ArticleBMC systems biology2010
The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression.
Article in BMC systems biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 20 citations in OpenAlex.
- RNF4 and USP7 coordinate spatial regulation of SLX4 stability within the PML nuclear bodies.Nucleic acids research · 2025Article
- C9orf72-linked arginine-rich dipeptide repeats aggravate pathological phase separation of G3BP1.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Membrane-less compartments in the nucleus: Separated or connected phases?Current opinion in cell biology · 2023Review
- Wiskott-Aldrich syndrome protein forms nuclear condensates and regulates alternative splicing.Nature communications · 2022Article
- Promyelocytic leukemia protein targets MK2 to promote cytotoxicity.EMBO reports · 2021Article
- Revisiting promyelocytic leukemia protein targeting by human cytomegalovirus immediate-early protein 1.PLoS pathogens · 2020Article
- N-terminal sequences in matrin 3 mediate phase separation into droplet-like structures that recruit TDP43 variants lacking RNA binding elements.Laboratory investigation; a journal of technical methods and pathology · 2019Article
- Characterization of gene regulation and protein interaction networks for Matrin 3 encoding mutations linked to amyotrophic lateral sclerosis and myopathy.Scientific reports · 2018Article
- Multimodal Light Microscopy Approaches to Reveal Structural and Functional Properties of Promyelocytic Leukemia Nuclear Bodies.Frontiers in oncology · 2018Review
- Specific genomic cues regulate Cajal body assembly.RNA biology · 2017Review
- Article
- Amyloids assemble as part of recognizable structures during oogenesis in Xenopus.Biology open · 2016Article
- NSort/DB: an intranuclear compartment protein database.Genomics, proteomics & bioinformatics · 2012Article
- Sorting the nuclear proteome.Bioinformatics (Oxford, England) · 2011Article
- PNAC: a protein nucleolar association classifier.BMC genomics · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCajal 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.
resultsBy 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.
conclusionsThe 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.