Transcription and DNA Replication Shapes DNA Break Dynamics in Long Neuronal Genes

Neural progenitor cells undergo tens of thousands of cell divisions to generate the 80 billion neurons in a human brain. These fast-dividing neural stem and progenitor cells rapidly incorporate somatic genome alteration. In neural stem and progenitor cells, genes encode proteins that control neuron connectivity and are hotspots for recurrent DNA break clusters (RDC). Concurrently, genes containing DNA break hotspots are genetically disrupted in patients with neuropsychiatric disorders and specific cancers. In addition, one-third of RDC-gene co-localize with copy number variations identified in the human frontal cortex, suggesting RDC may contribute to "programmed" CNV in the developing neural stem and progenitor cells. Yet, why genes associated with neuropsychiatric disorders are vulnerable to DNA breaks and copy number changes is not fully understood.We found that transcription and DNA replication dynamic determined the "programmed" DNA breaks. Long replication forks that are heavily transcribed favor RDCs formation. RDCs are DNA double-strand breaks at stalled or reprogrammed replication forks. Over 50% RDCs contain one pair of convergent replication forks. In these RDCs, the centromeric and telomeric DSB density gap behaves similarly to "twin peak" mitotic DNA synthesis and double fork failure.Lastly, R-loop is considered the major contributor to the head-on transcription-replication collision. However, most DNA break hotspots are in the R-loop desert. Nevertheless, head-on collision contributes 40% of DNA breaks higher than their co-direction counterpart. Our findings suggest R-loop-independent mechanisms in advancing convergent clash between DNA replication and transcription in the neuronal genes.