PIF2025 - The form and function of non-canonical DNA methylation during neural development - (PID2024-162911NB-I00)

Non-canonical DNA methylation (mCH) is emerging as a critical yet poorly understood epigenetic mark. In contrast to the well-characterised role of mCG, the abundance, developmental dynamics, and biological function of mCH remain enigmatic. In mammals, mCH accumulates in neural tissues, oocytes, and embryonic stem cells, and its dysregulation has been linked to cancer, cardiovascular disease, and neurodevelopmental disorders such as Rett syndrome (RTT) and Tatton-Brown–Rahman syndrome (TBRS). However, the causal mechanisms by which mCH contributes to normal development and disease remain unresolved. This proposal aims to uncover the in vivo function of mCH using cutting-edge genomics and the zebrafish as a powerful vertebrate model. We will combine CRISPR-based genome engineering, long-read sequencing, and quantitative multi-omics to establish the first systematic framework for studying mCH writing and reading in vivo. Our objectives are: (O1) to generate robust zebrafish models deficient in mCH writing and reading; (O2) to quantitatively define the developmental, cellular, and transcriptomic requirements for mCH; and (O3) to identify druggable pathways and molecular vulnerabilities arising from impaired mCH function. Together, these studies will deliver fundamental insight into mCH biology and uncover new mechanistic links between epigenomic dysregulation and human disease.