Homologous Chromosomes
 
Each diploid somatic nucleus contains two copies of each chromosome, known as homologues. The existence of pairs of homologous chromosomes is important for providing at least two copies of any particular gene. This provides the cell with two opportunities to generate a functional gene product. However, it also creates the problem of segregating the homologous chromosomes into the gametes. Homologous chromosomes always pair during the first meiotic cell division, when they have to be separated to help create haploid gametes (Fig.  1). In certain instances, homologous chromosomes also pair in the somatic interphase. This pairing is common in Dipteran insects and in some plants (1) . The techniques of fluorescent in situ hybridization (FISH) and confocal microscopy (see Denaturation Mapping) allow for the definition of chromosomal territories within the nucleus. Homologous chromosomes frequently occupy adjacent territories in insects and plants (2). Nevertheless, homologues do not often pair in the interphase of mammalian cells. Homologous chromosomes are occasionally found in contact with the same nuclear structures, such as the nucleolus or the nuclear membrane, but the distances between homologues are quite variable (3). 

Figure 1. Homologous chromosomes during meiosis. (a) Homologous chromosomes align during the pachytene of the first meiotic division. (b) Homologous chromosomes are separated during the anaphase of the first meiotic division.
Pairing of homologous chromosomes in meiosis occurs simultaneously with the beginning of chromosome condensation early in the prophase of the first meiotic division. In Coprinus, a fungus, the interaction between homologues, known as synapsis begins on the longitudinally aligned chromosomes at points towards the ends of the chromosomes and moves towards the centromere. It is probable that there are specific sites within the chromosome that have evolved to mediate chromosomal pairing (4). How homologous sequences are positioned next to each other during this chromosomal alignment process is also unknown, but recognition of similar nucleoprotein structures is likely to be involved. However heterochromatin association does not have a major role in this process, nor do the specialized chromosomal structures found at centromeres and telomeres. The end result of chromosomal adjustment is stable physical linkage of the homologues by the synaptonemal complex (SC) (5). This is a ribbonlike structure consisting of two electron-dense lateral elements (25 nm wide) that are separated by a less dense central region (105 nm wide). The major components of the SC are synthesized during the meiotic prophase. Most of the chromatin is located outside of the SC in loops attached to the lateral elements. The SC has important functions in providing a structural framework for efficient recombination, thereby stabilizing the crossover sites where chromatin bridges form at chiasmata (sites of crossing-over between homologous DNA sequences). SCs might also introduce constraints on the formation of chiasmata so that they cannot occur too close together. Visualization of SCs under the electron microscope after special staining procedures is a useful for revealing any misalignments of chromosomes due to deletions and duplications. This is a useful adjunct to conventional analysis of chromosomal bands.
 
References
1. B. John (1976) Chromosoma 46, 279–286. 
2. L. Avivi and M. Feldman (1989) Hum. Genet. 55, 281–285. 
3. L. Manmelides (1984) Proc. Natl. Acad. Sci. USA 181, 3123–3128. 
4. R. S. Hawley (1980) Genetics 94, 625–637. 
5. C. B. Gillies (1984) CRC Crit. Rev. Plant Sci. 2, 81–116.