Periodic Reporting for period 1 - EpiNoise (The role of epigenetic heterogeneity in cell fate decisions)
Okres sprawozdawczy: 2019-09-01 do 2021-08-31
Early mouse development is characterised by extensive remodelling of chromatin accessibility and DNA methylation (DNAme). These changes are essential for the establishment of the pluripotent state and for subsequent cell fate decisions. Mutants that fail to correctly remodel their accessibility or methylation landscapes display differentiation defects and often die before birth. But while it is clear that the correct establishment of chromatin accessibility and DNAme is essential for cell fate specification during development, the dynamic relationship between these two layers of regulation and their effects on gene expression over the course of development are largely unknown. This results from the fact that bulk methods for transcriptome, methylome and accessibility analysis provide population data and obscure relevant cellular heterogeneity which is abundant in the early embryo. The aim of this project was to uncover the roles of chromatin accessibility and DNA methylation in gene regulation and in cell fate specification during mouse development. This work may open up new avenues of applied research in amongst others regenerative medicine where the aim is to tightly control cell fate.
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.
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.
This project has contributed to the first single-cell multi-omics map of early mouse development and has identified an epigenetic bases for the hierarchical emergence of the three germ layers. It has also resulted in the first characterisation of individual gastrulation organoids at the single cell and epigenetic level. I will use the CRISPR/dCas9 tools that I developed for the project to perform the first interrogation of the function of lineage-specific regulatory elements in a multi-lineage system. Together, this work has not only will generated new insights in the fundamental biological process of cell fate specification, but may also open up new avenues of applied research in amongst others regenerative medicine where the aim is to tightly control cell fate. The expertise that I gained while working on this project enabled me to serve as a scientific expert on genome editing in a public engagement project. Here, I shaped and led discussion on genome editing with the general public to increase their awareness of genome editing tools and collect their opinion on the use of these tools in society.