Vector illustration Aim

Cell states are governed by complex heterotypic interactions between regulatory genes. Previous work has used genetic loss of function to study the complex interdependent roles of transcription factors controlling gene expression, differentiation, and morphogenesis. We have developed an industry partnership with Agilent to establish a scalable screening platform using standard CRISPR editing strategies.

Brief project outline

We will screen the transcriptional regulatory dependencies that underlie all possible pairwise perturbations of up to 20 different heterotypic regulatory genes in the first instance. We will leverage single cell bar-coding systems to perform scalable sequencing of samples using platforms developed at the WEHI (in collaboration with Shalin Naik).

Genomics-based innovative aspect of proposal

While previous studies have been limited to analysis of 1-3 regulatory genes in a combinatorial manner, in this project we aim to utilize scalable bar-coded RNA-seq with a library of multiplexed dual-gRNA gene knockouts to systematically map the heterotypic roles and interdependencies of transcription factors and epigenetic regulators controlling cell identity.

Broad applicability of the technique

The outcome of this project will enable two new platforms at UQ:

  1. A platform for arrayed CRISPR screening using multiple synthetic guide RNA. 
  2. A platform for Cell-seq2 based bulk RNA-seq.

Publications arising from this project

Cavin4 interacts with Bin1 to promote T-tubule formation and stability in developing skeletal muscle.

Harriet P. Lo, Ye-Wheen Lim, Zherui Xiong, Nick Martel, Charles Ferguson, Nicholas Ariotti, Jean Giacomotto, James Rae, Matthias Floetenmeyer, Shayli Varasteh Moradi, Ya Gao, Vikas A. Tillu, Di Xia, Huang Wang, Samira Rahnama, Susan J. Nixon, Michele Bastiani, Ryan D. Day, Kelly A. Smith, Nathan J. Palpant, Wayne A. Johnston, Kirill Alexandrov, Brett M. Collins, Thomas E. Hall, Robert G. Parton; Cavin4 interacts with Bin1 to promote T-tubule formation and stability in developing skeletal muscle. J Cell Biol 6 December 2021; 220 (12): e201905065. doi: https://doi.org/10.1083/jcb.201905065

 

Therapeutic Inhibition of Acid Sensing Ion Channel 1a Recovers Heart Function After Ischemia-Reperfusion Injury.

***NOTE: Correction to: Therapeutic Inhibition of Acid Sensing Ion Channel 1a Recovers Heart Function After Ischemia-Reperfusion Injury, https://www.ahajournals.org/doi/10.1161/CIR.0000000000001020***

Meredith A. Redd, Sarah E. Scheuer, Natalie J. Saez, Yusuke Yoshikawa, Han Sheng Chiu, Ling Gao, Mark Hicks, Jeanette E. Villanueva, Yashutosh Joshi, Chun Yuen Chow, Gabriel Cuellar-Partida, Jason N. Peart, Louise E. See Hoe, Xiaoli Chen, Yuliangzi Sun, Jacky Y. Suen, Robert J. Hatch, Ben Rollo, Di Xia, Mubarak A.H. Alzubaidi, Snezana Maljevic, Gregory A. Quaife-Ryan, James E. Hudson, Enzo R. Porrello, Melanie Y. White, Stuart J. Cordwell, John F. Fraser, Steven Petrou, Melissa E. Reichelt, Walter G. Thomas, Glenn F. King, Peter S. Macdonald, Nathan J. Palpant. https://www.ahajournals.org/doi/10.1161/CIRCULATIONAHA.121.054360

 

Project members

Research collaborators

Dr Nathan Palpant

Dr Nathan Palpant

Senior Research Fellow - GL
Institute for Molecular Bioscience

Genome Innovation Hub

Dr Di Xia

Dr Di Xia

Senior Research Assistant
Genome Innovation Hub
Dr Jun Ma

Dr Jun Ma

Research Assistant
Genome Innovation Hub