Dr Andy Eamens

Dr Andy Eamens

Lecturer

School of Environmental and Life Sciences

Career Summary

Biography

I was awarded my PhD from Charles Sturt University in 2004 and conducted the research component of my Thesis at CSIRO Plant Industry. My PhD focused on the development of a plant transformation vector for the generation of random insertion knockout mutants in rice, the model monocotyledonous plant species (Eamens et al., Plant Biotechnol J. 2004). During my time at CSIRO Plant Industry, I became highly interested in the ground breaking research conducted in the neighbouring Laboratory of Prof. Peter Waterhouse and Dr. Ming-Bo Wang on the mechanisms of RNA silencing in plants. In plants, animals and insects, RNA silencing is triggered by double-stranded RNA (dsRNA) that is converted into numerous classes of small RNA (sRNA). sRNAs are then loaded onto effector complexes that use the sRNA as a sequence specificity determinant to regulate the expression of complementary target sequences at either the transcriptional or post-transcriptional level. This interest prompted me to undertake a Postdoctoral Fellowship in the Laboratory of Dr. Louise Jones at the University of York in the United Kingdom (2003-2006). Louise and I, using a number of innovative molecular biology techniques, identified and characterised two new machinery proteins involved in the endogenous gene regulatory pathway of plants, the RNA-directed DNA methylation (RdDM) pathway. We went on to show that these two plant-specific RdDM machinery proteins are also required to mount an effective defence response against invading nucleic acids, namely those derived from viruses (Eamens et al., Plant J. 2008). In late 2006, I returned to CSIRO Plant Industry to work in the Laboratory of Prof. Waterhouse and Dr. Wang. During this Postdoctoral Fellowship (2006-2009), I developed an artificial microRNA (amiRNA) plant transformation vector that directs highly efficient and specific RNA silencing of a researcher’s gene(s) of interest (Eamens and Waterhouse, Methods Mol Biol. 2011). I subsequently used the amiRNA vector to functionally characterise DRB1, a central machinery protein of the Arabidopsis thaliana (Arabidopsis) miRNA pathway (Eamens et al., RNA. 2009), and to offer an alternate strategy to produce miRNA knockdown mutant plant lines (Eamens et al., Mol Plant. 2011; Eamens and Wang, Plant Signal Behav. 2011). The functional characterisation of DRB1 with the amiRNA plant transformation vector marked my entry into the DOUBLE-STRANDED RNA BINDING (DRB) protein world of plants (see Curtin et al., FEBS Lett. 2008). In mid-2009, I took up a Senior Research Fellowship at the University of Sydney to continue my research collaboration with Prof. Waterhouse. During this Fellowship (2009-2013), Peter and I showed that in addition to DRB1, DRB2 is required for the accurate and efficient production of a specific class of miRNAs from their dsRNA precursor transcripts in developmentally important tissues (Eamens et al., PLoS One. 2012). I went on to show, once again via the use of amiRNA technology, that DRB3 and DRB5 regulate the expression of DRB2-dependent miRNA target genes independently of target gene mRNA cleavage-based RNA silencing, the predominant mode of sRNA-directed RNA silencing in plants (Eamens et al., Plant Signal Behav. 2012). In 2013, I was recruited to the University of Newcastle as a Lecturer in Molecular Genetics. In addition to lecturing, I am taking a molecular approach to determine the role(s) of each of the five members of the Arabidopsis DRB protein family in the parallel sRNA-directed RNA silencing pathways of plants, specifically determining the 'DRB-dependence' of each sRNA species, and further to study the sRNA levels and sRNA target gene expression during abiotic stress, namely drought and salt stress.

Qualifications

  • PhD (Molecular Biology), Charles Sturt University
  • Bachelor of Applied Science (Med & App Biotech), Charles Sturt University
  • Bachelor of Applied Science (Med & App Biotech), Charles Sturt University

Keywords

  • Plant developmental biology
  • RNA biology
  • RNA silencing
  • epigenetics
  • gene expression regulation
  • microRNA (miRNAs)
  • small RNA

Languages

  • English (Mother)

Fields of Research

Code Description Percentage
060404 Epigenetics (incl. Genome Methylation and Epigenomics) 15
060702 Plant Cell and Molecular Biology 70
060405 Gene Expression (incl. Microarray and other genome-wide approaches) 15

Professional Experience

UON Appointment

Title Organisation / Department
Lecturer University of Newcastle
School of Environmental and Life Sciences
Australia

Professional appointment

Dates Title Organisation / Department
1/06/2009 - 4/02/2013 Senior Research Fellow

Senior Research Fellow

The University of Sydney
School of Molecular Bioscience
Australia
1/06/2006 - 1/06/2009 Postdoctoral Fellow

Postdoctoral Fellow

CSIRO - Commonwealth Scientific and Industrial Research Organisation
Plant Industry
1/01/2003 - 1/06/2006 Postdoctoral Fellow

Postdoctoral Fellow

The University of York
Department of Biology
United Kingdom

Teaching

Code Course Role Duration
BIOL3310 Plant Cell and Molecular Biology
Faculty of Science and Information Technology, The University of Newcastle | Australia
Lecturer
Lecturer 1/01/2013 - 1/01/2020
BIOL2050 Molecular Genetics
Faculty of Science and Information Technology, The University of Newcastle | Australia
Course Coordinator 1/01/2013 - 1/01/2020
BIOL2001 Molecular Biology Laboratory Skills
Faculty of Science and Information Technology, The University of Newcastle | Australia
Molecular Biology Laboratory Skills
Lecturer 1/01/2013 - 1/01/2020
BIOL4110/4220 Biology Honours
Faculty of Science and Information Technology, The University of Newcastle | Australia
Course Coordinator 1/01/2013 - 1/01/2020
BIOL3001 Advanced Molecular Biology Laboratory Skills
Faculty of Science and Information Technology, The University of Newcastle | Australia
Molecular Biology Laboratory Skills
Lecturer 1/01/2013 - 1/01/2020
BIOL1003 Professional Laboratory Skills
Faculty of Science and Information Technology, The University of Newcastle | Australia
Lecturer 1/01/2013 - 1/01/2020
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Publications

For publications that are currently unpublished or in-press, details are shown in italics.


Chapter (2 outputs)

Year Citation Altmetrics Link
2010 Eamens A, Curtin SJ, Waterhouse PM, 'RNA silencing in plants', Plant Developmental Biology 277-294 (2010)

RNA silencing-related mechanisms have been documented in almost all living organisms and RNA silencing is now used as board term to describe the vast array of related processes in... [more]

RNA silencing-related mechanisms have been documented in almost all living organisms and RNA silencing is now used as board term to describe the vast array of related processes involving RNA-RNA, RNA-DNA, RNA-protein or protein-protein interactions that ultimately result in the repression of gene expression. In plants, the parallel RNA silencing pathways have evolved to extraordinary levels of complexity and diversity, playing crucial roles in providing protection against invading nucleic acids derived from viruses or replicating transposons, controlling chromatin modifications as well as regulating endogenous gene expression to ensure normal plant growth and development. The aims of this chapter are (1) to provide an overview of the initial curious observations of RNA silencing-related phenomena in plants, (2) to outline the parallel gene silencing pathways of plants, and (3) to discuss current applications of RNA silencing technologies to not only study but also modify plant development. © 2010 Springer-Verlag Berlin Heidelberg.

DOI 10.1007/978-3-642-04670-4_15
Citations Scopus - 1
2007 Zhu QH, Eun MY, Han CD, Kumar CS, Pereira A, Ramachandran S, et al., 'Transposon insertional mutants: A resource for rice functional genomics', Rice Functional Genomics: Challenges, Progress and Prospects 223-271 (2007)

© 2007 Springer Science+Business Media, LLC. All rights reserved. With the completion of rice genome sequencing, the new challenge for the rice community is to unravel the biolog... [more]

© 2007 Springer Science+Business Media, LLC. All rights reserved. With the completion of rice genome sequencing, the new challenge for the rice community is to unravel the biological functions of approximately 40,000 rice genes. To achieve this goal, a wide range of functional genomics tools, such as microarray, serial analysis of gene expression (SAGE), RNA interference (RNAi), insertional mutagenesis, and bioinformatics, have been established and employed. Insertional (T-DNA, transposon or retrotransposon) mutagenesis has proven to be one of the most efficient methodolo gies, because studies of mutants with detectable phenotypes have given us the greatest insight into the mechanisms underlying a wide range of biological processes in plants. Compared with T-DNA insertional mutagenesis, transposon insertional mutagenesis (or transposon tagging) has distinct advantages. Large-scale transposon mutagenized populations can be produced using a relatively small number of starter lines, as many independent insertions can be generated among the progeny of a single line. The tagged gene can be confirmed by revertants resulting from excision of the transposon.

DOI 10.1007/0-387-48914-2_10
Citations Scopus - 15

Journal article (33 outputs)

Year Citation Altmetrics Link
2017 Hutcheon K, McLaughlin EA, Stanger SJ, Bernstein IR, Dun MD, Eamens AL, Nixon B, 'Analysis of the small non-protein-coding RNA profile of mouse spermatozoa reveals specific enrichment of piRNAs within mature spermatozoa.', RNA Biol, 1-15 (2017)
DOI 10.1080/15476286.2017.1356569
Co-authors Eileen Mclaughlin, Matt Dun, Brett Nixon
2016 Litholdo CG, Parker BL, Eamens AL, Larsen MR, Cordwell SJ, Waterhouse PM, 'Proteomic identification of putative MicroRNA394 target genes in arabidopsis thaliana identifies major latex protein family members critical for normal development', Molecular and Cellular Proteomics, 15 2033-2047 (2016) [C1]

© 2016 by The American Society for Biochemistry and Molecular Biology, Inc. Expression of the F-Box protein Leaf Curling Responsiveness (LCR) is regulated by microRNA, miR394, an... [more]

© 2016 by The American Society for Biochemistry and Molecular Biology, Inc. Expression of the F-Box protein Leaf Curling Responsiveness (LCR) is regulated by microRNA, miR394, and alterations to this interplay in Arabidopsis thaliana produce defects in leaf polarity and shoot apical meristem organization. Although the miR394-LCR node has been documented in Arabidopsis, the identification of proteins targeted by LCR F-box itself has proven problematic. Here, a proteomic analysis of shoot apices from plants with altered LCR levels identified a member of the Latex Protein (MLP) family gene as a potential LCR F-box target. Bioinformatic and molecular analyses also suggested that other MLP family members are likely to be targets for this post-translational regulation. Direct interaction between LCR F-Box and MLP423 was validated. Additional MLP members had reduction in protein accumulation, in varying degrees, mediated by LCR F-Box. Transgenic Arabidopsis lines, in which MLP28 expression was reduced through an artificial miRNA technology, displayed severe developmental defects, including changes in leaf patterning and morphology, shoot apex defects, and eventual premature death. These phenotypic characteristics resemble those of Arabidopsis plants modified to over-express LCR. Taken together, the results demonstrate that MLPs are driven to degradation by LCR, and indicate that MLP gene family is target of miR394-LCR regulatory node, representing potential targets for directly post-translational regulation mediated by LCR F-Box. In addition, MLP28 family member is associated with the LCR regulation that is critical for normal Arabidopsis development.

DOI 10.1074/mcp.M115.053124
Citations Scopus - 2Web of Science - 1
2016 Curtin SJ, Michno JM, Campbell BW, Gil-Humanes J, Mathioni SM, Hammond R, et al., 'MicroRNA maturation and microRNA target gene expression regulation are severely disrupted in soybean dicer-like1 double mutants', G3: Genes, Genomes, Genetics, 6 423-433 (2016) [C1]

© 2016 Curtin et al. Small nonprotein-coding microRNAs (miRNAs) are present in most eukaryotes and are central effectors of RNA silencing-mediated mechanisms for gene expression ... [more]

© 2016 Curtin et al. Small nonprotein-coding microRNAs (miRNAs) are present in most eukaryotes and are central effectors of RNA silencing-mediated mechanisms for gene expression regulation. In plants, DICER-LIKE1 (DCL1) is the founding member of a highly conserved family of RNase III-like endonucleases that function as core machinery proteins to process hairpin-like precursor transcripts into mature miRNAs, small regulatory RNAs, 21-22 nucleotides in length. Zinc finger nucleases (ZFNs) were used to generate single and doublemutants of putative soybean DCL1 homologs, DCL1a and DCL1b, to confirm their functional role(s) in the soybean miRNA pathway. Neither DCL1 single mutant, dcl1a or dcl1b plants, exhibited a pronounced morphological or molecular phenotype. However, the dcl1a/dcl1b double mutant expressed a strong morphological phenotype, characterized by reduced seed size and aborted seedling development, in addition to defective miRNA precursor transcript processing efficiency and deregulated miRNA target gene expression. Together, these findings indicate that the two soybean DCL1 paralogs, DCL1a and DCL1b, largely play functionally redundant roles in the miRNA pathway and are essential for normal plant development.

DOI 10.1534/g3.115.022137
Citations Scopus - 2Web of Science - 1
2016 Reis RS, Eamens AL, Roberts TH, Waterhouse PM, 'Chimeric DCL1-Partnering Proteins Provide Insights into the MicroRNA Pathway', FRONTIERS IN PLANT SCIENCE, 6 (2016) [C1]
DOI 10.3389/fpls.2015.01201
2016 Reilly JN, McLaughlin EA, Stanger SJ, Anderson AL, Hutcheon K, Church K, et al., 'Characterisation of mouse epididymosomes reveals a complex profile of microRNAs and a potential mechanism for modification of the sperm epigenome', SCIENTIFIC REPORTS, 6 (2016) [C1]
DOI 10.1038/srep31794
Citations Scopus - 6Web of Science - 5
Co-authors Janet Holt, Brett Nixon, Eileen Mclaughlin
2015 Reis RS, Hart-Smith G, Eamens AL, Wilkins MR, Waterhouse PM, 'Gene regulation by translational inhibition is determined by Dicer partnering proteins', NATURE PLANTS, 1 (2015) [C1]
DOI 10.1038/NPLANTS.2014.27
Citations Scopus - 18Web of Science - 16
2015 Reis RS, Eamens AL, Waterhouse PM, 'Missing Pieces in the Puzzle of Plant MicroRNAs', Trends in Plant Science, 20 721-728 (2015) [C1]

© 2015 Elsevier Ltd. Plant microRNAs (miRNAs) are important regulatory switches. Recent advances have revealed many regulatory layers between the two essential processes, miRNA b... [more]

© 2015 Elsevier Ltd. Plant microRNAs (miRNAs) are important regulatory switches. Recent advances have revealed many regulatory layers between the two essential processes, miRNA biogenesis and function. However, how these multilayered regulatory processes ultimately control miRNA gene regulation and connects miRNAs and plant responses with the surrounding environment is still largely unknown. In this opinion article, we propose that the miRNA pathway is highly dynamic and plastic. The apparent flexibility of the miRNA pathway in plants appears to be controlled by a number recently identified proteins and poorly characterized signaling cascades. We further propose that altered miRNA accumulation can be a direct consequence of the rewiring of interactions between proteins that function in the miRNA pathway, an avenue that remains largely unexplored. Plant miRNAs are produced in nuclear dicing bodies (D-bodies).Plant miRNAs can guide either transcript cleavage or translation inhibition, and these mechanisms of silencing are defined by the dicer partnering proteins, presumably in the D-bodies.Newly discovered proteins involved in D-body formation and activity suggest the presence of a complex network of connections among D-body activity, signaling cascades, and responses to the surrounding environment.

DOI 10.1016/j.tplants.2015.08.003
Citations Scopus - 7Web of Science - 6
2015 Reis RS, Hart-Smith G, Eamens AL, Wilkins MR, Waterhouse PM, 'MicroRNA regulatory mechanisms play different roles in arabidopsis', Journal of Proteome Research, 14 4743-4751 (2015) [C1]

© 2015 American Chemical Society. Plant microRNAs (miRNAs) operate by guiding the cleavage or translational inhibition of mRNA targets. They act as key gene regulators for develo... [more]

© 2015 American Chemical Society. Plant microRNAs (miRNAs) operate by guiding the cleavage or translational inhibition of mRNA targets. They act as key gene regulators for development and environmental adaptation, and Dicer-partnering proteins DRB1 and DRB2 govern which form of regulation plays the dominant role. Mutation of Drb1 impairs transcript cleavage, whereas mutation of Drb2 ablates translational inhibition. Regulation of gene expression by miRNA-guided cleavage has been extensively studied, but there is much less information about genes regulated through miRNA-mediated translation inhibition. Here, we compared the proteomes of drb1 and drb2 mutants to gain insight into the indirect effect of the different miRNA regulatory mechanisms in Arabidopsis thaliana. Our results show that miRNAs operatin g through transcript cleavage regulate a broad spectrum of processes, including catabolism and anabolism, and this was particularly obvious in the fatty acid degradation pathway. Enzymes catalyzing each step of this pathway were upregulated in drb1. In contrast, DRB2-associated translational inhibition appears to be less ubiquitous and specifically aimed toward responses against abiotic or biotic stimuli.

DOI 10.1021/acs.jproteome.5b00616
Citations Scopus - 3Web of Science - 3
2014 Eamens AL, McHale M, Waterhouse PM, 'The use of artificial MicroRNA technology to control gene expression in Arabidopsis thaliana', Methods in Molecular Biology, 1062 211-224 (2014)

In plants, double-stranded RNA (dsRNA) is an effective trigger of RNA silencing, and several classes of endogenous small RNA (sRNA), processed from dsRNA substrates by DICER-like ... [more]

In plants, double-stranded RNA (dsRNA) is an effective trigger of RNA silencing, and several classes of endogenous small RNA (sRNA), processed from dsRNA substrates by DICER-like (DCL) endonucleases, are essential in controlling gene expression. One such sRNA class, the microRNAs (miRNAs) control the expression of closely related genes to regulate all aspects of plant development, including the determination of leaf shape, leaf polarity, flowering time, and floral identity. A single miRNA sRNA silencing signal is processed from a long precursor transcript of nonprotein-coding RNA, termed the primary miRNA (pri-miRNA). A region of the pri-miRNA is partially self-complementary allowing the transcript to fold back onto itself to form a stem-loop structure of imperfectly dsRNA. Artificial miRNA (amiRNA) technology uses endogenous pri-miRNAs, in which the miRNA and miRNA*(passenger strand of the miRNA duplex) sequences have been replaced with corresponding amiRNA/ amiRNA*sequences that direct highly efficient RNA silencing of the targeted gene. Here, we describe the rules for amiRNA design, as well as outline the PCR and bacterial cloning procedures involved in the construction of an amiRNA plant expression vector to control target gene expression in Arabidopsis thaliana. © 2014 Springer Science+Business Media New York.

DOI 10.1007/978-1-62703-580-4_11
Citations Scopus - 4
2014 Eamens AL, McHale M, Waterhouse PM, 'The use of artificial MicroRNA technology to control gene expression in Arabidopsis thaliana', Methods in Molecular Biology, 1062 211-224 (2014) [C1]

In plants, double-stranded RNA (dsRNA) is an effective trigger of RNA silencing, and several classes of endogenous small RNA (sRNA), processed from dsRNA substrates by DICER-like ... [more]

In plants, double-stranded RNA (dsRNA) is an effective trigger of RNA silencing, and several classes of endogenous small RNA (sRNA), processed from dsRNA substrates by DICER-like (DCL) endonucleases, are essential in controlling gene expression. One such sRNA class, the microRNAs (miRNAs) control the expression of closely related genes to regulate all aspects of plant development, including the determination of leaf shape, leaf polarity, flowering time, and floral identity. A single miRNA sRNA silencing signal is processed from a long precursor transcript of nonprotein-coding RNA, termed the primary miRNA (pri-miRNA). A region of the pri-miRNA is partially self-complementary allowing the transcript to fold back onto itself to form a stem-loop structure of imperfectly dsRNA. Artificial miRNA (amiRNA) technology uses endogenous pri-miRNAs, in which the miRNA and miRNA*(passenger strand of the miRNA duplex) sequences have been replaced with corresponding amiRNA/ amiRNA*sequences that direct highly efficient RNA silencing of the targeted gene. Here, we describe the rules for amiRNA design, as well as outline the PCR and bacterial cloning procedures involved in the construction of an amiRNA plant expression vector to control target gene expression in Arabidopsis thaliana. © 2014 Springer Science+Business Media New York.

DOI 10.1007/978-1-62703-580-4_11
Citations Scopus - 4
2014 Eamens AL, Smith NA, Dennis ES, Wassenegger M, Wang M-B, 'In Nicotiana species, an artificial microRNA corresponding to the virulence modulating region of Potato spindle tuber viroid directs RNA silencing of a soluble inorganic pyrophosphatase gene and the development of abnormal phenotypes', VIROLOGY, 450 266-277 (2014) [C1]
DOI 10.1016/j.virol.2013.12.019
Citations Scopus - 21Web of Science - 19
2013 McHale M, Eamens AL, Finnegan EJ, Waterhouse PM, 'A 22-nt artificial microRNA mediates widespread RNA silencing in Arabidopsis', PLANT JOURNAL, 76 519-529 (2013) [C1]
DOI 10.1111/tpj.12306
Citations Scopus - 11Web of Science - 12
2012 Agius C, Eamens AL, Millar AA, Watson JM, Wang MB, 'RNA silencing and antiviral defense in plants', Methods in Molecular Biology, 894 17-38 (2012)

Given the widespread impact of RNA silencing on the Arabidopsis thaliana genome, it is indeed remarkable that this means of gene regulation went undiscovered for so long. Since th... [more]

Given the widespread impact of RNA silencing on the Arabidopsis thaliana genome, it is indeed remarkable that this means of gene regulation went undiscovered for so long. Since the publication of landmark papers in 1998 (Fire et al., Nature 391:806-811, 1998; Waterhouse et al., Proc Natl Acad Sci USA 95:13959-13964, 1998), intense research efforts have resulted in much progress from the speculation of Mello and colleagues that "the mechanisms underlying RNA interference probably exist for a biological purpose" (Fire et al., Nature 391:806-811, 1998). Across the eukaryotic kingdom, with the notable exception of Saccharomyces cerevisiae (Moazed, Science 326:544-550, 2009), the importance of small RNA-driven gene regulation has been recognized and implicated in central developmental processes as well as in aberrant and diseased states. Plants have by far the most complex RNA-based control of gene expression (Wang et al., Floriculture, ornamental and plant biotechnology, vol. III, 2006). Four distinct RNA silencing pathways have been recognized in plants, albeit with considerable conservation of the molecular components. These pathways are directed by various small RNA species, including microRNAs (miRNAs), trans-acting small interfering RNAs (siRNA) (ta-siRNAs), repeat-associated siRNAs (ra-siRNAs), and natural antisense transcript siRNAs (nat-siRNAs). The effective functionality of each of these pathways appear to be fundamental to the integrity of A. thaliana. Furthermore, in response to viral invasion, plants synthesize viral sRNAs as a means of defense. This process may in fact reflect the ancient origins of RNA silencing: plants may have evolved RNA silencing pathways as a defense mechanism against foreign nucleic acid species in the absence of an immune system (Wang and Metzlaff, Curr Opin Plant Biol 8:216-222, 2005). The generation of viral siRNAs is a particularly interesting illustration of RNA silencing as it provides a context to explore the potential to harness a naturally occurring system to the end goal of artificially engineering viral resistance. © 2012 Springer Science+Business Media, LLC.

DOI 10.1007/978-1-61779-882-5_2
Citations Scopus - 1
2012 Smith NA, Eamens AL, 'Isolation and detection of small RNAs from plant tissues', Methods in Molecular Biology, 894 155-172 (2012)

In plants, several classes of non-coding small RNA (sRNA) have been shown to be important regulators of gene expression in a wide variety of biological processes. The two main cla... [more]

In plants, several classes of non-coding small RNA (sRNA) have been shown to be important regulators of gene expression in a wide variety of biological processes. The two main classes of sRNA, the small-interfering RNA (siRNA) and microRNA (miRNA) classes, are well documented and several experimental approaches have been developed to allow for their routine isolation and detection from plant tissues. Here, we describe the current methods used for the isolation of total RNA and the subsequent enrichment of low-molecular-weight (LMW) RNA species, as well as to outline how sRNAs are detected from such nucleic acid preparations. © 2012 Springer Science+Business Media, LLC.

DOI 10.1007/978-1-61779-882-5_11
2012 Eamens AL, Kim KW, Waterhouse PM, 'DRB2, DRB3 and DRB5 function in a non-canonical microRNA pathway in Arabidopsis thaliana', Plant Signaling and Behavior, 7 (2012)

DOUBLE-STRANDED RNA BIN DIN G (DRB) proteins have been functionally characterized in viruses, prokaryotes and eukaryotes and are involved in all aspects of RNA biology. Arabidopsi... [more]

DOUBLE-STRANDED RNA BIN DIN G (DRB) proteins have been functionally characterized in viruses, prokaryotes and eukaryotes and are involved in all aspects of RNA biology. Arabidopsis thaliana (Arabidopsis) encodes five closely related DRB proteins, DRB1 to DRB5. DRB1 and DRB4 are required by DICER-LIKE (DCL) proteins DCL1 and DCL4 to accurately and efficiently process structurally distinct double-stranded RNA (dsRNA) precursor substrates in the microRNA (miRNA) and trans-acting small-interfering RNA (tasiRNA) biogenesis pathways respectively. We recently reported that DRB2 is also involved in the biogenesis of specific miRNA subsets. Furthermore, the severity of the developmental phenotype displayed by the drb235 triple mutant plant, compared with those expressed by either drb2, drb3 and drb5 single mutants, or double mutant combinations thereof, indicates that DRB3 and DRB5 function in the same non-canonical miRNA pathway as DRB2. Through the use of our artificial miRNA (amiRNA) plant expression vector, pBlueGreen 2,3 we demonstrate here that unlike DRB2, DRB3 and DRB5 are not involved in the dsRNA processing stages of the miRNA biogenesis pathway, but are required to mediate RNA silencing of target genes of DRB2-associated miRNA s. © 2012 Landes Bioscience.

Citations Scopus - 6
2012 Eamens AL, Wook Kim K, Waterhouse PM, 'DRB2, DRB3 and DRB5 function in a non-canonical microRNA pathway in Arabidopsis thaliana.', Plant signaling & behavior, 7 1224-1229 (2012)

DOUBLE-STRANDED RNA BINDING (DRB) proteins have been functionally characterized in viruses, prokaryotes and eukaryotes and are involved in all aspects of RNA biology. Arabidopsis ... [more]

DOUBLE-STRANDED RNA BINDING (DRB) proteins have been functionally characterized in viruses, prokaryotes and eukaryotes and are involved in all aspects of RNA biology. Arabidopsis thaliana (Arabidopsis) encodes five closely related DRB proteins, DRB1 to DRB5. DRB1 and DRB4 are required by DICER-LIKE (DCL) proteins DCL1 and DCL4 to accurately and efficiently process structurally distinct double-stranded RNA (dsRNA) precursor substrates in the microRNA (miRNA) and trans-acting small-interfering RNA (tasiRNA) biogenesis pathways respectively. We recently reported that DRB2 is also involved in the biogenesis of specific miRNA subsets. ( 1) Furthermore, the severity of the developmental phenotype displayed by the drb235 triple mutant plant, compared with those expressed by either drb2, drb3 and drb5 single mutants, or double mutant combinations thereof, indicates that DRB3 and DRB5 function in the same non-canonical miRNA pathway as DRB2. Through the use of our artificial miRNA (amiRNA) plant expression vector, pBlueGreen ( 2) (,) ( 3) we demonstrate here that unlike DRB2, DRB3 and DRB5 are not involved in the dsRNA processing stages of the miRNA biogenesis pathway, but are required to mediate RNA silencing of target genes of DRB2-associated miRNAs.

Citations Scopus - 17Web of Science - 19
2012 Agius C, Eamens AL, Millar AA, Watson JM, Wang MB, 'RNA silencing and antiviral defense in plants.', Methods in molecular biology (Clifton, N.J.), 894 17-38 (2012)

Given the widespread impact of RNA silencing on the Arabidopsis thaliana genome, it is indeed remarkable that this means of gene regulation went undiscovered for so long. Since th... [more]

Given the widespread impact of RNA silencing on the Arabidopsis thaliana genome, it is indeed remarkable that this means of gene regulation went undiscovered for so long. Since the publication of landmark papers in 1998 (Fire et al., Nature 391:806-811, 1998; Waterhouse et al., Proc Natl Acad Sci U S A 95:13959-13964, 1998), intense research efforts have resulted in much progress from the speculation of Mello and colleagues that "the mechanisms underlying RNA interference probably exist for a biological purpose" (Fire et al., Nature 391:806-811, 1998). Across the eukaryotic kingdom, with the notable exception of Saccharomyces cerevisiae (Moazed, Science 326:544-550, 2009), the importance of small RNA-driven gene regulation has been recognized and implicated in central developmental processes as well as in aberrant and diseased states. Plants have by far the most complex RNA-based control of gene expression (Wang et al., Floriculture, ornamental and plant biotechnology, vol. III, 2006). Four distinct RNA silencing pathways have been recognized in plants, albeit with considerable conservation of the molecular components. These pathways are directed by various small RNA species, including microRNAs (miRNAs), trans-acting small interfering RNAs (siRNA) (ta-siRNAs), repeat-associated siRNAs (ra-siRNAs), and natural antisense transcript siRNAs (nat-siRNAs). The effective functionality of each of these pathways appear to be fundamental to the integrity of A. thaliana. Furthermore, in response to viral invasion, plants synthesize viral sRNAs as a means of defense. This process may in fact reflect the ancient origins of RNA silencing: plants may have evolved RNA silencing pathways as a defense mechanism against foreign nucleic acid species in the absence of an immune system (Wang and Metzlaff, Curr Opin Plant Biol 8:216-222, 2005). The generation of viral siRNAs is a particularly interesting illustration of RNA silencing as it provides a context to explore the potential to harness a naturally occurring system to the end goal of artificially engineering viral resistance.

Citations Scopus - 8
2012 Smith NA, Eamens AL, 'Isolation and detection of small RNAs from plant tissues.', Methods in molecular biology (Clifton, N.J.), 894 155-172 (2012) [C1]

In plants, several classes of non-coding small RNA (sRNA) have been shown to be important regulators of gene expression in a wide variety of biological processes. The two main cla... [more]

In plants, several classes of non-coding small RNA (sRNA) have been shown to be important regulators of gene expression in a wide variety of biological processes. The two main classes of sRNA, the small-interfering RNA (siRNA) and microRNA (miRNA) classes, are well documented and several experimental approaches have been developed to allow for their routine isolation and detection from plant tissues. Here, we describe the current methods used for the isolation of total RNA and the subsequent enrichment of low-molecular-weight (LMW) RNA species, as well as to outline how sRNAs are detected from such nucleic acid preparations.

Citations Scopus - 6
2012 Eamens AL, Kim KW, Curtin SJ, Waterhouse PM, 'DRB2 Is Required for MicroRNA Biogenesis in Arabidopsis thaliana', PLOS ONE, 7 (2012) [C1]
DOI 10.1371/journal.pone.0035933
Citations Scopus - 26Web of Science - 23
2011 Smith NA, Eamens AL, Wang M-B, 'Viral Small Interfering RNAs Target Host Genes to Mediate Disease Symptoms in Plants', PLOS PATHOGENS, 7 (2011) [C1]
DOI 10.1371/journal.ppat.1002022
Citations Scopus - 98Web of Science - 91
2011 Eamens AL, Wang MB, 'Alternate approaches to repress endogenous microRNA activity in Arabidopsis thaliana', Plant Signaling and Behavior, 6 349-359 (2011)

MicroRnAs (miRnAs) are an endogenous class of regulatory small RnA (sRnA). in plants, miRnAs are processed from short non-protein-coding messenger RnAs (mRnAs) transcribed from sm... [more]

MicroRnAs (miRnAs) are an endogenous class of regulatory small RnA (sRnA). in plants, miRnAs are processed from short non-protein-coding messenger RnAs (mRnAs) transcribed from small miRnA genes (MIR genes). Traditionally in the model plant Arabidopsis thaliana (Arabidopsis), the functional analysis of a gene product has relied on the identification of a corresponding T-DnA insertion knockout mutant from a large, randomly-mutagenized population. However, because of the small size of MIR genes and presence of multiple, highly conserved members in most plant miRnA families, it has been extremely laborious and time consuming to obtain a corresponding single or multiple, null mutant plant line. Our recent study published in Molecular Plant 1 outlines an alternate method for the functional characterization of miRnA action in Arabidopsis, termed anti-miRnA technology. Using this approach we demonstrated that the expression of individual miRnAs or entire miRnA families, can be readily and efficiently knocked-down. Our approach is in addition to two previously reported methodologies that also allow for the targeted suppression of either individual miRnAs, or all members of a MIR gene family; these include miRnA target mimicry 2,3 and transcriptional gene silencing (TGS) of MIR gene promoters. 4 All three methodologies rely on endogenous gene regulatory machinery and in this article we provide an overview of these technologies and discuss their strengths and weaknesses in inhibiting the activity of their targeted miRnA(s). © 2011 Landes Bioscience.

DOI 10.4161/psb.6.3.14340
Citations Scopus - 7
2011 Eamens AL, Agius C, Smith NA, Waterhouse PM, Wang M-B, 'Efficient Silencing of Endogenous MicroRNAs Using Artificial MicroRNAs in Arabidopsis thaliana', MOLECULAR PLANT, 4 157-170 (2011)
DOI 10.1093/mp/ssq061
Citations Scopus - 32Web of Science - 29
2011 Eamens AL, Waterhouse PM, 'Vectors and methods for hairpin RNA and artificial microRNA-mediated gene silencing in plants.', Methods in molecular biology (Clifton, N.J.), 701 179-197 (2011) [C1]

In plant cells, DICER-LIKE4 processes perfectly double-stranded RNA (dsRNA) into short interfering (si) RNAs, and DICER-LIKE1 generates micro (mi) RNAs from primary miRNA transcri... [more]

In plant cells, DICER-LIKE4 processes perfectly double-stranded RNA (dsRNA) into short interfering (si) RNAs, and DICER-LIKE1 generates micro (mi) RNAs from primary miRNA transcripts (pri-miRNA) that form fold-back structures of imperfectly dsRNA. Both si and miRNAs direct the endogenous endonuclease, ARGONAUTE1 to cleave complementary target single-stranded RNAs and either small RNA (sRNA)-directed pathway can be harnessed to silence genes in plants. A routine way of inducing and directing RNA silencing by siRNAs is to express self-complementary single-stranded hairpin RNA (hpRNA), in which the duplexed region has the same sequence as part of the target gene's mRNA. Artificial miRNA (amiRNA)-mediated silencing uses an endogenous pri-miRNA, in which the original miRNA/miRNA* sequence has been replaced with a sequence complementary to the new target gene. In this chapter, we describe the plasmid vector systems routinely used by our research group for the generation of either hpRNA-derived siRNAs or amiRNAs.

Citations Scopus - 16
2010 Smith NA, Eamens AL, Wang M-B, 'The presence of high-molecular-weight viral RNAs interferes with the detection of viral small RNAs', RNA-A PUBLICATION OF THE RNA SOCIETY, 16 1062-1067 (2010) [C1]
DOI 10.1261/rna.2049510
Citations Scopus - 14Web of Science - 12
2009 Eamens AL, Smith NA, Curtin SJ, Wang M-B, Waterhouse PM, 'The Arabidopsis thaliana double-stranded RNA binding protein DRB1 directs guide strand selection from microRNA duplexes', RNA-A PUBLICATION OF THE RNA SOCIETY, 15 2219-2235 (2009) [C1]
DOI 10.1261/rna.1646909
Citations Scopus - 91Web of Science - 89
2008 Curtin SJ, Watson JM, Smith NA, Eamens AL, Blanchard CL, Waterhouse PM, 'The roles of plant dsRNA-binding proteins in RNAi-like pathways', FEBS LETTERS, 582 2753-2760 (2008)
DOI 10.1016/j.febslet.2008.07.004
Citations Scopus - 54Web of Science - 52
2008 Eamens A, Wang M-B, Smith NA, Waterhouse PM, 'RNA silencing in plants: Yesterday, today, and tomorrow', PLANT PHYSIOLOGY, 147 456-468 (2008) [C1]
DOI 10.1104/pp.108.117275
Citations Scopus - 156Web of Science - 131
2008 Eamens A, Vaistij FE, Jones L, 'NRPD1a and NRPD1b are required to maintain post-transcriptional RNA silencing and RNA-directed DNA methylation in Arabidopsis', PLANT JOURNAL, 55 596-606 (2008) [C1]
DOI 10.1111/j.1365-313X.2008.03525.x
Citations Scopus - 32Web of Science - 30
2006 Jones L, Keining T, Eamens A, Vaistij FE, 'Virus-induced gene silencing of Argonaute genes in Nicotiana benthamiana demonstrates that extensive systemic silencing requires Argonaute1-like and Argonaute4-like genes', PLANT PHYSIOLOGY, 141 598-606 (2006)
DOI 10.1104/pp.105.076109
Citations Scopus - 45Web of Science - 44
2006 Upadhyaya NM, Zhu QH, Zhou XR, Eamens AL, Hoque MS, Ramm K, et al., 'Dissociation (Ds) constructs, mapped Ds launch pads and a transiently-expressed transposase system suitable for localized insertional mutagenesis in rice', THEORETICAL AND APPLIED GENETICS, 112 1326-1341 (2006)
DOI 10.1007/s00122-006-0235-0
Citations Scopus - 38Web of Science - 32
2006 Zhu Q-H, Ramm K, Eamens AL, Dennis ES, Upadhyaya NM, 'Transgene structures suggest that multiple mechanisms are involved in T-DNA integration in plants', PLANT SCIENCE, 171 308-322 (2006)
DOI 10.1016/j.plantsci.2006.03.019
Citations Scopus - 20Web of Science - 15
2004 Eamens AL, Blanchard CL, Dennis ES, Upadhyaya NM, 'A bidirectional gene trap construct suitable for T-DNA and Ds-mediated insertional mutagenesis in rice (Oryza sativa L.)', PLANT BIOTECHNOLOGY JOURNAL, 2 367-380 (2004)
DOI 10.1111/j.1467-7652.2004.00081.x
Citations Scopus - 28Web of Science - 22
2002 Upadhyaya NM, Zhou XR, Zhu QH, Ramm K, Wu LM, Eamens A, et al., 'An iAc/Ds gene and enhancer trapping system for insertional mutagenesis in rice', FUNCTIONAL PLANT BIOLOGY, 29 547-559 (2002)
DOI 10.1071/PP01205
Citations Scopus - 51Web of Science - 49
Show 30 more journal articles

Conference (1 outputs)

Year Citation Altmetrics Link
2000 Upadhyaya NM, Zhou XR, Zhu QH, Eamens A, Wang MB, Waterhouse PM, Dennis ES, 'Transgenic rice', TRANSGENIC CEREALS (2000)
Citations Web of Science - 9
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Grants and Funding

Summary

Number of grants 8
Total funding $657,186

Click on a grant title below to expand the full details for that specific grant.


20147 grants / $652,217

Expansion and Upgrade of the Newcastle Plant Growth Facility$230,000

Funding body: ARC (Australian Research Council)

Funding body ARC (Australian Research Council)
Project Team Associate Professor David McCurdy, Professor Christopher Grof, Doctor Andy Eamens, Professor Yong-Ling Ruan, Conjoint Professor Christina Offler
Scheme Linkage Infrastructure Equipment & Facilities (LIEF)
Role Investigator
Funding Start 2014
Funding Finish 2014
GNo G1300636
Type Of Funding Scheme excluded from IGS
Category EXCL
UON Y

Expansion and Upgrade of the Newcastle Plant Growth Facility$195,000

Funding body: University of Newcastle

Funding body University of Newcastle
Project Team Associate Professor David McCurdy, Professor Christopher Grof, Doctor Andy Eamens, Professor Yong-Ling Ruan, Conjoint Professor Christina Offler
Scheme Equipment Grant
Role Investigator
Funding Start 2014
Funding Finish 2014
GNo G1300231
Type Of Funding Internal
Category INTE
UON Y

GRS – Darren Cullerne (UNC) The molecular characterisation of vernalisation in Safflower via the development of genomic and transcriptomic resources$58,073

Funding body: Grains Research and Development Corporation

Funding body Grains Research and Development Corporation
Project Team Doctor Andy Eamens, Mr Darren Cullerne, Mr Craig Wood
Scheme Grains Industry Research Scholarship
Role Lead
Funding Start 2014
Funding Finish 2016
GNo G1400797
Type Of Funding Other Public Sector - Commonwealth
Category 2OPC
UON Y

GRS – Darren Cullerne (UNC) The molecular characterisation of vernalisation in Safflower via the development of genomic and transcriptomic resources$58,073

Funding body: Grains Research and Development Corporation

Funding body Grains Research and Development Corporation
Project Team Doctor Andy Eamens, Mr Darren Cullerne, Mr Craig Wood
Scheme Grains Industry Research Scholarship
Role Lead
Funding Start 2014
Funding Finish 2016
GNo G1400797
Type Of Funding Other Public Sector - Commonwealth
Category 2OPC
UON Y

OCE Top-up PhD – Uni Newcastle – Kim Zimmerman - Wang$51,000

Funding body: CSIRO - Commonwealth Scientific and Industrial Research Organisation

Funding body CSIRO - Commonwealth Scientific and Industrial Research Organisation
Project Team Mr Kim Zimmerman, Doctor Andy Eamens, Ms Ming-Bo Wang
Scheme Postgraduate Scholarship
Role Lead
Funding Start 2014
Funding Finish 2016
GNo G1400654
Type Of Funding Other Public Sector - Commonwealth
Category 2OPC
UON Y

The molecular characterisation of vernalisation in Safflower via the development of genomic and transcriptomic resources$47,301

Funding body: CSIRO - Commonwealth Scientific and Industrial Research Organisation

Funding body CSIRO - Commonwealth Scientific and Industrial Research Organisation
Project Team Mr Darren Cullerne, Doctor Andy Eamens, Mr Craig Wood
Scheme Postgraduate Scholarship
Role Lead
Funding Start 2014
Funding Finish 2016
GNo G1400682
Type Of Funding Other Public Sector - Commonwealth
Category 2OPC
UON Y

The identification of DOUBLE-STRANDED RNA-BINDING protein dependent small RNAs.$12,770

Funding body: University of Newcastle - Faculty of Science & IT

Funding body University of Newcastle - Faculty of Science & IT
Project Team Doctor Andy Eamens
Scheme Strategic Initiative Research Fund (SIRF)
Role Lead
Funding Start 2014
Funding Finish 2014
GNo G1401037
Type Of Funding Internal
Category INTE
UON Y

20131 grants / $4,969

Discovering roles for the five members of the DOUBLE-STRANDED RNA BINDING (DRB) protein family in the small RNA-directed RNA silencing pathways of the model plant species Arabidopsis thaliana$4,969

Funding body: University of Newcastle

Funding body University of Newcastle
Project Team Doctor Andy Eamens
Scheme New Staff Grant
Role Lead
Funding Start 2013
Funding Finish 2013
GNo G1300981
Type Of Funding Internal
Category INTE
UON Y
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Research Supervision

Number of supervisions

Completed2
Current7

Total current UON EFTSL

Masters0.2
PhD2.55

Current Supervision

Commenced Level of Study Research Title Program Supervisor Type
2017 PhD Identification of Genetic Bottlenecks Limiting Assimilate Utilization in Plant Reproductive Organs PhD (Biological Sciences), Faculty of Science, The University of Newcastle Co-Supervisor
2016 PhD Molecular mechanisms underlying the transcriptional control of secondary cell wall biosynthesis in the stem of the C4 model plant Setaria viridis (Green foxtail) PhD (Biological Sciences), Faculty of Science, The University of Newcastle Co-Supervisor
2016 Masters Investigating the Profile of miRNAs in the Mammalian Male Reproductive Tract M Philosophy (Biological Sc), Faculty of Science, The University of Newcastle Co-Supervisor
2016 PhD Characterisation of Small RNA-Mediated Drought and Salt Stress Tolerance in the Model Plant Arabidopsis Thaliana PhD (Biological Sciences), Faculty of Science, The University of Newcastle Principal Supervisor
2014 PhD Small RNA-Directed, Auxin-Mediated Plant Defence Response to Fusarium Oxysporum Infection PhD (Biological Sciences), Faculty of Science, The University of Newcastle Principal Supervisor
2013 PhD The Development of Setaria Species as a Model System to Investigate Type II Cell Wall Construction, Deconstruction and Biomass Quality Traits PhD (Biological Sciences), Faculty of Science, The University of Newcastle Co-Supervisor
2013 PhD Identification of Regulatory Genes Controlling Cell Wall Invertase Expression in Arabidopsis Reproductive Organs PhD (Biological Sciences), Faculty of Science, The University of Newcastle Co-Supervisor

Past Supervision

Year Level of Study Research Title Program Supervisor Type
2017 PhD The Molecular Characterisation of the Vernalisation Response in Safflower via the Development of Genomic and Transcriptomic Resources PhD (Biological Sciences), Faculty of Science, The University of Newcastle Principal Supervisor
2017 PhD Contributions of DOUBLE-STRANDED RNA BINDING 2 to the Arabidopsis sRNA landscape PhD (Biological Sciences), Faculty of Science, The University of Newcastle Principal Supervisor
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Dr Andy Eamens

Position

Lecturer
Plant Science Group
School of Environmental and Life Sciences
Faculty of Science

Contact Details

Email andy.eamens@newcastle.edu.au
Phone (02) 4921 7784

Office

Room B105
Building Biology Building.
Location Callaghan
University Drive
Callaghan, NSW 2308
Australia
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