The Crithidia fasciculata replication protein A gene, RPA1, and topoisomerase II gene, TOP2, encode proteins involved in the replication of nuclear and mitochondrial DNA, respectively. Transcripts of both genes accumulate periodically during the cell cycle and attain their maximum levels just before S phase. Octamer consensus sequences within the 5-untranslated region (UTR) of both genes have been shown to be necessary for cycling of these transcripts. Using a gel retardation assay, we show here that nuclear extracts of C. fasciculata contain a protein factor(s) that binds specifically to RNA from 5-UTRs of TOP2 and RPA1 genes. In addition, mutations in the consensus octamer sequence abolish binding to the RNA in both cases. Ultraviolet cross-linking using a radiolabeled TOP2 5-UTR probe identified proteins with apparent molecular masses of 74 and 37 kDa in the RNA-protein complex. Nuclear extracts prepared from synchronized cells show that the binding activity varies during the cell cycle in parallel with TOP2 and RPA1 mRNA levels. These results suggest that the cell cycle regulation of the mRNA levels of trypanosomatid DNA replication genes may be mediated by binding of specific proteins to conserved sequences in the 5-UTR of their transcripts.The trypanosomatid Crithidia fasciculata is a protozoan parasite containing a single mitochondrion with an unusual form of DNA called kinetoplast DNA (kDNA) 1 (1, 2). The kDNA consists of a single network of catenated minicircles and maxicircles. During replication of kDNA, the minicircles are released from the network and are reattached to the network periphery after replication, whereas maxicircles replicate while still attached to the network (3). An unusual feature of DNA replication in trypanosomes is that both kinetoplast and nuclear DNA replicate in approximate synchrony (4, 5). In other eukaryotes, mitochondrial DNA replication occurs throughout the cell cycle (6, 7). Since both the kinetoplast and nuclear DNA replication genes are encoded in the nucleus, their coordinated expression may play a role in synchronizing nuclear and kDNA replication.Expression of protein-coding genes in trypanosomatids involves mechanisms that are different from those in most other eukaryotes. All mRNAs in trypanosomatids contain two exons, a 39-nucleotide miniexon at the 5Ј end of the mRNA and the main coding exon (8, 9). Genes are usually grouped in polycistronic transcription units, and the polycistronic pre-mRNAs are processed by 5Ј trans-splicing and 3Ј polyadenylation to yield monocistronic mRNAs. The differential expression of steady state mRNAs from a single polycistronic transcript involves post-transcriptional controls by mechanisms that are still unclear. Pre-mRNA turnover in combination with differential rates of trans-splicing and polyadenylation and of mRNA turnover may all play a role in regulating mRNA levels. So far, only two RNA polymerase II promoters for protein-coding genes have been described in trypanosomes, the Trypanosoma congolense glutamic acid/alanine-rich ...