Characterisation of endogenous KRAB zinc finger proteins

Abstract

The Krüppel-associated box (KRAB) zinc finger protein (ZFP) genes comprise one of the largest gene families in the mammalian genome, encoding transcription factors with an N-terminal KRAB domain and C-terminal zinc fingers. The KRAB domain interacts with a co-repressor protein, KAP-1, which can recruit various factors causing transcriptional repression of genes to which KRAB ZFPs bind. Little is currently known about the gene targets of the ~400 human and mouse KRAB ZFPs. Many KRAB ZFPs interact with factors other than KAP-1. To identify proteins that may interact with one particular KRAB ZFP, Zfp647, I previously carried out a yeast two-hybrid screen using the full-length Zfp647 sequence and a mouse embryonic cDNA library. I have now tested the interactions from this screen for their specificity for Zfp647. I show that Zfp647 can interact with itself and at least 20 other KRAB ZFPs through their zinc finger domains, and have confirmed the Zfp647 self-interaction by in vitro co-immunoprecipitation. In my yeast two-hybrid screen, Zfp647 bound to KAP-1 as well as another related protein, ARD1/Trim23. Zfp647 also interacts with proteins that function in ubiquitylation. I have found evidence to suggest that Zfp647 may also interact with proteins encoding jumonji domains both by yeast two-hybrid assay and by co-immunoprecipitation from NIH/3T3 cell extracts. We have previously found that Zfp647 localises to non-heterochromatic nuclear foci in differentiated ES cells, which also contain KAP-1 and HP1, and which lie adjacent to PML nuclear bodies in a high proportion of cells. I have found that these foci are also visible in pMEFs, but not NIH/3T3 tissue culture cells. Immunofluorescence studies with antibodies against proteins from the yeast twohybrid screen have not shown any significant co-localisation with Zfp647. KAP-1 is sumoylated ex vivo, as are two human KRAB ZFPs. Because Zfp647 lies adjacent to PML nuclear bodies and can associate with proteins involved in posttranslational modification, I tested whether Zfp647 is also modified. I characterised a sheep _-Zfp647 antibody previously created in the lab and have shown that it detects Zfp647 by western blot, but not by immunofluorescence. I show that treatment of NIH/3T3 cells with NEM, which prevents the removal of protein modifications, leads to the appearance of higher molecular weight forms of Zfp647. Modification of Zfp647 is not dependent on KAP-1, which is known to function as a SUMO E3 ligase. Attempts to classify the modification as either ubiquitin, SUMO or NEDD8 have suggested that Zfp647 may be mono-ubquitylated. The larger modified forms of Zfp647 are present in both NIH/3T3 and ES cells. Interestingly, I found that the modification profile of the protein changes over the course of ES cell differentiation, during which time Zfp647 relocalises to punctate nuclear foci; thus Zfp647 modification may be involved in this process.