The Influence of AHDC1 on the Output of Transcriptional Programs

Xia-Gibbs syndrome (XGS) is a rare neurodevelopmental disorder caused by pathogenic variants in AHDC1. However, the cellular and molecular functions of AHDC1 remain poorly defined. In this thesis, I investigated AHDC1 function by combining RNA silencing in a controlled steady-state neuronal-like model with reanalysis of AHDC1-mutant differentiation datasets. In SH-SY5Y cells, AHDC1 silencing activated ribosome-related transcriptional programs, increased MYCN expression, and was associated with a global increase in protein abundance. Chromatin analysis using the T2T-CHM13 human reference genome showed no evidence of HP1 redistribution after AHDC1 silencing across canonical constitutive heterochromatin. Instead, the strongest differences were detected in the Input signal, indicating that AHDC1 silencing affects chromatin-associated signals without causing a change in HP1 targeting. Increased signals over ribosomal protein genes and rDNA clusters further pointed to ribosome-linked chromatin compartments as sensitive to AHDC1 silencing. To assess whether the same pattern emerges during differentiation, I reanalyzed a published AHDC1-mutant differentiation dataset. Reanalysis of ATAC-seq at day 7 after induction of differentiation revealed an increase in chromatin accessibility at rDNA clusters in mutant cell lines. Crucially, single-cell RNA sequencing demonstrated an altered lineage composition and a temporal uncoupling of biosynthetic programs: early progenitor stages exhibited MYC upregulation without a coordinated induction of ribosomal genes, whereas later committed stages displayed lineage-dependent persistence of MYC and increase in ribosome-related programs. Together, these findings support a model in which AHDC1 influences biosynthetic transcriptional programs. Rather than acting as a canonical locus-specific repressor, AHDC1 appears to influence broader genome regulation, with impact at ribosome-linked and nucleolus-associated compartments.