Dr Iain Searle

Iain Searle
Deputy Head of Genetics and Evolution
School of Biological Sciences
Faculty of Sciences

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Dr Iain Searle

Our research in plant and animal epigenetics has been driven by a strong interest in understanding and elucidating the molecular mechanisms of how plants and animals adapt to environmental signalling and how speciation barriers evolve in plants.

Epigenetics, broadly defined, refers to all genetic information not encoded in the DNA sequence, with the best-understood consequence of epigenetic modifications being the regulation of gene expression. Although gene transcription and protein synthesis is required for plant development, the full repertoire of epigenetic mechanisms underpinning biological adaptation and speciation barriers remain equivocal. Post-translational modification of histone proteins (i.e. acetylation, ubiquitination, etc) and the covalent modification of DNA (i.e. adenine methylation, cytosine methylation and other recently discovered marks) can influence the function of the genome in a myriad of ways, for example regulation of alternative splicing. In addition, the majority of the genome is pervasively transcribed such that more than 90% of transcriptional activity is related to the production of various long non-coding RNAs (lncRNA), which possess no or limited protein-coding capacity. Expansion of these transcriptionally active non-coding sequences in plant and animal genomes appears to have occurred primarily in higher multicellular organisms.

Furthermore, emerging evidence from our laboratory and others that RNA modifications play an important role in extending the transcriptional space. Thus, both RNA modifications and lncRNAs represent attractive candidates for achieving context- and stimulus-specific epigenetic regulation of gene expression.

Fundamental Research-  We currently use a combination of molecular genetics, epigenomics and bioinformatics (high performance computing) to answer our research questions on long non-coding RNAs and RNA modifications. Honours, Masters, PhD and postdoctoral projects in genetics, epigenetics and bioinformatics are available.

Translational Research- We recently translated our wide-hybridisation technology to the Australian canola (Brassica napus) industry. In doing so we introduced disease resistance genes from either B. rapa or B. oleracea to synthesise B. napus (canola) with novel disease resistance. We are currently extending our translational canola research by connecting with international partners. Honours, Masters and PhD projects are available to develop the technology further in collaboration with industry partners. Are you a potential industry partner and want to connect? Don't hesitate to contact me.

Interested in joining our laboratory as an undergraduate placement student or postgraduate student? What to join our mentor programme? Ready to excel and be challenged with fascinating biological questions? Please don't hesitate to email me.

Publications- https://scholar.google.com.au/citations?user=F23tKLkAAAAJ&hl=en

Appointments

Date Position Institution name
2013 ARC Future Fellow University of Adelaide
2009 - 2013 ARC QEII Fellow Australian National University

Language Competencies

Language Competency
German Can speak and understand spoken

Education

Date Institution name Country Title
2004 University of Queensland Australia PhD
1996 University of Queensland Australia B Ag Sci Hons

Postgraduate Training

Date Title Institution Country
2007 - 2009 Wellcome Trust VIP Fellow University of Cambridge United Kingdom
2006 - 2007 Marie Curie Postdoctoral Fellow The Sainsbury Laboratory United Kingdom
2002 - 2006 Max Planck Postdoctoral Fellow Max Planck Institute for Plant Breeding Research Germany

Journals

Year Citation
2017 David, R., Burgess, A., Parker, B., Li, J., Pulsford, K., Sibbritt, T. ... Searle, I. (2017). Transcriptome-wide Mapping of RNA 5-Methylcytosine in Arabidopsis mRNAs and non-coding RNAs. The Plant cell, 29, 3, 16.00751-1-16.0075-30. 10.1105/tpc.16.00751
2017 Crisp, P., Ganguly, D., Smith, A., Murray, K., Estavillo, G., Searle, I. ... Pogson, B. (2017). Rapid recovery gene downregulation during excess-light stress and recovery in Arabidopsis. The Plant Cell, OnlinePubl, 8, 1-52. 10.1105/tpc.16.00828
2017 Wang, D., Qu, Z., Yang, L., Zhang, Q., Liu, Z., Do, T. ... Zhu, J. (2017). Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in plants. Plant Journal, 90, 1, 133-146. 10.1111/tpj.13481
2016 Burgess, A., David, R. & Searle, I. (2016). Deciphering the epitranscriptome: a green perspective. Journal of Integrative Plant Biology, 58, 10, 822-835. 10.1111/jipb.12483
2016 Chen, M., Xu, J., Devis, D., Shi, J., Ren, K., Searle, I. & Zhang, D. (2016). Origin and functional prediction of pollen allergens in plants. Plant Physiology, 172, 1, 341-357. 10.1104/pp.16.00625
2016 Ashby, R., Forêt, S., Searle, I. & Maleszka, R. (2016). MicroRNAs in Honey Bee Caste Determination. Scientific Reports, 6, 1, -. 10.1038/srep18794
2015 Liu, H., Searle, I. R., Mather, D. E., Able, A. J. & Able, J. A. (2015). Morphological, physiological and yield responses of durum wheat to pre-anthesis water-deficit stress are genotype-dependent. Crop and Pasture Science, 66, 10, 1024-1038. 10.1071/CP15013
2015 Liu, H., Searle, I., Watson-Haigh, N., Baumann, U., Mather, D., Able, A. & Able, J. (2015). Genome-wide identification of microRNAs in leaves and the developing head of four durum genotypes during water deficit stress. PLoS One, 10, 11, e0142799-1-e0142799-30. 10.1371/journal.pone.0142799
2015 Burgess, A., David, R. & Searle, I. (2015). Conservation of tRNA and rRNA 5-methylcytosine in the kingdom Plantae. BMC Plant Biology, 15, 1, 199-1-199-17. 10.1186/s12870-015-0580-8
2013 Cazzonelli, C., Vanstraelen, M., Simon, S., Yin, K., Carron-Arthur, A., Nisar, N. ... Pogson, B. (2013). Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. PLoS One, 8, 7, 1-14. 10.1371/journal.pone.0070069
2012 Campoli, C., Drosse, B., Searle, I., Coupland, G. & von Korff, M. (2012). Functional characterisation of HvCO1, the barley (Hordeum vulgare) flowering time ortholog of CONSTANS. The Plant Journal, 69, 5, 868-880. 10.1111/j.1365-313X.2011.04839.x
2011 Castro Marín, I., Loef, I., Bartetzko, L., Searle, I., Coupland, G., Stitt, M. & Osuna, D. (2011). Nitrate regulates floral induction in Arabidopsis, acting independently of light, gibberellin and autonomous pathways. Planta, 233, 3, 539-552. 10.1007/s00425-010-1316-5
2011 Gursanscky, N., Searle, I. & Carroll, B. (2011). Mobile microRNAs hit the target. Traffic, 12, 11, 1475-1482. 10.1111/j.1600-0854.2011.01253.x
2011 Burgess, A. & Searle, I. (2011). The clock primes defense at dawn. Immunology and Cell Biology, 89, 6, 661-662. 10.1038/icb.2011.30
2011 Indrasumunar, A., Searle, I., Lin, M., Kereszt, A., Men, A., Carroll, B. & Gresshoff, P. (2011). Nodulation factor receptor kinase 1α controls nodule organ number in soybean (Glycine max L. Merr). The Plant Journal, 65, 1, 39-50. 10.1111/j.1365-313X.2010.04398.x
2010 Searle, I., Pontes, O., Melnyk, C., Smith, L. & Baulcombe, D. (2010). JMJ14, a JmjC domain protein, is required for RNA silencing and cell-to-cell movement of an RNA silencing signal in Arabidopsis. Genes and Development, 24, 10, 986-991. 10.1101/gad.579910
2010 Indrasumunar, A., Kereszt, A., Searle, I., Miyagi, M., Li, D., Nguyen, C. ... Gresshoff, P. (2010). Inactivation of duplicated nod factor receptor 5 (NFR5) genes in recessive loss-of-function non-nodulation mutants of allotetraploid soybean (Glycine max L. Merr.). Plant and Cell Physiology, 51, 2, 201-214. 10.1093/pcp/pcp178
2009 Huang, L., Jones, A., Searle, I., Patel, K., Vogler, H., Hubner, N. & Baulcombe, D. (2009). An atypical RNA polymerase involved in RNA silencing shares small subunits with RNA polymerase II. Nature Structural and Molecular Biology, 16, 1, 91-93. 10.1038/nsmb.1539
2007 Corbesier, L., Vincent, C., Jang, S., Fornara, F., Fan, Q., Searle, I. ... Coupland, G. (2007). FT protein movement contributes to long-distance signaling in floral induction of Arabidopsis. Science, 316, 5827, 1030-1033. 10.1126/science.1141752
2007 Smith, L., Pontes, O., Searle, I., Yelina, N., Yousafzai, F., Herr, A. ... Baulcombe, D. (2007). An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. Plant Cell, 19, 5, 1507-1521. 10.1105/tpc.107.051540
2006 Searle, I., He, Y., Turck, F., Vincent, C., Fornara, F., Kröber, S. ... Coupland, G. (2006). The transcription factor FLC confers a flowering response to vernalization by repressing meristem competence and systemic signaling in Arabidopsis. Genes and Development, 20, 7, 898-912. 10.1101/gad.373506
2006 Corbesier, L., Vincent, C., Searle, I., Fomara, F. & Coupland, G. (2006). Analysis of the expression pattern of FT protein during flowering. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY, 143, 4, S166-S166.
2005 Berendzen, K., Searle, I., Ravenscroft, D., Koncz, C., Batschauer, A., Coupland, G. ... Ülker, B. (2005). A rapid and versatile combined DNA/RNA extraction protocol and its application to the analysis of a novel DNA marker set polymorphic between Arabidopsis thaliana ecotypes Col-0 and Landsberg erecta. Plant Methods, 1, 1, -. 10.1186/1746-4811-1-4
2004 Searle, I. & Coupland, G. (2004). Induction of flowering by seasonal changes in photoperiod. EMBO Journal, 23, 6, 1217-1222. 10.1038/sj.emboj.7600117
2003 Searle, I., Men, A., Laniya, T., Buzas, D., Iturbe-Ormaetxe, I., Carroll, B. & Gresshoff, P. (2003). Long-distance signaling in nodulation directed by a CLAVATA1-like receptor kinase. Science, 299, 5603, 109-112. 10.1126/science.1077937
2003 Waldron, J., Peace, C., Searle, I., Furtado, A., Wade, N., Findlay, I. ... Carroll, B. (2003). Randomly Amplified DNA Fingerprinting: A culmination of DNA marker technologies based on arbitrarily-primed PCR amplification. Journal of Biomedicine and Biotechnology, 2, 3, 141-150. 10.1155/S1110724302206026
2002 Waldron, J., Peace, C., Searle, I., Furtado, A., Wade, N., Findlay, I. ... Carroll, B. (2002). Randomly amplified DNA fingerprinting: A culmination of DNA marker technologies based on arbitrarily-primed PCR amplification. Journal of Biomedicine and Biotechnology, 2002, 3, 141-150. 10.1155/S1110724302206026
2002 May, K., Whisson, S., Zwart, R., Searle, I., Irwin, J., Maclean, D. ... Drenth, A. (2002). Inheritance and mapping of 11 avirulence genes in Phytophthora sojae. Fungal Genetics and Biology, 37, 1, 1-12. 10.1016/S1087-1845(02)00027-0
1999 Schenk, G., Ge, Y., Carrington, L., Wynne, C., Searle, I., Carroll, B. ... De Jersey, J. (1999). Binuclear metal centers in plant purple acid phosphatases: Fe-Zn in sweet potato and Fe-Zn in soybean. Archives of Biochemistry and Biophysics, 370, 2, 183-189. 10.1006/abbi.1999.1407

Conference Papers

Year Citation
2007 Searle, I., Mosher, R., Melnyk, C. & Baulcombe, D. (2007). Small RNAs hit the big time: Meetings. England. 10.1111/j.1469-8137.2007.02070.x

Conference Items

Year Citation
2015 David, R., Lim, H. M. & Searle, I. R. (2015). Identification of pla/ubp14, an Arabidopsis mutant that displays lengthened plastochron and larger organs. Annual Genetics Society of Australasia conference.

Theses

Year Citation
2016 Liu, H.; (2016); Genome-wide characterisation of microRNAs and their target genes in different durum wheat genotypes under water limiting conditions;

Datasets

Year Citation
2015 Liu, H., Searle, I., Watson-Haigh, , Baumann, , Mather, D. E., Able, A. J. & Able, J. A.; (2015); Genome-wide identification of differentially expressed microRNAs in leaves and the developing head of four durum genotypes during water deficit stress;

Competitive funding only listed below

  • Hermon Slade Foundation- Investigator Searle (2017-2020)
  • ACSRF Australia-China Joint Research Centre of Grains for Health- Investigators Gibosn, Searle, et al (2016-2019)
  • ASTE Travel Grant- Investigator Searle (2015)
  • ACSRF Australia-China Young Scientists Exchange Programme- Investigator Searle (2014)
  • ARC Future Fellowship FT130100525- Investigator Searle (2014-2018)
  • GRDC E-Innovation award- EzyCross- Investigators Searle & Salisbury (2013-2014)
  • GRDC Travel Grant- Investigator Searle (2013)
  • ANU Connect Ventures Direct Translation Fund- Investigators Lohe and Searle (2012)
  • CSIRO SEIF top-up PhD scholarship- Investigators Searle and Helliwell (2011-2013)
  • ARC Discovery Grant DP110103805- Investigators Searle and Helliwell (2011-2013)
  • ARC QEII Fellowship DP0988846- Investigator Searle (2009-2014)
  • Wellcome Trust Value-In-People Award- Investigator Searle (2008-2009)
  • Epigenome travel scholarship- Investigator Searle (2007)
  • Marie Curie International Incoming Fellowship- Investigator Searle (2006-2007)
  • MICRO 2500 - Microbiology II
  • GENETICS 2510 - Genetics IIA
  • GENETICS 3211 - Gene Expression & Human Developmental Genetics III
  • SCIENCE 3500- Opening Doors to the Middle Kingdom
  • Acting honours convenor March-September 2016

Research Assistant

  • Hoang Nguyen

PhD students- primary supervisor

  • Trung Do
  • Jun Li
  • Jing Zhao
  • Xingyu Wu
  •  

PhD students- co-supervisor

  • Haipei Liu
  • Deborah Devis

Masters students- primary supervisor

Honours Students- primary supervisor

  • Samuel Deed
  • Pei Qin

Undergraduate mentor programme

  • Pei Ng

Alumni

  • Rakesh David (Postdoctoral Fellow)
  • Alice Burgess (PhD)
  • Hua Deng (joint CSC PhD)
  • Peter Crisp (PhD)
  • Bruce Tsai (Masters)
  • Kalinya Pulsford (Honours)
  • Han Lim (Honours) 
  • Eliska Zlamalova (undergraduate)
  • Graham Gower (undergraduate)
  • Tyrone Chen (undergraduate)
  • Gauri Tarle (overseas visitor)
  • Arlet Estevez ​ (overseas visitor)
  • Franziska Gruhl (overseas visitor)

Editorial Boards

Date Role Editorial Board Name Country
2011 - ongoing Consulting Editor Frontiers in Genetics and Genomics

Offices Held

Date Office Name Institution Country
2016 - 2019 Deputy Head of the Department of Genetics and Evolution School of Biological Sciences, The University of Adelaide Australia
2015 - ongoing GSA South Australian Representative on Executive Genetics Society of AustralAsia Australia
Position
Deputy Head of Genetics and Evolution
Phone
83133266
Fax
8313 4362
Campus
North Terrace
Building
Molecular Life Sciences
Room Number
2 31
Org Unit
Genetics & Evolution

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