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.
Zheng Z, Wang N, Jalajakumari MB, Blackman L, Shen E, Verma S, Wang MB, Millar AA (2020) miR159 represses a constitutive pathogen defense response in tobacco. Plant Physiology 182, 2182-2198. doi: 10.1104/pp.19.00786
Millar AA (2020) The Function of miRNAs in Plants. Plants (Basel) 9, E198. doi:10.3390/plants9020198 (editorial).
Asadi Khanouki M, Rezanejad F, Millar AA (2019) Sequence and functional analysis of a TERMINAL FLOWER 1 homolog from Brassica juncea: a putative biotechnological tool for flowering time adjustment. GM Crops & Food doi: 10.1080/21645698.2019.1707340
Schumann U, Lee JM, Smith NA, Zhong C, Zhu JK, Dennis ES, Millar AA, Wang MB (2019) DEMETER plays a role in DNA demethylation and disease response in somatic tissues of Arabidopsis. Epigenetics 14, 1074–1087. doi: 10.1080/15592294.2019.1631113.
Millar AA, Lohe A, Wong G (2019) Biology and function of miR159. Plants (Basel) 8, 255. doi:10.3390/plants8080255
Wong G, Millar AA (2019) The use of microRNA decoy technologies to inhibit miRNA function in Arabidopsis. In, S de Folter (ed) Plant microRNAs: Methods and Protocols, Methods of Molecular Biology vol. 1932, Springer Science, New York, pp 227-238.
Wong G, Alonso-Peral M, Li B, Li J, Millar AA (2018) MicroRNA MIMIC binding sites: minor flanking nucleotide alterations can strongly impact MIMIC silencing efficacy in Arabidopsis. Plant Direct 2, e00088.
Crisp PA, Smith AB, Ganguly DR, Murray KD, Eichten SR, Millar AA, and Pogson BJ (2018) Pol II read-through promotes expression of neighbouring genes in SAL1-PAP-XRN retrograde signaling. Plant Physiology 178, 1614-1630.
Medina C, da Rocha M, Magliano M, Ratpopoulo A, Revel B, Marteu N, Magnone V, Lebrigand K, Cabrera J, Barcala M, Silva AC, Millar AA, Escobar C, Abad P, Favery B and Jaubert-Possamai S (2017) Characterization of microRNAs from Arabidopsis galls highlights a role for miR159 in the plant response to the root-knot nematode Meloidogyne incognita. New Phytologist 216, 882-896.
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, 1764-1778.
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.
PS Seminar Series - PhD Exit Seminar - A miRNA mystery: does miR159 play a role in plant defence response
Abstract - miRNAs are a class of small RNAs that negatively regulate gene expression in eukaryotes.