Computational and molecular biology

To understand the roles played by retrotransposons in early mammalian embryogenesis, and in neurons

Professor Faulkner’s research seeks to understand the role of retrotransposons, a type of “mobile DNA”, in causing genetic mosaicism in early mammalian embryogenesis, and in neurons.

This variation may be a fundamental aspect of healthy brain function, and appears to change in neurological diseases, including Rett syndrome, schizophrenia and Alzheimer's disease.

Professor Faulkner published a landmark work in Nature describing somatic retrotransposition in the human brain that was selected by the US National Institute of Mental Health as the 'joint No. 1 research advance of 2011' and has followed this work with four breakthrough articles in Cell and Molecular Cell. He is the recipient of the ASMR Queensland Premier’s Award (2009), the FEBS Anniversary Prize (2011), the Lorne Genome Millennium Science Award (2014), the Centenary Institute Lawrence Creative Prize (2014) and the Australian Academy of Science Ruth Stephens Gani Medal (2016).

Group leader

Professor Geoff Faulkner

Professor Geoff Faulkner

Group Leader, Computational and molecular biology

Professor, Neuroscience Queensland Brain Institute

  +61 7 334 66300
  g.faulkner@uq.edu.au
  UQ Researcher Profile

Better understand how the genome - our “book of life” - changes in normal and diseased brain cells.

QBI Professor awarded $1.25 million CSL Centenary Fellowship

Transient naive reprogramming corrects hiPS cells functionally and epigenetically
Buckberry, Sam, Liu, Xiaodong, Poppe, Daniel, Tan, Jia Ping, Sun, Guizhi, Chen, Joseph, Nguyen, Trung Viet, de Mendoza, Alex, Pflueger, Jahnvi, Frazer, Thomas, Vargas-Landín, Dulce B., Paynter, Jacob M., Smits, Nathan, Liu, Ning, Ouyang, John F., Rossello, Fernando J., Chy, Hun S., Rackham, Owen J. L., Laslett, Andrew L., Breen, James, Faulkner, Geoffrey J., Nefzger, Christian M., Polo, Jose M. and Lister, Ryan (2023). Transient naive reprogramming corrects hiPS cells functionally and epigenetically. Nature, 620 (7975), 863-872. doi: 10.1038/s41586-023-06424-7
Endogenous retroviruses can propagate TDP-43 proteinopathy

Ferreiro, Maria E. and Faulkner, Geoffrey J. (2023). Endogenous retroviruses can propagate TDP-43 proteinopathy. Trends in Neurosciences. doi: 10.1016/j.tins.2023.03.011

Elevated L1 expression in ataxia telangiectasia likely explained by an RNA-seq batch effect
Faulkner, Geoffrey J. (2023). Elevated L1 expression in ataxia telangiectasia likely explained by an RNA-seq batch effect. Neuron, 111 (5), 610-611. doi: 10.1016/j.neuron.2023.02.007
Impact of retrotransposon protein L1 ORF1p expression on oncogenic pathways in hepatocellular carcinoma: the role of cytoplasmic PIN1 upregulation
Zadran, Bassier, Sudhindar, Praveen Dhondurao, Wainwright, Daniel, Bury, Yvonne, Luli, Saimir, Howarth, Rachel, McCain, Misti Vanette, Watson, Robyn, Huet, Hannah, Palinkas, Fanni, Palmini, Rolando Berlinguer, Casement, John, Mann, Derek A., Oakley, Fiona, Lunec, John, Reeves, Helen, Faulkner, Geoffrey J. and Shukla, Ruchi (2023). Impact of retrotransposon protein L1 ORF1p expression on oncogenic pathways in hepatocellular carcinoma: the role of cytoplasmic PIN1 upregulation. British Journal of Cancer, 128 (7), 1236-1248. doi: 10.1038/s41416-023-02154-9
Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells
Gerdes, Patricia, Lim, Sue Mei, Ewing, Adam D., Larcombe, Michael R., Chan, Dorothy, Sanchez-Luque, Francisco J., Walker, Lucinda, Carleton, Alexander L., James, Cini, Knaupp, Anja S., Carreira, Patricia E., Nefzger, Christian M., Lister, Ryan, Richardson, Sandra R., Polo, Jose M. and Faulkner, Geoffrey J. (2022). Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells. Nature Communications, 13 (1) 7470, 1-18. doi: 10.1038/s41467-022-35180-x
Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (Nature Communications, (2021), 12, 1, (3297), 10.1038/s41467-021-23143-7)
Grapotte, Mathys, Saraswat, Manu, Bessière, Chloé, Menichelli, Christophe, Ramilowski, Jordan A., Severin, Jessica, Hayashizaki, Yoshihide, Itoh, Masayoshi, Tagami, Michihira, Murata, Mitsuyoshi, Kojima-Ishiyama, Miki, Noma, Shohei, Noguchi, Shuhei, Kasukawa, Takeya, Hasegawa, Akira, Suzuki, Harukazu, Nishiyori-Sueki, Hiromi, Frith, Martin C., Abugessaisa, Imad, Aitken, Stuart, Aken, Bronwen L., Alam, Intikhab, Alam, Tanvir, Alasiri, Rami, Alhendi, Ahmad M. N., Alinejad-Rokny, Hamid, Alvarez, Mariano J., Andersson, Robin, Arakawa, Takahiro ... Lecellier, Charles-Henri (2022). Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (Nature Communications, (2021), 12, 1, (3297), 10.1038/s41467-021-23143-7). Nature Communications, 13 (1) 1200. doi: 10.1038/s41467-022-28758-y
Somatic retrotransposition in the developing rhesus macaque brain
Billon, Victor, Sanchez-Luque, Francisco J, Rasmussen, Jay, Bodea, Gabriela O, Gerhardt, Daniel J, Gerdes, Patricia, Cheetham, Seth W, Schauer, Stephanie N, Ajjikuttira, Prabha, Meyer, Thomas J, Layman, Cora E, Nevonen, Kimberly A, Jansz, Natasha, Garcia-Perez, Jose L, Richardson, Sandra R, Ewing, Adam D, Carbone, Lucia and Faulkner, Geoffrey J (2022). Somatic retrotransposition in the developing rhesus macaque brain. Genome Research, 32 (7), gr.276451.121-1314. doi: 10.1101/gr.276451.121
HUSH, retrotransposon RNA, you're NEXT to decay
Faulkner, Geoffrey J. (2022). HUSH, retrotransposon RNA, you're NEXT to decay. Molecular Cell, 82 (9), 1610-1612. doi: 10.1016/j.molcel.2022.04.013
Retrotransposons: still mobile in humans
Faulkner, Geoffrey J. (2022). Retrotransposons: still mobile in humans. Nature Reviews Genetics, 23 (8), 458-459. doi: 10.1038/s41576-022-00485-6
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
Grapotte, Mathys, Saraswat, Manu, Bessière, Chloé, Menichelli, Christophe, Ramilowski, Jordan A., Severin, Jessica, Hayashizaki, Yoshihide, Itoh, Masayoshi, Tagami, Michihira, Murata, Mitsuyoshi, Kojima-Ishiyama, Miki, Noma, Shohei, Noguchi, Shuhei, Kasukawa, Takeya, Hasegawa, Akira, Suzuki, Harukazu, Nishiyori-Sueki, Hiromi, Frith, Martin C., Abugessaisa, Imad, Aitken, Stuart, Aken, Bronwen L., Alam, Intikhab, Alam, Tanvir, Alasiri, Rami, Alhendi, Ahmad M. N., Alinejad-Rokny, Hamid, Alvarez, Mariano J., Andersson, Robin, Arakawa, Takahiro ... Lecellier, Charles-Henri (2021). Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature Communications, 12 (1) 3297. doi: 10.1038/s41467-021-23143-7
The evolving gene regulatory landscape—a tinkerer of complex creatures
Faulkner, Geoffrey J. (2021). The evolving gene regulatory landscape—a tinkerer of complex creatures. Genome Biology, 22 (1) 199, 199. doi: 10.1186/s13059-021-02412-0
Hcv activates somatic l1 retrotransposition—a potential hepatocarcinogenesis pathway
Sudhindar, Praveen D., Wainwright, Daniel, Saha, Santu, Howarth, Rachel, McCain, Misti, Bury, Yvonne, Saha, Sweta S., McPherson, Stuart, Reeves, Helen, Patel, Arvind H., Faulkner, Geoffrey J., Lunec, John and Shukla, Ruchi (2021). Hcv activates somatic l1 retrotransposition—a potential hepatocarcinogenesis pathway. Cancers, 13 (20) 5079. doi: 10.3390/cancers13205079
Processed pseudogenes: a substrate for evolutionary innovation. Retrotransposition contributes to genome evolution by propagating pseudogene sequences with rich regulatory potential throughout the genome
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
An early proinflammatory transcriptional response to tau pathology is age‐specific and foreshadows reduced tau burden
Rasmussen, Jay, Ewing, Adam D., Bodea, Liviu‐Gabriel, Bodea, Gabriela O., Gearing, Marla and Faulkner, Geoffrey J. (2021). An early proinflammatory transcriptional response to tau pathology is age‐specific and foreshadows reduced tau burden. Brain Pathology, 32 (3) e13018, e13018. doi: 10.1111/bpa.13018
No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing
Smits, Nathan, Rasmussen, Jay, Bodea, Gabriela O., Amarilla, Alberto A., Gerdes, Patricia, Sanchez-Luque, Francisco J., Ajjikuttira, Prabha, Modhiran, Naphak, Liang, Benjamin, Faivre, Jamila, Deveson, Ira W., Khromykh, Alexander A., Watterson, Daniel, Ewing, Adam D. and Faulkner, Geoffrey J. (2021). No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing. Cell Reports, 36 (7) 109530, 109530. doi: 10.1016/j.celrep.2021.109530
Absence of coding somatic single nucleotide variants within well-known candidate genes in late-onset sporadic Alzheimer's Disease based on the analysis of multi-omics data
Min, Shishi, Li, Zongchang, Shieh, Annie, Giase, Gina, Bao, Riyue, Zhang, Chunling, Kuney, Liz, Kopp, Richard, Asif, Huma, Alliey-Rodriguez, Ney, Qin, Lixia, Craig, David Wesley, Faulkner, Geoffrey J., Gershon, Elliot S., Tang, Beisha, Chen, Chao and Liu, Chunyu (2021). Absence of coding somatic single nucleotide variants within well-known candidate genes in late-onset sporadic Alzheimer's Disease based on the analysis of multi-omics data. Neurobiology of Aging, 108, 207-209. doi: 10.1016/j.neurobiolaging.2021.07.010
Hippocampal neurogenesis mediates sex-specific effects of social isolation and exercise on fear extinction in adolescence
Drummond, Katherine D., Waring, Michelle L., Faulkner, Geoffrey J., Blewitt, Marnie E., Perry, Christina J. and Kim, Jee Hyun (2021). Hippocampal neurogenesis mediates sex-specific effects of social isolation and exercise on fear extinction in adolescence. Neurobiology of Stress, 15 100367, 1-16. doi: 10.1016/j.ynstr.2021.100367
Endogenous retroviruses in the origins and treatment of cancer
Jansz, Natasha and Faulkner, Geoffrey J. (2021). Endogenous retroviruses in the origins and treatment of cancer. Genome Biology, 22 (1) 147, 1-22. doi: 10.1186/s13059-021-02357-4
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
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
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
L1 mosaicism in mammals: extent, effects, and evolution
Faulkner, Geoffrey J. and Garcia-Perez, Jose L. (2017). L1 mosaicism in mammals: extent, effects, and evolution. Trends in Genetics, 33 (11), 802-816. doi: 10.1016/j.tig.2017.07.004
Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells
Klawitter, Sabine, Fuchs,Nina V., Upton, Kyle R., Munoz-Lopez, Martin, Shukla, Ruchi, Wang, Jichang, Garcia-Canadas, Marta, Lopez-Ruiz, Cesar, Gerhardt, Daniel J., Sebe, Attila, Grabundzija, Ivana, Merkert, Sylvia, Gerdes, Patricia, Pulgarin, J. Andres, Bock, Anja, Held, Ulrike, Witthuhn, Anett, Haase, Alexandra, Sarkadi, Balazs, Lower, Johannes, Wolvetang, Ernst J., Martin, Ulrich, Ivics, Zoltan, Izsvak, Zsuzsanna, Garcia-Perez, Jose L., Faulkner, Geoffrey J. and Schumann, Gerald G. (2016) Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells. Nature Communications, 7 1-14. doi:10.1038/ncomms10286
Ubiquitous L1 mosaicism in hippocampal neurons
Upton, Kyle R., Gerhardt, Daniel J., Jesuadian, J. Samuel, Richardson, Sandra R., Sanchez-Luque, Francisco J., Bodea, Gabriela O., Ewing, Adam D., Salvador-Palomeque, Carmen, van der Knaap, Mario S., Brennan, Paul M., Vanderver, Adeline and Faulkner, Geoffrey J. (2015) Ubiquitous L1 mosaicism in hippocampal neurons. Cell, 161 2: 228-239. doi:10.1016/j.cell.2015.03.026
L1 retrotransposons and somatic mosaicism in the brain
Richardson, Sandra R., Morell, Santiago and Faulkner, Geoffrey J. (2014) L1 retrotransposons and somatic mosaicism in the brain. Annual Review of Genetics, 48 1-27. doi:10.1146/annurev-genet-120213-092412
Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma
Shukla, Ruchi, Upton, Kyle R., Muñoz-Lopez, Martin, Gerhardt, Daniel J., Fisher, Malcolm E., Thu Nguyen, Brennan, Paul M., Baillie, J. Kenneth, Collino, Agnese, Ghisletti, Serena, Sinha, Shruti, Iannelli, Fabio, Radaelli, Enrico, Dos Santos, Alexandre, Rapoud, Delphine, Guettier, Catherine, Samuel, Didier, Natoli, Gioacchino, Carninci, Piero, Ciccarelli, Francesca D., Luis Garcia-Perez, Jose, Faivre, Jamila and Faulkner, Geoffrey J. (2013) Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell, 153 1: 101-111. doi:10.1016/j.cell.2013.02.032
Somatic retrotransposition alters the genetic landscape of the human brain
Baillie, J. Kenneth, Barnett, Mark W., Upton, Kyle R., Gerhardt, Daniel J., Richmond, Todd A., De Sapio, Fioravante, Brennan. Paul M., Rizzu, Patrizia, Smith, Sarah, Fell, Mark, Talbot, Richard T., Gustincich, Stefano, Freeman, Thomas C., Mattick, John S., Hume, David A., Heutink, Peter, Carninci, Piero, Jeddeloh, Jeffrey A. and Faulkner, Geoffrey J. (2011) Somatic retrotransposition alters the genetic landscape of the human brain. Nature, 479 7374: 534-537. doi:10.1038/nature10531
The regulated retrotransposon transcriptome of mammalian cells
Faulkner, Geoffrey J., Kimura, Yasumasa, Daub, Carsten O., Wani, Shivangi, Plessy, Charles, Irvine, Katharine M., Schroder, Kate, Cloonan, Nicole, Steptoe, Anita L., Lassmann, Timo, Waki, Kazunori, Hornig, Nadine, Arakawa, Takahiro, Takahashi, Hazuki, Kawai, Jun, Forrest, Alistair R. R., Suzuki, Harukazu, Hayashizaki, Yoshihide, Hume, David A., Orlando, Valerio, Grimmond, Sean M. and Carninci, Piero (2009) The regulated retrotransposon transcriptome of mammalian cells. Nature genetics, 41 5: 563-571. doi:10.1038/ng.368