Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Crosslinking mass spectrometry of the p300 catalytic core complexed with the nucleosome

ABSTRACT: p300 is a histone acetyltransferase that associates with crucial biological processes. p300 acetylates all four histones in the nucleosome, a basic unit of chromatin, and alters chromatin structure and dynamics. In this study, we performed structural and biochemical analysis to understand the nucleosome binding by p300. Crosslinking mass spectrometry suggests that the p300 catalytic core binds to nucleosomes in multiple binding forms to acetylate different histone tails.

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Hitoshi Kurumizaka

PROVIDER: PXD033804 | JPOST Repository | Wed Jun 29 00:00:00 BST 2022

REPOSITORIES: jPOST

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	210518hatXL06_0728F90_2ul.mzXML	Mzxml
	210518hatXL07_0728F90_2ul.mzXML	Mzxml
	210518hatXL10_0728F90_2ul.mzXML	Mzxml
	210518hatXL11_0728F90_2ul.mzXML	Mzxml
	210518hatXL12_0728F90_2ul.mzXML	Mzxml

Items per page:

1 - 5 of 20

Publications

Structural basis for binding diversity of acetyltransferase p300 to the nucleosome.

Hatazawa Suguru S Liu Jiuyang J Takizawa Yoshimasa Y Zandian Mohamad M Negishi Lumi L Kutateladze Tatiana G TG Kurumizaka Hitoshi H

iScience 20220609 7

p300 is a human acetyltransferase that associates with chromatin and mediates vital cellular processes. We now report the cryo-electron microscopy structures of the p300 catalytic core in complex with the nucleosome core particle (NCP). In the most resolved structure, the HAT domain and bromodomain of p300 contact nucleosomal DNA at superhelical locations 2 and 3, and the catalytic site of the HAT domain are positioned near the N-terminal tail of histone H4. Mutations of the p300-DNA interfacial ...[more]

PMID: 35754730

Similar Datasets

Nucleosome binding by the pioneer transcription factor OCT4

Project description:The nucleosome is a fundamental unit of chromatin in eukaryotes, and generally prevents the binding of transcription factors to genomic DNA. Pioneer transcription factors overcome the nucleosome barrier, and bind their target DNA sequences in chromatin. OCT4 is a representative pioneer transcription factor that plays a role in stem cell pluripotency. In the present study, we biochemically analyzed the nucleosome binding by OCT4. Crosslinking mass spectrometry showed that OCT4 binds the nucleosome.

2020-05-13 | PXD019160 | JPOST Repository

Comprehensive nucleosome interactome screen establishes fundamental principles of nucleosome binding

Project description:Nuclear proteins bind chromatin to execute and regulate genome-templated processes. While structural and biochemical studies of individual nucleosome interactions have suggested that an acidic patch on the nucleosome disk surface may be a common site for recruitment to chromatin, the pervasiveness of acidic patch binding and whether other nucleosome surface binding hot-spots exist remains unclear. Here, we use nucleosome affinity proteomics with a library of nucleosomes that collectively disrupts all exposed histone surfaces to establish the universal principles of nucleosome binding. We find that the acidic patch and two adjacent surfaces are the primary hot-spots for nucleosome disk binding and are critical for the majority of nucleosome-protein interactions. In contrast, nearly half of the nucleosome disk surface participates only minimally in protein binding. In addition to establishing the fundamental principles of chromatin binding, our screen defines nucleosome surface requirements of nearly 300 nucleosome interacting proteins implicated in diverse nuclear processes including transcription, DNA damage repair, cell cycle regulation, and nuclear architecture. Building from our screen, we demonstrate that the Anaphase-Promoting Complex/Cyclosome directly binds the acidic patch and elucidate a redundant charge-based mechanism of acidic patch binding by nuclear pore protein ELYS. Overall, our interactome screen illuminates a highly competitive nucleosome binding hub for chromatin-targeted activities and curates a list of nucleosome interacting proteins that will enable mechanistic exploration of many unexpected chromatin-templated nuclear processes.

2020-06-24 | PXD018690 | Pride

Structure of nucleosome-bound human PBAF complex

Project description:BAF and PBAF are mammalian SWI/SNF family chromatin remodeling complexes that possess multiple histone/DNA-binding subunits and create nucleosome-depleted/free regions for transcription activation. Despite previous structural studies and recent advance of SWI/SNF family complexes, it remains incompletely understood how PBAF-nucleosome complex is organized. Here we determined structure of 13-subunit human PBAF in complex with acetylated nucleosome in ADP-BeF3-bound state. Four PBAF-specific subunits work together with nine BAF/PBAF-shared subunits to generate PBAF-specific modular organization, distinct from that of BAF at various regions. PBAF-nucleosome structure reveals six histone-binding domains and four DNA-binding domains/modules, the majority of which directly bind histone/DNA. This multivalent nucleosome-binding pattern, not observed in previous studies, suggests that PBAF may integrate comprehensive chromatin information to target genomic loci for function. Our study reveals molecular organization of subunits and histone/DNA-binding domains/modules in PBAF-nucleosome complex and provides structural insights into PBAF-mediated nucleosome association complimentary to the recently reported PBAF-nucleosome structure.

2023-03-11 | PXD036708 | Pride

Histone variant H2A.Z regulates nucleosome unwrapping and CTCF binding in mouse ES cells

Project description:Nucleosome is the basic structural unit of chromatin, and its dynamics plays critical roles in the regulation of genome functions. However, how the nucleosome structure is regulated by histone variants in vivo is still largely uncharacterized. Here, by employing Micrococcal nuclease (MNase) digestion of crosslinked chromatin followed by chromatin immunoprecipitation (ChIP) and paired-end sequencing (MNase-X-ChIP-seq), we mapped genome-wide unwrapping states of nucleosomes containing histone variant H2A.Z in mouse embryonic stem (ES) cells. We found that H2A.Z is enriched with unwrapped nucleosomes. Interestingly, the function of +1 H2A.Z nucleosome in transcriptional regulation is correlated with the unwrapping states. We further showed that H2A.Z nucleosomes adjacent the CTCF binding sites (CBS) may adopt an open conformation. We confirmed the unwrapping state of H2A.Z nucleosomes under native condition by re-ChIP of H2A.Z after CTCF CUT&RUN in mouse ES cells. Importantly, we found that depletion of H2A.Z results in increased CTCF binding, indicating dynamic competition between the unwrapped H2A.Z nucleosomal intermediates and CTCF at the CBS. Taken together, our results showed that histone variant H2A.Z regulates transcription and CTCF binding through modulating the nucleosome unwrapping.

2020-04-27 | GSE146082 | GEO

Analysis of the overlapping tri-nucleosome association with genomic and synthetic DNA

Project description:Nucleosome consists of a histone octamer wrapped by 145 bps of DNA and serves as a fundamental unit of chromatin. The overlapping di-nucleosome (OLDN) is found as another chromatin unit, in which 250 bps of DNA continuously wraps around the intimately associated histone octamer-hexamer complex. In the present study, our genome-wide analysis found a higher nucleosome stacking structure, overlapping tri-nucleosome (OLTN), in which about 350 bps of DNA wrap around the histone octamer-hexamer-hexamer complex. We quantified the length of DNA associated with the 20-mer histone core, and also we found that the OLTN localizes downstream of the transcription start sites as well as the OLDN does. The results suggest that nucleosome stacking structures may be formed for gene regulation.

2024-01-17 | GSE224789 | GEO

H4K20me2 SILAC Nucleosome Affinity Purification

Project description:Goal of this project was the identification of chromatin interacting proteins whose binding is differentially regulated by di-methylation of lysine 20 on histone H4 (H4K20me2). To achieve this unodified and H4K20me2-modified histone H4 were generated by native chemical ligation and assembled into recombinant di-nucleosomes. The di-nucleosomes were immobilized on streptavidin-coated beads via the biotinylated di-nucleosomal DNA and used for nucleosome affinity purifications to identify proteins regulated by H4K20me2 from SILAC-labelled HeLaS3 nuclear extracts (Arg10 and Lys8). SILAC affinity purifications were carried out in "forward" (heavy extract on modified nucleosome and light extract on unmodified nucleosome) and "reverse" (light extract on modified nucleosome and heavy extract on unmodified nucleosome) label-swap experiments and protein abundances were quantified by MaxQuant.

2019-02-27 | PXD009281 | Pride

Direct Nucleosome Binding of Borealin Secures Chromosome Association of the Chromosomal Passenger Complex

Project description:CPC-NCP complexes were crosslinked using EDC and analysed by mass spectrometry. The results showed Borealin is critical for nucleosome binding made extensive contacts with NCPs, whereas Survivin interactions are mostly limited to the BIR domain and the H3 N-terminal tail as expected. Mapping the crosslinks onto the three dimensional structures of NCP and CPC suggests a model where the localisation module of the CPC together with a highly basic N-terminal tail of Borealin docks onto the acidic patch formed by H2A and H2B, a surface commonly involved in nucleosome recognition. This interaction may orient the Survivin BIR domain to facilitate binding of histone H3 tail phosphorylated at Thr3. Notably, Borealin loop residues trace along the DNA-histone interface implying its major contribution to nucleosome binding involves both protein-histone and possibly protein-DNA contacts.

2019-09-30 | PXD012882 | Pride

Structural basis of paralog-specific KDM2A/B nucleosome recognition

Project description:The nucleosome acidic patch is a major interaction hub for chromatin, providing a platform for enzymes to dock and orient for nucleosome-targeted activities. In order to define the molecular basis of acidic patch recognition proteome-wide, we performed an amino acid resolution acidic patch interactome screen. We discovered that the histone H3 lysine 36 (H3K36) demethylase KDM2A, but not its closely related paralog, KDM2B, requires the acidic patch for nucleosome binding. These KDM2 family JumonjiC (JmjC) domain lysine demethylases are critical to heterochromatin formation and are commonly misregulated in cancer. Despite fundamental roles in transcriptional regulation in health and disease, the molecular mechanisms governing nucleosome substrate specificity of KDM2A/B, or any other JmjC lysine demethylases, remain unclear. We used a covalent JmjC inhibitor to solve cryo-EM structures of KDM2A and KDM2B trapped in action on the nucleosome. Our structures show that KDM2-nucleosome binding is paralog-specific and facilitated by dynamic nucleosomal DNA unwrapping and histone charge shielding that mobilize the H3K36 sequence for demethylation.

2023-02-14 | PXD032791 | Pride

Histone modification and nucleosome mapping in human liver cancer cells

Project description:The nucleosome is a fundamental unit of chromatin architecture, but it has been under-evaluated during the analysis of histone modification using ChIP-Seq. Thus, we developed a novel approach for defining histone modification at single nucleosome resolution by synergistic analyses of histone modification data from ChIP-Seq and high-resolution nucleosome mapping data from native MNase-Seq using a PCR-free strategy. With this approach, we have generated histone modification data at the single nucleosome resolution in human embryonic stem cells, normal hepatocytes, and liver cancer cells of both genders, and performed quantitative analysis of epigenetic regulation in stem cell differentiation into hepatocytes and neoplastic transformation of liver cancer.

2020-04-10 | GSE76344 | GEO

Gcn5-mediated histone acetylation governs nucleosome dynamics in spermiogenesis [ATAC-seq]

Project description:During mammalian spermatogenesis, male germ cells undergo dramatic reorganization of chromatin, whereby 90-99% of histones are evicted and replaced by protamines. This reorganization prominently features histone acetylation to loosen chromatin structure. Given the potential role of retained histones in fertility and early embryonic development, the genomic location of retained nucleosomes is of great interest. However, the ultimate position and mechanisms underlying nucleosome eviction/retention are poorly understood, including several studies utilizing MNase-seq methodologies, but reporting remarkably dissimilar locations. Here, we utilized ATAC-seq to determine the location of retained nucleosomes in mouse sperm and found enrichment at promoters, but also retention at inter- and intragenic regions, and repetitive elements. We further investigated nucleosome eviction/retention by generating pre-meiotic, germ cell specific, conditional knockout mice for the histone acetyltransferase Gcn5, a key histone acetyltransferase. Gcn5cKO germ cells exhibited abnormal chromatin dynamics during spermiogenesis, including diminished nucleosome eviction leading to increased histone retention in sperm. These mice exhibited severe reproductive phenotypes: abnormal sperm production, sperm morphology, and ultimately, male infertility. Our findings demonstrate Gcn5 mediated histone acetylation promotes chromatin accessibility and nucleosome eviction in spermiogenesis, and that loss of histone acetylation leads to defects that disrupt male fertility and potentially, early embryogenesis.

2019-11-07 | GSE134825 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data