DNA from Kinetoplastida contains the unusual modified base 
beta-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.