MERVL/Zscan4 network activation results in transient genome-wide DNA demethylation of mESCs

Supplemental Information includes Supplemental Experimental Procedures, six figures, and four tables and can be found with this article online at http:// dx.doi.org/10.1016/j.celrep.2016.08.087.Mouse embryonic stem cells are dynamic and heterogeneous. For example, rare cells cycle through a state characterized by decondensed chromatin and expression of transcripts, including the Zscan4 cluster and MERVL endogenous retrovirus, which are usually restricted to preimplantation embryos. Here, we further characterize the dynamics and consequences of this transient cell state. Single-cell transcriptomics identified the earliest upregulated transcripts as cells enter the MERVL/Zscan4 state. The MERVL/Zscan4 transcriptional network was also upregulated during induced pluripotent stem cell reprogramming. Genome-wide DNA methylation and chromatin analyses revealed global DNA hypomethylation accompanying increased chromatin accessibility. This transient DNA demethylation was driven by a loss of DNA methyltransferase proteins in the cells and occurred genome-wide. While methylation levels were restored once cells exit this state, genomic imprints remained hypomethylated, demonstrating a potential global and enduring influence of endogenous retroviral activation on the epigenome.EMBO Fellowship (ALTF938-2014) and Marie Sklodowska-Curie Individual FellowshipDFG grant WA1029 within the SFB1027BBSRC (grant BB/K010867/1)Wellcome Trust (grant 095645/Z/11/Z)EU EpiGeneSysBLUEPRINTThe authors thank all members of the W.R. laboratory for helpful discussions. We also thank Ferdinand von Meyenn and Mario Iurlaro for serum-2i transcriptome data, Simon Andrews for bioinformatics support, Simon Walker for imaging support, Nathalie Smerdon for high-throughput sequencing assistance, David Oxley for mass spectrometry, Rachael Walker for flow cytometry assistance, Ruslan Strogantsev for genomic imprinting discussions, Minoru Ko for the Zscan4c::EGFP plasmid, Samuel Pfaff for the MERVL::tdTomato plasmid, and Haruhiko Koseki for Dnmt1fl/fl ESCs. M.A.E.-M. is supported by an EMBO Fellowship (ALTF938-2014) and Marie Sklodowska-Curie Individual Fellowship. P.G. was supported by DFG grant WA1029 within the SFB1027. Research in W.R.’s lab is supported by the BBSRC (grant BB/ K010867/1), Wellcome Trust (grant 095645/Z/11/Z), EU EpiGeneSys, and BLUEPRINT