Mini-heterochromatin domains constrain the cis-regulatory impact of SVA transposons in human brain development and disease

SVA retrotransposons remain active in humans and contribute to individual genetic variation. Polymorphic SVA alleles harbor gene-regulatory potential and can cause genetic disease. However, how SVA insertions are controlled and functionally impact human disease is unknown. Here, we dissect the epigenetic regulation and influence of SVAs in cellular models of X-linked dystonia-parkinsonism (XDP), a neurodegenerative disorder caused by an SVA insertion at the TAF1 locus. We demonstrate that the KRAB zinc finger protein ZNF91 establishes H3K9me3 and DNA methylation over SVAs, including polymorphic alleles, in human neural progenitor cells. The resulting mini-heterochromatin domains attenuate the cis-regulatory impact of SVAs. This is critical for XDP pathology; removal of local heterochromatin severely aggravates the XDP molecular phenotype, resulting in increased TAF1 intron retention and reduced expression. Our results provide unique mechanistic insights into how human polymorphic transposon insertions are recognized, and their regulatory impact constrained by an innate epigenetic defense system. In this study we used XDP patient and unaffected individual (Control) derived neural progenitor cells (NPCs) and induced pluripotent stem cell (iPSCs). RNA sequencing data with TRIM28 CRISPRi, ZNF91 CRISPRi, DNMT1 CRISPR cut, ZNF91&DNMT1 CRISPRi samples is included. In all the CRISPR experiments LacZ was used as a non-targeting control. In most cases four replicates were generated for both CRISPRi and CRISPRi control (LacZ). Except for XNES1_DNMT1_LZ, CNES1_DNMT1_ZF91_KD, CNES1_DNMT1_LZ, CNES1_DNMT1_KO and XNES1_ZF91lacZ where we have three replicates. CUT&RUN analysis was done in both ZNF91-CRISPRi and TRIM28-CRISPRi, including CRISPRi-Ctrl (lacZ). Data is provided for one replicate per condition. *************************************************************** Submitter states that missing raw files are due to patient privacy concerns. ***************************************************************