CRISPRi-targeted raw RNA-seq data in iPSC-derived neurons. In this study, we performed RNA-sequencing to test transcriptomic changes of CRISPRi-targetd MIR family TE (chr11: 47608036-47608220) in iPSC-derived neurons.

Despite its broad role in human disease, transposable element (TE) dysregulation of quantitative trait loci (QTL) has not been well-characterized in brain aging or Alzheimer’s disease (AD). Here, we leveraged large-scale human RNA-sequencing (RNA-seq), whole-genome sequencing (WGS), and QTL data (xQTL) from three brain biobanks to comprehensively characterize dysregulation of TE expression dysregulation across diverse pathobiology of AD, including tau, amyloid-β, APOE genotypes, and sex. Joint-analysis of WGS and RNA-seq data identified 26,188 genome-wide significant TE expression QTLs (teQTLs) that were associated with expression of 1,453 locus-TEs in human aging brains. Subsequent colocalization analysis of teQTLs with GWAS loci from 278,950 AD cases and 1,780,303 controls further identified likely causal genes for AD (FDFT1 and C1QTNF4) that were regulated by brain teQTLs. In addition, an elevated intergenic TE from the MIR family (chr11: 47608036-47608220) was found to suppress expression of the anti-inflammation related gene C1QTNF4 (its nearest gene) via long-range enhancer-promoter chromatin interaction in neurons. Lastly, CRISPR interference (CRISPRi) assays identified a neuron-specific suppressive role of the activated MIR family TE on expression of anti-inflammatory genes in human induced pluripotent stem cells (iPSC)-derived neurons, including C1QTNF4. In conclusion, we demonstrate that TEs play crucial functional roles in gene regulation in the aging human brain and that analysis of teQTLs identifies AD risk genes and advances our understanding of brain aging and AD. This approach could aid investigation of other complex brain disorders as well.