Nuclease mapping and DNA sequence analysis of transcripts from the dihydrofolate reductase-thymidylate synthase (R) region of Leishmania major

Trypanosomatid protozoan parasites utilize a number of nonstandard mechanisms in expressing their genes. To probe these phenomena in a genetically accessible system, we have mapped termini of eight transcripts arising from the amplified R region including the DHFR-TS gene of methotrexate-reslstant Leishmania major. Poly(A)⁺ RNAs transcribed from the DHFR-TS-coding strand exhibit features similar to those observed around other trypanosomatid protein-coding genes. These include close spacing, the presence of a trans-spliced minlexon on the 5′ termini, heterogeneity at both 5′ and 3′ ends, and in some cases S1 nuclease protection of intertranscript regions. Other than the splice acceptor site, no consensus sequence elements associated with either 5′ or 3′ ends were detected, although polydinucleotide tracts tended to be near inter-transcript regions. Two poly(A)⁺ RNAs transcribed from the opposite strand of the upstream flanking regions lacked the miniexon. Sequencing of DNA encoding the overlapping 1.7 kb opposite strand transcripts (one bearing and one lacking the miniexon, both found on polysomes) revealed no reading frames likely to encode proteins, suggesting that at least some of these RNAs could be nonfunctional by-products of RNA processing.