Chromosome Organization and Function in the Cell Nucleus
We are taking a multi-disciplinary approach by combining the tools of cell biology, genomics, high resolution three dimensional microscopy and in-house developed state-of-the art computer imaging approaches to study the spatial organization and function of DNA replication sites, transcriptional sites and, most recently, chromosome territories inside the cell nucleus. Of major interest is to develop these studies in human cancer cells where perturbations occur in genomic organization and regulation and during differentiation of human skin cells where major switches in transcriptional programming occur.
Our studies of large subsets of chromosomes (8-10 chromosome pairs) have elucidated probabilistically preferred 3-D interchromosomal networks that are cell type specific in normal diploid human fibroblasts, keratinocytes and luminal epithelial breast cells. In addition, characteristic changes in the interchromosomal networks were found as the cells progressed through the cell cycle and during differentiation of keratinocytes into skin cells. Most strikingly, we discovered a nearly complete reorganization of the interchromosomal network in a malignant human breast cell (MCF10Ca1A) which was originally derived from a normal luminal ductal epithelial breast cell line (MCF10A). We propose that these alterations in chromosomal organization are reflecting corresponding alterations in the genomic programing of these cells. Consistent with this, gene expression microarray analysis revealed massive changes in gene expression between the normal and malignant cell lines.
In a related project, we are studying the 3-D organization (topology) of individual chromosome territories in the cell nucleus using a 6-probe multi-FISH approach that extends from one end of each chromosome to the other. We are particularly interested in determining whether the specific chromosomes in the malignant cells show characteristic alterations in their 3-D organization.