Dataset Information

The proteomic composition of constitutive heterochromatin in mouse tissues

ABSTRACT: 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.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Brain, Liver

SUBMITTER: M. Cristina Cardoso

LAB HEAD: M. Cristina

PROVIDER: PXD045223 | Pride | 2024-05-23

REPOSITORIES: Pride

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			Action	DRS
	Gladys_20140926_OP_MM_MSC10346.raw	Raw
	Gladys_20140926_OP_MM_MSC10347.raw	Raw
	Gladys_20140926_OP_MM_MSC10348.raw	Raw
	Gladys_20140926_OP_MM_MSC10349.raw	Raw
	Grobi_20140519_OP_MMddm_MSC09714_A.raw	Raw

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Publications

The Proteomic Composition and Organization of Constitutive Heterochromatin in Mouse Tissues.

Schmidt Annika A Zhang Hui H Schmitt Stephanie S Rausch Cathia C Popp Oliver O Chen Jiaxuan J Cmarko Dusan D Butter Falk F Dittmar Gunnar G Lermyte Frederik F Cardoso M Cristina MC

Cells 20240111 2

Pericentric heterochromatin (PCH) forms spatio-temporarily distinct compartments and affects chromosome organization and stability. Albeit some of its components are known, an elucidation of its proteome and how it differs between tissues in vivo is lacking. Here, we find that PCH compartments are dynamically organized in a tissue-specific manner, possibly reflecting compositional differences. As the mouse brain and liver exhibit very different PCH architecture, we isolated native PCH fractions ...[more]

PMID: 38247831

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