Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration [Hi-C]

Persistent DNA double-strand breaks (DSBs) in neurons are an early pathological hallmark of neurodegenerative diseases including Alzheimer's Disease (AD), with the potential to disrupt genome integrity. We used single-nucleus RNA-seq in human post-mortem prefrontal cortex samples and found that excitatory neurons in AD were enriched for somatic mosaic gene fusions. Gene fusions were particularly enriched in excitatory neurons with DNA damage repair and senescence gene signatures. In addition, somatic genome structural variations and gene fusions were enriched in neurons burdened with DSBs in the CK-p25 mouse model of neurodegeneration. Neurons enriched for DSBs also had elevated levels of cohesin along with progressive multiscale disruption of the 3D genome organization aligned with transcriptional changes in synaptic, neuronal development, and histone genes. Overall, this study demonstrates the disruption of genome stability and the 3D genome organization by DSBs in neurons as pathological steps in the progression of neurodegenerative diseases. Overall design: In situ Hi-C was performed as previously described in Rao et al., 2014. 80-120k FANS isolated nuclei were used for CK-p25. Nuclei were permeabilized. DNA was digested with 100 units of MboI, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ~400 bp, at which point ligation junctions were pulled down with streptavidin beads and prepped for Illumina sequencing. Illumina libraries were sequenced in 38 bp paired-end mode. Three replicates were performed, where each replicate was a pool of 3 CK-p25 mice forebrains. P301S Tau mice and primary neuronal culture Hi-C were performed using 120-170k FANS isolated nuclei with the Dovetail Hi-C kit (SKU: 21004) according to the manufacturer's instructions. Hi-C was analyzed using the HOMER Hi-C analysis pipeline (http://homer.ucsd.edu/homer/interactions2/index.html) and Juicer.