Position of human chromosomes is conserved in mouse nuclei indicating a species-independent mechanism for maintaining genome organization

Abstract

The nonrandom positioning of chromosome territories in eukaryotic cells is largely correlated with gene density and is conserved throughout evolution. Gene-rich chromosomes are predominantly central, while gene-poor chromosomes are peripherally localized in interphase nuclei. We previously demonstrated that artificially introduced human chromosomes assume a position equivalent to their endogenous homologues in the diploid colon cancer cell line DLD-1. These chromosomal aneuploidies result in a significant increase in transcript levels, suggesting a relationship between genomic copy number, gene expression, and chromosome position. We previously proposed that each chromosome is marked by a "zip code" that determines its nonrandom position in the nucleus. In this paper, we investigated (1) whether mouse nuclei recognize such determinants of nuclear position on human chromosomes to facilitate their distinct partitioning and (2) if chromosome positioning and transcriptional activity remain coupled under these trans-species conditions. Using three-dimensional fluorescence in situ hybridization, confocal microscopy, and gene expression profiling, we show (1) that gene-poor and gene-rich human chromosomes maintain their divergent but conserved positions in mouse-human hybrid nuclei and (2) that a foreign human chromosome is actively transcribed in mouse nuclei. Our results suggest a species-independent conserved mechanism for the nonrandom positioning of chromosomes in the three-dimensional interphase nucleus.

Fig. 1

Human chromosomes occupy discrete territories in both mouse and human nuclei. Structurally preserved nuclei were hybridized with painting probes specific for HSA7 (red), HSA18 (yellow) and HSA19 (green). Confocal image stacks were merged and maximum intensity projections were generated from each of the A9 mouse-human monochromosomal fibroblast nuclei (a, c and e) as well as from DLD-1 derivatives (b, d and f), Scale bar: 10 μm. (a and b) HSA7 territories visualized in A9+7 (a) and DLD-1+7 (b). (c and d) HSA18 territories visualized in A9+18 (c) and DLD-1+18 (d). (e and f) HSA19 territories visualized in A9+19 (e) and DLD-1+19 (f)

Fig. 2. Human chromosomes assume a conserved radial position in both mouse and human nuclei that correlates with their gene densities

(a, c and e) 3D radial distance profiles of chromosome territories HSA7 (a), HSA18 (c) and HSA19 (e). X-axis: % Radial Distance, 0% - nuclear center, 100% - nuclear periphery and Y-axis: % Frequency of chromosome territories. (b, d and f) Raw distributions of 3D radial distance measurements. X-axis: Cell line, Y-axis: % Radial Distance.

Fig. 3. Human chromosomes are transcriptionally active in mouse A9 cells

(a) Gene expression profiles of HSA7, 18 and 19 in A9 and A9 hybrid cells. Red dots: cell line/human reference ratio >1.5 log₂, Green dots: cell line/human reference ratio < -1.5 log₂. Grey boxes indicate the human chromosome in each cell line. aCGH: Genomic profile of A9+19 relative to the A9 mouse cell line on a human oligonucleotide-based CGH microarray. Increased copy number for chromosome arm 19p is clearly indicated, while no change in 19q is observed. (b) Top Panel: Quantification of Fig. 3a displaying the percentage of genes showing greater than a 1.5 log₂ increase (red), more than a 1.5 log₂ decrease (green) or no significant change (yellow) in gene expression levels for each of the human chromosomes in the A9 monochromosomal hybrid cell lines. Bottom Panel: HSA19 was further divided into p and q arms to demonstrate the difference in detected expression of these two chromosome arms.

Fig. 4

Human chromosome 19 is partially deleted in A9+19 mouse-human hybrid cells. FISH analyses of A9+19 metaphase reveals deleted HSA19q. Green: 19p and Red: 19q Inset: enlarged image of HSA19.