Sequence Determinants of mRNA Fate in Neuronal Differentiation
Supervisors: Prof Grzegorz Kudla and Dr Marina Chekulaeva
Codon usage bias, the preference for certain synonymous codons, is one of the strongest known predictors of protein abundance, mRNA stability and subcellular mRNA localisation. In particular, the partitioning of mRNA into the cell nucleus, cytoplasm, P-bodies, stress granules and neurites have recently been shown to depend on codon optimality. The functional consequences of codon usage also vary by tissue type – but the molecular mechanisms that underlie these effects are poorly understood.
To study the role of codon usage in tissue-specific gene regulation, we will integrate libraries of genetic variants into human induced pluripotent stem cells (hiPSCs), and track their mRNA fate as the cells undergo differentiation into motor neurons. To achieve this, we will combine state-of-the-art synthetic biology and genome engineering approaches used in the Kudla lab, with neuronal cell culture and functional genomics assays from the Chekulaeva group. Specific questions we will ask include: (1) what properties of the coding sequence influence tissue-specific gene regulation during neuronal differentiation; (2) do differences emerge at the level of transcription, mRNA stability, or translation; (3) does codon usage differentially affect translation in neuronal cell bodies and in neurites; (4) how these processes are affected in amyotrophic lateral sclerosis (ALS) models derived from patient hiPSCs. We anticipate that these experiments will uncover new layers of regulatory information hidden within the genetic code.
Selected references:
Radrizzani S, Kudla G, Izsvák Z, Hurst LD (2024) Selection on synonymous sites: the unwanted transcript hypothesis. Nature Reviews Genetics 2024 Jan 31. https://doi.org/10.1038/s41576-023-00686-71-18
Mendonsa S., (...), and Chekulaeva M. (2023) Massively parallel identification of mRNA localization elements in primary cortical neurons. Nature Neuroscience 26: 394–405. https://www.nature.com/articles/s41593-022-01243-x
Loedige I., (...) and Chekulaeva M. (2023). mRNA stability and m6A are major determinants of subcellular mRNA localization in neurons. Molecular Cell 83(15): 2613-2828. https://doi.org/10.1016/j.molcel.2023.06.021
Mordstein C, (...) and Kudla G (2020) Codon Usage and Splicing Jointly Influence mRNA Localization. Cell Syst 10(4): 351-362. https://doi.org/10.1016/j.cels.2020.03.001
Marina Chekulaeva Research Group
For informal enquiries about this project, please contact Greg Kudla (Grzegorz.Kudla@ed.ac.uk).