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5,047 results for “histones”
Data for: A histone demethylase links the loss of plasticity to nongenetic inheritance and morphological change
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Data from: Evidence of centromeric histone 3 chaperone involved in DNA damage repair pathway in budding yeast
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Selfish chromosomal drive shapes recent centromeric histone evolution in monkeyflowers
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Phosphorylated histone variant γH2Av is associated with chromatin insulators in Drosophila
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Histone acetylation readers Bdf1 and Yaf9 direct SWR1 remodeler to +1 nucleosome
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Sex affects immunolabeling for histone 3 K27me3 in the trophectoderm of the bovine blastocyst but not labeling for histone 3 K18ac
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The histone demethylase Kdm3 prevents auto-immune piRNAs production in Drosophila
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Data from: Asexuality associated with marked genomic expansion of tandemly repeated rRNA and histone genes
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Data from: Diverse nucleosome site-selectivity among histone deacetylase complexes
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Palmitoyltransferase ZDHHC19 regulates histone-to-protamine exchange during spermiogenesis in mice
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Transcriptome analysis of WT versus H2A.J-KO MEFs for the paper entitled: The H2A.J histone variant contributes to Interferon-Stimulated Gene expression in senescence by its weak interaction with H1 and the derepression of repeated DNA sequences
<p>Abstract for overall study:</p> <p>The histone variant H2A.J was previously shown to accumulate in senescent human fibroblasts with persistent DNA damage to promote inflammatory gene expression, but its mechanism of action was unknown. We show that H2A.J accumulation contributes to weakening the association of histone H1 to chromatin and increasing its turnover. Decreased H1 in senescence is correlated with increased expression of some repeated DNA sequences, increased expression of STAT/IRF transcription factors, and transcriptional activation of Interferon-Stimulated Genes (ISGs). The H2A.J-specific Val-11 moderates the transcriptional activity of H2A.J, and H2A.J-specific Ser-123 can be phosphorylated in response to DNA damage with potentiation of its transcriptional activity by the phospho-mimetic S123E mutation. Our work demonstrates the functional importance of H2A.J-specific residues and potential mechanisms for its function in promoting inflammatory gene expression in senescence.</p> <p>Specific description for this dataset:</p> <p>We further tested a role for H2A.J in Interferon-Stimulated Gene expression by analyzing the transcriptome of WT and H2A.J MEFs induced into senescence by etoposide. TruSeq stranded DNA libraries were prepared from polyA-selected RNA and sequenced as 43 bp paired-end reads. The fastq sequences were mapped to Gencode.vM24.transcripts.fa.gz (GRCm38 transcriptome) with salmon. Read counts were then aggregated to the gene level with tximeta, and differential gene expression was analysed with DESeq2, edgeR, and limma-voom. Gene set enrichment analysis was performed with camera.</p> <p>The transciptomes of senescent WT and H2AFJ-KO showed strong separation from proliferating MEFs, and a weaker separation distinguished WT and H2A.J-KO MEFs. Strikingly, gene set enrichment analysis indicated highly significant defects in Interferon Response Gene Expression in the H2A.J-KO MEFs in senescence with significant down-regulation in senescent H2A.J-KO cells of a series of oligoadenylate synthase genes (Oas1g, Oas1a, Oasl1, Oas2, Oasl2) and several ISGs. Thus, H2A.J also contributes to ISG expression in the heterologous context of senescent MEFs.</p>
Histone H1 variants in Arabidopsis are subject to numerous post-translational modifications, both conserved and previously unknown in histones, suggesting complex functions of H1 in plants - raw data
<p>Data from HPLC coupled with mass spectrometer acquired during experiments.<br /> </p>
Characterisation of core histone sequences and nuclear mobility using a reproducible research approach
<p>Dataset required to build the PhD thesis. Includes the public sequences that would otherwise be downloaded anew.</p>
A histone methyltransferase-independent function of PRC2 controls small RNA dynamics during programmed DNA elimination in Paramecium
<p><span lang="EN-US">To limit transposable element (TE) mobilization, most eukaryotes have evolved small RNAs to silence TE activity via homology-dependent mechanisms. Small RNAs, 20-30 nucleotides in length, bind to PIWI proteins and guide them to nascent transcripts by sequence complementarity, triggering the recruitment of histone methyltransferase enzymes on chromatin to repress the transcriptional activity of TEs and other repeats. In<span> the ciliate <em>Paramecium tetraurelia</em>,</span> 25-nt scnRNAs corresponding to TEs recruit Polycomb Repressive Complex 2 (PRC2), and trigger their elimination during the formation of the somatic nucleus. Here, we sequenced sRNAs during the entire sexual cycle with unprecedented resolution. Our data confirmed that scnRNAs are produced from the entire germline genome, from TEs and non-TE sequences, during meiosis. Non-TE scnRNAs are selectively degraded, which results in the specific selection of TE-scnRNAs. We demonstrate that PRC2 is essential for the selective degradation of non-TE-scnRNAs, independently of its histone methyltransferase activity. We further show that the PRC2 cofactor Rf4 mediates the physical interaction between the scnRNA-binding protein Ptiwi09 and the zinc finger protein Gtsf1, pointing to an architectural role of PRC2 in scnRNA degradation.</span></p>
Molecular Dynamics simulation dataset for : Hypoxia increases the methylated histones to prevent histone clipping and redistribution of heterochromatin during Raf-induced senescence.
<p>Files are Initial structures of Cathepsin L(CTSL) with histone H3 peptides (naive and K23me3) and their Molecular Dynamics simulation trajectories. AutoDock Vina and Charmm were used in H3 peptide docking. </p> <p>Wild type CTSL was modeled with apo-Cathepsin L C25A mutant(PDB ID : 3K24) using Charmm-GUI. Trimethylated histone H3 peptide was generated with PyMol. H3 peptide Molecular Dynamics simulations were performed with GPU-accelerated OpenMM.</p>
The histone code of the fungal genus Aspergillus uncovered by evolutionary and proteomic analyses
<p>The fasta, trimmed alignment, and maximum-likelihood phylogenetic tree files associated with the manuscript 'The histone code of the fungal genus Aspergillus uncovered by evolutionary and proteomic analyses' can be found in Supplementary Data 1 and 2 (zip). </p>
STED immunofluorescence imaging of histone protein H3K27 in a 2-cell stage mice embryo
<p>In either confocal or STED mode, immunofluorescence was performed as previously described in [1], using an upright Zeiss microscope with a mounted STEDYCON module and a Zeiss 100x 1.46 NA objective. Primary antibodies used were anti-H3K27ac (Active Motif, 39034) and anti-H3K27me3 (Abcam, ab6002), both at 1:200 dilution. Secondary anti-mouse and anti-rabbit antibodies used were labeled with STAR Red (Sigma-Aldrich, 52283) and STAR Orange (Sigma-Aldrich, 41367), respectively. Excitation was provided by 640 nm (@3%) and 775 nm (@96.5%) lasers for the STAR Red channel, whereas 561 nm (@7.8%) and 775 nm (@100%) lasers were used for the STAR Orange channel. Imaging of the samples was performed with 5 µs pixel dwell time, 64 µm pinhole aperture, 15-line accumulations and a pixel size of 20 nm.</p> <p>Experimental procedures were approved by the EMBL Rome Animal Facility in accordance with European and Italian legislations.</p> <p>1. Bošković, A., Bender, A., Gall, L., Ziegler-Birling, C., Beaujean, N., & Torres-Padilla, M.-E. Analysis of active chromatin modifications in early mammalian embryos reveals uncoupling of h2a.z acetylation and h3k36 trimethylation from embryonic genome activation. Epigenetics 7, 747–757 (2012).</p>
MD simulation trajectories for paper "Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms"
<div> <div>The dataset includes the MD simulation trajectories for the paper "Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms". </div> <div>Citation: Zhou BR, Feng H, Kale S, Fox T, Khant H, de Val N, Ghirlando R, Panchenko AR, Bai Y. Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms. Mol Cell. 2021 Jan 7;81(1):166-182.e6. PMID: 33238161; PMCID: PMC7796963.</div> </div>
Analysis of opposing histone modifications H3K4me3 and H3K27me3 reveals candidate diagnostic biomarkers for triple negative breast cancer and gene set prediction combinations
<p>Supplementary data of manuscript <strong>'Analysis of opposing histone modifications H3K4me3 and H3K27me3 reveals candidate diagnostic biomarkers for triple negative breast cancer and gene set prediction combinations </strong><strong>Analysis of opposing histone modifications H3K4me3 and H3K27me3 reveals candidate diagnostic biomarkers for triple negative breast cancer and gene set prediction combinations'</strong></p>
HDAC11 cellular assay development- histones deacetylation
<p>I looked at the effect of overexpression of HDAC11 on exogenous histone acetylation in HEK293T cells.</p>
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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.