Targeting histone deacetylase complexes via KRAB-zinc finger proteins: thePHD and bromodomains of KAP-1 form a cooperative unit that recruits a novel isoform of the Mi-2 alpha subunit of NuRD

Macromolecular complexes containing histone deacetylase and ATPase activiti es regulate chromatin dynamics and are vitally responsible for transcriptio nal gene silencing in eukaryotes. The mechanisms that target these assembli es to specific loci are not as well understood. We show that the corepresso r KAP-1, via its PHD (plant homeodomain) and bromodomain, links the superfa mily of Kruppel associated box (KRAB) zinc finger proteins (ZFP) to the NuR D complex. We demonstrate that the tandem PHD finger and bromodomain of KAP -1, an arrangement often found in cofactor proteins but functionally ill-de fined, form a cooperative unit that is required for transcriptional repress ion. Substitution of highly related PHD fingers or bromodomains failed to r estore repression activity, suggesting high specificity in their cooperativ e function. Moreover, single amino acid substitutions in either the bromodo main or PHD finger, including ones that mimic disease-causing mutations in the hATRX PHD finger, abolish repression. A search for effecters of this re pression function yielded a navel isoform of the Mi-2 alpha protein, an int egral component of the NuRD complex. Endogenous KAP-1 is associated with Mi -2 alpha and other components of NuRD, and KAP-1-mediated silencing require s association with NuRD and HDAC activity. These data suggest the KRAB-ZFP superfamily of repressors functions to target the histone deacetylase and c hromatin remodeling activities of the NuRD complex to specific gene promote rs in vivo.