title: The quantitative nuclear matrix proteome as a biochemical snapshot of nuclear organization.
abstract: 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.
authors.affiliation: Max Planck Institute of Immunobiology and Epigenetics , Stübeweg 51, 79108 Freiburg, Germany.
authors.forename: Rudolf
authors.initials: R
authors.lastname: Engelke
authors.forename: Julia
authors.initials: J
authors.lastname: Riede
authors.forename: Jan
authors.initials: J
authors.lastname: Hegermann
authors.forename: Andreas
authors.initials: A
authors.lastname: Wuerch
authors.forename: Stefan
authors.initials: S
authors.lastname: Eimer
authors.forename: Joern
authors.initials: J
authors.lastname: Dengjel
authors.forename: Gerhard
authors.initials: G
authors.lastname: Mittler
mesh_terms: D002460:Cell Line; D002467:Cell Nucleus / Q000737:chemistry / Q000378:metabolism; D005434:Flow Cytometry; D006801:Humans; D015530:Nuclear Matrix / Q000737:chemistry*; D034521:Nuclear Matrix-Associated Proteins / Q000032:analysis* / Q000737:chemistry; D020543:Proteome / Q000032:analysis* / Q000737:chemistry; D040901:Proteomics / Q000379:methods*
chemical_list: D034521:Nuclear Matrix-Associated Proteins; D020543:Proteome