Sequence-specific DNA-binding of evolutionary divergent KRAB-zinc finger proteins

University Of California At Davis, Davis CA

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Abstract

DESCRIPTION (provided by applicant): KRAB domain-containing zinc finger proteins (KRAB-ZNFs) are a large, but poorly characterized family of transcriptional regulators in mammals. KRAB-ZNFs are thought to function as transcriptional repressors through a KRAB box-mediated interaction with the KAP1 corepressor complex. Despite much biochemical evidence, there are very few known target genes of KRAB-ZNFs and the physiological roles of these regulators remain essentially unknown. The genes encoding zinc finger proteins are typically found in clusters located on several different chromosomes. These clusters are thought to have arisen from tandem duplications and are present in much higher numbers in mammalian species. Recent phylogenetic analysis suggests that the KRAB ZNF gene clusters on human chromosome 19 and mouse chromosome 7 are highly related; it appears that a single mouse gene Zfp61 has given rise to a cluster of 10 human genes on chromosome 19. Each of these genes contains a KRAB transcriptional repressor domain and has varying numbers of C2H2 zinc finger DNA binding domains. Such lineage specific duplications of KRAB-ZNFs may have important implications for defining species-specific transcriptional networks and may have significant implications on development. I propose that the evolution of human specific KRAB-ZNF genes has a significant impact on lineage-specific transcriptional networks. Specifically, the divergence within the C2H2 regions of the cluster of KRAB-ZNF genes leads to diverse DNA binding activities of the 10 KRAB-ZNF transcriptional repressors. These separate factors are therefore capable of regulating 10 distinct subsets of genes that are otherwise only controlled by a single transcription repressor in mouse. I will express tagged versions of the 10 human genes and one mouse gene and analyze their targets using an in vivo chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq).