E.coli bacterial cellsAims

To develop robust protocols for long-read transcriptomics in bacteria. 

Brief project outline

Operons are clusters of genes that are co-transcribed. In bacteria their critical function in regulation is well-established through detailed exploration of archetypes such as the lac operon. However, a genome-wide understanding of operons remains an intractable problem with current RNA-Seq technology. Short-read (Illumina) transcriptomics cannot reliably distinguish different transcript isoforms or define transcription start and end sites. Furthermore, the lack of poly-A tails in bacterial transcripts makes transcriptomics challenging compared with eukaryotes.

This project seeks to develop new protocols for long-read transcriptomics in bacteria using PacBio and Nanopore data. This in itself will revolutionise our ability to understand the regulatory networks of bacteria.  

Genomics-based innovative aspect of proposal

The broad aim of this project is to develop long-read transcriptomic capabilities for bacteria at UQ.

Broad applicability of the technique

The protocols developed in this project will be directly applicable to researchers interested in gene regulation in bacteria. We expect that the protocols post-RNA preparation will be suitable for inclusion within the portfolio of a UQ sequencing centre. Bioinformatics software will be made freely available through a Github site.

Future directions: Developing the protocols for bacterial isolates will be a critical first step in the development of long-read meta-transcriptomic protocols. The data and protocols produced here will be important for validating and interpreting novel meta-transcriptomic datasets by establishing ground-truth benchmarking sets and providing raw data for “spike-in” experiments.

Project members

Research collaborators

Professor Scott Beatson

Associate Professor Scott Beatson

Associate Professor
School of Chemistry and Molecular Biosciences, Faculty of Science
Affiliate Associate Professor
UQ Centre for Clinical Research, Faculty of Medicine
 Professor Mark Walker

Professor Mark Walker

Professor
School of Chemistry and Molecular Biosciences, Faculty of Science
Professor Mark Schembri

Professor Mark Schembri

Professor
School of Chemistry and Molecular Biosciences, Faculty of Science

Dr Minh-Duy Phan

Postdoctoral Research Fellow
School of Chemistry and Molecular Biosciences, Faculty of Science
Dr Brian Forde

Dr Brian Forde

Advance Queensland Industry Research Fellow
UQ Centre for Clinical Research Faculty of Medicine

Dr Amanda Walker

Laboratory Coordinator/Research Assistant
School of Chemistry and Molecular Biosciences

Genome Innovation Hub

Stacey Andersen

Stacey Andersen

Senior Research Assistant
Genome Innovation Hub
Senior Research Assistant
IMB Sequencing Facility
Valentine Murigneux

Valentine Murigneux

Senior research assistant
Genome Innovation Hub
Bioinformatician
QCIF Facility for Advanced Bioinformatics
Dr Subash Rai

Dr Subash Rai

Research Assistant
Genome Innovation Hub