PXD045223

PXD045223 is an original dataset announced via ProteomeXchange.

Title	The proteomic composition of constitutive heterochromatin in mouse tissues
Description	Pericentric 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.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:42:06.899.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	M. Cristina Cardoso
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2023-09-08 06:30:21	ID requested
1	2024-05-23 00:00:48	announced
⏵ 2	2024-10-22 06:42:15	announced	2024-10-22: Updated project metadata.

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;

submitter keyword: mouse, brain, liver, HPLC-MS/MS

M. Cristina
contact affiliation	Cardoso Lab, Department of Biology, Technische Universität Darmstadt, Germany
contact email	cardoso@bio.tu-darmstadt.de
lab head
M. Cristina Cardoso
contact affiliation	Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
contact email	cardoso-lab@bio.tu-darmstadt.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/05/PXD045223

PRIDE project URI

• PRIDE
  1. PXD045223
     1. Label: PRIDE project
     2. Name: The proteomic composition of constitutive heterochromatin in mouse tissues