Project ID CM-HD2023_26

ThemeCM-HD

Co Supervisor 1A Centre for Developmental Neurobiology, IoPPNWebsite

Co Supervisor 1B Centre for Developmental Neurobiology, IoPPNWebsite

Gene regulation mechanisms underlying interneuron diversity

Cortical interneurons comprise over 20 types of cells with distinct morphologies and functions. Correct development of this group of neurons is essential for normal neural and cognitive functions. How different types of interneurons emerge from common progenitor populations remains a largely unresolved problem. This PhD project will address it by pursuing three interrelated objectives: (1) understanding how alternative splicing contributes to development of distinct types of interneurons; (2) setting up a hybridization-proximity (HyPro) labelling to analyse interneuron type-specific transcriptomes and proteomes; and (3) using this new spatial “omics” technology to understand regulation mechanisms of interneuron type-specific splicing. Work on the first objective will involve in-depth bioinformatics analyses of single-cell sequencing data and it will be carried out mostly during the rotation. Optimization of the HyPro technology (objective 2) will begin during the rotation and may require the entire year 2 to complete. Years 3-4 will be used to analyse interneuron-specific transcriptomes and proteomes and validate the key insights using gene knockout and gain-of-function experiments, neuron imaging and appropriate molecular assays (objective 3) and to write the thesis. The expertise of the Makeyev group in bioinformatics, biochemistry and cell-based assays will ensure adequate training of the student and successful completion of the relevant parts of the project. The Marin lab, a leader in the interneuron field, will provide an ideal environment to perform critical ex-vivo and in-vivo experiments. Overall, the project will uncover fundamental mechanisms underlying establishment of unique neuronal identities and will inform future biomedical studies in this exciting field.

One representative publication from each co-supervisor:

• Yap K, Chung TH, and Makeyev EV (2022) Hybridization-proximity labeling reveals spatially ordered interactions of nuclear RNA compartments. Mol Cell 82, 463-478.

• Mi D, Li Z, Lim L, Li M, Moissidis M, Yang Y, Gao T, Hu TX, Pratt T, Price DJ, Sestan N, and Marín O (2018) Early emergence of cortical interneuron diversity in the mouse embryo. Science 360, 81-85.