HypoSUMOylation in embryonic stem cells generates head-and-trunk embryo-like structure [Methyl-seq]

Recent advances in synthetic mammalian embryo models have opened new avenues to understand the complex events controlling lineage decisions and morphogenetic processes occurring during peri-implantation and early organogenesis. Two main strategies have been developed to build embryo-like structures (ELS): by assembling extraembryonic and embryonic stem cells (ESCs) or by subjecting ESCs to various morphogens. Here, we show that mouse ESCs solely exposed to chemical inhibition of SUMOylation, a posttranslational modification which acts as a general barrier to cell-fate transitions, generates early ELSs comprising both anterior neural and trunk-associated regions. HypoSUMOylated ESCs give rise to adherent spheroids which, once in suspension, self-organize into gastrulating structures containing cell types spatially and functionally related to embryonic and extraembryonic compartments. Alternatively, spheroids cultured in an optimized droplet-microfluidic device form elongated structures characterized by a multi-axial organization reminiscent of natural embryo morphogenesis. Single-cell RNA-sequencing further revealed a variety of cellular lineages including properly positioned anterior neuronal cell types, Schwann cell precursors and paraxial mesoderm segmented into somite-like structures. Mechanistically, transient SUMOylation suppression gradually increases DNA methylation genome-wide and repressive marks deposition at Nanog, enhancing ESC plasticity. Our approach provides a proof of principle for a potential new strategy to study early embryogenesis by targeting reprogramming roadblocks to shape multicellular architecture. Overall design: Examination of the level of methylation in ES cells treated or not with the SUMO inhibitor, in triplicate, using Illumina Illumina Hiseq 4000.