Discovery of new regulatory networks with long-read transcriptomics

Aims

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.