Chromosome pairing is usually discussed in the context of meiosis. Association of homologues in germ cells enables chromosome segregation and is necessary for fertility. A few organisms, such as flies, also pair their entire genomes in somatic cells. Most others, including mammals, display little homologue pairing outside of the germline. Experimental evidence from both flies and mammals suggests that communication between homologues contributes to normal genome regulation. This paper will contrast the role of pairing in transmitting information between homologues in flies and mammals. In mammals, somatic homologue pairing is tightly regulated, occurring at specific loci and in a developmentally regulated fashion. Inappropriate pairing, or loss of normal pairing, is associated with gene misregulation in some disease states. While homologue pairing in flies is capable of influencing gene expression, the significance of this for normal expression remains unknown. The sex chromosomes pose a particularly interesting situation, as females are able to pair X chromosomes, but males cannot. The contribution of homologue pairing to the biology of the X chromosome will also be discussed. 1. Introduction One of the most intriguing aspects of somatic homologue pairing is that such a basic condition has enormous variability between species. Homologues pair vigorously in Drosophila, as illustrated by the remarkable alignment of polytene chromosomes. In fact, homologue pairing is pervasive throughout the Diptera, but in other organisms the occurrence and extent of homologue pairing is often unknown [1, 2]. Close association of homologous chromosomes in vegetative diploid budding yeast has been reported, but a careful reexamination suggested that little, if any, pairing occurs [3]. In diploid fission yeast both homologues occupy the same chromosome territory and centromeric pairing is observed in most cells [4]. Early studies suggested somatic homologue pairing in numerous plant species (Reviewed in [2]). Recent work supports the idea of homologue pairing in some grains and fungi, but also casts doubt on other reports of pairing in plants [5–8]. 2. Mammals: Pairing to Share Information Mammals have perhaps the most elaborate manifestation of homologue pairing. While complete pairing of the mammalian genome is not reported outside of the germline, somatic pairing of specific chromosomal regions does occur, but is tightly regulated. For example, homologous association of pericentromeric regions of human chromosome 1 is detected in cerebellar, but not cerebral, tissue
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