%0 Journal Article %A Damian Kao %A Yuliana Mihaylova %A Samantha Hughes %A Alvina Lai %A A. Aziz Aboobaker %T Epigenetic analyses of the planarian genome reveals conservation of bivalent promoters in animal stem cells %D 2017 %R 10.1101/122135 %J bioRxiv %P 122135 %X Background Planarian flatworms have an indefinite capacity to regenerate due to a population of pluripotent adult stem cells (neoblasts). Previous studies have suggested that they have features in common with both pluripotent mammalian embryonic stem cells and germ line stem cells. However, little is known about the importance of epigenetic regulation in these cells, which is likely to be crucial for neoblast biology and regeneration. We set out to develop analytical and experimental tools for planarians to allow the study of epigenetic marks in neoblasts and allow direct comparison of this model system with other animals.Results We developed an optimized ChIP-seq protocol for planarian neoblasts that allowed us to generate genome wide profiles for H3K4me1, H3K4me3 and H3K27me3. These were found to correlate as expected with genome wide expression profiles from analyses of planarian RNA-seq data. We found that many genes that are silent in neoblasts and then switch in post-mitotic progeny during differentiation have both H3K4me3 and H3K27me3 at promoter regions and are therefore bivalent. Further analysis suggested that bivalency is present at hundreds of loci in the pluripotent neoblast population.Conclusions We confirm that epigenetic regulation is key to neoblast biology and that bivalent promoters are not confined to vertebrate lineages, but may be a conserved feature of animal stem cells. Our work further establishes planarian neoblasts as a powerful model system for understanding the epigenetic regulation of pluripotency and regeneration. %U https://www.biorxiv.org/content/biorxiv/early/2017/03/29/122135.full.pdf