THE KRUPPEL-ASSOCIATED BOX (KRAB) ZINC-FINGER PROTEIN KID-1 AND THE WILMS-TUMOR PROTEIN WT1, 2 TRANSCRIPTIONAL REPRESSOR PROTEINS, BIND TO HETERODUPLEX DNA

Zinc finger proteins of the Cys(2)His(2) class represent a large group of DNA-binding proteins. A major subfamily of those proteins, the Kru ppel-associated box (KRAB) domain-containing Cys(2)His(2)-zinc finger proteins, have been described as potent transcriptional repressors. So far, however, no DNA-binding sites for KRAB domain-containing zinc fi nger proteins have been isolated. Using a polymerase chain reaction-ba sed selection strategy with double-and single-stranded DNA, we failed to reveal a binding site for Kid-1, one member of KRAB-zinc finger pro teins. Binding of Kid-1 both to single-and homoduplex double-stranded DNA was negligible. We now present evidence that Kid-1 binds to hetero duplex DNA. Similar to Kid-1, the non-KRAB-zinc finger protein WT1 als o bound avidly to heteroduplex DNA (both the -KTS and +KTS splice vari ant of WT1), whereas the POU domain protein Oct-6, the ets domain prot ein Ets-1 and the RING finger of BRCA-1 did not bind to heteroduplex D NA. Binding of WT1 to heteroduplex DNA was markedly reduced in natural ly occurring mutants. The recognition of certain DNA structures by tra nscriptional repressor proteins may therefore represent a more common phenomenon than previously thought.