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

Rubika Balendra; Igor Ruiz de Los Mozos; Hana M Odeh; Idoia Glaria; Carmelo Milioto; Katherine M Wilson; Agnieszka M Ule; Martina Hallegger; Laura Masino; Stephen Martin; Rickie Patani; James Shorter; Jernej Ule; Adrian M Isaacs

doi:10.26508/lsa.202201824

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

Life Sci Alliance. 2023 Jul 12;6(9):e202201824. doi: 10.26508/lsa.202201824. Print 2023 Sep.

Authors

Rubika Balendra^{1

2}, Igor Ruiz de Los Mozos^{3

4

5}, Hana M Odeh⁶, Idoia Glaria^{1

2

7}, Carmelo Milioto^{1

2}, Katherine M Wilson^{1

2}, Agnieszka M Ule⁵, Martina Hallegger³, Laura Masino⁸, Stephen Martin⁸, Rickie Patani^{3

5}, James Shorter⁶, Jernej Ule^{9

5

10}, Adrian M Isaacs^{11

2}

Affiliations

¹ UK Dementia Research Institute at UCL, London, UK.
² Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK.
³ The Francis Crick Institute, London, UK.
⁴ Department of Personalized Medicine, NASERTIC, Government of Navarra, Pamplona, Spain.
⁵ Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK.
⁶ Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
⁷ Research Support Service, Institute of Agrobiotechnology, CSIC-Government of Navarra, Mutilva, Spain.
⁸ Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK.
⁹ The Francis Crick Institute, London, UK jernej.ule@kcl.ac.uk.
¹⁰ UK Dementia Research Institute at King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK.
¹¹ UK Dementia Research Institute at UCL, London, UK a.isaacs@ucl.ac.uk.

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

C9orf72 Protein / genetics
Dipeptides
Gene Expression Profiling*
Humans
Poly A
RNA / genetics
Transcriptome* / genetics

Substances

C9orf72 Protein
Poly A
Dipeptides
RNA
C9orf72 protein, human

Abstract

Publication types

MeSH terms

Substances

Grants and funding