OTX2 controls chromatin accessibility to direct somatic versus germline differentiation [CUT&Run]

The choice between somatic and germline fates is essential for species survival. This choice occurs in embryonic epiblast cells, as these cells are competent for both somatic and germline differentiation. Transcription factors (TFs) play a central role in this process by binding to specific chromatin loci to modulate gene expression and determine cell identity. The TF OTX2 regulates the choice between somatic and germline fates, as Otx2-null epiblast-like cells (EpiLCs) form primordial germ cell-like cells (PGCLCs) with enhanced efficiency. However, the mechanisms by which OTX2 achieves this function are not fully characterized. Here we show that OTX2 controls chromatin accessibility to enable somatic differentiation. By performing CUT&RUN for OTX2 and ATAC-seq in wild-type and Otx2-null embryonic stem cells and EpiLCs, we identified regions where OTX2 binding opens chromatin. Enforced OTX2 expression maintains accessibility at these regions and induces opening of 4,000 additional somatic-associated regions in the presence of PGC-inducing cytokines. Once cells have acquired germline identity, the 4,000 additional somatic associated regions do not respond to OTX2 and remain closed. Our results indicate that OTX2 works in cells with dual competence for both somatic and germline differentiation to increase accessibility of somatic regulatory regions and induce the somatic fate at the expense of the germline. Overall design: Chromatin accessiblity profiling by ATAC-seq of WT and OTX2-/- ESCs, EpiLCs, PGCLC or somatic cell aggregates. Chromatin profiling of OTX2-/- EpiLCs and aggregates after enforced expression of OTX2 using a tamoxifen-induced system.