Identifying gene locus associations with promyelocytic leukemia nuclear bodies using immuno-TRAP

Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.
The Journal of Cell Biology (Impact Factor: 9.83). 04/2013; 201(2):325-35. DOI: 10.1083/jcb.201211097
Source: PubMed


Important insights into nuclear function would arise if gene loci physically interacting with particular subnuclear domains could be readily identified. Immunofluorescence microscopy combined with fluorescence in situ hybridization (immuno-FISH), the method that would typically be used in such a study, is limited by spatial resolution and requires prior assumptions for selecting genes to probe. Our new technique, immuno-TRAP, overcomes these limitations. Using promyelocytic leukemia nuclear bodies (PML NBs) as a model, we used immuno-TRAP to determine if specific genes localize within molecular dimensions with these bodies. Although we confirmed a TP53 gene-PML NB association, immuno-TRAP allowed us to uncover novel locus-PML NB associations, including the ABCA7 and TFF1 loci and, most surprisingly, the PML locus itself. These associations were cell type specific and reflected the cell's physiological state. Combined with microarrays or deep sequencing, immuno-TRAP provides powerful opportunities for identifying gene locus associations with potentially any nuclear subcompartment.

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Available from: David Bazett-Jones, Apr 04, 2014
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    • "The eukaryotic nucleus contains domains organized by master proteins, such as promyelocytic leukemia (PML), which drives the formation of PML nuclear bodies (NBs; Lallemand-Breitenbach and de Thé, 2010). PML NBs are stress-regulated, dynamic structures that concentrate hundreds of proteins and nely tune multiple pathways including senescence, stemness, stress response, and defense against viruses (Koken et al., 1995; Dellaire and Bazett-Jones, 2004; Bernardi and Pandol, 2007; Ching et al., 2013). Functionally, NB disruption through expression of the PML/RARA oncogene has been implicated in acute promyelocytic leukemia (APL) pathogenesis. "
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