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The modified base J is the target for a nove lDNA‐binding protein in kinetoplastid protozoans

DNA from Kinetoplastida contains the unusual modified base β‐D‐glucosyl(hydroxymethyl)uracil, called J. Base J is found predominantly in repetitive DNA and correlates with epigenetic silencing of telomeric variant surface glycoprotein genes in Trypanosoma brucei. We have now identified a protein in nuclear extracts of bloodstream stage T.brucei that binds specifically to J‐containing duplex DNA. J‐specific DNA binding was also observed with extracts from the kinetoplastids Crithidia fasciculata and Leishmania tarentolae. We purified the 90 kDa C.fasciculata J‐binding protein 50 000‐fold and cloned the corresponding gene from C.fasciculata, T.brucei and L.tarentolae. Recombinant proteins expressed in Escherichia coli demonstrated J‐specific DNA binding. The J‐binding proteins show 43–63% identity and are unlike any known protein. The discovery of a J‐binding protein suggests that J, like methylated cytosine in higher eukaryotes, functions via a protein intermediate.