Find research datasets worth reusing

opencc-by-4.0Nov 2020View details →

Transcriptome analysis of the effect of over-expressing H2A.J mutants in proliferating WI38 fibroblasts 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

Abstract for overall study: 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. Specific description for this dataset: H2A.J differs from canonical H2A only by a valine at position 11 instead of alanine, and the 7 C-terminal amino acids containing a potential minimal phosphorylation site SQ for DNA-damage response kinases. To test the functional importance of these H2A.J-specific sequences, we mutated Val-11 to Ala as is found in all canonical H2A sequences, and we mutated Ser-123 to either Glu to mimic a phospho-serine residue or to Ala to prevent phosphorylation. We also substituted the C-terminus of H2A.J with the C-terminus of H2A. These mutants, WT-H2A.J and canonical H2A-type1 were ectopically expressed in proliferating fibroblasts, and their microarray transcriptomes were compared to that of proliferating and senescent fibroblasts without ectopic histone expression. Genome-wide transcriptome analysis indicated that senescent fibroblasts clustered distinctly from proliferating fibroblasts, and proliferating fibroblasts expressing the H2A.J-V11A and H2A.J-S123E mutants clustered distinctly from fibroblasts expressing the other H2A.J mutants, WT-H2A.J, and H2A. Hallmark gene set enrichment analysis of the transcriptomes of fibroblasts expressing H2A.J-V11A or H2A.J-S123E versus control proliferating fibroblasts indicated that they showed the same highly significant enrichment for the Epithelial-Mesenchyme Transition, TNF-Alpha Signaling Via NF-kB, and Inflammatory Response gene sets. Notable inflammatory genes including IL1A, IL1B, IL6, CXCL8, and CCL2 are contained in these gene sets and are often induced in senescence as part of the senescence-associated secretory phenotype. Heat maps showed that the H2A.J-V11A and H2A.J-S123E mutants were particularly apt at activating the expression of these inflammatory genes in proliferating fibroblasts

opencc-zeroApr 2019View details →

Bohdan-Khomtchouk/ENCODE_histone_geneXtendeR_analysis: ENCODE_histone_geneXtendeR_analysis

geneXtendeR analysis on 198 human histone modification ChIP-seq ENCODE datasets used in <a href="https://bioconductor.org/packages/geneXtendeR/">https://bioconductor.org/packages/geneXtendeR/</a>

opencc-by-4.0Jul 2021View details →

Suppl. Information to "The tropical coral Pocillopora acuta displays an unusual chromatin structure and shows histone H3 clipping plasticity upon bleaching"

Supplementary File 1: Multiple alignment for protein sequences of core histones with Pocillopora acuta, Pocillopora damicornis, Acropora digitifera, Nematostella vectensis, Hydra vulgaris, Schistosoma mansoni and Mus musculus. A. Histone H2A; B. Histone H2B; C. Histone H3; D. Histone H4. An asterisk (*) means that the amino acid is conserved between all species. Supplementary File 2: Original (uncropped and unedited) images used for Figures 1 to 4. Supplementary File 3: P. acuta nuclei and Symbiodinium count on a Thoma cell counting chamber done over three different nuclei extractions. For each extraction, two counts were performed. P. acuta nuclei were stained with Hoechst 33342 and display a blue fluorescence at 350 nm. Symbiodinium are not damaged by our extraction method and are not permeable to Hoechst. They display a red fluorescence because of their chlorophyl content. Observations were done on a Leica DMLB with objective PL Fluotar 40x and 100x. A text version of the data in the Excel file below. Extraction #1 replicate 1: 102 P. acuta nuclei (Blue) ; 2 Symbiodinium (Red) Extraction #1 replicate 2: 112 P. acuta nuclei (Blue) ; 2 Symbiodinium (Red) Extraction #1 replicate 1: 42 P. acuta nuclei (Blue) ; 0 Symbiodinium (Red) Extraction #1 replicate 2: 55 P. acuta nuclei (Blue) ; 1 Symbiodinium (Red) Extraction #1 replicate 1: 215 P. acuta nuclei (Blue) ; 3 Symbiodinium (Red) Extraction #1 replicate 2: 257 P. acuta nuclei (Blue) ; 5 Symbiodinium (Red) Made at IHPE.

opencc-by-4.0Sep 2021View details →

Mammary single-cell RNA-seq analysis and prostate cancer survival as a function of H2AFJ expression for the paper entitled: The histone variant H2A.J is enriched in luminal epithelial cells

opencc-by-4.0Aug 2022View details →

Nanoscale Shape-Dependent Histone Modifications

Recent observations suggest a role for complex nanoscale particulate shape in regulation of specific immune-related cellular and in vivo processes. We suspect that cellular recognition of nanostructure architecture could involve non-molecular inputs, including cellular transduction of nanoscale spatially resolved stresses induced by complex shape. Here we report nanoscale shape-dependent control of the cellular epigenome. ChIP-Seq sequencing datasets are provided.

opencc-by-4.0Jun 2024View details →

Supporting data for "Chromatin conformation and histone modification profiling across human kidney anatomic regions"

Here we deposit supporting data for our manuscript entitled "Chromatin conformation and histone modification profiling across human kidney anatomic regions". <ul> <li>donor_info.pdf: Additional clinical information of the donor involved in the study</li> <li>Large zip files with names starting as "hic": Juicer Hi-C outputs aligned with hg38 genome <ul> <li>Note: hg19 alignment outputs are available at GEO.</li> </ul> </li> <li>hg19_loop_domain.zip: Hi-C chromatin contact domain finding results with Arrowhead and chromatin loop finding results with HiCCUPs (implemented in Juicer tools), aligned with hg19 genome</li> <li>hg38_loop_domain.zip: Hi-C chromatin contact domain finding results with Arrowhead and chromatin loop finding results with HiCCUPs (implemented in Juicer tools), aligned with hg38 genome</li> <li>CUTRUN_peak_hg19.tar.gz: CUT&RUN peaks.stringent.bed data outputs generated by hg19 alignment</li> <li>CUTRUN_peak_hg38.tar.gz: CUT&RUN peaks.stringent.bed data outputs generated by hg38 alignment</li> <li>CUTRUN_bigwig_hg38.tar.gz: CUT&RUN bigwig outputs generated by hg38 alignment <ul> <li>Note: hg19 alignment outputs are available at GEO.</li> </ul> </li> <li>CUTRUN_overlapped_peaks.xlsx: Overlaps between H3K27me3 and H3K4me3 in each anatomical region. Peaks were loaded from ‘.peaks.stringent.bed’ files in R and converted to GRanges objects using package ‘GenomicRanges’. R function ‘intersect’ was used to calculate the overlap between two GRanges objects, represented as each row in the table. <ul> <li>Here we list the details of overlaps between H3K27me3 and H3K4me3 in each anatomical region, as well as overlaps for each of the histone markers across anatomical regions.</li> </ul> </li> </ul>

opencc-by-4.0Jun 2016View details →

Human Histone Deacetylase 6 (HDAC6); A Target Enabling Package

HDAC6 is a cytosolic deacetylase with diverse roles in cellular trafficking, autophagy and cell signalling. Specifically targeting the unique zinc-finger ubiquitin-binding domain (ZnF-UBD) of HDAC6 may be an attractive strategy in myeloma and lymphoma but no inhibitor has been reported to date. Presented here are 4 co-crystal structures of HDAC6 ZnF-UBD in complex with different compounds, and associated SPR, ITC and FP assays.

opencc-by-4.0Jan 2019View details →

Histone tail dynamics in partially disassembled nucleosomes during chromatin remodeling: Simulation dataset

Dataset of molecular dynamics simulations of partially disassembled nucleosomes. - Input: Parameters and initial structures - Output: Trajectories NAMD 2.12 (multi-core with CUDA) was used for the simulations.

opencc-by-4.0Dec 2022View details →

Simultaneous profiling of histone modifications and DNA methylation via nanopore sequencing

Datasets that contain a minimum of nanopore reads sufficient for hidden Markov model training and for evaluating the performance of our computational tool - nanoHiMe at simultaneously calling CpG and/or adenine methylation on individual nanopore reads. Ecoli_PCR_amplicons_100k.tgz, Ecoli_PCR_MSssI_100k.tar.gz and Ecoli_PCR_pA-Hia5_100k.tar.gz are used for training new parameters of the emission distributions of individual k-mers from DNA template without modification, with fully methylated CpGs, and with partially methylated adenines, respectively. nanoHiMe_H3K27me3.fast5.tgz are the nanopore sequencing reads from H3K27me3 nanoHiMe-seq experiments in GM12878 cells and used for evaluating the performance of nanoHiMe at jointly calling CpG and adenine methylation.

ClinicalTrials.gov40/100

Selective Estrogen Receptor Modulators to Enhance the Efficacy of Viral Reactivation With Histone Deacetylase Inhibitors

ClinicalTrials.gov study NCT03382834. IPD Sharing: YES. Countries: 2. Publications: 1.

controlledIPD-YESFeb 2026View details →

opencc-zeroMay 2020View details →

Data from: Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction

The H2A.Z histone variant, a genome-wide hallmark of permissive chromatin, is enriched near transcription start sites in all eukaryotes. H2A.Z is deposited by the SWR1 chromatin remodeler and evicted by unclear mechanisms. We tracked H2A.Z in living yeast at single-molecule resolution, and found that H2A.Z eviction is dependent on RNA Polymerase II (Pol II) and the Kin28/Cdk7 kinase, which phosphorylates Serine 5 of heptapeptide repeats on the carboxy-terminal domain of the largest Pol II subunit Rpb1. These findings link H2A.Z eviction to transcription initiation, promoter escape and early elongation activities of Pol II. Because passage of Pol II through +1 nucleosomes genome-wide would obligate H2A.Z turnover, we propose that global transcription at yeast promoters is responsible for eviction of H2A.Z. Such usage of yeast Pol II suggests a general mechanism coupling eukaryotic transcription to erasure of the H2A.Z epigenetic signal.

opencc-zeroAug 2020View details →

Data from: Diverse nucleosome site-selectivity among histone deacetylase complexes

Histone acetylation regulates chromatin structure and gene expression and is removed by histone deacetylases (HDACs). HDACs are commonly found in various protein complexes to confer distinct cellular functions, but how the multi-subunit complexes influence deacetylase activities and site-selectivities in chromatin is poorly understood. Recent studies on the HDAC1 containing CoREST complex and acetylated nucleosome substrates revealed a notable preference for deacetylation of histone H3 acetyl-Lys9 vs. acetyl-Lys14 (M. Wu et al, 2018). Here we analyze the enzymatic properties of five class I HDAC complexes: CoREST, NuRD, Sin3B, MiDAC and SMRT with site-specific acetylated nucleosome substrates. Our results demonstrate that these HDAC complexes show a wide variety of deacetylase rates in a site-selective manner. A Gly13 in the histone H3 tail is responsible for a sharp reduction in deacetylase activity of the CoREST complex for H3K14ac. These studies provide a framework for connecting enzymatic and biological functions of specific HDAC complexes.

opencc-zeroJan 2020View details →

Sex affects immunolabeling for histone 3 K27me3 in the trophectoderm of the bovine blastocyst but not labeling for histone 3 K18ac

The mammalian embryo displays sexual dimorphism in the preimplantation period. Moreover, competence of the embryo to develop is dependent on the sire from which the embryo is derived and can be modified by embryokines produced by the endometrium such as colony stimulating factor 2 (CSF2). The preimplantation period is characterized by large changes in epigenetic modifications of DNA and histones. It is possible, therefore, that effects of sex, sire, and embryo regulatory molecules are mediated by changes in epigenetic modifications. Here it was tested whether global levels of two histone modifications in the trophectoderm of the bovine blastocyst were affected by sex, sire, and CSF2. It was found that amounts of immunolabeled H3K27me3 were greater (P=0.030) for male embryos than female embryos. Additionally, labeling for H3K27me3 and H3K18ac depended upon the bull from which embryos were derived. Although CSF2 reduced the proportion of embryos developing to the blastocyst, there was no effect of CSF2 on labeling for H3K27me3 or H3K18ac. Results indicate that the blastocyst trophoctoderm can be modified epigenetically by embryo sex and paternal inheritance through alterations in histone epigenetic marks.

opencc-by-4.0Feb 2016View details →

X-ray diffraction images for DPF3 tandem PHD fingers co-crystallized with an acetylated histone-derived peptide

This submission includes a tar archive of bzipped diffraction images recorded with the ADSC Q315r detector at the Advanced Photon Source of Argonne National Laboratory, Structural Biology Center beam line 19-ID. Relevant meta data can be found in the headers of those diffraction images. Please find below the content of an input file XDS.INP for the program XDS (Kabsch, 2010), which may be used for data reduction. The "NAME_TEMPLATE_OF_DATA_FRAMES=" item inside XDS.INP may need to be edited to point to the location of the downloaded and untarred images. !!! Paste lines below in to a file named XDS.INP DETECTOR=ADSC  MINIMUM_VALID_PIXEL_VALUE=1  OVERLOAD= 65000 DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0 DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0 TRUSTED_REGION=0.0 1.05 MAXIMUM_NUMBER_OF_JOBS=10 ORGX=   1582.82  ORGY=   1485.54 DETECTOR_DISTANCE= 150 ROTATION_AXIS= -1.0 0.0 0.0 OSCILLATION_RANGE=1 X-RAY_WAVELENGTH= 1.2821511 INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0 FRACTION_OF_POLARIZATION=0.90 POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0 SPACE_GROUP_NUMBER=20 UNIT_CELL_CONSTANTS= 100.030   121.697    56.554    90.000    90.000    90.000 DATA_RANGE=1  180 BACKGROUND_RANGE=1 6 SPOT_RANGE=1 3 SPOT_RANGE=31 33 MAX_CELL_AXIS_ERROR=0.03 MAX_CELL_ANGLE_ERROR=2.0 TEST_RESOLUTION_RANGE=8.0 3.8 MIN_RFL_Rmeas= 50 MAX_FAC_Rmeas=2.0 VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 6000 30000 INCLUDE_RESOLUTION_RANGE=50.0 1.7 FRIEDEL'S_LAW= FALSE STARTING_ANGLE= -100      STARTING_FRAME=1 NAME_TEMPLATE_OF_DATA_FRAMES= ../x247398/t1.0???.img !!! End of XDS.INP

opencc-zeroNov 2023View details →

Data for: A histone demethylase links the loss of plasticity to nongenetic inheritance and morphological change

Plasticity is a widespread feature of development, enabling phenotypic change based on the environment. Although the evolutionary loss of plasticity has been linked both theoretically and empirically to increased rates of phenotypic diversification, molecular insights into how this process might unfold are generally lacking. Here, we show that a regulator of nongenetic inheritance links evolutionary loss of plasticity in nature to changes in plasticity and morphology as selected in the laboratory. Across nematodes of Diplogastridae, which ancestrally had a polyphenism, or discrete plasticity, in their feeding morphology, we use molecular evolutionary analyses to screen for change associated with independent losses of plasticity. Having inferred a set of ancestrally polyphenism-biased genes from phylogenetically informed gene-knockouts and gene-expression comparisons, selection signatures associated with plasticity's loss identify the histone H3K4 di/monodemethylase gene spr-5/LSD1/KDM1A. Manipulations of this gene affect both sensitivity and variation in plastic morphologies, and artificial selection of manipulated lines drives multigenerational shifts in these phenotypes. Our findings thus give mechanistic insight into how traits are modified as they traverse the continuum of greater to lesser environmental sensitivity.

opencc-by-4.0Dec 2023View details →

Replica-Exchange with Solute Tempering (REST2) Simulations of Histone Tails

Replica at 300 K 1 bar 1 µs trajectories and corresponding parameter files for histone tails alone or with a DNA fragment. The parameter files containing IDP modification are indicated as "idp".  With DNA fragment, the trajectories are given without solvent and ion and called "nosol".

opencc-by-4.0Mar 2024View details →

STORM Data: Transcriptionally active chromatin loops contain both 'active' and 'inactive' histone modifications that exhibit exclusivity at the level of nucleosome clusters

The dataset underlying the SMLM STORM super-resolution images of 'Transcriptionally active chromatin loops contain both ‘active’ and ‘inactive’ histone modifications that exhibit exclusivity at the level of nucleosome clusters'. See Biorxiv paper for details on sample preparation: <a href="https://www.biorxiv.org/content/10.1101/2023.09.03.555774v1.full.pdf">https://www.biorxiv.org/content/10.1101/2023.09.03.555774v1.full.pdf</a>, Pyranose Oxidase STORM buffer on Elyra 7 Zeiss Microscope, processed with Zen Black. Samples are named according to which figures they occur in the above paper.

opencc-by-4.0Nov 2023View details →

Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending

This repository contains the DNA affinity purification sequencing (DAP-seq) data, for two biological replicates, as used in the following manuscript: Yimin Hu, Samuel Schwab, Silvia Deiss, Pedro Escudeiro, Joe D. Joiner, Marcus D. Hartmann, Andrei N. Lupas, Birte Hernandez Alvarez, Vikram Alva, and Remus T. Dame. 'Bacterial Histone HBb from Bdellovibrio Bacteriovorus Compacts DNA by Bending'. bioRxiv, 27 September 2023. https://doi.org/10.1101/2023.02.26.530074. There are four types of data in this repository:<ul><li>Paired-end FASTQ files, containing the raw Illumina reads (raw_reads folder).</li><li>Raw read QC reports, generated by the nf-core/chipseq pipeline (fastqc folder).</li><li>BAM files, generated by the nf-core/chipseq pipeline (bam folder).</li><li>bigWig files, generated by the nf-core/chipseq pipeline (bigwig folder).</li></ul>Abstract: Histones are essential for genome compaction and transcription regulation in eukaryotes, where they assemble into octamers to form the nucleosome core. In contrast, archaeal histones assemble into dimers that form hypernucleosomes upon DNA binding. Although histone homologs have recently been identified in bacteria, their DNA-binding characteristics remain largely unexplored. Our study reveals that the bacterial histone HBb is indispensable for the survival of Bdellovibrio bacteriovorus, suggesting critical roles in DNA organization and gene regulation. We also elucidate the crystal structure of the HBb dimer at 1.06 Å resolution and employ various biophysico-chemical approaches to show its ability to bind and compact DNA in a sequence-independent manner. This binding induces DNA bending, similar to that observed with bacterial HU/IHF family proteins. Finally, using DNA affinity purification and sequencing, we reveal that HBb binds along the entire genomic DNA of B. bacteriovorus without sequence specificity. These unique DNA-binding properties of bacterial histones, distinct from their archaeal and eukaryotic counterparts, highlight the diverse roles that histones can play in DNA organization across the domains of life. To whom correspondence should be addressed (E-mail): birte.hernandez@tuebingen.mpg.de, or vikram.alva@tuebingen.mpg.de, or rtdame@chem.leidenuniv.nl