The mouse genome displays highly dynamic populations of KRAB-zinc finger protein genes and related genetic units. Mus musculus

We present a thorough analysis of KZFP genes and related units in the murine genome. We first identified about twice more elements than previously annotated either as KZFP genes or pseudogenes, we then could delineate an organization in clusters distributed throughout the genome, with signs of recombination, translocation, duplication and seeding of new sites by retrotransposition of KZFP genes and related genetic units (KZFP/rGUs). Finally, we could demonstrate that the KAP1-SETDB1 repressor complex tames the expression of KZFP/rGUs within clusters, yet that the primary target of this regulation was not the KZFP/rGUs themselves but enhancers contained in neighboring endogenous retroelements. Overall design: Analysis of KZFP/rGUs genomic distribution (ChIP-seq), expression profiles (RNA-seq), related transcripts and associated histone modifications (ChIP-seq). Characterization of binding and transcriptional control of KAP1 in KZFP/rGUs clusters via ChIP-seq and RNA-seq.