Base J, β-d-glucosyl-hydroxymethyluracil, is an epigenetic modification of 
thymine in the nuclear DNA of flagellated protozoa of the order Kinetoplastida. 
J is enriched at sites involved in RNA polymerase (RNAP) II initiation and 
termination. Reduction of J in Leishmania tarentolae via growth in BrdU resulted 
in cell death and indicated a role of J in the regulation of RNAP II 
termination. To further explore J function in RNAP II termination among 
kinetoplastids and avoid indirect effects associated with BrdU toxicity and 
genetic deletions, we inhibited J synthesis in Leishmania major and Trypanosoma 
brucei using DMOG. Reduction of J in L. major resulted in genome-wide defects in 
transcription termination at the end of polycistronic gene clusters and the 
generation of antisense RNAs, without cell death. In contrast, loss of J in T. 
brucei did not lead to genome-wide termination defects; however, the loss of J 
at specific sites within polycistronic gene clusters led to altered 
transcription termination and increased expression of downstream genes. Thus, J 
regulation of RNAP II transcription termination genome-wide is restricted to 
Leishmania spp., while in T. brucei it regulates termination and gene expression 
at specific sites within polycistronic gene clusters.