Thesis Defense Maria Florescu: “Cutting edge tools to reveal lineages and epigenetic modifications in single cells”

Every cell in the human body has a past, present and future. During each of these phases, cells experience events that influence their biomolecules, such as their DNA. For example, a cell’s history can be documented in the form of small changes in its DNA. The cell passes these changes on to all its offspring. In order to predict the future of a certain cell, it is helpful to look at the cell’s past and present. Researchers use so-called sequencing technology to measure biomolecules.

Barcode

CRISPR-Cas9 is a cutting-edge technology that can change biomolecules, including DNA. It cuts the DNA in two, which damages the surrounding nucleotides – DNA’s building blocks. When the DNA repairs itself, it removes the damaged nucleotides and replaces them with new ones. This process leaves a scar or ‘barcode’ in the DNA. The cell passes this barcode on to all its offspring. During her PhD, Florescu together with her colleagues used CRISPR-Cas9 to introduce such a barcode in a large number of cells in zebrafish embryos. Once the embryos grew into adult zebrafish, she and her colleagues scanned the cells of various organs for this barcode. This way, they traced the descent of cells: their history.

Cell identity

Besides researching the history of cells, it is also valuable to study their current identity. To that end, Florescu and her colleagues introduce a new technology called ScarTrace. This technique combines the measurement of barcodes left by CRISPR-Cas9 with sequencing technology. The researchers introduced barcodes in a large number of cells in the embryos of zebrafish. With ScarTrace, they were among the first ones to study both the history and current identity of various cells using only one technique.

Histone modifications

DNA is wrapped around histone complexes – groups of proteins that order DNA. The ways in which DNA is wrapped around these complexes determines which genes are active and which are not. But the wrapping of DNA around histone complexes can also change. When this happens, we speak of histone modifications. Researchers from the Van Oudenaarden group previously developed a technology – scChIC-seq – that allows measurement of one such histone modification per individual cell. During her PhD, Florescu and colleagues expanded the capacity of this technology – calling the improved version scChIX – and made it possible to measure not one but two histone modifications per cell.

Embryonic research

With her thesis, Florescu introduces two valuable techniques for embryonic research, and elaborates on their challenges and opportunities for further studies.