title: Sorting the nuclear proteome.
abstract: BACKGROUND
  Quantitative experimental analyses of the nuclear interior reveal a morphologically structured yet dynamic mix of membraneless compartments. Major nuclear events depend on the functional integrity and timely assembly of these intra-nuclear compartments. Yet, unknown drivers of protein mobility ensure that they are in the right place at the time when they are needed.
  
  
  RESULTS
  This study investigates determinants of associations between eight intra-nuclear compartments and their proteins in heterogeneous genome-wide data. We develop a model based on a range of candidate determinants, capable of mapping the intra-nuclear organization of proteins. The model integrates protein interactions, protein domains, post-translational modification sites and protein sequence data. The predictions of our model are accurate with a mean AUC (over all compartments) of 0.71. We present a complete map of the association of 3567 mouse nuclear proteins with intra-nuclear compartments. Each decision is explained in terms of essential interactions and domains, and qualified with a false discovery assessment. Using this resource, we uncover the collective role of transcription factors in each of the compartments. We create diagrams illustrating the outcomes of a Gene Ontology enrichment analysis. Associated with an extensive range of transcription factors, the analysis suggests that PML bodies coordinate regulatory immune responses.
authors.affiliation: Queensland Brain Institute, School of Chemistry and Molecular Biosciences, Queensland Facility for Advanced Bioinformatics, The University of Queensland, St Lucia, Australia.
authors.forename: Denis C
authors.initials: DC
authors.lastname: Bauer
authors.forename: Kai
authors.initials: K
authors.lastname: Willadsen
authors.forename: Fabian A
authors.initials: FA
authors.lastname: Buske
authors.forename: Kim-Anh
authors.initials: KA
authors.lastname: Lê Cao
authors.forename: Timothy L
authors.initials: TL
authors.lastname: Bailey
authors.forename: Graham
authors.initials: G
authors.lastname: Dellaire
authors.forename: Mikael
authors.initials: M
authors.lastname: Bodén
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D002467:Cell Nucleus / Q000737:chemistry* / Q000378:metabolism; D015870:Gene Expression; D045586:Intranuclear Inclusion Bodies / Q000737:chemistry / Q000378:metabolism; D051379:Mice; D009687:Nuclear Proteins / Q000378:metabolism; D011499:Protein Processing, Post-Translational; D021381:Protein Transport; D020543:Proteome / Q000032:analysis*; D014157:Transcription Factors / Q000032:analysis* / Q000378:metabolism
chemical_list: D009687:Nuclear Proteins; D020543:Proteome; D014157:Transcription Factors