RNA polymerase II of trypanosomes, early diverging eukaryotes, transcribes long polycistronic messages, which are not capped but are processed by trans-splicing and polyadenylation to form mature mRNAs. The same RNA polymerase II also transcribes the genes coding for the spliced leader RNA, which are capped, exported to the cytoplasm, processed, and reimported into the nucleus before they are used as splicing donors to form mRNAs from pre-mRNA polycistronic transcripts. As pre-mRNA and spliced leader transcription events appear to be uncoupled, we studied how the RNA polymerase II is distributed in the nucleus of Trypanosoma cruzi. Using specific antibodies to the T. cruzi RNA polymerase II unique carboxy-terminal domain, we demonstrated that large amounts of the enzyme are found concentrated in a domain close to the parasite nucleolus and containing the spliced leader genes. The remaining RNA polymerase II is diffusely distributed in the nucleoplasm. The spliced leader-associated RNA polymerase II localization is dependent on the cell transcriptional state. It disperses when transcription is blocked by ␣-amanitin and actinomycin D. Tubulin genes are excluded from this domain, suggesting that it may exclusively be the transcriptional site of spliced leader genes. Trypomastigote forms of the parasite, which have reduced spliced leader transcription, show less RNA polymerase II labeling, and the spliced leader genes are more dispersed in the nucleoplasm. These results provide strong evidences that transcription of spliced leader RNAs occurs in a particular domain in the T. cruzi nucleus.Trypanosomes belong to a group of early diverging flagellated protozoa that causes several parasitic diseases, including Chagas' disease, leishmaniosis, and African trypanosomiasis. As with most eukaryotes, they also have three RNA polymerases characterized by a variable sensitivity to ␣-amanitin (15, 48). In trypanosomatids, the ␣-amanitin-sensitive RNA polymerase II (RNA Pol II), which transcribes most of the protein coding genes, catalyzes the transcription of long polycistronic messages (25, 47). These long polycistronic messages are then processed in a trans-splicing reaction by addition of a 30-to 40-nucleotide sequence derived from the spliced leader (SL) RNA at the 5Ј end of each cistron, followed by addition of a poly(A) tail at the 3Ј end (3, 42). The cap is added at the 5Ј end of the SL RNA during its transcription, and then it is transferred with the 30 to 40 nucleotides to the mature mRNA in the trans-splicing reaction (21, 29, 37). Transcription is constitutive for almost all genes characterized to date and varies in overall rates according to the parasite developmental stages (18). Thus, most regulation of gene expression in these organisms seems to occur posttranscriptionally either by the stability of the processed mRNAs or by translational controls as discussed in several reviews (8,23,44,49). Recently, a bidirectional promoter was identified in strand-switch regions of chromosomes 1 (31) and 3 (30) of Leishmania ...