Chromosomal Organization: Mingling with the Neighbors

C hromosomes, the packaged DNA carriers of heredity and instructions for proper cell functioning, undergo dramatic morphological transformations during the cell-division cycle. In metaphase, which includes the alignment of chromosomes before their separation between the two daughter cells, the 46 chromosomes in a human cell are condensed to such a degree that they can be observed by light microscopy as clearly separate individual entities. In cells that have entered the subsequent interphase, the chromosomes partially decondense into chromosome territories [1]. The information contained in chromosomes is retrieved and acted upon in their (partly) decondensed state. A precise understanding of how decondensed interphase chromosomes interact is important because close contact between and within chromosomes has implications for such fundamental processes as transcription and DNA damage repair; chromosome association can infl uence gene expression [2,3], and misrepair of DNA double-strand breaks can promote genome instability in the form of chromosome translocations [4,5]. A key issue in chromosome biology is to determine if, and if so to what extent, different chromosomes interact in the nucleus. A number of arrangements are possible (Figure 1). At one end, there is a complete lack of interaction: chromosomes may be contiguous without intermingling, or they may be separated by interchromatin domains. Interchromatin domains are nuclear areas mostly void of chromatin where important chromosomal transactions such as transcription, pre-mRNA splicing, DNA damage repair, and DNA replication occur. At the other extreme, chromatin loops of different chromosomes can freely intermingle, leading to a situation where the borders between chromosome territories and chromosome subdomains are no longer clearly defi ned. Understanding which of these models is correct requires a geographical survey of the chromosomes in the cell nucleus by microscopy. The quality of the information with regard to spatial distribution of the components in the nucleus is determined in the fi rst instance by the resolution of the microscope, which is on the order of several hundred nanometers for visual light microscopy and several nanometers for electron microscopy. In general, confocal light microscopy is used for a global overview of the three-dimensional organization of structures in the nucleus, while electron microscopy is useful for detailed two-dimensional views of a small nuclear area. In addition to the type of microscopy employed, the resolution and quality of data obtained are also infl uenced by changes in the organization of the nuclear components that may occur during preparation of the sample. Fluorescently labeled …