The proteins of intra-nuclear bodies: A data-driven analysis of sequence, interaction and expression

Mohamad, Nurul and Bodén, Mikael (2010) The proteins of intra-nuclear bodies: A data-driven analysis of sequence, interaction and expression. BMC Systems Biology, 4 44: 1-12. doi:10.1186/1752-0509-4-44

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Author Mohamad, Nurul
Bodén, Mikael
Title The proteins of intra-nuclear bodies: A data-driven analysis of sequence, interaction and expression
Journal name BMC Systems Biology   Check publisher's open access policy
ISSN 1752-0509
Publication date 2010-04-13
Sub-type Article (original research)
DOI 10.1186/1752-0509-4-44
Open Access Status DOI
Volume 4
Issue 44
Start page 1
End page 12
Total pages 12
Editor Melissa Norton
Place of publication London, U.K.
Publisher BioMed Central
Collection year 2011
Language eng
Formatted abstract
Background Cajal bodies, nucleoli, PML nuclear bodies, and nuclear speckles are morpohologically distinct intra-nuclear structures that dynamically respond to cellular cues. Such nuclear bodies are hypothesized to play important regulatory roles, e.g. by sequestering and releasing transcription factors in a timely manner. While the nucleolus and nuclear speckles have received more attention experimentally, the PML nuclear body and the Cajal body are still incompletely characterized in terms of their roles and protein complement.

Results By collating recent experimentally verified data, we find that almost 1000 proteins in the mouse nuclear proteome are known to associate with one or more of the nuclear bodies. Their gene ontology terms highlight their regulatory roles: splicing is confirmed to be a core activity of speckles and PML nuclear bodies house a range of proteins involved in DNA repair. We train support-vector machines to show that nuclear proteins contain discriminative sequence features that can be used to identify their intra-nuclear body associations. Prediction accuracy is highest for nucleoli and nuclear speckles. The trained models are also used to estimate the full protein complement of each nuclear body. Protein interactions are found primarily to link proteins in the nuclear speckles with proteins from other compartments. Cell cycle expression data provide support for increased activity in nucleoli, nuclear speckles and PML nuclear bodies especially during S and G2 phases.

Conclusions The large-scale analysis of the mouse nuclear proteome sheds light on the functional organization of physically embodied intra-nuclear compartments. We observe partial support for the hypothesis that the physical organization of the nucleus mirrors functional modularity. However, we are unable to unambiguously identify proteins' intra-nuclear destination, suggesting that critical drivers behind of intra-nuclear translocation are yet to be identified.
© 2010 Mohamad and Bodén; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Keyword Cajal bodies
Proteomic analysis
DNA-damage
PML
Localization
Nucleolus
Body
Kernels
Cells
Model
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2011 Collection
Institute for Molecular Bioscience - Publications
 
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Citation counts: TR Web of Science Citation Count  Cited 6 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 8 times in Scopus Article | Citations
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Created: Sun, 16 May 2010, 10:07:42 EST