The interplay of RNA structure and protein disorder in protein-RNA condensates

Flora C Y Lee^1,2, Anob M Chakrabarti¹, Miha Modic^1,2,3, Klara Kuret^1,3, Martina Hallegger^1,2, Jernej Ule^1,2,3

¹ The Francis Crick Institute, 1 Midland Road, London NW1 1AT

² UK Dementia Research Institute at King's College London, London, UK.

³ National Institute of Chemistry, Hajdrihova ulica 19, 1000 Ljubljana, Slovenia

In recent years, it has become clear that intrinsically disordered regions (IDRs) of RBPs, and the structure of RNAs, often contribute to the condensation of RNPs. To understand the transcriptomic features of such RNP condensates, we’ve used an improved individual nucleotide resolution CLIP protocol (iiCLIP), which produces highly sensitive and specific data, and thus enables quantitative comparisons of interactions across conditions (Lee et al., 2021).

This showed how the IDR-dependent condensation properties of TDP-43 interplay with multivalent RNA motifs to specify its RNA binding and regulatory repertoire (Hallegger et al., 2021), and how post-translational modification in the IDR of LIN28A similarly modify its multivalent RNA assembly in early development (Modic et al, in preparation). Moreover, we developed software for discovery and visualisation of RNA binding motifs that uncovered common importance of binding regions composed of multivalent motifs (Kuret et al, 2021).

Finally, we used hybrid iCLIP (hiCLIP) to characterise the RNA structures mediating the assembly of Staufen RNPs across mammalian brain development, which demonstrated the roles of long-range RNA duplexes in the compaction of long 3’UTRs.

I will present how these studies taken together are helping us towards a unified view of the characteristics of multivalent RNA regions, RNA structures and IDRs in RBPs that contribute to formation and functions of RNP condensates.

References:

Hallegger, M., Chakrabarti, A.M., Lee, F.C.Y., Lee, B.L., Amalietti, A.G., Odeh, H.M., Copley, K.E., Rubien, J.D., Portz, B., Kuret, K., et al. (2021). TDP-43 condensation properties specify its RNA-binding and regulatory repertoire. Cell 184, 4680–4696.e22.

Kuret, K., Amalietti, A.G., and Ule, J. (2021). Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP. bioRxiv.

Lee, F.C.Y., Chakrabarti, A.M., Hänel, H., Monzón-Casanova, E., Hallegger, M., Militti, C., Capraro, F., Sadée, C., Toolan-Kerr, P., Wilkins, O., et al. (2021). An improved iCLIP protocol. bioRxiv