African trypanosomes are protozoan parasites causing serious and potentially fatal diseases of humans and domestic livestock. They have a digenetic life cycle, with one phase in the tsetse fly vector and another in the tissue fluids and bloodstream of the mammalian host (70). Antigenic variation, the continual switching of the variant surface glycoprotein (VSG) which constitutes the surface coat, allows evasion of mammalian immunity (16). The VSG coat is encoded by around 1,000 genes, most of which are thought to be in long tandem arrays in chromosomes but some of which are at telomeres (68). Only one VSG gene is expressed at a time, and for most genes this is achieved by duplicative transposition, where a copy of a VSG gene is synthesized and inserted into a transcriptionally active, telomeric, bloodstream expression site (3). There are estimated to be around 20 expression sites for VSG genes expressed in the bloodstream (39), and switching between VSGs is accomplished by a number of mechanisms which involve either changing the expression site that is active or replacing the VSG gene in the active expression site (3). Bloodstream expression sites have a common architecture; the VSG gene is at the 3Ј end, adjacent to the simple repeats of the telomere, and is coexpressed with various 5Ј flanking expression siteassociated genes (ESAGs) from a promoter located 40 to 60 kb upstream (51). These complex expression sites are subject to a range of control mechanisms. Within the bloodstream life cycle stage, expression of individual genes within the active expression site is regulated posttranscriptionally (40,(48)(49)(50)73) but switching between expression sites is by regulation of transcription initiation (54). However, in the procyclic stage in the insect, where VSG is not expressed, expression sites are downregulated, partly at the level of transcription initiation (55) and partly by transcription attenuation close to the promoter itself (14,37,48,49,55,69,73). Thus, in addition to control mechanisms for individual genes within life cycle stages, there are further mechanisms that control between stages.When trypanosomes are taken up by the tsetse fly, they undergo a rapid differentiation to the procyclic stage. Procyclic trypanosomes are not coated with VSG, expressing instead a new surface coat composed of the protein procyclin, also known as PARP (procyclic acidic repetitive protein) (45,53). Expression of VSG is reinitiated only during differentiation to the nondividing metacyclic stage in the salivary glands of the tsetse fly (62). This is the stage infective for mammals, and its coating with VSG is thought to be essential for parasite survival and proliferation following transfer into the host. Only a small, specific subset of VSGs are expressed (Ͻ28; 1 to 2% of the total repertoire) in the metacyclic population (17,22,65). The metacyclic VSG (M-VSG) genes are activated randomly in the metacyclic stage, yielding a polyclonal population, each individual of which expresses only one VSG (62). Further, clonal anal...