM) imaging of the same cells. We demonstrated that threads of intranucleolar condensed chromatin are localized in a complex 3D network of vacuoles. Upon AMD treatment, these structures coalesce before migrating toward the perinucleolar condensed chromatin, to which they finally fuse. During their migration, FCs, which are all linked to ICC, are pulled by the latter to gather as caps disposed at the periphery of nucleoli.
Data from: Nucleolar sub-compartments in motion during rRNA synthesis inhibition: contraction of nucleolar condensed chromatin and gathering of fibrillar centers are concomitant
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The Histone Variant H2A.W Defines Heterochromatin and Promotes Chromatin Condensation in Arabidopsis
GEO Series GSE50942. Arabidopsis thaliana. 10 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
Extrachromosomal DNA Associates with Nuclear Condensates and Reorganizes Chromatin Structures to Enhance Oncogenic Transcription
GEO Series GSE275060. Homo sapiens. 117 samples. Type: Other.
N6-adenosine Methylation of Enhancer RNAs and YTHDC1 Facilitate Transcriptional Condensate Formation and 3D Chromatin Organization
GEO Series GSE143441. Homo sapiens. 62 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
Extrachromosomal DNA Associates with Nuclear Condensates and Reorganizes Chromatin Structures to Enhance Oncogenic Transcription [ChIA-PET]
GEO Series GSE275054. Homo sapiens. 12 samples. Type: Other.
An essential cell cycle regulator drives chromatin condensation in maturing erythroblasts
GEO Series GSE83809. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Condensin-dependent chromatin condensation represses transcription globally during quiescence
GEO Series GSE120606. Saccharomyces cerevisiae. 48 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.
SUMOylation of Linker Histone H1 Drives Chromatin Condensation and Restriction of Embryonic Cell Fate Identity [ChIP-seq]
GEO Series GSE153040. Mus musculus. 10 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Extrachromosomal DNA Associates with Nuclear Condensates and Reorganizes Chromatin Structures to Enhance Oncogenic Transcription [RNA-seq]
GEO Series GSE275702. Homo sapiens. 20 samples. Type: Expression profiling by high throughput sequencing.
SUMOylation of Linker Histone H1 Drives Chromatin Condensation and Restriction of Embryonic Cell Fate Identity
GEO Series GSE153041. Mus musculus. 36 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
Histone H2A.X Phosphorylation Activates Caspase-Induced Chromatin Condensation in Late Stage Erythropoiesis
GEO Series GSE159422. Homo sapiens. 22 samples. Type: Expression profiling by high throughput sequencing.
SUMOylation of Linker Histone H1 Drives Chromatin Condensation and Restriction of Embryonic Cell Fate Identity [ATAC-seq]
GEO Series GSE153039. Mus musculus. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Extrachromosomal DNA Associates with Nuclear Condensates and Reorganizes Chromatin Structures to Enhance Oncogenic Transcription [ChIA-Drop]
GEO Series GSE275053. Homo sapiens. 6 samples. Type: Other.
Condensate-promoting ENL mutation induces tumorigenesis via chromatin remodeling
GEO Series GSE239470. Mus musculus. 74 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
The three-dimensional genomic organization changes in terminal erythropoiesis reveal independence of chromatin condensation from nuclear condensation
GEO Series GSE185470. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.