Comparative analysis of KRAB zinc finger proteins in rodents and man: Evidence for several evolutionarily distinct subfamilies of KRAB zinc finger genes

Although the KRAB zinc finger proteins probably constitute the single large st class of transcription factors within the human genome, almost nothing i s known about their biological function. To increase our knowledge about th is interesting and relatively unexplored family of potent transcriptional r epressors, we here present the cloning, structural analysis, and expression study of three novel mouse KRAB zinc finger proteins. In addition, we pres ent an extensive comparative analysis of various members of this gene famil y based on the structure of the common KRAB A motif, At least three larger subfamilies of KR;IB zinc finger proteins are identified: one carrying the classical KRAB A motif only, another holding both a classical KRAB A and a classical KRAB B motif, and a third holding a classical KRAB A and a highly divergent KRAB B domain, named b, A large variation both in size and in pr imary amino acid sequence was observed in the linker region between the KRA B domain and the C-terminally located zinc finger repeats. This variability indicates that this region is of minor importance for the biological funct ion of KRAB-containing zinc finger proteins, The fact that in many zinc fin ger genes, the entire or almost the entire linker region is composed of deg enerate finger motifs substantiates this conclusion. The absence of identif iable KRAB A and B motifs in the genome of yeast, Saccharomyces cerevisiae, indicates a relatively late appearance of the KRAB domain in evolution and may suggest that the biological functions are restricted to multicellular organisms. In addition, we show that the expression of individual members o f one subfamily of KRAB zinc finger genes is restricted to specific hematop oietic cell lineages. This finding suggests that KRAB zinc finger proteins may play a role in lineage commitment, possibly silencing leakage transcrip tion from nonlineage-expressed genes.