The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression
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 fac...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Published: |
BioMed Central
2010
|
| Subjects: |
| _version_ | 1796946769539497984 |
|---|---|
| author | Mohamad, N. Bodén, M. |
| author_facet | Mohamad, N. Bodén, M. |
| author_sort | Mohamad, N. |
| collection | UM |
| description | 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. |
| first_indexed | 2024-03-06T05:36:49Z |
| format | Article |
| id | um.eprints-14595 |
| institution | Universiti Malaya |
| last_indexed | 2024-03-06T05:36:49Z |
| publishDate | 2010 |
| publisher | BioMed Central |
| record_format | dspace |
| spelling | um.eprints-145952015-11-06T02:23:15Z http://eprints.um.edu.my/14595/ The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression Mohamad, N. Bodén, M. QH Natural history 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. BioMed Central 2010-04-13 Article PeerReviewed Mohamad, N. and Bodén, M. (2010) The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression. BMC Systems Biology, 4 (44). ISSN 1752-0509, DOI https://doi.org/10.1186/1752-0509-4-44 <https://doi.org/10.1186/1752-0509-4-44>. http://www.biomedcentral.com/1752-0509/4/44 doi:10.1186/1752-0509-4-44 |
| spellingShingle | QH Natural history Mohamad, N. Bodén, M. The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression |
| title | The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression |
| title_full | The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression |
| title_fullStr | The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression |
| title_full_unstemmed | The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression |
| title_short | The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression |
| title_sort | proteins of intra nuclear bodies a data driven analysis of sequence interaction and expression |
| topic | QH Natural history |
| work_keys_str_mv | AT mohamadn theproteinsofintranuclearbodiesadatadrivenanalysisofsequenceinteractionandexpression AT bodenm theproteinsofintranuclearbodiesadatadrivenanalysisofsequenceinteractionandexpression AT mohamadn proteinsofintranuclearbodiesadatadrivenanalysisofsequenceinteractionandexpression AT bodenm proteinsofintranuclearbodiesadatadrivenanalysisofsequenceinteractionandexpression |