title: Identifying gene locus associations with promyelocytic leukemia nuclear bodies using immuno-TRAP.
abstract: 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.
authors.affiliation: Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.
authors.forename: Reagan W
authors.initials: RW
authors.lastname: Ching
authors.forename: Kashif
authors.initials: K
authors.lastname: Ahmed
authors.forename: Paul C
authors.initials: PC
authors.lastname: Boutros
authors.forename: Linda Z
authors.initials: LZ
authors.lastname: Penn
authors.forename: David P
authors.initials: DP
authors.lastname: Bazett-Jones
mesh_terms: D002843:Chromatin / Q000378:metabolism; D002846:Chromatography, Affinity / Q000379:methods*; D004273:DNA, Neoplasm / Q000235:genetics / Q000302:isolation & purification; D056726:Genetic Association Studies; D056426:Genetic Loci; D006801:Humans; D007163:Immunosorbent Techniques; D017404:In Situ Hybridization, Fluorescence; D045586:Intranuclear Inclusion Bodies / Q000235:genetics* / Q000276:immunology* / Q000648:ultrastructure; D019169:Jurkat Cells; D015473:Leukemia, Promyelocytic, Acute / Q000235:genetics* / Q000473:pathology*; D009928:Organ Specificity; D011401:Promoter Regions, Genetic / Q000235:genetics
chemical_list: D002843:Chromatin; D004273:DNA, Neoplasm