Epigenetics and Non-Coding RNAs in Plants
We are interested in understanding the molecular mechanisms underlying reproductive development and currently focus on non-coding RNAs (miRNAs, siRNAs, long non-coding RNAs) and post-transcriptional RNA modifications.
- Chief Investigator
- Dr Iain Searle, ARC Research fellow
- Samuel Deed
- Pei Qin (Sabrina)
- Rakesh David (Postdoctoral Fellow)
- Alice Burgess (PhD)
- Hua Deng (PhD)
- Peter Crisp (PhD)
- Bruce Tsai (Masters)
- Xingyu Wu (Masters)
- Kalinya Pulsford (Honours)
- Han Lim (Honours)
- Eliska Zlamalova (undergraduate)
- Graham Gower (undergraduate)
- Tyrone Chen (undergraduate)
- Natasha Bradley (Summer student)
- Gauri Tarle (overseas visitor)
- Arlet Estevez (overseas visitor)
- Franziska Gruhl (overseas visitor)
For available Honours and PhD projects please contact Dr Iain Searle
Image credit: Alice Burgess
Image credit: Chris Wong
Our overarching aim is to use the model plant Arabidopsis thaliana to understand the molecular basis of complex traits and translate these discoveries into crop plants like canola and cereals (e.g. barley, wheat and rice).
We hypothesise that a hidden layer of regulation exists at the post-transcriptional level in mRNAs in eukaryotes and parkaryotes. We are undertaking genome-wide identification of the RNA modifications (e.g. 5-methyl cytosine) during the early stages of enodperm and embryo development in Arabidopsis. We have identified a number of RNA methylases required for m5C and are intersted in understanding the mechanism directing and removing these RNA modifications.
Project One- Seed Development and long non-coding RNAs
Recently we discovered thousands of novel long non-coding RNAs (lncRNAs) in the Arabidopsis thaliana and other plant genomes using cutting-edge next generation Illumina sequencing and bioinformatics (e.g. Wang et al., 2017, The Plant Journal). This project will involve using molecular genetic techniques, like CRISPR/CAS9 genome editing, to functional characterize a subset of lncRNAs during endosperm development. Honours, Masters and PhD projects are available on this topic.
Skills learned- bioinformatics, second-generation illumina sequencing, molecular genetics
Project Two- Post-transcriptional RNA modifications in plants and animals
We have recently discovered a hidden layer of post-transcriptional (RNA) regulation- cytosine methylation (m5C)- in Arabidopsis using bisulphite conversion techniques (Burgess et al., BMC Plant Biology 2015, David et al., 2017 The Plant Cell). We are currently determining the genome-wide distribution of cytosine methylation using Illumina sequencing and the reversible nature of the modification. We are exploring the targeting mechanism of the RNA methyltransferases, the role of m5C during development and the enzymes that remove m5C. Honours, Masters and PhD projects are available on this topic.
Skills learned- bioinformatics, third-generation Nanopore sequencing, molecular genetics
With collaborators at the University of Adelaide's Robinson Research Institute are exploring the role of RNA modifications during reproductive development in mice.
Project Three- Generation of healthy common vetch
Common vetch (Vicia sativa) is a leguminous, annual crop plant that provides valuable soil nitrogen to farming systems and is a palatable, cheap, high protein feed source with potential as feed for livestock and humans. One significant reason of its limited agricultural use is that anti-nutritional compounds exist in seeds, especially β-cyano-alanine and γ-glutamyl-β-cyano-alanine (GBA), which has toxicity to monogastric animals, like poultry, pigs, and humans.
We are using phylogenomics to identify candidate genes regulating toxin production and genome to edit these genes using CRISPR/CAS9 to produce healthy (zero toxin) vetch. Honours, Masters and PhD projects are available on this topic.
Skills learned- bioinformatics, third-generation PacBio and Nanopore sequencing, molecular genetics, plant biology
For a list of lab publications, please visit the researcher profile of Dr Iain Searle.
- Dabing Zhang - Shanghai Jiao Tong University (China)
- Rupert Fray - The University of Nottingham (UK)