Research Output per year
Personal profile
Previous positions
2009-2011: California Institute for Regenerative Medicine Postdoctoral Trainee (Joseph Ecker), The Salk Institute for Biological Studies, La Jolla, CA, USA.
2006-2009: Human Frontier Science Project Postdoctoral Fellow (Joseph Ecker), The Salk Institute for Biological Studies, La Jolla, CA, USA.
2005-2006: Postdoctoral Fellow (James Whelan), Department of Biochemistry and Molecular Biology, The University of Western Australia, Perth, Australia.
2001-2005: Ph.D. (James Whelan), Department of Biochemistry and Molecular Biology, The University of Western Australia, Perth, Australia.
2006-2009: Human Frontier Science Project Postdoctoral Fellow (Joseph Ecker), The Salk Institute for Biological Studies, La Jolla, CA, USA.
2005-2006: Postdoctoral Fellow (James Whelan), Department of Biochemistry and Molecular Biology, The University of Western Australia, Perth, Australia.
2001-2005: Ph.D. (James Whelan), Department of Biochemistry and Molecular Biology, The University of Western Australia, Perth, Australia.
Research
Exploring the Epigenome
Just as the fixed notes of a musical instrument can be played in different combinations, orders and strengths to create unique songs, different cells in a complex multicellular organism can produce their distinctive form and function by each expressing particular combinations of genes from the genome. By modulating accessibility to the information encoded in the genome, epigenetic modifications can affect gene activation and repression to execute distinct transcriptional programs and impart a heritable state of transcriptional activity. In essence, the epigenome is a regulatory code that is superimposed upon the genome that can modify the cellular readout of the underlying information encoded in the DNA sequence. Developing a comprehensive understanding of how the cell utilizes epigenetic modifications is essential in order to both understand the critical roles it plays in eukaryotic development and stress response, and to develop effective strategies to remedy its disruption in disease states.
We use advanced DNA sequencing, molecular, genetic and computational techniques in a diverse range of complex multicellular organisms, including plants, humans, mice, and social insects, to study the epigenome and epigenetic mechanisms at the molecular scale. Recent advances in DNA sequencing technology now enable us to rapidly identify precisely where epigenetic modifications, such as DNA methylation and histone modifications, occur throughout entire plant and animal genomes1-3. The research in my laboratory aims to understand how the information encoded in the DNA of plant and animal genomes is controlled by epigenetic mechanisms during development, how the epigenome may be altered by the surrounding environment, and to develop molecular tools to reprogram it.
Just as the fixed notes of a musical instrument can be played in different combinations, orders and strengths to create unique songs, different cells in a complex multicellular organism can produce their distinctive form and function by each expressing particular combinations of genes from the genome. By modulating accessibility to the information encoded in the genome, epigenetic modifications can affect gene activation and repression to execute distinct transcriptional programs and impart a heritable state of transcriptional activity. In essence, the epigenome is a regulatory code that is superimposed upon the genome that can modify the cellular readout of the underlying information encoded in the DNA sequence. Developing a comprehensive understanding of how the cell utilizes epigenetic modifications is essential in order to both understand the critical roles it plays in eukaryotic development and stress response, and to develop effective strategies to remedy its disruption in disease states.
We use advanced DNA sequencing, molecular, genetic and computational techniques in a diverse range of complex multicellular organisms, including plants, humans, mice, and social insects, to study the epigenome and epigenetic mechanisms at the molecular scale. Recent advances in DNA sequencing technology now enable us to rapidly identify precisely where epigenetic modifications, such as DNA methylation and histone modifications, occur throughout entire plant and animal genomes1-3. The research in my laboratory aims to understand how the information encoded in the DNA of plant and animal genomes is controlled by epigenetic mechanisms during development, how the epigenome may be altered by the surrounding environment, and to develop molecular tools to reprogram it.
Research expertise keywords
- Epigenetics
- Epigenomics
- DNA methylation
- Genomics (plant, animal)
- Stem cells
- Induced pluripotent stem cells
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Research Output
Conserved and divergent features of DNA methylation in embryonic stem cell-derived neurons
Martin, S., Poppe, D., Olova, N., O'Leary, C., Ivanova, E., Pflueger, J., Dechka, J., Simmons, R. K., Cooper, H. M., Reik, W., Lister, R. & Wolvetang, E., 9 Jan 2020, bioRxiv, 2020, 01.08 61 p.Research output: Contribution to specialist publication › Article
Open Access
Evolution of DNA methylome diversity in eukaryotes
de Mendoza, A., Lister, R. & Bogdanovic, O., 13 Mar 2020, In : Journal of Molecular Biology. 432, 6, p. 1687-1705Research output: Contribution to journal › Review article
3
Citations
(Scopus)
Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings
Almudi, I., Vizueta, J., Wyatt, C. D. R., de Mendoza, A., Marlétaz, F., Firbas, P. N., Feuda, R., Masiero, G., Medina, P., Alcaina-Caro, A., Cruz, F., Gómez-Garrido, J., Gut, M., Alioto, T. S., Vargas-Chavez, C., Davie, K., Misof, B., González, J., Aerts, S., Lister, R. & 6 others, , 26 May 2020, In : Nature Communications. 11, 1, 2631.Research output: Contribution to journal › Article
Open Access
Mitochondrial CLPP2 assists coordination and homeostasis of respiratory complexes
Petereit, J., Duncan, O., Murcha, M. W., Fenske, R., Cincu, E., Cahn, J., Pruzinska, A., Ivanova, A., Kollipara, L., Wortelkamp, S., Sickmann, A., Lee, J., Lister, R., Millar, A. H. & Huang, S., 22 Jun 2020, In : Plant Physiology.Research output: Contribution to journal › Article
Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows
Denisenko, E., Guo, B. B., Jones, M., Hou, R., de Kock, L., Lassmann, T., Poppe, D., Clément, O., Simmons, R. K., Lister, R. & Forrest, A. R. R., 2 Jun 2020, In : Genome Biology. 21, 1, p. 130Research output: Contribution to journal › Article
Open Access
Datasets
Data from: Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements
Secco, D. (Creator), Wang, C. (Creator), Shou, H. (Creator), Schultz, M. D. (Creator), Chiarenza, S. (Creator), Nussaume, L. (Creator), Ecker, J. R. (Creator), Whelan, J. M. (Creator) & Lister, R. (Creator), Dryad Digital Repository, 6 Aug 2015
DOI: 10.5061/dryad.40gd6, https://datadryad.org/resource/doi:10.5061/dryad.40gd6
Dataset
GSM1977638: xl_st10.5_MethylC-seq
Bogdanovic, O. (Creator) & Lister, R. (Creator), Gene Expression Omnibus (NCBI), 26 Aug 2016
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1977638
Dataset
Projects
2020 - Aperio VERSA 8, Brightfield and Fluorescence (automated digital slide scanner) - Main System
Ganss, R., Laing, N., Filipovska, A., Lister, R., Forrest, A., Leedman, P., Yeoh, G., Keelan, J., Nowak, A., Xu, J., Blancafort, P., Trinder, D., Pavlos, N., Ravenscroft, G., Hamzah, J., Juan Pardo, E., Winteringham, L., Kennedy, B., Pixley, F., Redwood, A., Lesterhuis, W., Endersby, R., He, B., Richman, T., Kabir, T., Siira, S., Mowla, A. & Taylor, R.
National Health & Medical Research Council NHMRC
1/01/20 → 31/12/20
Project: Research
Co-funding of Skilled Personnel for the ACRF Centre for Advanced Cancer Genomics
Forrest, A., Leedman, P. & Lister, R.
Australian Cancer Research Foundation
1/08/19 → 30/07/22
Project: Research
ACRF Centre for Advanced Cancer Genomics (NovaSeq)
Forrest, A., Leedman, P., Lister, R., Lassmann, T., Saunders, C., Farah, C., Robinson, B., Nowak, A., Kees, U., Johns, T., Ganss, R., Erber, W., Lake, R., Millward, M., Ziman, M. & Amanuel, B.
Australian Cancer Research Foundation
30/10/18 → 29/10/21
Project: Research
Investigating the molecular signature of ASD through integrative genomics
Lister, R., Voineagu, I. & Gratten, J.
National Health & Medical Research Council NHMRC
1/01/18 → 31/12/20
Project: Research