Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The structure and composition of native human nucleosomes

ABSTRACT: In this study, we analysed the composition of histone modifications on native nucleosomes purified from HEK293 cells.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Jason Low

LAB HEAD: Joel Mackay

PROVIDER: PXD064241 | Pride | 2026-01-12

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	HEK293Nuc_H2AVariants_Rep1.sky.zip	Other
	HEK293Nuc_H2AVariants_Rep2.sky.zip	Other
	HEK293Nuc_H2AVariants_Rep3.sky.zip	Other
	HEK293Nuc_Rep1_H3.sky.zip	Other
	HEK293Nuc_Rep1_H4.sky.zip	Other

Items per page:

1 - 5 of 31

Publications

The BRD4-nucleosome interaction is enhanced modestly and non-selectively by histone acetylation.

Lambrechts Lucien S LS Reid Xavier J XJ Kambanis Lucas L Luong Clement C Kobakhidze Erekle E Daners Andrea A Zhong Yichen Y Patel Karishma K Franck Charlotte K CK Sani Hakimeh Moghaddas HM Taylor Cameron C Low Jason K K JKK Payne Richard J RJ Mackay Joel P JP

Nucleic acids research 20251101 22

BRD4 regulates gene transcription in complex eukaryotes, in part through the binding of its tandem bromodomains to acetylated lysine residues found in histones and transcription factors. Despite pharmacological inhibition of these domains showing promise in preclinical studies, clinical trial data have been less encouraging so far. A stronger understanding of BRD4 biochemistry could provide a route to better outcomes. To advance on prior work, which has focused almost entirely on the binding of ...[more]

PMID: 41459750

Similar Datasets

Targeting cholesterol homeostasis eliminates drug-tolerant persister cells in glioblastoma

Project description:The transition of cancer cells between drug-sensitive and drug-tolerant persister phenotypes drives treatment failures. Using glioblastoma models, we identified MRK-740, an inhibitor of H3K4 methyltransferase PRDM7/9, as a potent enhancer of chemotherapy-induced cell death, resulting in elimination of glioblastoma persister cells. Mechanistic investigations as well as analysis of glioblastoma specimens revealed that H3K4me3 is a transcription-activating mark at the promoters of key genes involved in cholesterol biosynthesis. The inhibition of H3K4 methylation in cells treated with microtubule-targeting agents led to the disruption of cholesterol homeostasis and LXR-dependent cholesterol efflux, ultimately depleting intracellular cholesterol and causing the death of persisters. Furthermore, we have developed a brain permeable microtubule-targeting agent to validate these mechanistic findings in vivo. We show that a combination of our novel chemotherapeutic agent and a brain permeable LXR agonist significantly extends survival in a glioblastoma mouse model. These results uncover the importance of balanced cholesterol homeostasis in chemotherapy tolerance.

2025-12-22 | PXD050643 | Pride

The BRD4-nucleosome interaction is enhanced modestly and non-selectively by histone acetylation

Project description:BRD4 regulates gene transcription in complex eukaryotes, in part through the binding of its tandem bromodomains to acetylated lysine residues found in histones and transcription factors. Despite pharmacological inhibition of these binding events showing significant promise in preclinical studies, clinical trial data have been less encouraging so far. A stronger understanding of BRD4 biochemistry could provide a route to better outcomes. To advance on prior work, which has focused almost entirely on the binding properties of isolated bromodomains and acetylated peptides, we have sought the preferred nucleosomal binding partner of full-length BRD4. Here we performed affinity pulldowns of HEK293 mononucleosomes against BRD4 to ascertain binding preferences in the nucleosomal context.

2026-01-12 | PXD064221 | Pride

Mind Your Spectra: Points to be Aware of when Validating the Identification of Isobaric Histone Peptidoforms

Project description:Mass spectrometry (MS) is now well recognized as a powerful technique to identify and quantify post-translational modifications (PTMs), overcoming many of the limitations of antibody-based methods. Histones, which play a central role in all DNA-templated processes, are regulated by a wealth of dynamic modifications, particularly on their numerous lysine residues. Reliable identification of histone PTMs remains challenging and still requires manual data curation. In this study, we focused on the Lys27-Arg40 stretch of histone H3 and considered four sequence variants, an increasing number of lysine PTMs, and chemical artefacts coming from the specific protocol of histone sample processing, which resulted in many peptides with the same atomic composition. Our analysis revealed the value of low-mass b1 and cyclic immonium fragment ions for validation of the identification of the distinct peptide forms. We examined how MS/MS spectra are transformed by several common software tools during the conversion of raw files into peak lists, and highlighted how some parameters may erase the informative low-mass fragments. We established the fragmentation profiles and retention times for forty H3 K27-R40 variant×PTM combinations, including the mouse-specific variants H3mm7 and H3mm13, and targeted their detection in histone samples extracted from mouse testis and brain via a scheduled parallel reaction monitoring (PRM) analysis. These two mouse-specific variants were reported to be highly abundant at the transcript level in these tissues and may seem to be identified at the protein level by data-dependent MS acquisition. However, we only detected very low levels of the unmodified form of H3mm7 and found no trace of H3mm13 by PRM. Our work contributes to reliably deciphering the histone code shaped by distinct sequence variants and numerous combinations of PTMs.

2025-04-22 | PXD057347 | Pride

A repurposed, non-canonical cytochrome c, chaperones calcium binding by PilY1 for type IVa pili formation - Dataset 2/2

Project description:Type IVa pili (T4aP) are versatile bacterial cell surface structures that undergo extension/adhesion/retraction cycles powered by the cell envelope-spanning T4aP machine. In this machine, a complex composed of four minor pilins and PilY1 primes T4aP extension and is also present at the pilus tip mediating adhesion. Similar to many other bacteria, Myxococcus xanthus contains multiple minor pilins/PilY1 sets, the function of which remains unknown.Here, we report that minor pilins and PilY1 of cluster_1 (PilY1.1) form calcium-responsive priming and tip complexes contingent on a non-canonical cytochrome c (TfcP) with an unusual His/Cys heme ligation. We provide evidence that TfcP is unlikely to participate in electron transport and has been repurposed to promote calcium binding by PilY1.1 at low calcium concentrations, thereby stabilising PilY1.1 and enabling its function in a broader range of calcium concentrations. These results identify a novel function of cytochromes c and illustrate how incorporating an accessory factor expands the environmental range under which the T4aP system functions.

2022-01-30 | PXD031267 | Pride

De novo mutations of MSL3 cause a novel X-linked syndrome due to impaired histone H4 lysine 16 acetylation

Project description:Epigenetic regulation by histone acetylation plays a key role in cellular homeostasis and its misregulation is associated with human disease. Histone 4 Lysine 16 acetylation (H4K16ac) serves a unique role amongst the many histone modifications as it directly affects chromatin structure1. The Male Specific Lethal (MSL) complex associated MOF/KAT8 histone acetyl transferase is responsible for bulk H4K16ac in flies and mammals. Yet, its importance during human development and a potential involvement in human pathologies remains largely unknown. Here, we uncover that pathogenic variants in MSL3, a component of the MSL complex, are causative for a new recognizable X-linked syndrome affecting Histone 4 Lysine 16 acetylation (H4K16ac) in both male and female individuals. Common clinical features of the syndrome include global developmental delay comprising profound speech delay, delayed ability to walk and craniofacial dysmorphism. Using patient-derived primary fibroblasts, we demonstrate that de novo variants or deletions of MSL3 affect the assembly and enzymatic activity of the MSL complex, hence impacting on global H4K16ac levels. Transcriptome analysis from patient cells showed misregulation of cellular pathways involved in serotonergic signaling, morphogenesis, axon guidance and cell structure. Finally, using HDAC inhibitor treatment, we can rescue expression of downregulated target genes, offering potential therapeutic avenues for MSL3-mutated patients. Taken together, we characterize a novel syndrome, named ILyADe (Impaired Lysine 16 acetylation associated disorder), which is caused by mutations of an epigenetic regulator, allowing us for the first time to unravel the crucial role of H4K16ac during human development. ILyaDe thus constitutes a new class of syndromes associated with misregulation of a single epigenetic modification caused by a genetic alteration.

2018-09-18 | PXD009317 | Pride

Mass spectrometry of histone post-translational modifications in WT and KMT2C/2D dKO urothelial cells

Project description:KMT2C and KMT2D are two of the frequently mutated epigenetic modifiers in urothelial cancer. To compare the histone post-translational modification with Kmt2c/d loss, we performed mass spectrometry analysis of histones from Kmt2c/d WT and dKO urothelial cells.

2025-01-08 | PXD056439 | Pride

Mass spectrometry analysis of in vitro PLK1 phosphorylation

Project description:Polo-like kinase 1 (PLK1) protects against genome instability by ensuring timely and accurate mitotic cell division, and its activity is tightly regulated throughout the cell cycle. Although the pathways that initially activate PLK1 in G2 are well-characterized, the factors that directly regulate PLK1 in mitosis remain poorly understood. Here, we identify that human PLK1 activity is sustained by the DNA damage response kinase Checkpoint kinase 2 (Chk2) in mitosis. Chk2 directly phosphorylates PLK1 T210, a residue on its T-loop whose phosphorylation is essential for full PLK1 kinase activity. Loss of Chk2-dependent PLK1 activity causes increased mitotic errors, including chromosome misalignment, chromosome missegregation, and cytokinetic defects. Moreover, Chk2 deficiency increases sensitivity to PLK1 inhibitors, suggesting that Chk2 status may be an informative biomarker for PLK1 inhibitor efficacy. This work demonstrates that Chk2 sustains mitotic PLK1 activity and protects genome stability through discrete functions in interphase DNA damage repair and mitotic chromosome segregation.

2024-11-01 | PXD053933 | Pride

Automated high-throughput biological sex identification from archaeological human dental enamel using targeted proteomics

Project description:Biological sex is a key information for archaeological and forensic studies, which can be assessed in enamel using proteomics. However, the lack of a standard approach for fast and accurate sex identification limits the reach of proteomics applications. Here, we introduce a targeted proteomics-based workflow that builds on a rapid, non-destructive, sensitive, and quantitative mass spectrometry (MS) strategy for the determination of biological sex from human dental enamel, including a R-Shiny interface for the data analysis. The method was first developed and optimised using modern teeth material and then validated on an independent set of modern deciduous teeth of known sex. The assay was then applied to archaeological material and demonstrated unprecedented specificity and scalability for molecular sex inference, with the possibility of analysing > 300 individuals in less than two days of MS measurement time, and with subsequent confident sex assignment in less than a day of data analysis.

2024-10-17 | PXD049326 | Pride

Mitochondrial respiratory chain is essential for hematopoietic stem cell function

Project description:Adult and fetal hematopoietic stem cells (HSCs) display a glycolytic phenotype, which is required for maintenance of stemness; however, whether mitochondrial respiration is required to maintain HSC function is not known. Here we report that loss of the mitochondrial complex III subunit Rieske iron sulfur protein (RISP) in fetal mouse HSCs allows them to proliferate but impairs their differentiation, resulting in anemia and prenatal death. RISP null fetal HSCs displayed impaired respiration resulting in a decreased NAD+/NADH ratio. RISP null fetal HSCs and progenitors exhibited an increase in both DNA and histone methylation concomitant with increases in 2-hydroxyglutarate (2-HG), a metabolite known to inhibit DNA and histone demethylases. RISP inactivation in adult HSCs also impaired respiration resulting in loss of quiescence resulting in severe pancytopenia and lethality. Thus, respiration is dispensable for adult or fetal HSC proliferation, but essential for fetal HSC differentiation and maintenance of adult HSC quiescence.

2017-09-13 | PXD006054 | Pride

A novel chemical biology high-content strategy for the identification of novel HMT inhibitors reveals a crosstalk between DOT1L and CARM1

Project description:Epigenetic regulation is a dynamic and reversible process that controls gene expression. Abnormal function results in downregulation or upregulation of pathways leading to diseases, such as cancer. The enzymes that establish and maintain epigenetic marks, such as histone methyltransferases (HMTs), are therapeutic targets as their and, importantly, the epigenetic modifications are reversible. Noteworthy, HMTs, as the other epigenetic enzymes and readers, form together multiprotein complexes that in concert regulate histone marks. To probe the epigenetic protein complexes in a biological system, we developed a reliable chemical biology high-content imaging strategy to screen compound libraries on multiple histone marks inside cells simultaneously. The advantage is double: (1) it identifies directly a drug that is active in cells on a specific histone mark and (2) it reveals the crosstalk between the epigenetic marks. By this approach, we identified that compound 4, a published CARM1 (PRMT4) inhibitor, inhibits both histone mark H3R2me2a (regulated by CARM1) and H3K79me2 (regulated by DOT1L) pointing out a synergistic interaction between the two HMTs. The results obtained by the screening assay were validated by mass spectrometry and other techniques confirming the crosstalk between the two marks and HMTs. Prompted by the interaction between CARM1 and DOT1L we combined compound 4 and DOT1L inhibitor EPZ-5676 resulting in a stronger cell proliferation inhibition and apoptosis, indicating that our approach provides also a novel strategy to identify effective synergistic drug combinations for cancer therapy.

2022-05-19 | PXD022873 | Pride