THE CYSTEINE-RICH LIM DOMAINS INHIBIT DNA-BINDING BY THE ASSOCIATED HOMEODOMAIN IN ISL-1

Recently, a new class of homeobox genes has been identified, called LI M-homeobox genes. These genes encode proteins which have two tandemly repeated cysteine motifs, referred to as LIM domains, in addition to a homeodomain. In addition, proteins with only LIM domains have been de scribed but the function of the LIM domain is unknown. We have analyse d the function of LIM domains using Isl-1 as a representative LIM-home odomain protein. Employing protein prepared in bacterial cells, we sho w that the presence of the LIM domain in Isl-1 inhibits binding of the homeodomain to its DNA target. This in vitro inhibition can be releas ed either by denaturation/renaturation of the protein or by truncation of the LIM domains. A similar inhibition is observed in vivo using re porter constructs. In addition we show that LIM domains in a chimeric protein can inhibit binding of the Ubx homeodomain to its target. The ability of LIM domains to inhibit DNA binding by the homeodomain provi des a possible basis for negative regulation of LIM-homeodomain protei ns in vivo.