Setting an immuno-TRAP for PML nuclear bodies

P romyelocytic leukemia nuclear bodies (PML NBs) are nucleoplasmic particles that contain numerous proteins , including the PML protein itself. In patients with promyelocytic leukemia, PML is fused to retinoic acid receptor ␣, resulting in a loss of PML NBs and a block in promy-elocyte differentiation. Yet the precise function of PML NBs remains unclear. To learn more about these particles, Ching et al. identify regions of the genome that associate with PML NBs, using a novel method that could easily be adapted for other subnuclear structures as well (1). Though PML NBs are found in most somatic cells, their constitution can vary even between particles in the same nucleus. Alongside PML, PML NBs can contain sig-naling proteins, transcription factors, and chromatin-modifying enzymes, implicating these structures in multiple aspects of ge-nome regulation (2). " When you look at PML bodies by electron spectroscopic imaging, you see a protein-based core with obvious connections to chromatin fi bers, " says David Bazett-Jones from The Hospital for Sick Children in Toronto. " So the ge-nome and these nuclear bodies are intimately linked in some way. " Indeed, fl uorescence in situ hybridiza-tion (FISH) studies have shown that PML NBs can interact with spe-cifi c regions of the genome, including the TP53 and MHC loci (3, 4), but, says Bazett-Jones, " the disadvantage of FISH is that you have to have an a priori idea of what to probe for. " Bazett-Jones and colleagues , led by graduate student Reagan Ching, therefore wanted to develop an unbiased method to identify genomic loci associated with PML NBs, basing their approach on a technique used previously to identify chromatin regions in the vicinity of an actively transcribing gene (5). Ching et al.'s adapted approach, named immuno-TRAP, involved labeling PML NBs with an anti-PML antibody and a secondary antibody coupled to horseradish peroxidase (1). This enzyme can then conjugate biotin-tyramide onto nearby proteins, including histones, allowing Ching et al. to isolate biotinylated chromatin and identify genomic loci that are close to PML NBs. Using immuno-TRAP, Ching et al. confirmed the TP53 locus as a PML NB– associated region of the genome, but they also identifi ed several new loci that are enriched around these nuclear particles. " We pulled out a number of examples, clearly showing that PML bodies have links to specifi c gene elements, " says Bazett-Jones. The loci associated with PML NBs varied in …