title: Specialized compartments of cardiac nuclei exhibit distinct proteomic anatomy.
abstract: As host to the genome, the nucleus plays a critical role as modulator of cellular phenotype. To understand the totality of proteins that regulate this organelle, we used proteomics to characterize the components of the cardiac nucleus. Following purification, cardiac nuclei were fractionated into biologically relevant fractions including acid-soluble proteins, chromatin-bound molecules and nucleoplasmic proteins. These distinct subproteomes were characterized by liquid chromatography-tandem MS. We report a cardiac nuclear proteome of 1048 proteins--only 146 of which are shared between the distinct subcompartments of this organelle. Analysis of genomic loci encoding these molecules gives insights into local hotspots for nuclear protein regulation. High mass accuracy and complementary analytical techniques allowed the discrimination of distinct protein isoforms, including 54 total histone variants, 17 of which were distinguished by unique peptide sequences and four of which have never been detected at the protein level. These studies are the first unbiased analysis of cardiac nuclear subcompartments and provide a foundation for exploration of this organelle's proteomes during disease.
authors.affiliation: Department of Anesthesiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA. sfranklin@mednet.ucla.edu
authors.forename: Sarah
authors.initials: S
authors.lastname: Franklin
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Zhang
authors.forename: Haodong
authors.initials: H
authors.lastname: Chen
authors.forename: Anna K
authors.initials: AK
authors.lastname: Paulsson
authors.forename: Scherise A
authors.initials: SA
authors.lastname: Mitchell-Jordan
authors.forename: Yifeng
authors.initials: Y
authors.lastname: Li
authors.forename: Peipei
authors.initials: P
authors.lastname: Ping
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Vondriska
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D002451:Cell Compartmentation; D002467:Cell Nucleus / Q000378:metabolism* / Q000648:ultrastructure; D016678:Genome / Q000235:genetics; D006657:Histones / Q000378:metabolism; D008297:Male; D013058:Mass Spectrometry; D051379:Mice; D008807:Mice, Inbred BALB C; D008969:Molecular Sequence Data; D009206:Myocardium / Q000166:cytology* / Q000378:metabolism* / Q000648:ultrastructure; D009687:Nuclear Proteins / Q000737:chemistry / Q000378:metabolism; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D013347:Subcellular Fractions / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D006657:Histones; D009687:Nuclear Proteins; D010455:Peptides; D020543:Proteome; D014157:Transcription Factors
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