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- Title
Sorting the nuclear proteome.
- Authors
Bauer, Denis C.; Willadsen, Kai; Buske, Fabian A.; Lê Cao, Kim-Anh; Bailey, Timothy L.; Dellaire, Graham; Bodén, Mikael
- Abstract
Motivation: 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.Contact: m.boden@uq.edu.auSupplementary information: Supplementary data are available at Bioinformatics online.
- Subjects
PROTEIN analysis; BIOINFORMATICS; TRANSCRIPTION factors; AMINO acid sequence; QUANTITATIVE research; CELL morphology; MOLECULAR structure
- Publication
Bioinformatics, 2011, Vol 27, Issue 13, pi7
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btr217