Faulkner publications

Dynamic and ongoing de novo L1 retrotransposition contributes to genome plasticity and intrapatient heterogeneity in ovarian cancer

Pradhan, Barun, Oikkonen, Jaana, Zhang, Kaiyang, Botto, Juan Manuel, Eriksson, Minna R., Sundaresan, Srividhya, Genç, Fatih, Pisanic, Thomas R., Marin Falco, Matias, Li, Yilin, Pikkusaari, Sanna, Lavikka, Kari, Micoli, Giulia, Marchi, Giovanni, Muranen, Taru A., Huhtinen, Kaisa, Vähärautio, Anna, Badge, Richard, Burns, Kathleen H., Hietanen, Sakari, Hynninen, Johanna, Faulkner, Geoffrey J., Hautaniemi, Sampsa, and Kauppi, Liisa (2026). Dynamic and ongoing de novo L1 retrotransposition contributes to genome plasticity and intrapatient heterogeneity in ovarian cancer. Cancer Research 86 (4) 1073-1088. https://doi.org/10.1158/0008-5472.can-24-4419

Combination antiretroviral therapy and MCL-1 inhibition mitigate HTLV-1 infection in vivo

Cooney, James P., Hirons, Ashley, Jansz, Natasha, Allison, Cody C., Hickey, Peter, Teh, Charis E., Tan, Tania, Dagley, Laura F., Yousef, Jumana, Yurick, David, Khoury, Georges, Preston, Simon P., Arandjelovic, Philip, Davidson, Kathryn C., Williams, Lewis J., Bader, Stefanie M., Wang, Le, Bhandari, Reet, Mackiewicz, Liana, Dayton, Merle, Clow, William, Faulkner, Geoffrey J., Gray, Daniel H., Einsiedel, Lloyd, Purcell, Damian F.J., Doerflinger, Marcel, and Pellegrini, Marc (2025). Combination antiretroviral therapy and MCL-1 inhibition mitigate HTLV-1 infection in vivo. Cell 188 (18) 4896-4912.e19. https://doi.org/10.1016/j.cell.2025.06.023

OGT prevents DNA demethylation and suppresses the expression of transposable elements in heterochromatin by restraining TET activity genome-wide

Sepulveda, Hugo, Li, Xiang, Arteaga-Vazquez, Leo J., López-Moyado, Isaac F., Brunelli, Melina, Hernández-Espinosa, Lot, Yue, Xiaojing, Angel, J. Carlos, Brown, Caitlin, Dong, Zhen, Jansz, Natasha, Puddu, Fabio, Modat, Aurélie, Scotcher, Jamie, Creed, Páidí, Kennedy, Patrick H., Manriquez-Rodriguez, Cindy, Myers, Samuel A., Crawford, Robert, Faulkner, Geoffrey J., and Rao, Anjana (2025). OGT prevents DNA demethylation and suppresses the expression of transposable elements in heterochromatin by restraining TET activity genome-wide. Nature Structural and Molecular Biology 32 (7) 3 1282-1296. https://doi.org/10.1038/s41594-025-01505-9

A mutant ASXL1-BAP1-EHMT complex contributes to heterochromatin dysfunction in clonal hematopoiesis and chronic monomyelocytic leukemia

Dong, Zhen, Sepulveda, Hugo, Arteaga-Vazquez, Leo J., Blouin, Chad, Fernandez, Jenna, Binder, Moritz, Chou, Wen-Chien, Tien, Hwei-Fang, Patnaik, Mrinal M., Faulkner, Geoffrey J., Myers, Samuel A., and Rao, Anjana (2025). A mutant ASXL1-BAP1-EHMT complex contributes to heterochromatin dysfunction in clonal hematopoiesis and chronic monomyelocytic leukemia. Proceedings of the National Academy of Sciences 122 (1) e2413302121 1-12. https://doi.org/10.1073/pnas.2413302121

Chromatin-based memory as a self-stabilizing influence on cell identity

Bell, Charles C., Faulkner, Geoffrey J., and Gilan, Omer (2024). Chromatin-based memory as a self-stabilizing influence on cell identity. Genome Biology 25 (1) 320 1-13. https://doi.org/10.1186/s13059-024-03461-x

Two HUSH complexes connect a direct LINE to innate immunity

Faulkner, Geoffrey J. (2024). Two HUSH complexes connect a direct LINE to innate immunity. Molecular Cell 84 (15) 2801-2803. https://doi.org/10.1016/j.molcel.2024.07.010

LINE-1 retrotransposons contribute to mouse PV interneuron development

Bodea, Gabriela O., Botto, Juan M., Ferreiro, Maria E., Sanchez-Luque, Francisco J., de los Rios Barreda, Jose, Rasmussen, Jay, Rahman, Muhammed A., Fenlon, Laura R., Jansz, Natasha, Gubert, Carolina, Gerdes, Patricia, Bodea, Liviu-Gabriel, Ajjikuttira, Prabha, Da Costa Guevara, Darwin J., Cumner, Linda, Bell, Charles C., Kozulin, Peter, Billon, Victor, Morell, Santiago, Kempen, Marie-Jeanne H. C., Love, Chloe J., Saha, Karabi, Palmer, Lucy M., Ewing, Adam D., Jhaveri, Dhanisha J., Richardson, Sandra R., Hannan, Anthony J., and Faulkner, Geoffrey J. (2024). LINE-1 retrotransposons contribute to mouse PV interneuron development. Nature Neuroscience 27 (7) 1-34. https://doi.org/10.1038/s41593-024-01650-2

Comparative cofactor screens show the influence of transactivation domains and core promoters on the mechanisms of transcription

Bell, Charles C., Balic, Jesse J., Talarmain, Laure, Gillespie, Andrea, Scolamiero, Laura, Lam, Enid Y. N., Ang, Ching-Seng, Faulkner, Geoffrey J., Gilan, Omer, and Dawson, Mark A. (2024). Comparative cofactor screens show the influence of transactivation domains and core promoters on the mechanisms of transcription. Nature Genetics 56 (6) 1181-1192. https://doi.org/10.1038/s41588-024-01749-z

Viral genome sequencing methods: benefits and pitfalls of current approaches

Jansz, Natasha and Faulkner, Geoffrey J. (2024). Viral genome sequencing methods: benefits and pitfalls of current approaches. Biochemical Society Transactions 52 (3) 1431-1447. https://doi.org/10.1042/bst20231322

HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and function

Friedman, Clayton E., Cheetham, Seth W., Negi, Sumedha, Mills, Richard J., Ogawa, Masahito, Redd, Meredith A., Chiu, Han Sheng, Shen, Sophie, Sun, Yuliangzi, Mizikovsky, Dalia, Bouveret, Romaric, Chen, Xiaoli, Voges, Holly K., Paterson, Scott, De Angelis, Jessica E., Andersen, Stacey B., Cao, Yuanzhao, Wu, Yang, Jafrani, Yohaann M.A., Yoon, Sohye, Faulkner, Geoffrey J., Smith, Kelly A., Porrello, Enzo, Harvey, Richard P., Hogan, Benjamin M., Nguyen, Quan, Zeng, Jian, Kikuchi, Kazu, Hudson, James E. and 1 more (2024). HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and function. Developmental Cell 59 (1) 91-107.e6. https://doi.org/10.1016/j.devcel.2023.11.012

Stimulation of the muscarinic receptor M4 regulates neural precursor cell proliferation and promotes adult hippocampal neurogenesis

Madrid, Lidia I., Hafey, Katelyn, Bandhavkar, Saurabh, Bodea, Gabriela O., Jimenez-Martin, Javier, Milne, Michael, Walker, Tara L., Faulkner, Geoffrey J., Coulson, Elizabeth J., and Jhaveri, Dhanisha J. (2024). Stimulation of the muscarinic receptor M4 regulates neural precursor cell proliferation and promotes adult hippocampal neurogenesis. Development 151 (1) dev201835 1-13. https://doi.org/10.1242/dev.201835

Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development

Gerdes, Patricia, Chan, Dorothy, Lundberg, Mischa, Sanchez-Luque, Francisco J., Bodea, Gabriela O., Ewing, Adam D., Faulkner, Geoffrey J., and Richardson, Sandra R. (2023). Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development. Genome Research 33 (9) 1465-1481. https://doi.org/10.1101/gr.278003.123

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. https://doi.org/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 46 (6) 413-414. https://doi.org/10.1016/j.tins.2023.03.011

Single-neuron whole genome sequencing identifies increased somatic mutation burden in Alzheimer's disease related genes

Li, Zongchang, Min, Shishi, Alliey-Rodriguez, Ney, Giase, Gina, Cheng, Lijun, Craig, David Wesley, Faulkner, Geoffrey J., Asif, Huma, Liu, Chunyu, and Gershon, Elliot S. (2023). Single-neuron whole genome sequencing identifies increased somatic mutation burden in Alzheimer's disease related genes. Neurobiology of Aging 123 222-232. https://doi.org/10.1016/j.neurobiolaging.2022.12.002

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. https://doi.org/10.1016/j.neuron.2023.02.007

The complexity of transferring genetic information

Strader, Lucia C., Staller, Max V., Willis, Anne E., Faulkner, Geoffrey J., Beggs, Jean D., and Cech, Thomas R. (2023). The complexity of transferring genetic information. Molecular Cell 83 (3) 320-323. https://doi.org/10.1016/j.molcel.2023.01.002

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. https://doi.org/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. https://doi.org/10.1038/s41467-022-35180-x

Nanopore Sequencing to Identify Transposable Element Insertions and Their Epigenetic Modifications

Smits, Nathan and Faulkner, Geoffrey J. (2022). Nanopore Sequencing to Identify Transposable Element Insertions and Their Epigenetic Modifications. Transposable Elements: Methods and Protocols. New York, NY United States: Springer.151-171.https://doi.org/10.1007/978-1-0716-2883-6_9