Specific RNA interactions promote TDP‐43 multivalent phase separation and maintain liquid properties

• Published in: EMBO reports Vol. 22; no. 12; pp. e53632 - n/a
• Main Authors: Grese, Zachary R, Bastos, Alliny CS, Mamede, Lohany D, French, Rachel L, Miller, Timothy M, Ayala, Yuna M
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 06.12.2021; John Wiley and Sons Inc
• Subjects: Amyotrophic lateral sclerosis; Amyotrophic Lateral Sclerosis - genetics; Amyotrophic Lateral Sclerosis - metabolism; Animals; Binding sites; Condensates; Condensation; Dementia disorders; DNA-Binding Proteins - metabolism; Domains; Frontotemporal dementia; Frontotemporal Dementia - genetics; Gene expression; Gene sequencing; Homeostasis; Liquid phases; Liquidity; liquid‐liquid phase separation; Mutation; Neurodegenerative diseases; Nucleotide sequence; Pathogenesis; Phase separation; Protein interaction; Proteins; Ribonucleic acid; ribonucleoprotein (RNP) granules; RNA; RNA - genetics; RNA-Binding Proteins - genetics; RNA‐binding protein; TDP‐43; ribonucleoprotein (RNP) granules; RNA-binding protein; liquid-liquid phase separation; amyotrophic lateral sclerosis; TDP-43
• ISSN: 1469-221X; 1469-3178
• DOI: 10.15252/embr.202153632

TDP‐43 is an RNA‐binding protein that forms ribonucleoprotein condensates via liquid‐liquid phase separation (LLPS) and regulates gene expression through specific RNA interactions. Loss of TDP‐43 protein homeostasis and dysfunction are tied to neurodegenerative disorders, mainly amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. Alterations of TDP‐43 LLPS properties may be linked to protein aggregation. However, the mechanisms regulating TDP‐43 LLPS are ill‐defined, particularly how TDP‐43 association with specific RNA targets regulates TDP‐43 condensation remains unclear. We show that RNA binding strongly promotes TDP‐43 LLPS through sequence‐specific interactions. RNA‐driven condensation increases with the number of adjacent TDP‐43‐binding sites and is also mediated by multivalent interactions involving the amino and carboxy‐terminal TDP‐43 domains. The physiological relevance of RNA‐driven TDP‐43 condensation is supported by similar observations in mammalian cellular lysate. Importantly, we find that TDP‐43‐RNA association maintains liquid‐like properties of the condensates, which are disrupted in the presence of ALS‐linked TDP‐43 mutations. Altogether, RNA binding plays a central role in modulating TDP‐43 condensation while maintaining protein solubility, and defects in this RNA‐mediated activity may underpin TDP‐43‐associated pathogenesis. SYNOPSIS Liquid‐liquid phase separation of the RNA‐binding protein TDP‐43 is regulated by specific RNA sequences. In addition to modulating phase separation, RNA is crucial for maintaining the liquid state of TDP‐43 condensates. GU‐repeat RNA specifically promotes TDP‐43 liquid‐liquid phase separation and this increases with multiple binding sites. Binding of specific RNA sequences to the TDP‐43 RNA‐binding domains maintains liquidity of TDP‐43 condensates. Both the N‐ and C‐terminal TDP‐43 domains are required for RNA‐driven liquid‐liquid phase separation, constituting a multivalent network. The liquid properties of RNA‐driven TDP‐43 condensates are disrupted in a subset of ALS‐linked TDP‐43 mutations. Liquid‐liquid phase separation of the RNA‐binding protein TDP‐43 is regulated by specific RNA sequences. In addition to modulating phase separation, RNA is crucial for maintaining the liquid state of TDP‐43 condensates.