PXD002537 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | A quantitative proteomic analysis of in vitro assembled chromatin |
Description | The structure of chromatin is critical for many aspects of cellular physiology and is considered to be the primary medium to store epigenetic information. It is defined by the histone molecules that constitute the nucleosome, the positioning of the nucleosomes along the DNA and the non-histone proteins that associate with it. These factors help to establish and maintain a largely DNA sequence-independent but surprisingly stable structure. Chromatin is extensively disassembled and reassembled during DNA replication, repair, recombination or transcription in order to allow the necessary factors to gain access to their substrate. Despite such constant interference with chromatin structure, the epigenetic information is generally well maintained. Surprisingly, the mechanisms that coordinate chromatin assembly and ensure proper assembly are not particularly well understood. Here, we use SWATH-MS to describe the kinetics of in vitro assembled chromatin supported by an embryo extract prepared from preblastoderm Drosophila melanogaster embryos. This system allows easy manipulation of distinct aspects of chromatin assembly such as post-translational histone modifications, the levels of histone chaperones and the concentration of distinct DNA binding factors. Our findings support the idea that chromatin assembly factors and factors important for chromatin structure bind chromatin in an ordered manner, which is -at least in part- regulated by histone deacetylation. We are able to identify functional clusters of proteins based on their different binding kinetics. Whereas many proteins bind exclusively during the onset of chromatin assembly, a few proteins show a clear tendency towards matured chromatin. |
HostingRepository | PRIDE |
AnnounceDate | 2016-01-27 |
AnnouncementXML | Submission_2016-01-27_07:24:18.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Andreas Schmidt |
SpeciesList | scientific name: Drosophila melanogaster (Fruit fly); NCBI TaxID: 7227; |
ModificationList | acetylated residue; iodoacetamide derivatized residue |
Instrument | TripleTOF 6600; LTQ Orbitrap |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2015-07-14 01:29:56 | ID requested | |
⏵ 1 | 2016-01-27 07:24:19 | announced | |
Publication List
V, ö, lker-Albert MC, Pusch MC, Fedisch A, Schilcher P, Schmidt A, Imhof A, A Quantitative Proteomic Analysis of In Vitro Assembled Chromatin. Mol Cell Proteomics, 15(3):945-59(2016) [pubmed] |
Keyword List
curator keyword: Biological |
submitter keyword: Acetylation |
Affinity proteomics |
Chromatin function or biology |
Label-free quantification |
Macromolecular Assemblages |
Contact List
Axel Imhof |
contact affiliation | Prof. Dr. Axel Imhof Histone Modifications Group Zentrallabor für Proteinanalytik BioMedical Center Ludwig-Maximilians-University of Munich Großhdernerstr. 9 82152 Planegg-Martinsried Tel.: --49 89 2180 75420 Fax.: --49 89 2180 75440 e-mail: imhof@lmu.de |
contact email | imhof@lmu.de |
lab head | |
Andreas Schmidt |
contact affiliation | Adolf-Butenandt-Institut |
contact email | A.Schmidt@med.uni-muenchen.de |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD002537
- Label: PRIDE project
- Name: A quantitative proteomic analysis of in vitro assembled chromatin