Thomas E Bureau
Molecular evolution of genes and genomes, with an emphasis on the involvement of mobile elements in the evolution of developmentally important genes. Determination of the transposition mechanisms of novel mobile elements, including MITEs (miniature inverted-repeat transposable elements). Development of genomics-based approaches to study genome evolution. Examination of the role of retroelement-mediated cellular gene transduction in the evolution of retroviruses.
Though transposons make up a large fraction of almost all eukaryotic genomes, until recently little was known concerning their role in host evolution. Our research has established that transposons can in fact interact or contribute to the host gene repertoire. For example, DNA transposons can acquire gene fragments in a process called transduplication.
Though the vast majority of detectable transduplication events result in pseudogene formation, some appear to be transcribed (non-coding RNA genes) and even rarely be part of novel protein-coding genes. In the latter case, the persistence of host conserve domains within transposons suggests that transduplication events may have profound element-specific selective advantage. Transposons can also abandon their mobile lifestyle and be so-called domesticated by their host.
We are profiling domesticated transposons to pinpoint the genomic signatures of domesticated transposons. Far from being the odd one-off, domestication of transposons appears to be frequent events.
To uncover their elusive functional role, we are characterized the suites of domesticated transposons from several model plant and other eukaryotic species. These results not only suggest they have a function and are bona fide “host genes” but also that they play a fundamentally important role in development and evolution.
We are using cutting-edge genomics protocols to uncover functionally and agronomically important regions within the so-called non-coding regions of plant genomes.
We are looking for master students in molecular biology and bioinformatics to be part of a multidisciplinary project (description below).
Climate change and environmental pollution will have a great impact on food security worldwide. The temperature increases cause, and will continue causing, more frequent drought events and, as such, an increasing concentrations of soluble chemicals (such as salt) in the field. In addition, the persistent expansion of aridity will carry a drastic "over use" of fields causing the depletion of essential nutritional components of the soil such as nitrogen. Therefore, it is prudent to respond by developing major improvements in plant breeding programs and agricultural technology.
The powerful combination of functional genomics, bioinformatics and phenomics is key to achieve this objective. In recent years, the use of non-coding RNAs as important targets for breeding agricultural trait-improvements have been spotlighted because of their role in environmental conditions regulating genes related to the growth and yield productivity of crops.
Phenomics is the large scale study of the dynamic characteristics (physical and biochemical traits or phenotype) of an organism. Modern phenomics platforms use specialize sensors with different spectral characteristics to capture subtle phenotypic changes over time at high-throughput in a non-invasive way such as growth rate, height, canopy structure, water content in leaves, pre-wilting condition, and transpiration rate. In such a way, the responses of non-coding RNA genes under different (abiotic) stress conditions can be evaluated. Camelina sativa is an important economical crop in Canada due to its nutritional properties (high content of omega-3 and omega-l fatty acids and vitamin E) as well as its potential use for biofuel production. In this project, we proposed to screen hundreds of non-coding RNAs under different stress conditions using a combined approach of genomics and phenomics in different environments to identify Camelina sativa responsive genes to agricultural important traits. This study will not only provide a set of most promising germplasm lines but also a complete phenotypic profile at different development stages under diverse stress conditions as essential elements in breeding and bio-engineering programs to develop climate-change-resilient plants.
For further information, please do not hesitate to contact Emilio Vello at emilio.vello [at] mcgill.ca.
Emilio Vello, M.Sc.
Academic Associate & Bioinformatician
McGill Plant Phenomics Platform Manager
Department of Biology, McGill University
1205 Dr. Penfield Avenue
Montreal, Quebec, H3A 1B1
Office: Stewart Biology, S3/19 | Lab: Stewart Biology, N4/3 | Phone: 514-398-4237 | Email: emilio.vello [at] mcgill.ca
- Joly-Lopez, Z., Bureau, T. (2018) Exaptation of transposable element coding sequences. Current Opinions in Genetics and Development. doi: 10.1016/j.gde.2018.02.011.
- Zhang, H., Zhou, Q., Wang, P., Xiong, X., Luchetti, A., Raoult, D., Levasseur, A., Santini, S., Abergel, C., Legendre, M., Drezen, J., Béliveau, C., Cusson, M., Jiang, S., Bao, H., Sun, C., Bureau, T., Cheng, P., Han, M., Zhang, Z., Zhang, X., Dai, F. (2018) Unexpected invasion success of miniature inverted-repeat transposable elements in viral genome. Mobile DNA. doi: 10.1186/s13100-018-0125-4.
- Joly-Lopez, Z., Forczek, E., Vello, E., Hoen, D., Tomita, A., Bureau, T. (2017) Abiotic Stress Phenotypes Are Associated with Conserved Genes Derived from Transposable Elements. Frontiers in Plant Science. doi: 10.3389/fpls.2017.02027.
- Hoen, D. Bourque, G., Casacuberta, J., Cordaux, R., Feschotte, C., Fiston-Lavier, A.-S., Hua-Van, A., Hubley, R., Kapusta, A., Lerat, E., Maumus, F., Pollock, D., Quesneville, H., Smit, A., Wheeler, T., Bureau, T. and Blanchette, M. (2015) A call for benchmarking transposable element annotation methods. Mobile DNA 6:13 DOI 10.1186/s13100-015-0044-6.
- Hoen, D. and Bureau, T. (2015) Discovery of novel genes derived from transposable elements using integrative genomic analysis. Molecular Biology and Evolution 32(6):1487–1506 doi:10.1093/molbev/msv042.
- Vello, E,. Tomita, A., Diallo, A.-O., and Bureau, T. (2015) A comprehensive approach to assess Arabidopsis survival phenotype in waterlimited condition using a non-invasive high-throughput phenomics platform. Frontiers in Plant Science 6:1101. doi: 10.3389/fpls.2015.01101.
- Edger, P., Heidel-Fischer, H., Bekaert, M., Rota, J., Glöckner, G., Platts, A., Heckel, D., Der, J., Wafula, E., Tang, M., Hofberger, J., Smithson, A., Hall, J., Blanchette, M., Bureau, T., Wright, S., dePamphilis, C., Schranz, M., Barker, M., Conant, G., Wahlberg, N., Vogel, H., Pires, J., and Wheat. C. (2015) The butterfly plant arms-race escalated by gene and genome duplication. Proceedings of the National Academy of Sciences USA 112: 8362–8366.
- Joly-Lopez, Z. and Bureau, T. (2014)Diversity and evolution of transposable elements in Arabidopsis. Chromosomal Research 22, 203-216.
- Bureau, T. (2014) MUG1 and MUG2 of the domesticated transposon gene family MUSTANG are necessary for Arabidopsis thaliana fitness, poster presentation, International Conference on Arabidopsis Research, Portland, Oregon USA, July 2014.
- Bureau, T. (2014) MUSTANG 7: A domesticated transposable element with a low temperature stress phenotype, poster presentation, International Conference on Arabidopsis Research, Portland, Oregon USA, July 2014.
- Bureau, T. (2014) Functional characterization of Tophat, a domesticated hAT-like transposable element gene, poster presentation, International Conference on Arabidopsis Research, Portland, Oregon USA, July 2014.
- Bureau, T. (2014) High-throughput screening to detect drought tolerance genotypes in Arabidopsis using a non-invasive phenomics platform, poster presentation, International Conference on Arabidopsis Research, Portland, Oregon USA, July 2014.
- Haudry, A., Platts, A., Vello, E., Hoen, D., Leclercq, M., Williamson, R., Forczek, E., Joly-Lopez, Z., Steffen, J., Hazzouri, K., Dewar, K., Stinchcombe, J., Schoen, D., Wang, X., Schmutz, J., Town, C., Edger, P., Pires, J., Schumaker, K., Jarvis, D., Mandáková, T., Lysak, M., Schranz, M., van den Bergh, E., Harrison, P., Moses, A.*, Bureau, T.*, Wright, S.*, Blanchette, M.* (2013) An Atlas of over 90,000 Conserved Non-Coding Sequences Yields a Detailed Map of Crucifer Regulatory Regions. Nature Genetics doi:10.1038/ng.2684.
- Zoé Joly-Lopez, Ewa Forczek, Douglas R. Hoen, Nikoleta Juretic, and Thomas E. Bureau (2012). A Gene Family Derived from Transposable Elements during Early Angiosperm Evolution Has Reproductive Fitness Benefits in Arabidopsis thaliana. PLoS Genetics 8: e1002931.
- Hoen, D. and Bureau, T. (2012) Transposable Element Exaptation in Plants. Plant Transposable Elements: Topics in Current Genetics 24: 219-251.
- Elrouby, N. and Bureau, T.E. (2011) Modulation of AUXIN-BINDING PROTEIN 1 gene expression in maize and the teosintes by transposon insertions in its promoter. Molecular Genomics and Genetics, 267: 143-153. (Talk highlighted in the article Transposable elements – Are they good for you after all? By John Brookfield, Genetics Society News, 65, pp. 20-24.)
- Elrouby, N. and Bureau, T. (2010) Bs1, a new chimeric gene formed by retrotransposon-mediated exon shuffling in maize. Plant Physiology 153:1413-1424.
- McNally, K., Childs, K., Bohnert, R., Davidson, R. Zhao, K., Ulat, V., Zeller, G., Clark, R., Hoen, D., Bureau, T., Stokowski, R., Ballinger, D., Frazer, K., Cox, D., Padhukasahasram, B., Bustamante, C., Weigel, D., Mackill, D., Bruskiewich, R., Rätsch, G., Buell, C., Leung, H., and Leach, J. (2009) Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proceedings of the National Academy of Sciences USA 106:12273-12278.
- Kwon, S.-J., Park, K.C., Son, J.-H., Bureau, T., Park, C.-H. and Kim, N.-S. (2009) Sequence diversity of a domesticated transposase gene, MUG1, in Oryza species. Molecules and Cells 27:459-465.
- Hoen, D. and Bureau, T. as part of the Rice Annotation Project (2008) The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Research 36:1028-1033.
- Kim, N.-S., Park, K.-C., Kwon, S.-J., Kim, P.-H and Bureau, T. (2008) Gene structure dynamics and divergence of the polygalacturonase gene family of plants and fungus. Genome 51: 30-40.
- Hoen, D. and Bureau, T. as part of the Rice Annotation Project (2007) Curated Genome Annotation of Oryza sativa ssp. Japonica and Comparative Genome Analysis with Arabidopsis thaliana. Genome Research 17:175-183.
- Hoen, D., Park, K.-C., Elrouby, N., Yu, Z., Mohabir, N., Cowan, R. and Bureau, T. (2006) Transposon-mediated expansion and diversification of a family of ULP-like genes. Molecular Biology and Evolution 23:1254-1268.
- Cowan, R., Hoen, D., Schoen, D. and Bureau, T. (2005) MUSTANG is a novel family of domesticated transposase genes found in diverse angiosperms. Molecular Biology and Evolution 22:2084-2089.
- Juretic, N., Hoen, D., Huynh, M., Harrison, P. and Bureau, T. (2005) The evolutionary fate of MULE-mediated duplications of host gene fragments in rice. Genome Research 15: 1292-1297. Rated “9.0” or exceptional by the Faculty of 1000.
- IRGSP (Transposon section: Juretic, N., Hoen, D., Wright, S., Bruskiewich, R. and Bureau, T.) (2005) The map-based sequence of the rice genome. Nature 436: 793-800.
- MacKenzie, J., Saade, F., Le, Q.-H., Bureau, T., and Schoen, D. (2005) Effects of UV-B exposure on rates of genomic mutation and transposon mobility in Arabidopsis thaliana. Genetics 171:715-723.
- Juretic, N., Bureau, T., and Bruskiewich, R. (2004) Transposable element annotation of the rice genome. Bioinformatics 20: 155-160.
- Le, Q.-H. and Bureau, T. (2004) Prediction and quality assessment of Transposon Insertion Display data. BioTechniques 36:222-224.
- Wright, S., Agrawal, N. and Bureau, T. (2003) Effects of recombination and gene density on transposable element distributions in Arabidopsis thaliana. Genome Research 13:1887-1903.
- Turcotte, K. and Bureau, T. (2002) The Stowaway family of plant transposons is part of the IS630/Tc1/Mariner superfamily. Genome 45: 82-90.
- Bevan, M., Mayer, K., White, O., Eisen J., Preuss, D., Bureau, T., Salzberg, S. and Mewes, H.-W. (2001) Sequence and analysis of the Arabidopsis genome. Current Opinions in Plant Biology 4: 105-110.
- Turcotte, K., Srinivasan, S., and Bureau, T. (2001) Survey of transposable elements from rice genomic sequences. Plant Journal 25:169-179.
- Le, Q.-H., Turcotte, K. and Bureau, T. (2001) Tc8, a member of the IS4/Tourist transposon superfamily in C. elegans. Genetics 158:1081-1088.
- Wright, S., Le, Q.-H., Schoen, D. and Bureau, T. (2001) Population dynamics of an Ac-like transposable element in self- and cross-pollinating Arabidopsis. Genetics 158:1279-1288.
- Witte, C.-P., Le, Q.-H., Bureau, T., and Kumar, A. (2001) Terminal-repeat Retrotransposons in Miniature (TRIM) are involved in restructuring the host-plant genome. PNAS (USA) 98:13778-13783.
- Elrouby, N. and Bureau, T. (2001) A novel hybrid ORF formed by multiple gene transductions by a plant LTR retroelement. Journal of Biological Chemistry 276:41963-41968.
- Chang, R., O’Donoughue, L. and Bureau, T. (2001) Inter-MITE Polymorphisms (IMP): A high throughput transposon-based genome mapping and fingerprinting approach. Theoretical and Applied Genetics 102:773-778.
- Le, Q.-H., Wright, S., Yu, Z. and Bureau, T. (2000) Transposon discovery in Arabidopsis thaliana. PNAS (USA) 97: 7376-7381.
- AGI (Transposon section: Le, Q.-H., Agrawal, N., Lagault, B., Yu, Z., Martinessan, R. and Bureau, T.) (2000) Analysis of the genome of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
- Elrouby, N. and Bureau, T. (2000) Molecular characterization of the Abp1 5’-flanking region in maize and the teosintes. Plant Physiology 124:369-377.
- Yu, Z. Wright, S. and Bureau, T. (2000) Mutator-Like Elements (MULEs) in Arabidopsis thaliana: Structure, diversity and evolution. Genetics 156:2019-2031.
- Le, Q.-H., Wright, S., Yu, Z. and Bureau, T. (2000) Transposon discovery in Arabidopsis thaliana. PNAS (USA) 97: 7376-7381.