Ciliated protists are model organisms for a number of molecular phenomena including telomerase function, self-splicing introns, and an RNA interference-related mechanism in programmed DNA elimination. Despite this relevance, our knowledge about promoters and transcriptional regulation in these organisms is very limited. The macronuclear genome of stichotrichous ciliates consists of minichromosomes which typically encode a single gene. The 5 nontranscribed spacers are usually no longer than 400 bp and highly suitable for promoter characterizations. We used microinjection of two artificial and differently tagged ␣1 tubulin minichromosomes into the macronucleus of Stylonychia lemnae as a means to characterize in detail the corresponding promoter. Clonal cell lines that stably maintained both minichromosomes were generated, enabling comparative expression analysis by primer extension assays. Deletion and block substitution mutations of one of the minichromosomes revealed a TATA-like element, a putative initiator element, and two distinct upstream sequence elements (USEs). Determination of transcription initiation sites and a sequence alignment indicated that both TATA-like and initiator elements are conserved components of S. lemnae minichromosomes, whereas the USEs appear to be specific for the ␣1 tubulin minichromosome. The ␣2 tubulin minichromosome promoter is very short, comprising the two proximal elements but not the USEs. Despite the latter finding, up-regulation of ␣-tubulin expression in cells treated with concanavalin A activated the ␣2 but not the ␣1 tubulin promoter. These results therefore show that gene expression regulation in S. lemnae occurs at the level of transcription initiation on the basis of structurally different promoters.In the past, research on ciliates has revealed generally important discoveries such as self-splicing introns (18), telomerase (9), and, recently, small RNAs involved in DNA elimination (26). Despite this relevance and despite evidence that ciliates regulate their genes at the transcriptional level (2, 36, 37), determinants of transcription in these organisms have not been a major focus. In Tetrahymena thermophila, promoter elements have been experimentally identified in the rRNA gene (6, 25), the telomerase RNA gene (11), and the RAD51 gene (35). However, no detailed analysis of a ciliate promoter has been achieved thus far. In ciliates, gene expression is restricted to macronuclei, which develop from micronuclei after conjugation. In this process, micronuclear DNA is fragmented, in part eliminated, and macronucleus-destined DNA is amplified (reviewed in reference 15). In stichotrichous ciliates, the extent of these DNA manipulations is extreme. For example, in Stylonychia lemnae, more than 90% of the micronuclear DNA is eliminated, DNA fragmentation leads to gene-sized minichromosomes, and DNA amplification results in gene-specific copy numbers that can exceed 100,000 per cell (12,38). A typical macronuclear minichromosome in these organisms harbors a single gene and very ...