A hexanucleotide repeat expansion (HRE), (GGGGCC)n, in C9orf72 is the most common genetic cause of the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here we identify a molecular mechanism by which structural polymorphism of the HRE leads to ALS/FTD pathology and defects. The HRE forms DNA and RNA G-quadruplexes with distinct structures and promotes RNA•DNA hybrids (R-loops). The structural polymorphism causes a repeat-length-dependent accumulation of transcripts aborted in the HRE region. These transcribed repeats bind to ribonucleoproteins in a conformation-dependent manner. Specifically, nucleolin, an essential nucleolar protein, preferentially binds the HRE G-quadruplex, and patient cells show evidence of nucleolar stress. Our results demonstrate that distinct C9orf72 HRE structural polymorphism at both DNA and RNA levels initiates molecular cascades leading to ALS/FTD pathologies, and provide the basis for a mechanistic model for repeat-associated neurodegenerative diseases. Structurally polymorphic C9orf72 hexanucleotide repeats cause an impairment in transcriptional processivity and lead to accumulation of truncated repeat-containing transcripts that bind to specific ribonucleoproteins, such as nucleolin, in a conformation-dependent manner resulting in nucleolar stress and C9orf72-linked pathology in amyotrophic lateral sclerosis and frontotemporal dementia. Repeat expansions — mutations in which extra copies of tandemly repeated DNA sequence are generated — underlie more than 40 genetic diseases, which typically lead to neurological and neuromuscular problems. The C9orf72 hexanucleotide repeat expansion has been identified as a cause for both amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Normal C9orf72 contains up to 25 repeats, whereas those in afflicted individuals can have thousands. This study suggests that a gain in RNA toxicity underlies C9orf72-linked pathology in ALS/FTD. Transcribed C9orf72 hexanucleotide repeats are shown to bind to specific ribonucleoproteins, such as nucleolin, in a conformation-dependent manner; as a result nucleolin is mislocalized and functionally impaired, leading to nucleolar stress.

C9orf72 nucleotide repeat structures initiate molecular cascades of disease