Studying disease-causing polymorphic transposable element insertions using nanopore sequencing

Abstract X-Linked Dystonia-Parkinsonism (XDP) is a mendelian neurodegenerative disorder. Recently, a polymorphic transposable element (TE) insertion in the 32nd intron of the TAF1 gene has been identified as the genetic factor responsible for this disease. The XDP-TE is associated with TAF1 mis-regulation, but the mechanisms behind this phenomenon remain elusive. We hypothesize that repressive epigenetic marks on the XDP-TE are key players in this process. Thus, here we aim to dissect the molecular intricacies that keep the XDP-TE at bay and identify how it triggers aberrant TAF1 expression, ultimately leading to XDP. Leveraging advanced sequencing techniques and XDP patient-derived iPSCs and neural progenitor cells, we employed CUT&RUN and nanopore sequencing to identify epigenetic marks on the XDP-TE. To illuminate what factors establish these marks, and their effect on gene expression, we did CRISPR inhibition of various candidate genes coupled with RNA sequencing. We demonstrate that ZNF91 — a TE-binding KRAB-zinc-finger protein — establishes H3K9me3 and DNA methylation over the XDP-TE in a cell type specific manner in patient-derived cells. Moreover, removal of DNA methylation, or both H3K9me3 and DNA methylation, severely aggravates the XDP molecular phenotype, causing a reduced TAF1 expression and increased intron retention. Biography Vivien Horvath completed her PhD in Biomedicine at Pompeu Fabra University, Barcelona. Currently, she is a senior postdoctoral researcher at Lund University/Lund Stem Cell Center. Her research focuses on the non-coding genome, particularly transposable elements, in age-related neurodegenerative disorders. Vivien investigates how repetitive sequences and their epigenetic regulators, like DNA methylation, affect gene expression and disease progression, currently focusing on X-Linked Dystonia-Parkinsonism. In her research she uses nanopore sequencing to identify methylation patterns over transposable elements and to discover previously hidden non-coding insertions.