Genetic deletion of a recently evolved 2.4 Mb tandem zinc finger gene cluster causes retrotransposon activation in mice

Authors

• G Wolf
• M Tinkham
• D Hoang
• TS Macfarlan

Abstract

Krüppel-associated box zinc finger proteins (KRAB-ZFPs) are potent transcriptional repressors that bind DNA in a sequence-specific manner through tandem arrays of C2H2-type zinc fingers. The KRAB-ZFP family rapidly amplified and diversified in mammals, possibly reflecting an ongoing arms race between KRAB-ZFPs and potentially hazardous retrotransposons. However, very few KRAB-ZFPs have been thoroughly investigated to date. To gain new insights into KRAB-ZFP gene evolution and function, we determined the genomic binding sites of approximately 10% of the more than 300 murine KRAB-ZFPs, including 17 KRAB-ZFPs that are encoded within a 2.4 Mb gene cluster that is not conserved in other mammals. Consistent with the arms-race hypothesis, we show that the majority of these mouse-specific KRAB-ZFPs bind mouse-specific retrotransposons. Genetic deletion of the entire 2.4 Mb KRAB-ZFP cluster in embryonic stem cells (ESCs) using CRISPR/Cas9 technology revealed a strong reactivation of retrotransposons, accompanied by a local loss of repressive histone modifications in KRAB-ZFP cluster knockout ESCs. Furthermore, we observed upregulation of several genes that are located near reactivated retrotransposons, indicating that KRAB-ZFPs can act on genes by binding to nearby retrotransposons. Our data supports an arms-race model in which KRAB-ZFPs primarily evolve to repress potentially hazardous retrotransposons. However, a consequence of this arms race is the establishment of species-specific gene regulatory patterns guided by KRAB-ZFP/target retrotransposon pairs. Finally, we show that CRISPR/Cas9 technology is suitable to genetically delete large KRAB-ZFP clusters in ESCs, opening a promising opportunity to generate mouse models in which human diseases associated with retrotransposon activity may be simulated.

Scientific Focus Area: Molecular Biology and Biochemistry

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