Studentship | Genome-wide screening approach to uncover novel regulators of organelle-selective autophagy

MRC Funded
Project with

Autophagy was once thought to be a bulk, non-selective degradative pathway that cells employ during nutrient deprivation to rapidly break down cellular content for energy generation. With the improvement in biochemistry and microscopy techniques, it is becoming increasingly clear that different organelles and intracellular structures can be selectively recognised for targeted degradation in response to different stresses or stimuli. However, many key regulatory genes that are involved in each specialised autophagic pathway remain unclear, let alone the logic and importance of degrading each organelle in the face of each stress. 

The Liang Lab specialises in using state-of-the-art CRISPR/Cas-derived genetic manipulation approaches to perform loss- and gain-of-function screens at the genomic level to interrogate factors that are required in each pathway (including different organelle-autophagies) (Liang and Corn, 2022). By performing a CRISPR-interference (CRISPRi) screen for key players in endoplasmic reticulum-specific autophagy (ER-phagy), we previously demonstrated that a Ubiquitin-like modification, known as UFMylation, is involved in the ER-phagy and ER stress regulation (Liang et al., 2020, Liang et al. 2018). Clinical mutation of genes involved in the UFMylation pathway results in striking neurodevelopmental, immunological and hematopoetic defects, underscoring the potential involvement of UFMylation mediated ER homeostasis in these processes. 

As an extension to our previous ER-phagy screening effort, we are looking for a highly-driven student to perform both loss-of-function and gain-of-function screens (using CRISPR-interference and CRISPR-activation approaches) to further delineate the common and unique factors involved in the turnover of different organelles. This undertaking has the potential to significantly improve our current understanding on the need to promote or inhibit the clearance of a particular organelle/intracellular structure in physiological and pathological contexts. This project will involve first-hand experience in performing genome-wide screens, data analysis, and prioritisation of candidate hits. Biochemical assays, molecular biology, flow cytometry, and fluorescence confocal microscopy will be employed for downstream validation and characterisation of novel factors that are identified to demonstrate their relevance in each organelle turnover and to explore their potential clinical/pathological relevance. 

References:

  1. Liang, J.R. and Corn, J.E. 2022. A CRISPR view on autophagy. Trends in Cell Biology.
  2. Liang JR, Lingeman E, Luong T, Ahmed S, Muhar M, Nguyen T, Olzmann JA, Corn JE (2019) A genome-wide screen for ER autophagy highlights key roles of mitochondrial metabolism and ER-resident UFMylation Cell 180 1160-1177
  3. Liang JR, Lingeman E, Ahmed S, Corn JE (2018) Atlastins remodel the endoplasmic reticulum for selective autophagy. Journal of Cell Biology J Cell Biol 217 3354-3367




Application Procedure

We are currently accepting applications for our 2023 programme. To apply, please send the following to mrcppu-phd-admin@dundee.ac.uk
 

  • Cover letter explaining your interest in our work. Please also indicate which group(s) you are most interested in, and whether you prefer rotations or would like to join one lab directly.
  • CV with contact details of three referees.


Applications from overseas students are welcome. The closing date for the first round of applications is January 31st 2022