Oral Presentation 16th Asian Conference on Transcription 2019

Development of new bioinformatic tools for identification and characterisation of CRISPR ncRNA and protein coding operons (1185)

Te-yuan Chyou 1 , Saadlee Shehreen 1 , Tom Nicholson 1 , Simon Jackson 2 , Paul Gardner 1 , Peter Fineran 2 3 , Chris Brown 1 3
  1. Department of Biochemistry, University of Otago, Dunedin, New Zealand
  2. Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
  3. Genetics Otago, University of Otago, Dunedin, New Zealand

There are now about 400,000 complete bacterial and archaeal genome sequences in the easily accessible public databases, and huge amounts of data from less traditional sources. To mine this we have developed computational tools and pipelines to predict and analyse genomes on this scale. We are interested in determining the functions of both coding and non-coding RNAs in bacterial antiviral systems.

One set of systems that exploit both coding and non-coding RNAs are the CRISPR-Cas adaptive immune systems. These CRISPR-Cas systems use ncRNA to target foreign DNA in most archaea and about 30% of bacteria. We have used our integrated suite of software (CRISPRSuite) to identify viral and non-viral targets of the CRISPR-Cas system and study all three components (CRISPR RNA, tracrRNA and Cas proteins). CRISPRSuite has also facilitated our analysis of the beneficial, or negative, effects of CRISPR-Cas in pathogenic bacteria and the mechanisms of rapid primed spacer acquisition in bacteria. For example, we recently discovered evidence of primed CRISPR adaptation by type II (Cas9) systems.

Data from new high-throughput technologies, notably precise mapping of transcription termination sites (term-seq), has allowed us to re-examine long standing paradigms for bacterial transcription termination in both coding and ncRNA.

The results from these studies will be presented and our bioinformatic tools are available through the bioanalysis.otago.ac.nz gateway.