Technology and Innovation Scientist
Honorary Research Fellow
Overview
Dr Seth Cheetham is a NHMRC Early Career Fellow and holds a Career Track Fellow position at Mater Research Institute-University of Queensland. After his Bachelor of Science (Hons) at the University of Queensland, he completed his PhD at the University of Cambridge, supported by the Herchel Smith Research Studentship. He joined Mater Research in 2017 and is based at the Translational Research Institute. Seth is a molecular biologist and geneticist with a focus on epigenetics and RNA biology. He has a long-term interest in the functions of the so-called ‘junk’ DNA—noncoding DNA regions scattered throughout the genome with no obvious function— and its role in human biology. Seth leads a team within the Genome Plasticity and Disease group, where he is primary supervisor of two PhD students and is associate supervisor of one. He has authored 16 publications, including eight as a first author and three as a corresponding author. He has published in some of the most influential molecular biology journals including Science, Molecular Cell, Nature Reviews Genetics , Genome Biology and Nature Structural and Molecular Biology. His work has attracted > $1M in funding from an NHMRC Fellowship (2019), a Cancer Australia Grant (2021), Mater Foundation seeding grant (2019), a UQ ECR grant (2019) and the UQ Genome Innovation Hub (2020). In 2021 Seth was award the Genetics Society of Australasia Alan Wilton ECR award for his research in the field of noncoding RNA and epigenetics.
Publications
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Journal Article: Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome
Troskie, Robin-Lee, Jafrani, Yohaann, Mercer, Tim R., Ewing, Adam D., Faulkner, Geoffrey J. and Cheetham, Seth W. (2021). Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome. Genome Biology, 22 (1) 146, 1-15. doi: 10.1186/s13059-021-02369-0
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Journal Article: Nanopore sequencing enables comprehensive transposable element epigenomic profiling
Ewing, Adam D., Smits, Nathan, Sanchez-Luque, Francisco J., Faivre, Jamila, Brennan, Paul M., Richardson, Sandra R., Cheetham, Seth W. and Faulkner, Geoffrey J. (2020). Nanopore sequencing enables comprehensive transposable element epigenomic profiling. Molecular Cell, 80 (5), 915-928.e5. doi: 10.1016/j.molcel.2020.10.024
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Journal Article: Overcoming challenges and dogmas to understand the functions of pseudogenes
Cheetham, Seth W., Faulkner, Geoffrey J. and Dinger, Marcel E. (2020). Overcoming challenges and dogmas to understand the functions of pseudogenes. Nature Reviews Genetics, 21 (3), 191-201. doi: 10.1038/s41576-019-0196-1
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Journal Article: RNA-DamID reveals cell-type-specific binding of roX RNAs at chromatin-entry sites
Cheetham, Seth W and Brand, Andrea H (2017). RNA-DamID reveals cell-type-specific binding of roX RNAs at chromatin-entry sites. Nature structural & molecular biology, 25 (1), 109-114. doi: 10.1038/s41594-017-0006-4
Grants
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Long-read genetic and epigenetic profiling in lung cancer for precision medicine
(2021–2024) Priority-driven Collaborative Cancer Research Scheme
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Deciphering global and locus-specific regulation of LINE-1 retrotransposons in cancer
(2019–2022) NHMRC Early Career Fellowships
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Are inhibitory pseudogenes key players in cancer?
(2019) UQ Early Career Researcher
Supervision
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Epigenetic lineage tracing using Dam and alternate DNA methylases
Doctor Philosophy
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Functional coding and noncoding pseudogenes in the human genome
Doctor Philosophy
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Deciphering global and locus-specific regulation of LINE-1 (L1) retrotransposons in cancer
Doctor Philosophy
Available Projects
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Deciphering global and locus-specific regulation of LINE-1 retrotransposons in cancer
In cancer, but not healthy cells, ~100 L1 “jumping genes” can copy and paste themselves into the human genome. L1s can contribute to cancer initiation by activating oncogenes and inactivating tumour suppressor genes and can drive tumour evolution, underpinning resistance to chemotherapy. This project aims to determine the cause of L1 activation in cancer. This project will identify novel factors that regulate L1 expression in cancer, transforming our understanding of the mechanism of L1 activation. As L1 expression is highly correlated with cancer severity, these factors may hold important prognostic and diagnostic value.
Publications
Featured Publications
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Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome
Troskie, Robin-Lee, Jafrani, Yohaann, Mercer, Tim R., Ewing, Adam D., Faulkner, Geoffrey J. and Cheetham, Seth W. (2021). Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome. Genome Biology, 22 (1) 146, 1-15. doi: 10.1186/s13059-021-02369-0
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Nanopore sequencing enables comprehensive transposable element epigenomic profiling
Ewing, Adam D., Smits, Nathan, Sanchez-Luque, Francisco J., Faivre, Jamila, Brennan, Paul M., Richardson, Sandra R., Cheetham, Seth W. and Faulkner, Geoffrey J. (2020). Nanopore sequencing enables comprehensive transposable element epigenomic profiling. Molecular Cell, 80 (5), 915-928.e5. doi: 10.1016/j.molcel.2020.10.024
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Overcoming challenges and dogmas to understand the functions of pseudogenes
Cheetham, Seth W., Faulkner, Geoffrey J. and Dinger, Marcel E. (2020). Overcoming challenges and dogmas to understand the functions of pseudogenes. Nature Reviews Genetics, 21 (3), 191-201. doi: 10.1038/s41576-019-0196-1
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RNA-DamID reveals cell-type-specific binding of roX RNAs at chromatin-entry sites
Cheetham, Seth W and Brand, Andrea H (2017). RNA-DamID reveals cell-type-specific binding of roX RNAs at chromatin-entry sites. Nature structural & molecular biology, 25 (1), 109-114. doi: 10.1038/s41594-017-0006-4
Book Chapter
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Mapping RNA-Chromatin interactions in vivo with RNA-DamID
Cheetham, Seth W. and Brand, Andrea H. (2020). Mapping RNA-Chromatin interactions in vivo with RNA-DamID. RNA-Chromatin Interactions. (pp. 255-264) edited by Ulf Andersson Vang Ørom. New York, NY, United States: Humana Press. doi: 10.1007/978-1-0716-0680-3_18
Journal Article
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Reduced chromatin accessibility correlates with resistance to Notch activation
van den Ameele, Jelle, Krautz, Robert, Cheetham, Seth W., Donovan, Alex P. A., Llorà-Batlle, Oriol, Yakob, Rebecca and Brand, Andrea H. (2022). Reduced chromatin accessibility correlates with resistance to Notch activation. Nature Communications, 13 (1) 2210. doi: 10.1038/s41467-022-29834-z
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In vivo targeted DamID identifies CHD8 genomic targets in fetal mouse brain
Wade, A. Ayanna, van den Ameele, Jelle, Cheetham, Seth W., Yakob, Rebecca, Brand, Andrea H. and Nord, Alex S. (2021). In vivo targeted DamID identifies CHD8 genomic targets in fetal mouse brain. iScience, 24 (11) 103234, 103234. doi: 10.1016/j.isci.2021.103234
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Troskie, Robin-Lee, Faulkner, Geoffrey J. and Cheetham, Seth W. (2021). Processed pseudogenes: a substrate for evolutionary innovation. Retrotransposition contributes to genome evolution by propagating pseudogene sequences with rich regulatory potential throughout the genome. BioEssays, 43 (11) 2100186, 2100186. doi: 10.1002/bies.202100186
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Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome
Troskie, Robin-Lee, Jafrani, Yohaann, Mercer, Tim R., Ewing, Adam D., Faulkner, Geoffrey J. and Cheetham, Seth W. (2021). Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome. Genome Biology, 22 (1) 146, 1-15. doi: 10.1186/s13059-021-02369-0
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Microdeletion of 9q22.3: a patient with minimal deletion size associated with a severe phenotype
Ewing, Adam D., Cheetham, Seth W., McGill, James J., Sharkey, Michael, Walker, Rick, West, Jennifer A., West, Malcolm J. and Summers, Kim M. (2021). Microdeletion of 9q22.3: a patient with minimal deletion size associated with a severe phenotype. American Journal of Medical Genetics Part A, 185 (7) ajmg.a.62224, 2070-2083. doi: 10.1002/ajmg.a.62224
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Nanopore sequencing enables comprehensive transposable element epigenomic profiling
Ewing, Adam D., Smits, Nathan, Sanchez-Luque, Francisco J., Faivre, Jamila, Brennan, Paul M., Richardson, Sandra R., Cheetham, Seth W. and Faulkner, Geoffrey J. (2020). Nanopore sequencing enables comprehensive transposable element epigenomic profiling. Molecular Cell, 80 (5), 915-928.e5. doi: 10.1016/j.molcel.2020.10.024
-
Overcoming challenges and dogmas to understand the functions of pseudogenes
Cheetham, Seth W., Faulkner, Geoffrey J. and Dinger, Marcel E. (2020). Overcoming challenges and dogmas to understand the functions of pseudogenes. Nature Reviews Genetics, 21 (3), 191-201. doi: 10.1038/s41576-019-0196-1
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LINE-1 Evasion of epigenetic repression in humans
Sanchez-Luque, Francisco J., Kempen, Marie-Jeanne H.C., Gerdes, Patricia, Vargas-Landin, Dulce B., Richardson, Sandra R., Troskie, Robin-Lee, Jesuadian, J. Samuel, Cheetham, Seth W., Carreira, Patricia E., Salvador-Palomeque, Carmen, García-Cañadas, Marta, Muñoz-Lopez, Martin, Sanchez, Laura, Lundberg, Mischa, Macia, Angela, Heras, Sara R., Brennan, Paul M., Lister, Ryan, Garcia-Perez, Jose L., Ewing, Adam D. and Faulkner, Geoffrey J. (2019). LINE-1 Evasion of epigenetic repression in humans. Molecular Cell, 75 (3), 590-604.e12. doi: 10.1016/j.molcel.2019.05.024
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DamID as a versatile tool for understanding gene regulation
Aughey, Gabriel N., Cheetham, Seth W. and Southall, Tony D. (2019). DamID as a versatile tool for understanding gene regulation. Development, 146 (6) dev173666, dev173666. doi: 10.1242/dev.173666
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Targeted DamID reveals differential binding of mammalian pluripotency factors
Cheetham, Seth W., Gruhn, Wolfram H., van den Ameele, Jelle, Krautz, Robert, Southall, Tony D., Kobayashi, Toshihiro, Surani, M. Azim and Brand, Andrea H. (2018). Targeted DamID reveals differential binding of mammalian pluripotency factors. Development, 145 (20) dev170209, dev.170209. doi: 10.1242/dev.170209
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RNA-DamID reveals cell-type-specific binding of roX RNAs at chromatin-entry sites
Cheetham, Seth W and Brand, Andrea H (2017). RNA-DamID reveals cell-type-specific binding of roX RNAs at chromatin-entry sites. Nature structural & molecular biology, 25 (1), 109-114. doi: 10.1038/s41594-017-0006-4
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Gloss, Brian S., Signal, Bethany, Cheetham, Seth W., Gruhl, Franziska, Kaczorowski, Dominik C., Perkins, Andrew C. and Dinger, Marcel E. (2017). High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci. Scientific Reports, 7 (1) 6731, 6731. doi: 10.1038/s41598-017-06110-5
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Marshall, Owen J., Southall, Tony D., Cheetham, Seth W. and Brand, Andrea H. (2016). Cell-type-specific profiling of protein-DNA interactions without cell isolation using targeted DamID with next-generation sequencing. Nature Protocols, 11 (9), 1586-1598. doi: 10.1038/nprot.2016.084
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The Evx1/Evx1as gene locus regulates anterior-posterior patterning during gastrulation
Bell, Charles C., Amaral, Paulo P., Kalsbeek, Anton, Magor, Graham W., Gillinder, Kevin R., Tangermann, Pierre, di Lisio, Lorena, Cheetham, Seth W., Gruhl, Franziska, Frith, Jessica, Tallack, Michael R., Ru, Ke-Lin, Crawford, Joanna, Mattick, John S., Dinger, Marcel E. and Perkins, Andrew C. (2016). The Evx1/Evx1as gene locus regulates anterior-posterior patterning during gastrulation. Scientific Reports, 6 (1) 26657, 26657. doi: 10.1038/srep26657
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Freedom of expression: cell-type-specific gene profiling
Otsuki, Leo, Cheetham, Seth W. and Brand, Andrea H. (2014). Freedom of expression: cell-type-specific gene profiling. Wiley Interdisciplinary Reviews: Developmental Biology, 3 (6), 429-443. doi: 10.1002/wdev.149
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Long noncoding RNAs and the genetics of cancer
Cheetham, S. W., Gruhl, F., Mattick, J. S. and Dinger, M. E. (2013). Long noncoding RNAs and the genetics of cancer. British Journal of Cancer, 108 (12), 2419-2425. doi: 10.1038/bjc.2013.233
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Cheetham, Seth W. and Brand, Andrea H. (2013). Insulin finds its niche. Science, 340 (6134), 817-818. doi: 10.1126/science.1238525
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Gascoigne, Dennis K., Cheetham, Seth W., Cattenoz, Pierre B., Clark, Michael B., Amaral, Paulo P., Taft, Ryan J., Wilhelm, Dagmar, Dinger, Marcel E. and Mattick, John S. (2012). Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes. Bioinformatics, 28 (23), 3042-3050. doi: 10.1093/bioinformatics/bts582
Grants (Administered at UQ)
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Long-read genetic and epigenetic profiling in lung cancer for precision medicine
(2021–2024) Priority-driven Collaborative Cancer Research Scheme
-
Deciphering global and locus-specific regulation of LINE-1 retrotransposons in cancer
(2019–2022) NHMRC Early Career Fellowships
-
Are inhibitory pseudogenes key players in cancer?
(2019) UQ Early Career Researcher
PhD and MPhil Supervision
Current Supervision
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Epigenetic lineage tracing using Dam and alternate DNA methylases
Doctor Philosophy — Principal Advisor
Other advisors:
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Functional coding and noncoding pseudogenes in the human genome
Doctor Philosophy — Principal Advisor
Other advisors:
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Deciphering global and locus-specific regulation of LINE-1 (L1) retrotransposons in cancer
Doctor Philosophy — Associate Advisor
Other advisors:
Possible Research Projects
Note for students: The possible research projects listed on this page may not be comprehensive or up to date. Always feel free to contact the staff for more information, and also with your own research ideas.
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Deciphering global and locus-specific regulation of LINE-1 retrotransposons in cancer
In cancer, but not healthy cells, ~100 L1 “jumping genes” can copy and paste themselves into the human genome. L1s can contribute to cancer initiation by activating oncogenes and inactivating tumour suppressor genes and can drive tumour evolution, underpinning resistance to chemotherapy. This project aims to determine the cause of L1 activation in cancer. This project will identify novel factors that regulate L1 expression in cancer, transforming our understanding of the mechanism of L1 activation. As L1 expression is highly correlated with cancer severity, these factors may hold important prognostic and diagnostic value.
