Project description

The nucleus is organized into membraneless, yet functionally distinct compartments. We now know that many nuclear compartments are organized by an array of non-coding RNAs implicated in diverse gene-regulatory processes including embryonic development, cell type-specific phenotypes and cancer. These RNAs acts as hubs/scaffolds for effector proteins forming complex biomolecular assemblies.

Intrinsically disordered regions (IDRs) have recently emerged as key players in the formation of biomolecular assemblies by driving weak, multivalent protein-protein interactions. We have previously identified that the IDRs of the transcriptional corepressor SPEN are essential for protein concentration within large ribonucleoprotein complexes. This supramolecular assembly is essential for gene regulation. However, how IDR interactions form, their selectivity and contribution to multivalency or how interactions are perturbed in disease remains unclear.

This project will employ a multidisciplinary approach across scales to elucidate the function of these assemblies, their molecular organization, dynamic protein-protein and RNA-protein interactions. We will integrate state-of-the-art methods in stem cell biology and genome editing with super-resolution microscopy, biophysical and structural methods. We will use in silico structure predictions to determine the IDR-containing regions that are critical for self-interaction and assembly. We will express minimal RNA-protein assemblies and conduct structural studies by cryo-EM and NMR. We will next perturb these interactions, in vitro through peptide inhibitors which will guide in vivo genetic perturbations followed by downstream analyses within cells by super-resolution microscopy and quantitative image analyses.

Relevant publications

Markaki Y et al., Cell. 2021. doi: 10.1016/j.cell.2021.10.022

Kraus F et al., Markaki Y. Nat Protoc. 2017. doi: 10.1038/nprot.2017.020

Ariyoshi A & Schwabe JWR, Genes Dev. 2003. doi: 10.1101/gad.266203

For more information about the project please contact: yolanda.markaki@le.ac.uk