Correct spatial and temporal gene expression underpins life. Such knowledge is not only required to understand organisms function, but underpins all important traits, including that of our crop species. Gene expression has been predominantly studied at the transcriptional level (transcription factors, histones, epigenetics), however, how the transcriptome is translated into the proteome is an exceedingly complex process. Termed, Post-Transcriptional Gene Regulation (PTGR), this is the predominant interest of the lab which we have focused on two main areas.
These are small RNAs (sRNA) which scan the transcriptome, binding to high complementary mRNA targets, which they repress through a complex mechanism of transcript degradation and translational inhibition. They are highly important in development and response to environmental factors, and hence many control important agricultural traits. Our major questions are;
- miRNA target recognition; although high complementarity is a pre-requisite for a strong miRNA-target interaction, we have recently shown that factors beyond complementarity are highly important, such as the RNA 2o structure of target mRNA. We continue to explore such factors.
- The biology of miRNAs in model and crop species. We are investigating the functional role of miRNAs, largely by manipulating their expression in planta. This gives insights into the function they are performing in plant, and their possible use for altering important crop traits.
RNA binding proteins (RBPs).
RNA does not exist as an isolated entity, but rather as a RNA-protein complex with RBPs, which determine all aspects of the fate of an RNA, including their processing, expression, sub-cellular localisation and half-life. However, despite this fundamental importance and their ubiquity (the number of RBPs and transcription factors are comparable), very little is known how RBPs regulate the expression of the transcriptome. Our major questions are;
- Develop and exploit mRNA-interactome capture, a method for determining the portion of the proteome bound to mRNA in planta. We developed this method in Arabidopsis, and now aim to apply this to plants subjected to abiotic stresses, where there are known PTGR mechanism that are required for survival, with the goal to identify key stress survival genes.
- Functionally characterize novel families of RBPs. Our first interactome identified many uncharacterized and unexpected RBPs. Through a variety of approaches, we aim to determine to which RNAs these proteins bind and the function they perform in the plant.
Open to students
Characterizing the mRNA-protein “interactome” of plants (Undergraduate, Summer scholar course, Honours, Graduate, Masters coursework & research, Higher degree by research)
Developing molecular tools for functional analysis of microRNA-mediated gene silencing (Summer scholar course, Honours, Masters coursework & research, Higher degree by research)
Factors impacting gene silencing efficacy in plants (Summer scholar course, Honours, Graduate, Higher degree by research)
MicroRNA target recognition; the role of the target RNA secondary structure. (Summer scholar course, Honours, Masters coursework & research, Higher degree by research)
The role of RNA binding proteins in post-transcriptional gene regulation and plant biology. (Summer scholar course, Honours, Masters coursework & research, Higher degree by research)
Zheng Z, Reichel M, Deveson I, Wong G, Li J and Millar AA (2017) Target RNA secondary structure is a major determinant of miR159 efficacy. Plant Physiology 174, (in press).
Reichel M, Liao Y, Rettel M, Ragan C, Evers M, Alleaume A-M, Horos R, Hentze MW, Preiss T and Millar AA (2016) In planta determination of the mRNA-binding proteome of Arabidopsis etiolated seedlings. The Plant Cell 28, 2435-2452.
Li Y, Alonso-Peral M, Wong G, Wang M-B and Millar AA (2016) Ubiquitous miR159 repression of MYB33/65 in Arabidopsis rosettes is robust and is not perturbed by a wide range of stresses. BMC Plant Biology 16, 179.
Reichel M and Millar AA (2015) Specificity of plant microRNA target MIMICs: Cross-targeting of miR159 and miR319. Journal of Plant Physiology 180, 45-48.
Reichel M, Li Y, Li J and Millar AA (2015) Inhibiting plant microRNA activity: molecular SPONGEs, target MIMICs and STTMs all display variable efficacies against target microRNAs. Plant Biotechnology Journal 13, 915-926.
Li J, Reichel M, Li Y and Millar AA (2014) The functional scope of plant microRNA-mediated silencing. Trends in Plant Science 19, 750-756.
Li, J, Reichel, M and Millar AA (2014) Determinants beyond both complementarity and cleavage govern miR159 efficacy in Arabidopsis. PLoS Genetics 10, e1004232.
Deveson I, Li J and Millar AA (2013) MicroRNAs with analogous target complementarities perform with highly variable efficacies in Arabidopsis. FEBS Letters 587, 3703-3708.
Allen RS, Nakasugi K, Doran R, Millar AA and Waterhouse PM (2013) Facile mutant identification via a single parental backcross method and application of whole genome sequencing based mapping pipelines. Frontiers in Plant Science 4, 362.
Deveson I, Li J and Millar AA (2013) Expression of human ARGONAUTE 2 inhibits endogenous microRNA activity in Arabidopsis. Frontiers in Plant Science 4, 96.
Li J and Millar AA (2013) Expression of a microRNA-resistant target transgene misrepresents the functional significance of the endogenous microRNA:target gene relationship. Molecular Plant 6, 577-580.
- Alonso-Peral MM, Sun C and Millar AA (2012) MircoRNA159 can act as a switch or tuning microRNA independently of its abundance in Arabidopsis. PLoS ONE 7, e34751.
- Fahim M, Millar AA, Wood CC and Larkin PJ (2012) Resistance to Wheat streak mosaic virus generated by expression of an artificial polycistronic microRNA in wheat. Plant Biotechnology Journal. 10, 150-163.
- Reichel M, Li J and Millar AA (2011) Silencing the silencer: strategies to inhibit microRNA activity. Biotechnology Letters 33, 1285-92.
- Allen, RS, Li J, Alonso-Peral MM, White RG, Gubler F and Millar AA (2010) MicroR159 regulation of most conserved targets in Arabidopsis has negligible phenotypic effects. Silence 1:18
- Alonso-Peral MM, Li J, Li Y, Allen RS, Schnippenkoetter W, Ohms S, White RG, Millar AA (2010) The microR159 regulated GAMYB-like genes inhibit growth and promote programmed cell death in Arabidopsis. Plant Physiology 154, 757-771
- Fahim M, Ayala-Navarrete L, Millar AA, Larkin PJ (2010) Hairpin RNA derived from viral NIa gene confers immunity to wheat streak mosaic virus infection in transgenic wheat plants. Plant Biotechnology Journal 8, 821-834.
- Allen, RS, Li J, Stahle MI, Dubroué A, Gubler F, Millar AA (2007) Genetic analysis demonstrates functional redundancy and the major target genes of the Arabidopsis miR159 family. Proceedings of the National Academy of Sciences, USA 104, 16371-16376.
- Millar AA, Jacobsen JV, Ross JJ, Helliwell CA, Poole AT, Scofield G, Reid JB, Gubler F. (2006) Seed dormancy and ABA metabolism in Arabidopsis and barley: the role of ABA 8’ hydroxylase. The Plant Journal 45, 942-954.
- Millar AA, Waterhouse PM (2005) Plant and animal microRNAs: similarities and differences. Functional and Integrative Genomics 5, 129-135.
- Gubler F, Millar AA, Jacobsen JV (2005) Dormancy release, ABA and pre-harvest sprouting. Current Opinion in Plant
- Millar AA, Gubler F (2005) The Arabidopsis GAMYB-like genes, MYB33 and MYB65, are microRNA-regulated genes that redundantly facilitate anther development. The Plant Cell 17, 705-721.