The quantitative nuclear matrix proteome as a biochemical snapshot of nuclear organization

Rudolf Engelke, Julia Riede, Jan Hegermann, Andreas Wuerch, Stefan Eimer, Joern Dengjel, Gerhard Mittler

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22 Citations (Scopus)


The nuclear matrix (NM) is an operationally defined structure of the mammalian cell nucleus that resists stringent biochemical extraction procedures applied subsequent to nuclease-mediated chromatin digestion of intact nuclei. This comprises removal of soluble biomolecules and chromatin by means of either detergent (LIS: lithium diiodosalicylate) or high salt (AS: ammonium sulfate, sodium chloride) treatment. So far, progress toward defining bona fide NM proteins has been hindered by the problem of distinguishing them from copurifying abundant contaminants and extraction-method-intrinsic precipitation artifacts. Here, we present a highly improved NM purification strategy, adding a FACS sorting step for efficient isolation of morphologically homogeneous lamin B positive NM specimens. SILAC-based quantitative proteome profiling of LIS-, AS-, or NaCl-extracted matrices versus the nuclear proteome together with rigorous statistical filtering enables the compilation of a high-quality catalogue of NM proteins commonly enriched among the three different extraction methods. We refer to this set of 272 proteins as the NM central proteome. Quantitative NM retention profiles for 2381 proteins highlight elementary features of nuclear organization and correlate well with immunofluorescence staining patterns reported in the Human Protein Atlas, demonstrating that the NM central proteome is significantly enriched in proteins exhibiting a nuclear body as well as nuclear speckle-like morphology.

Original languageEnglish
Pages (from-to)3940-3956
Number of pages17
JournalJournal of Proteome Research
Issue number9
Publication statusPublished - 1 Jan 2014
Externally publishedYes



  • flow cytometry
  • nuclear compartment
  • nuclear matrix
  • Nuclear organization
  • organellar proteomics
  • SILAC quantitative proteomics

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)
  • Medicine(all)

Cite this

Engelke, R., Riede, J., Hegermann, J., Wuerch, A., Eimer, S., Dengjel, J., & Mittler, G. (2014). The quantitative nuclear matrix proteome as a biochemical snapshot of nuclear organization. Journal of Proteome Research, 13(9), 3940-3956.