PhD & Postdoc

Charlotte Dubois

Epigenetics · Université Paris-Saclay

Charlotte Dubois maps the epigenetic landscape of 5-hydroxymethylcytosine (5hmC) — an oxidative derivative of 5-methylcytosine that is especially enriched in brain tissue — across the stepwise differentiation trajectory from human induced pluripotent stem cells to mature cortical neurons. At Université Paris-Saclay's I2BC institute, supervised by Prof. Edith Moreau, she exploits Oxford Nanopore long-read sequencing's unique ability to directly detect 5hmC modifications without chemical conversion, enabling haplotype-resolved epigenetic profiling at single-molecule resolution for the first time in human neurogenesis. Her analysis of 14 differentiation time-points has revealed a wave of 5hmC accumulation at enhancers of genes encoding synaptic scaffold proteins between days 21 and 35 of differentiation — a previously unrecognised epigenetic checkpoint whose disruption she links to improper dendritic morphology in neurodevelopmental disorder iPSC lines. Charlotte has developed a Snakemake bioinformatics pipeline for joint calling of 5mC, 5hmC, and chromatin accessibility, which she has deposited as open-source software used by three other labs. Her completed industry internship at Illumina France and active applications to genomics CRO positions signal her readiness to translate this expertise.

Thesis Topic

Profiling 5-Hydroxymethylcytosine Dynamics in Human Neural Progenitor Differentiation Using Nanopore Long-Read Sequencing

Transition Signals