ZSCAN4-binding motif - TGCACAC is conserved and enriched in CA/TG microsatellites in both mouse and human genomes [ChIP-Seq]

The Zinc finger and SCAN domain containing 4 (Zscan4) protein, expressed transiently in pluripotent stem cells as well as in gamete and embryonic development, regulates genome stability in addition to telomere elongation and karyotype correction in mouse ES cells. However, the mechanism underlying Zscan4’s ability to counter the toxic effects of DNA/chromatin remodeling is not fully understood. In this study, we used ChIP-seq technology with Zscan4 antibodies to identify genome-wide binding sites in mouse and human ES cells. We discovered that both mouse and human Zscan4 bind to specific simple sequence repeats, (TG/CA)n, that have a propensity to induce genomic instability through a left-handed helix and stem-loop structure. Furthermore, we found that Zscan4 removes active histone marks from (TG/CA)n regions to maintain the closed/inactive chromatin state. These results demonstrate that Zscan4 protects unstable genomic regions by directing chromatin condensation. Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for 1) Zscan4 in mouse embryonic fibroblasts (MEF), mouse ES cells (ES), and retinoic acid treated mouse ES cells (RA), and 2) ZSCAN4 in human ES cells treated with or without DUX4