Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are two neurodegenerative diseases that share genetic and neuropathological features. The most common genetic cause of both ALS and FTD is a GGGGCC repeat expansion in the C9orf72 gene. How C9orf72 mutations contribute to neurodegeneration is not fully understood. To study the cellular mechanisms driving neurodegeneration, we developed a platform to interrogate the chromatin accessibility landscape and transcriptional program within neurons in response to pathogenic protein accumulation. We provide evidence that neurons expressing the dipeptide repeat protein poly(proline-arginine), translated from the C9orf72 hexanucleotide repeat expansion, activate a highly specific transcriptional program, exemplified by a single transcription factor, p53. Ablating p53 in mice completely rescued neurons from cell death and axonal degeneration and markedly increased survival in a C9orf72 mouse model. Furthermore, p53 reduction was sufficient to rescue C9orf72 ALS/FTD patient iPSC-derived motor neurons from DNA damage and mitigate neurodegeneration in a C9orf72 fly model. Mechanistically, we show that p53 is stabilized, binds to DNA and activates a downstream transcriptional program, including Puma, which drives neurodegeneration. Finally, integrating human genetics data with protein interaction networks reveals p53 as a central hub gene within a functional protein interaction network specific to ALS but not several other neurodegenerative diseases. These data demonstrate a neurodegenerative mechanism dynamically regulated through transcription factor binding events controlling gene expression programs and provide a framework to apply chromatin accessibility and transcription program profiles to neurodegeneration.