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PXD045223

PXD045223 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleThe proteomic composition of constitutive heterochromatin in mouse tissues
DescriptionPericentric heterochromatin (PCH) forms spatially and temporarily distinct compartments from other nuclear fractions and plays an important role in nuclei organization and genome stability. This highlights the necessity of elucidating the protein compositions of PCH. We find that the PCH compartments are dynamically regulated in a tissue-dependent manner in mice due to the assumable compositional difference. Here, we isolate the native PCH fractions from mouse brain and liver, analyze the protein compositions using quantitative mass spectrometry, figure out the common and tissue-specific PCH proteins by comparing their protein abundance in PCH. Besides heterochromatin enriched proteins, the PCH proteome contains also common chromatin proteins and RNA/transcription and nuclear-membrane related proteins, which do not accumulate at PCH compartments. In quantitative mass spectrometry data, these proteins show much lower protein abundance at PCH than PCH enriched proteins. Thus, we further cut out PCH unspecific protein candidates based on their abundance at PCH. MeCP2 is classified into the brain PCH enriched protein sets, while histone H1 not. To confirm, We analyze the interplay of MeCP2 and H1 and find that H1 and MeCP2 compete with each other at PCH regions and regulate PCH morphology in an opposite way in cultured cells. Thus, our workflow of PCH isolation, quantitative mass spectrometry, and confirmation-based data analysis is capable of identifying proteins that are commonly and tissue-specifically enriched at PCH regions.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_06:42:06.899.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterM. Cristina Cardoso
SpeciesList scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationListNo PTMs are included in the dataset
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-09-08 06:30:21ID requested
12024-05-23 00:00:48announced
22024-10-22 06:42:15announced2024-10-22: Updated project metadata.
Publication List
Schmidt A, Zhang H, Schmitt S, Rausch C, Popp O, Chen J, Cmarko D, Butter F, Dittmar G, Lermyte F, Cardoso MC, The Proteomic Composition and Organization of Constitutive Heterochromatin in Mouse Tissues. Cells, 13(2):(2024) [pubmed]
10.3390/cells13020139;
Keyword List
submitter keyword: mouse, brain, liver, HPLC-MS/MS
Contact List
M. Cristina
contact affiliationCardoso Lab, Department of Biology, Technische Universität Darmstadt, Germany
contact emailcardoso@bio.tu-darmstadt.de
lab head
M. Cristina Cardoso
contact affiliationCell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
contact emailcardoso-lab@bio.tu-darmstadt.de
dataset submitter
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