Cell Type Specific Chromosome Territory Organization in the Interphase Nucleus of Normal and Cancer Cells NARASIMHARAO V. MARELLA, 1 SAMBIT BHATTACHARYA, 2 LOPAMUDRA MUKHERJEE, 3 JINHUI XU, 3 AND RONALD BEREZNEY 1 * 1 Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, New York 2 Department of Mathematics and Computer Science, Fayetteville State University, Fayetteville, North Carolina 3 Department of Computer Sciences and Engineering, University at Buffalo, State University of New York, Buffalo, New York Numerous studies indicate that the genome of higher eukaryotes is organized into distinct chromosome territories and that the 3-D arrangement of these territories may be closely connected to genomic function and the global regulation of gene expression. Despite this progress, the degree of non-random arrangement remains unclear and no overall model has been proposed for chromosome territory associations. To address this issue, a re-FISH approach was combined with computational analysis to analysis the pair-wise associations for six pairs of human chromosomes (chr #1, 4, 11, 12, 16, 18) in the G 0 state of normal human WI38 lung fibroblast and MCF10A epithelial breast cells. Similar levels of associations were found in WI38 and MCF10A for several of the chromosomes whereas others showed striking differences. A novel computational geometric approach, the generalized median graph (GMG), revealed a preferred probabilistic arrangement distinct for each cell line. Statistical analysis demonstrated that 50% of the associations depicted in the GMG models are present in each individual nucleus. A nearly twofold increase of chromosome 4/16 associations in a malignant breast cancer cell line (MCFCA1a) compared to the related normal epithelial cell line (MCF10A) further demonstrates cancer related changes in chromosome arrangements. Our findings of highly preferred chromosome association profiles that are cell type specific and undergo alterations in cancer cells, lead us to propose a probabilistic chromosome code whereby the 3-D association profile of chromosomes contributes to the functional landscape of the cell nucleus, the global regulation of gene expression and the epigenetic state of chromatin. J. Cell. Physiol. 221: 130–138, 2009. ß 2009 Wiley-Liss, Inc. Recent studies have highlighted the importance of higher order nuclear structure and compartmentalization in the regulation of gene expression and the conservation of epigenetic mechanisms in various cell types (Berezney, 2002; Stein et al., 2003, 2008; Misteli, 2005, 2007; Lanctot et al., 2007; Kumaran et al., 2008). At the highest level of chromatin organization it is now established that individual chromosomes within the interphase mammalian nucleus occupy discrete regions referred to as ‘‘chromosome territories’’ (Manuelidis, 1990; Cremer and Cremer, 2001; Pederson, 2004; Cremer et al., 2006; Meaburn and Misteli, 2007). Numerous studies based largely on the radial positioning of chromosomes in the cell nucleus demonstrate a probabilistic non-random arrangement based on chromosome size or gene density (Croft et al., 1999; Sun et al., 2000; Boyle et al., 2001; Cremer et al., 2001; Parada et al., 2003; Bolzer et al., 2005; Meaburn and Misteli, 2007). This organization is maintained as the cells transverse the cell cycle in interphase (Gerlich and Ellenberg, 2003; Gerlich et al., 2003; Walter et al., 2003) and is evolutionarily preserved across species (Tanabe et al., 2002). Only very limited studies, however, have investigated whether there are changes in chromosome arrangements in different cell and tissue types (Parada et al., 2004a; Mayer et al., 2005; Neusser et al., 2007), during cell differentiation, development (Kuroda et al., 2004; Stadler et al., 2004; Wiblin et al., 2005) and in cancer cells (Parada et al., 2002; Cremer et al., 2003). Another less investigated aspect of chromosome territory organization is the question of preferential chromosomal neighborhoods (Nagele et al., 1999). Chromosomal neighborhoods refer to the spatial positioning of chromosomes relative to each other. Proximity between chromosomes in the interphase nucleus has been proposed to determine the rate of translocation frequency and other karyotypic rearrangements between the chromosomes (Roix et al., 2003; Soutoglou et al., 2007; Folle, 2008). Moreover, the position of a gene within the chromosome territory has been linked to its activity (Volpi et al., 2000; Chambeyron and Bickmore, 2004; Zink et al., 2004; Ling et al., 2006; Morey et al., 2007) and recent investigations have revealed the importance of interchromosomal interactions for gene regulation and epigenetic maintenance (Osborne et al., 2004; Spilianakis et al., 2005; Lomvardas et al., 2006). In this study, the chromosome territory organization of a subset of six chromosome pairs (chr #1, 4, 11, 12, 16, 18) were studied in the normal human fibroblast cell line WI38 and a normal human breast epithelial cell line MCF10A. A re-FISH This article is dedicated to Professor Donald S. Coffey on the occasion of his 50th year at The Johns Hopkins University School of Medicine. Additional Supporting Information may be found in the online version of this article. Contract grant sponsor: National Institute of Health; Contract grant number: GM-072131. Narasimharao V. Marella’s present address is Cancer Genetics Inc., 201 Meadows Office Complex, Route 17 North, Rutherford, NJ 07070. *Correspondence to: Ronald Berezney, Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260. E-mail: berezney@buffalo.edu Received 17 April 2009; Accepted 21 April 2009 Published online in Wiley InterScience (www.interscience.wiley.com.), 3 June 2009. DOI: 10.1002/jcp.21836 ORIGINAL ARTICLE 130 Journal of Journal of Cellular Physiology Cellular Physiology ß 2009 WILEY-LISS, INC.