Three-dimensional spectral precision distance microscopy of chromatin nanostructures after triple-colour DNA labelling: a study of the BCR region on chromosome 22 and the Philadelphia chromosome

Topological analysis of the three-dimensional (3D) chromatin nanostructure and its function in intact cell nuclei implies the use of high resolution f ar field light microscopy, e.g, confocal laser scanning microscopy (CLSM). However, experimental evidence indicates that, in practice, under biologica lly relevant conditions, the spatial resolution of CLSM is limited to about 300 nm in the lateral direction and about 700 nm in the axial direction. T o overcome this shortcoming, the use of a recently developed light microsco pical approach, spectral precision distance microscopy (SPDM) is establishe d. This approach is based on the precise localization of small labelling si tes of a given target in spectrally differential images. By means of quanti tative image analysis, the bary centres (intensity weighted centroid analog ous to the centre of mass) of these independently registered labelling site s can be used as point markers for distance and angle measurements after ap propriate calibration of optical aberrations (here, polychromatic shifts). In combination with specific labelling of very small chromatin target sites with dyes of different spectral signatures by fluorescence in situ hybridi zation (FISH), SPDM presently allows us to analyse the nuclear topology in three-dimensionally conserved nuclei with a 'resolution equivalent', many t imes smaller than the conventional optical resolution. Chronic myelogeneous leukaemia (CML) is genetically characterized by the fu sion of parts of the BCR and ABL genes on chromosomes 22 and 9, respectivel y. In most cases, the fusion leads to a translocation t(9; 22) producing th e Philadelphia chromosome. SPDM was applied to analyse the 3D chromatin str ucture of the BCR region on the intact chromosome 22 and the BCR-ABL fusion gene on the Philadelphia chromosome (Ph) by using a new triple-colour FISH protocol: two different DNA probes were used to detect the BCR region and the third DNA probe was used to identify the location of the ABL gene. Cons istent 3D distance measurements down to values considerably smaller than 10 0 nm were performed. The angle distributions between the three labelled sit es on the Philadelphia chromosome territory were compared to two state-of-t he-art computer models of nuclear chromatin structure. Significant differen ces between measured and simulated angle distributions were obtained, indic ating a complex and non-random angle distribution.