031-23 – SVA retrotransposons as novel regulatory domains in key neurodegenerative disease related loci

SINE-VNTR-Alu (SVA) retrotransposons are transposable elements within the human genome, a subset of which are capable of propagation and thereby drive genomic mutation and diversity. SVAs have been directly linked with at least 24 diseases including X-linked dystonia Parkinsonism (XDP) with increasing evidence of associations to other neurological disorders such as autism, schizophrenia, Parkinson’s disease and amyotrophic lateral sclerosis. They can disrupt normal gene regulation via a variety of mechanisms, however the exact mechanisms behind these disease modifying effects remains unclear. We have undertaken an array of molecular and genomic studies to delineate the signalling pathways that regulate their function. I will present data that multiple transcription factors, including the SVA specific KRAB-zinc finger protein ZNF91 and its associated co-factor KAP1, as important factors that bind to SVA sequences and may contribute to the previously observed diseases. Using both in vitro and in vivo protocols, including Chromatin Immuno-precipitation (ChIP) and CRISPR approaches in established cell line models, we demonstrate that epigenetic regulation is one mechanism involved in SVA mediated regulation of gene expression. When comparing endogenous and knockout SVA cell lines for a specific SVA insertion at a model locus (LRIG2), we observed a significant reduction in the binding of KAP1 which correlated with a previously observed increase in expression of LRIG2 and reduction in DNA methylation in the promoter as measured by qPCR and bisulphite pyrosequencing, respectively. KAP1 is a key regulator across the human genome and acts as a scaffold to recruit epigenetic modifiers such as histone de-acetylases, histone methyl-transferases and DNA methyl-transferases. We hypothesise that SVAs can act as regulatory domains through epigenetic manipulation via the actions of ZNF91 and KAP1, and that these mechanisms would be disrupted in neurodegenerative diseases.