Driver, M. D. | bioRxiv Science

bioRxiv2024

The effect of dipeptide repeat proteins on FUS/TDP43-RNA condensation in C9orf72 ALS/FTD

Condensation of RNA binding proteins (RBPs) with RNA is essential for cellular function. The most common familial cause of the diseases ALS and FTD are C9orf72 repeat expansion disorders that produce dipeptide repeat proteins (DPRs). We explore the hypothesis that DPRs disrupt the native condensation behaviour of RBPs and RNA through molecular interactions resulting in toxicity. FUS and TDP43 are two RBPs known to be affected in ALS/FTD. We use our previously developed 1-bead-per-amino acid and a newly developed 3-bead-per-nucleic acid molecular dynamics model to explore ternary phase diagrams of FUS/TDP43-RNA-DPR systems. We show that the most toxic arginine containing DPRs (R-DPRs), can disrupt the RBP condensates through cation-{pi} interactions, and can strongly sequester RNA through electrostatic interactions. The native droplet morphologies are already modified at small additions of R-DPRs leading to non-native FUS/TDP43-encapsulated condensates with a marbled RNA/DPR core.

biophysics↗

bioRxiv2024

Selective phase separation of transcription factors is driven by orthogonal molecular grammar

Protein production is critically dependent on gene transcription rates, which are regulated by RNA polymerase and a large collection of transcription factors (TFs). Previous studies identified the formation of super enhancer regions where increased transcriptional activity is observed. This has been linked to phase separation, in which the differential condensation behaviour of separate TF families has been hypothesised to cause the selectivity in gene expression. The underlying molecular forces that are responsible for this selectivity, however, are unknown. Here, we conduct phase separation studies on six TFs (FUS, EWS, TAF15, SP1, SP2, and HNF1A) from three different TF families by carrying out residue-scale coarse-grained molecular dynamics simulations. Our exploration of ternary TF phase diagrams revealed four dominant sticker motifs and two orthogonal driving forces, consisting of hydrophobic (aromatic, aliphatic) interactions and electrostatic/cation-{pi} interactions. The contribution of these driving forces to the homotypic and heterotypic intermolecular strengths dictate the resultant condensate morphology. These results point to sequence-dependent orthogonal grammar as a generic mechanism responsible for selective transcriptional condensation in gene expression. Interestingly, our results also show how RNA polymerase is able to overcome this orthogonality to coalesce with TF condensate providing a framework in which co-condensation is the primary nuclear organisational principle that controls selective partitioning of RNAP to targeted genes for transcription.

biophysics↗