During this project I have performed parallel single-cell sequencing of nucleosome position (chromatin accessibility), DNAme and transcription (scNMT-seq) on a timeseries of mouse embryos spanning from pluripotency to the onset of lineage specification (E4.5 E5.5 E6.5 E7.5) to uncover their relationships. I found that epigenetic changes at promoters regulate the shutdown of the pluripotency program during development. Subsequent lineage differentiation was associated with epigenetic differences at enhancers. Notably, enhancers associated with the ectoderm are accessible and hypomethylated and therefore epigenetically primed in the early epiblast, prior to cell fate specification. Conversely, enhancers of the endoderm and mesoderm are epigenetically remodelled during specification when they become accessible and lose DNAme. Together, these results provide a molecular framework for the hierarchical emergence of the three germ layers. These results have been published in an international peer-reviewed journal and have been presented at international and local seminars.
Argelaguet, R.*, Clark, S.J.* Mohammed, H.*, Stapel, L.C.* Krueger, C., Kapourani, C-A., Imaz-Rosshandler, I., Lohoff, T., Ziang, Y., Hanna, C., Smallwood, S., Ibarra-Soria, X., Buettner, F., Sanguinetti, G., Xie, W., Krueger, F., Gottgens, B., Rugg-Gunn, P., Kelsey, G., Dean, W., Nichols, J., Stegle, O., Marioni, J.C. Reik, W. Multi-omics profiling of mouse gastrulation at single cell resolution. Nature. 576, 487-491 (2019).
* authors contributed equally
Following up on these results I have identified lineage-specific epigenetic profiles and have developed CRISPR/dCas9-based genome editing tools to interrogate their function. In parallel, I have characterised an in vitro model of early mouse development at the single cell level and compared it to the mouse embryo to determine its use for high-throughput functional screening. I am currently writing up a paper on the characterisation of the in vitro model and envision an additional paper using the genome editing tools in the future. Furthermore, I have presented these results at international and local seminars. I have also been involved in a public engagement project to gather the public’s opinion on genome editing tools and their use. My participation in this project won me the public engagement award from my institute.
