Characterization of the 1.35 kilobase DNA repeat unit containing the conserved 35 nucleotides at the 5'-termini of variable surface glycoprotein mRNAs in Trypanosoma brucei.

We have cloned and determined the sequence of the 1.35 kb trypanosome DNA repeat unit that contains the conserved 35 nucleotides found at the 5'-ends of variable surface glycoprotein (VSG) mRNAs and present in many other trypanosome RNAs. Our data indicate that the genomic repeats, estimated by others to be present in 200-250 copies in the haploid genome (18, 21), are structurally very highly conserved but with dispersed point changes. The 1.35 kb repeat unit has an unusual stretch of multiple repetitive elements starting about 100 bp downstream from the 35 nucleotide sequence; in addition there are several potential eukaryotic transcription initiation sites throughout the repeat unit. Genomic mapping studies using portions of the repeat unit as hybridization probes suggest that the entire repeat is conserved at its multiple genomic locations.