Transcriptome-wide RNA binding analysis of C9orf72 poly(PR) dipeptides

• Published in: Life science alliance Vol. 6; no. 9; p. e202201824
• Main Authors: Balendra, Rubika, Ruiz de los Mozos, Igor, Odeh, Hana M, Glaria, Idoia, Milioto, Carmelo, Wilson, Katherine M, Ule, Agnieszka M, Hallegger, Martina, Masino, Laura, Martin, Stephen, Patani, Rickie, Shorter, James, Ule, Jernej, Isaacs, Adrian M
• Format: Journal Article
• Language: English
• Published: United States Life Science Alliance LLC 01.09.2023
• Subjects: C9orf72 Protein - genetics; Dipeptides; Gene Expression Profiling; Humans; Poly A; RNA - genetics; Transcriptome - genetics
• ISSN: 2575-1077; 2575-1077
• DOI: 10.26508/lsa.202201824

An intronic GGGGCC repeat expansion in C9orf72 is a common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. The repeats are transcribed in both sense and antisense directions to generate distinct dipeptide repeat proteins, of which poly(GA), poly(GR), and poly(PR) have been implicated in contributing to neurodegeneration. Poly(PR) binding to RNA may contribute to toxicity, but analysis of poly(PR)-RNA binding on a transcriptome-wide scale has not yet been carried out. We therefore performed crosslinking and immunoprecipitation (CLIP) analysis in human cells to identify the RNA binding sites of poly(PR). We found that poly(PR) binds to nearly 600 RNAs, with the sequence GAAGA enriched at the binding sites. In vitro experiments showed that poly(GAAGA) RNA binds poly(PR) with higher affinity than control RNA and induces the phase separation of poly(PR) into condensates. These data indicate that poly(PR) preferentially binds to poly(GAAGA)-containing RNAs, which may have physiological consequences.