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978 results for “chromatin remodeling”
Dynamic 1D search and processive nucleosome translocations by RSC and ISW2 chromatin remodelers
<p>Eukaryotic gene expression is linked to chromatin structure and nucleosome positioning by ATP-dependent chromatin remodelers that establish and maintain nucleosome-depleted regions (NDRs) near transcription start-sites. Conserved yeast RSC and ISW2 remodelers exert antagonistic effects on nucleosomes flanking NDRs, but the temporal dynamics of remodeler search, engagement and directional nucleosome mobilization for promoter accessibility are unknown. Using optical tweezers and 2-color single-particle imaging, we investigated the Brownian diffusion of RSC and ISW2 on free DNA and sparse nucleosome arrays. RSC and ISW2 rapidly scan DNA by one-dimensional hopping and sliding respectively, with dynamic collisions between remodelers followed by recoil or apparent co-diffusion. Static nucleosomes block remodeler diffusion resulting in remodeler recoil or sequestration. Remarkably, both RSC and ISW2 use ATP hydrolysis to translocate mono-nucleosomes processively at ~30 bp/sec for surprising distances on extended linear DNA. Processivity and opposing push-pull directionalities of nucleosome translocation shown by RSC and ISW2 shape the distinctive landscape of promoter chromatin.</p>
ATP binding facilitates target search of SWR1 chromatin remodeler by promoting one-dimensional diffusion on DNA
<p>One-dimensional (1D) target search is a well-characterized phenomenon for many DNA-binding proteins but is poorly understood for chromatin remodelers. Herein, we characterize the 1D scanning properties of SWR1, a conserved yeast chromatin remodeler that performs histone exchange on +1 nucleosomes adjacent to a nucleosome-depleted region (NDR) at gene promoters. We demonstrate that SWR1 has a kinetic binding preference for DNA of NDR length as opposed to gene-body linker length DNA. Using single and dual color single-particle tracking on DNA stretched with optical tweezers, we directly observe SWR1 diffusion on DNA. We found that various factors impact SWR1 scanning, including ATP which promotes diffusion through nucleotide binding rather than ATP hydrolysis. A DNA-binding subunit, Swc2, plays an important role in the overall diffusive behavior of the complex, as the subunit in isolation retains similar, although faster, scanning properties as the whole remodeler. ATP-bound SWR1 slides until it encounters a protein roadblock, of which we tested dCas9 and nucleosomes. The median diffusion coefficient, 0.024 μm2/s, in the regime of helical sliding, would mediate rapid encounter of NDR-flanking nucleosomes at length scales found in cellular chromatin.</p>
Data from: Dissecting gene activation and chromatin remodeling dynamics in single human cells undergoing reprogramming
<p>During cell fate transitions, cells remodel their transcriptome, chromatin, and epigenome; however, it has been difficult to determine the temporal dynamics and cause-effect relationship between these changes at the single-cell level. Here, we employ the heterokaryon-mediated reprogramming system as a single-cell model to dissect key temporal events during early stages of pluripotency conversion using super-resolution imaging. We reveal that, following heterokaryon formation, the somatic nucleus undergoes global chromatin decompaction and removal of repressive histone modifications H3K9me3 and H3K27me3 without acquisition of active modifications H3K4me3 and H3K9ac. The pluripotency gene OCT4 (POU5F1) shows nascent and mature RNA transcription within the first 24 h after cell fusion without requiring an initial open chromatin configuration at its locus. NANOG, conversely, has significant nascent RNA transcription only at 48 h after cell fusion but, strikingly, exhibits genomic reopening early on. These findings suggest that the temporal relationship between chromatin compaction and gene activation during cellular reprogramming is gene context dependent. </p>
Histone tail dynamics in partially disassembled nucleosomes during chromatin remodeling: Simulation dataset
<p>Dataset of molecular dynamics simulations of partially disassembled nucleosomes.</p> <p>- Input: Parameters and initial structures</p> <p>- Output: Trajectories</p> <p>NAMD 2.12 (multi-core with CUDA) was used for the simulations.</p>
Data from: Dissecting gene activation and chromatin remodeling dynamics in single human cells undergoing reprogramming
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ATP binding facilitates target search of SWR1 chromatin remodeler by promoting one-dimensional diffusion on DNA
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Dynamic 1D search and processive nucleosome translocations by RSC and ISW2 chromatin remodelers
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Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to transposable elements
<p>Structural variant calls, RepeatMasker annotations, and genome assemblies of diverse mouse genomes. </p>
Code and data for "Bordetella adenylate cyclase toxin elicits chromatin remodeling and transcriptional reprogramming that blocks differentiation of monocytes into macrophages"
<p># Code and data for "Bordetella adenylate cyclase toxin elicits chromatin remodeling and transcriptional reprogramming that blocks differentiation of monocytes into macrophages"</p> <p><br> - `pipeline` contains scripts for processing raw reads with `nf-core/rnaseq` Nextflow pipeline<br> - `setup_conda.sh` sets up a conda environment for Nextflow<br> - `samplesheet.csv` describes the samples<br> - `rna-seq-nextflow.sh` runs the analysis<br> - `data` contains the quantifications by Salmon from the pipeline and data for the CRE motif (see `analysis.Rmd` for more details)<br> - `analysis.Rmd` an R notebook containing a code to reproduce conclusions and figures in the paper and additional comments.</p> <p>The R environment (all packages) is reproducibly reconstructed via `renv` - run `renv::restore()` after loading the project.</p> <p>The generated figures and tables are stored in the `outputs` directory.</p> <p> </p>
Chromatin conformation, gene transcription, and nucleosome remodeling as an emergent system
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Data from: Serine ADP-ribosylation marks nucleosomes for ALC1-dependent chromatin remodeling
<p>Serine ADP-ribosylation (ADPr) is a DNA damage-induced post-translational modification catalyzed by the PARP1/2:HPF1 complex. As the list of PARP1/2:HPF1 substrates continues to expand, there is a need for technologies to prepare mono- and poly-ADP-ribosylated proteins for biochemical interrogation. Here we investigate the unique peptide ADPr activities catalyzed by PARP1 in the absence and presence of HPF1. We then exploit these activities to develop a method that facilitates installation of ADP-ribose polymers onto peptides with precise control over chain length and modification site. Importantly, the enzymatically mono- and poly-ADP-ribosylated peptides are fully compatible with protein ligation technologies. This chemoenzymatic protein synthesis strategy was employed to assemble a series of full-length, ADP-ribosylated histones and show that ADPr at H2BS6 or H3S10 converts nucleosomes into robust substrates for the chromatin remodeler ALC1. We found ALC1 preferentially remodels 'activated' substrates within heterogeneous mononucleosome populations and asymmetrically ADP-ribosylated dinucleosome substrates, and that nucleosome serine ADPr is sufficient to stimulate ALC1 activity in nuclear extracts. Our study identifies a biochemical function for nucleosome serine ADPr and describes a new, highly modular approach to explore the impact that site-specific serine mono- and poly-ADPr have on protein function.</p>
Data from: Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes
The yeast Chd1 protein acts to position nucleosomes across genomes. Here, we model the structure of the Chd1 protein in solution and when bound to nucleosomes. In the apo state, the DNA-binding domain contacts the edge of the nucleosome while in the presence of the non-hydrolyzable ATP analog, ADP-beryllium fluoride, we observe additional interactions between the ATPase domain and the adjacent DNA gyre 1.5 helical turns from the dyad axis of symmetry. Binding in this conformation involves unravelling the outer turn of nucleosomal DNA and requires substantial reorientation of the DNA-binding domain with respect to the ATPase domains. The orientation of the DNA-binding domain is mediated by sequences in the N-terminus and mutations to this part of the protein have positive and negative effects on Chd1 activity. These observations indicate that the unfavorable alignment of C-terminal DNA-binding region in solution contributes to an auto-inhibited state.
Chromatin Remodeling via Retinoic Acid Action During Mu-rine Spermatogonial Development
<p>Spermatogonial differentiation is a process that commits germ cells to the complex process of spermatogenesis. Spermatogonial differentiation is mediated by the action of retinoic acid, which triggers major morphological and transcriptional changes. While these transcriptional changes have been well explored, there has been little effort devoted to epigenetic regulation surrounding spermatogonial development. This study aimed to uncover the timing and dynamics of chromatin organization during spermatogonial development within the context of these transcriptional changes. Using germ cell synchrony and the assay for transposase accessible chromatin and next generation sequencing (ATAC-seq) to isolate subpopulations of developing spermatogonia and identify accessible regions within their genome, we found 50% of accessible regions in undifferentiated spermatogonia were condensed following retinoic acid action within 18 hours. Surprisingly, genes with known functional relevance during spermatogonial development were accessible at all times, indicating that chromatin state does not impact transcription at these sites. While there was an overall decrease in gene accessibility during spermatogonial development, we found that transcriptionally active regions were not predictive of chromatin state.</p>
Data from: Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes
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Data from: Serine ADP-ribosylation marks nucleosomes for ALC1-dependent chromatin remodeling
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Data from: Evf2 lncRNA/BRG1/DLX1 interactions reveal RNA-dependent inhibition of chromatin remodeling
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SS18::SSX redistributes BAF chromatin remodelers selectively to activate and repress transcription [ChIP-Seq, Hi-ChIP]
GEO Series GSE269770. Mus musculus. 71 samples. Type: Other.
BPTF is required for c-MYC-induced remodelling of target chromatin and transcriptional activation [ChIP-Seq]
GEO Series GSE65544. Homo sapiens. 3 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Upstream regulator of genomic imprinting in rice is a small RNA-associated chromatin remodeler [Bisulfite_seq]
GEO Series GSE260651. Oryza sativa. 2 samples. Type: Methylation profiling by high throughput sequencing.
Genome-Wide Specificity of DNA-Binding, Gene Regulation, and Chromatin Remodeling by TALE- and CRISPR/Cas9-Based Transcription Factors
GEO Series GSE68341. Homo sapiens. 9 samples. Type: Expression 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.