title: Electrophoretic characterization of the Mammalian nuclear matrix proteome, nuclear envelope, nucleoli and covalently bound ADP-ribose polymers: potential applications to cancer.
abstract: OBJECTIVE
  Nucleic acid metabolism is biochemically compartmentalized to the nucleus. Thus, it is necessary to define the proteome of the various macromolecular structures within this organelle.
  
  
  METHODS
  We isolated the nuclear matrix (NM) fraction from rat liver by sequential centrifugation steps at 13,000 rpm, staggered between endogenous nuclease treatment for 2 h at 37°C, followed by high-salt (H.S.; 2.0 M NaCl) and non-ionic detergent extractions (0.1%- or 1.0% Triton X-100) to eliminate the bulk of chromosomal DNA/RNA, histone proteins and the nuclear envelope (NE).
  
  
  RESULTS
  Integrity of the NM and NE structures was confirmed by electron microscopy. Next, we analyzed the NM proteome on a 20% polyacrylamide gel using the PhastSystem. We observed the absence of histone proteins and the characteristic presence of the lamins by Coomassie blue staining. By contrast, upon silver staining, following electrophoretic separation with a Tris-Borate-EDTA buffer, we observed the NM-associated nucleic RNA and protein-free ADP-ribose polymers. While polymers are found in much lower concentration than RNA in NM, they were purified by affinity chromatography on boronate resin prior to electrophoresis. We observed the electrophoretic resolution of free ADP-ribose chains (5-25 units) by silver staining.
  
  
  CONCLUSIONS
  The significance of our observations to cancer studies and carcinogenesis is discussed.
authors.affiliation: Graduate School of Biomedical Sciences, University of North Texas Health Science Center at Fort Worth, Fort Worth, TX, U.S.A.
authors.forename: Xavier G
authors.initials: XG
authors.lastname: Aranda
authors.affiliation: Texas College of Osteopathic Medicine, UNT Health Science Center, Fort Worth, TX, U.S.A.
authors.forename: Ronald G
authors.initials: RG
authors.lastname: Racho
authors.affiliation: Graduate School of Biomedical Sciences, University of North Texas Health Science Center at Fort Worth, Fort Worth, TX, U.S.A.
authors.forename: Gustavo
authors.initials: G
authors.lastname: Pacheco-Rodríguez
authors.affiliation: Institute for Cancer Research, University of North Texas System, Fort Worth, TX, U.S.A.
authors.forename: Rafael
authors.initials: R
authors.lastname: Alvarez-González
mesh_terms: D000818:Animals; D002466:Cell Nucleolus / Q000737:chemistry / Q000378:metabolism; D004586:Electrophoresis / Q000379:methods; D009369:Neoplasms / Q000737:chemistry* / Q000378:metabolism; D009685:Nuclear Envelope / Q000737:chemistry* / Q000378:metabolism; D015530:Nuclear Matrix / Q000737:chemistry* / Q000378:metabolism; D034521:Nuclear Matrix-Associated Proteins / Q000737:chemistry* / Q000378:metabolism; D011065:Poly(ADP-ribose) Polymerases / Q000737:chemistry* / Q000378:metabolism; D020543:Proteome / Q000737:chemistry* / Q000378:metabolism; D051381:Rats; D017207:Rats, Sprague-Dawley
chemical_list: D034521:Nuclear Matrix-Associated Proteins; D020543:Proteome; D011065:Poly(ADP-ribose) Polymerases
keywords: Nuclear matrix; PhastSystem; affinity chromatography; boronate resin; chromatin; electrophoresis; epigenetics; histones; lamins; nuclear envelope; nucleoli; poly(ADP-ribose); proteomics