Professor Ryan Lister
Plant Energy Biology, ARC Centre of Excellence
- Contact details
- Plant Energy Biology, ARC Centre of Excellence
The University of Western Australia (M519)
35 Stirling Highway
CRAWLEY WA 6009
- +61 8 6488 4407
- Room 4.74, Bayliss Building, Perth campus
- PhD W.Aust.
- Key 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.
- Wierzbicki AT*, Cocklin R*, Mayampurath A*, Lister R, Rowley MJ, Gregory BD, Ecker JR, Tang H, Pikaard CS. (2012) Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome. Genes and Development, 26(16):1825-36.
Dowen RH, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, Nery JR, Dixon JE, Ecker JR. (2012) Widespread dynamic DNA methylation in response to biotic stress. PNAS 109(32):E2183-91.
Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, Camargo AA, Stevenson BJ, Ecker JR, Bafna V, Strausberg RL, Simpson AJ, Ren B. (2011) Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Research, 22(2):246-58.
Pastor WA*, Pape UJ*, Huang Y*, Henderson HR, Lister R, Ko M, McLoughlin EM, Brudno Y, Mahapatra S, Kapranov P, Tahiliani M, Daley GQ, Liu XS, Ecker JR, Milos PM, Agarwal S, Rao A. (2011) Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 473(7347):394-397.
Lister R*, Pelizzola M*, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O’Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, Evans RM, Ecker JR. (2011) Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 471(7336):68-73.
Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnology 28(10):1026-1028.
Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, Pelizzola M, Edsall LE, Kuan S, Luu Y, Klugman S, Antosiewicz-Bourget J, Ye Z, Espinoza C, Agarwahl S, Shen L, Ruotti V, Wang W, Stewart R, Thomson JA, Ecker JR, Ren B. (2010) Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell May 7;6(5):479-91.
Lister R*, Pelizzola M*, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462(7271):315-22.
Lister R, Ecker JR. (2009) Finding the fifth base: Genome-wide sequencing of cytosine methylation. Genome Research 19(6):959-66.
Lister R, Gregory BD, Ecker JR. (2009) Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. Current Opinions in Plant Biology 12(2):107-18.
Sappl PG, Carroll AJ, Clifton R, Lister R, Whelan J, Harvey Millar A, Singh KB. (2009) The Arabidopsis glutathione transferase gene family displays complex stress regulation and co-silencing multiple genes results in altered metabolic sensitivity to oxidative stress. Plant Journal 58(1):53-68.
Lister R*, O'Malley RC*, Tonti-Filippini J*, Gregory BD, Berry CC, Millar AH, Ecker JR. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133(3):523-36.
Gregory BD, O'Malley RC, Lister R, Urich MA, Tonti-Filippini J, Chen H, Millar AH, Ecker JR. (2008) A link between RNA metabolism and silencing affecting Arabidopsis development. Developmental Cell 14(6):854-66.
Ho LH, Giraud E, Uggalla V, Lister R, Clifton R, Glen A, Thirkettle-Watts D, Van Aken O, Whelan J. (2008) Identification of regulatory pathways controlling gene expression of stress-responsive mitochondrial proteins in Arabidopsis. Plant Physiology 147(4):1858-73.
Lister R, Carrie C, Duncan O, Ho LH, Howell KA, Murcha MW, Whelan J. (2007) Functional definition of outer membrane proteins involved in preprotein import into mitochondria. Plant Cell 19(11):3739-59.
Murcha MW, Elhafez D, Lister R, Tonti-Filippini J, Baumgartner M, Philippar K, Carrie C, Mokranjac D, Soll J, Whelan J. (2007) Characterization of the preprotein and amino Acid transporter gene family in Arabidopsis. Plant Physiology 143(1):199-212.
Ho LHM, Giraud E, Lister R, Thirkettle-Watts D, Low J, Clifton R, Howell KA, Carrie C, Donald T, Whelan J. (2007) Characterisation of the regulatory and expression context of an alternative oxidase gene provides insights into cyanide insensitive respiration during growth and development. Plant Physiology 143(1):199-212.
Clifton R, Lister R, Parker KL, Sappl PG, Elhafez D, Millar AH, Day DA, Whelan J. (2005) Stress-induced co-expression of alternative respiratory chain components in Arabidopsis thaliana. Plant Molecular Biology 58:193-212.
Lister R, Chew O, Lee MN, Heazlewood JL, Clifton, R., Parker KL, Millar AH, Whelan J. (2004) A Transcriptomic and Proteomic Characterization of the Arabidopsis Mitochondrial Protein Import Apparatus and Its Response to Mitochondrial Dysfunction. Plant Physiology 134:777-789.
Chew O, Lister R, Qbadou S, Heazlewood JL, Soll J, Schleiff E, Millar AH, Whelan, J. (2004) A plant outer mitochondrial membrane protein with high amino acid sequence identity to a chloroplast protein import receptor. FEBS letters 557:109-114.
Murcha MW, Lister R, Ho AY, Whelan, J. (2003) Identification, expression, and import of components 17 and 23 of the inner mitochondrial membrane translocase from Arabidopsis. Plant Physiology 131:1737-1747.
Lister R, Mowday B, Whelan J, Millar AH (2002) Zinc dependent intermembrane space proteins stimulate carrier import into plant mitochondria. The Plant Journal 30:555-566.
Lister R, Murcha MW, Whelan J (2003) The mitochondrial protein import machinery of plants (MPIMP) database. Nucleic Acids Research 31:325-327.
Lister R, Chew O, Rudhe C, Lee MN, Whelan J. (2001) Arabidopsis thaliana ferrochelatase-I and -II are not imported into Arabidopsis mitochondria. FEBS letters 506: 291-295.
Note: * denotes authors who contributed equally to the study.
- Honours and awards
- 2012: Australian Research Council Future Fellow (2012 - 2016)
2011: Paper #4 in “The Hottest Research of 2011” (Thomson ISI): Lister et al. 2011 (Nature) - #1 in Life Sciences
2009-2011: California Institute for Regenerative Medicine Postdoctoral training grant, The Salk Institute for Biological Studies
2010: Genome Technology - Young Investigators Award
2009: #2 Scientific Discovery of 2009 (TIME magazine)
2006-2009: Human Frontier Science Project long-term Fellowship, The Salk Institute for Biological Studies
- 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.
- Research profile
Research profile and publications