The University of Queensland

Heritable L1 retrotransposition in the mouse primordial germline and early embryo

Richardson, Sandra R., Gerdes, Patricia, Gerhardt, Daniel J., Sanchez-Luque, Francisco J., Bodea, Gabriela-Oana, Muñoz-Lopez, Martin, Jesuadian, J. Samuel, Kempen, Marie-Jeanne H. C., Carreira, Patricia E., Jeddeloh, Jeffrey A., Garcia-Perez, Jose L., Kazazian Jr., Haig H., Ewing, Adam D. and Faulkner, Geoffrey J. (2017). Heritable L1 retrotransposition in the mouse primordial germline and early embryo. Genome Research, 27 (8), 1395-1405. doi: 10.1101/gr.219022.116

Analysis of somatic LINE-1 insertions in neurons

Sanchez-Luque, Francisco J., Richardson, Sandra R. and Faulkner, Geoffrey J. (2017). Analysis of somatic LINE-1 insertions in neurons. Genomic mosaicism in neurons and other cell types. (pp. 219-251) edited by José María Frade and Fred H. Gage. New York, United States: Humana Press. doi: 10.1007/978-1-4939-7280-7_12

LINE-1 cultured cell retrotransposition assay

Kopera, Huira C., Larson, Peter A., Moldovan, John B., Richardson, Sandra R., Liu, Ying and Moran, John V. (2016). LINE-1 cultured cell retrotransposition assay. Transposons and retrotransposons: methods and protocols. (pp. 139-156) edited by Jose L. Garcia-Pérez. New York, NY, United States: Humana Press . doi: 10.1007/978-1-4939-3372-3_10

Retrotransposon capture sequencing (RC-Seq): a targeted, high-throughput approach to resolve somatic L1 retrotransposition in humans

Sanchez-Luque, Francisco J., Richardson, Sandra R. and Faulkner, Geoffrey J. (2016). Retrotransposon capture sequencing (RC-Seq): a targeted, high-throughput approach to resolve somatic L1 retrotransposition in humans. Transposons and retrotranspons: methods and protocols. (pp. 47-77) edited by Jose L. Garcia-Pérez. New York, NY, United States: Springer. doi: 10.1007/978-1-4939-3372-3_4

The Influence of LINE-1 and SINE Retrotransposons on Mammalian Genomes

Richardson, Sandra R., Doucet, Aurélien J., Kopera, Huira C., Moldovan, John B., Garcia-Perez, José Luis and Moran, John V. (2015). The Influence of LINE-1 and SINE Retrotransposons on Mammalian Genomes. Mobile DNA III. (pp. 1165-1208) Washington, DC, USA: ASM Press. doi: 10.1128/9781555819217.ch51

Every repeat is unique: Exploring the genomic impact of human L1 retrotransposons at locus-specific resolution

Workman, Stephanie and Richardson, Sandra R. (2024). Every repeat is unique: Exploring the genomic impact of human L1 retrotransposons at locus-specific resolution. Cell Genomics, 4 (2) 100504, 100504. doi: 10.1016/j.xgen.2024.100504

Safe Babies, Safe Moms: A Multifaceted, Trauma Informed Care Initiative

Patchen, Loral, Mccullers, Asli, Beach, Charmain, Browning, Melanie, Porter, Shy, Danielson, Aimee, Asegieme, Evelyn, Richardson, S. Roxana, Jost, Ali, Jensen, Caitlin Schille and Ahmed, Naheed (2023). Safe Babies, Safe Moms: A Multifaceted, Trauma Informed Care Initiative. Maternal and Child Health Journal, 28 (1), 31-37. doi: 10.1007/s10995-023-03840-z

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. doi: 10.1101/gr.278003.123

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

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

LINE-1 retrotransposon activation intrinsic to interneuron development

Bodea, Gabriela O., Ferreiro, Maria E., Sanchez-Luque, Francisco J., Botto, Juan M., Rasmussen, Jay, Rahman, Muhammed A., Fenlon, Laura R., Gubert, Carolina, Gerdes, Patricia, Bodea, Liviu-Gabriel, Ajjikuttira, Prabha, Kozulin, Peter, Billon, Victor, Morell, Santiago, Kempen, Marie-Jeanne H.C., Love, Chloe J., Palmer, Lucy M., Ewing, Adam D., Jhaveri, Dhanisha J., Richardson, Sandra R., Hannan, Anthony J. and Faulkner, Geoffrey J. (2022). LINE-1 retrotransposon activation intrinsic to interneuron development.

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

Dynamic methylation of an L1 transduction family during reprogramming and neurodifferentiation

Salvador-Palomeque, Carmen, Sanchez-Luque, Francisco J., Fortuna, Patrick R. J., Ewing, Adam D., Wolvetang, Ernst J., Richardson, Sandra R. and Faulkner, Geoffrey J. (2019). Dynamic methylation of an L1 transduction family during reprogramming and neurodifferentiation. Molecular and Cellular Biology, 39 (7) e00499-18, 1-19. doi: 10.1128/mcb.00499-18

Heritable L1 retrotransposition events during development: understanding their origins: examination of heritable, endogenous L1 retrotransposition in mice opens up exciting new questions and research directions

Richardson, Sandra R. and Faulkner, Geoffrey J. (2018). Heritable L1 retrotransposition events during development: understanding their origins: examination of heritable, endogenous L1 retrotransposition in mice opens up exciting new questions and research directions. BioEssays, 40 (6) 1700189, e1700189. doi: 10.1002/bies.201700189

L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis

Schauer, Stephanie N., Carreira, Patricia E., Shukla, Ruchi, Gerhardt, Daniel J., Gerdes, Patricia, Sanchez-Luque, Francisco J., Nicoli, Paola, Kindlova, Michaela, Ghisletti, Serena, Santos, Alexandre Dos, Rapoud, Delphine, Samuel, Didier, Faivre, Jamila, Ewing, Adam D., Richardson, Sandra R. and Faulkner, Geoffrey J. (2018). L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis. Genome Research, 28 (5), 639-653. doi: 10.1101/gr.226993.117

L1 retrotransposon heterogeneity in ovarian tumor cell evolution

Nguyen, Thu H. M., Carreira, Patricia E., Sanchez-Luque, Francisco J., Schauer, Stephanie N., Fagg, Allister C., Richardson, Sandra R., Davies, Claire M., Jesuadian, J. Samuel, Kempen, Marie-Jeanne H. C., Troskie, Robin-Lee, James, Cini, Beaven, Elizabeth A., Wallis, Tristan P., Coward, Jermaine I. G., Chetty, Naven P., Crandon, Alexander J., Venter, Deon J., Armes, Jane E., Perrin, Lewis C., Hooper, John D., Ewing, Adam D., Upton, Kyle R. and Faulkner, Geoffrey J. (2018). L1 retrotransposon heterogeneity in ovarian tumor cell evolution. Cell Reports, 23 (13), 3730-3740. doi: 10.1016/j.celrep.2018.05.090

Heritable L1 retrotransposition in the mouse primordial germline and early embryo

Richardson, Sandra R., Gerdes, Patricia, Gerhardt, Daniel J., Sanchez-Luque, Francisco J., Bodea, Gabriela-Oana, Muñoz-Lopez, Martin, Jesuadian, J. Samuel, Kempen, Marie-Jeanne H. C., Carreira, Patricia E., Jeddeloh, Jeffrey A., Garcia-Perez, Jose L., Kazazian Jr., Haig H., Ewing, Adam D. and Faulkner, Geoffrey J. (2017). Heritable L1 retrotransposition in the mouse primordial germline and early embryo. Genome Research, 27 (8), 1395-1405. doi: 10.1101/gr.219022.116

TET enzymes: double agents in the transposable element-host genome conflict

Gerdes, Patricia, Richardson, Sandra R. and Faulkner, Geoffrey J. (2016). TET enzymes: double agents in the transposable element-host genome conflict. Genome Biology, 17 (1) 259. doi: 10.1186/s13059-016-1124-8

Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme

Carreira, Patricia E., Ewing, Adam D., Li, Guibo, Schauer, Stephanie N., Upton, Kyle R., Fagg, Allister C., Morell, Santiago, Kindlova, Michaela, Gerdes, Patricia, Richardson, Sandra R., Li, Bo, Gerhardt, Daniel J., Wang, Jun, Brennan, Paul M. and Faulkner, Geoffrey J. (2016). Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme. Mobile DNA, 7 (1) 21, 1-14. doi: 10.1186/s13100-016-0076-6

Transposable elements in the mammalian embryo: pioneers surviving through stealth and service

Gerdes, Patricia, Richardson, Sandra R., Mager, Dixie L. and Faulkner, Geoffrey J. (2016). Transposable elements in the mammalian embryo: pioneers surviving through stealth and service. Genome Biology, 17 (1) 100. doi: 10.1186/s13059-016-0965-5

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

The influence of LINE-1 and SINE retrotransposons on mammalian genomes

Richardson, Sandra R., Doucet, Aurélien J., Kopera, Huira C., Moldovan, John B., Garcia-Perez, José Luis and Moran, John V. (2015). The influence of LINE-1 and SINE retrotransposons on mammalian genomes. Microbiology Spectrum, 3 (2) MDNA3-0061-2014. doi: 10.1128/microbiolspec.MDNA3-0061-2014

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

APOBEC3A deaminates transiently exposed single-strand DNA during LINE-1 retrotransposition

Richardson, Sandra R., Narvaiza, Iñigo, Planegger, Randy A., Weitzman, Matthew D. and Moran, John V. (2014). APOBEC3A deaminates transiently exposed single-strand DNA during LINE-1 retrotransposition. eLife, 2014 (3) e02008. doi: 10.7554/eLife.02008

Diversity through duplication: Whole-genome sequencing reveals novel gene retrocopies in the human population

Richardson, Sandra R., Salvador-Palomeque, Carmen and Faulkner, Geoffrey J. (2014). Diversity through duplication: Whole-genome sequencing reveals novel gene retrocopies in the human population. BioEssays, 36 (5), 475-481. doi: 10.1002/bies.201300181

L1 retrotransposons, cancer stem cells and oncogenesis

Carreira, Patricia E., Richardson, Sandra R. and Faulkner, Geoffrey J. (2014). L1 retrotransposons, cancer stem cells and oncogenesis. FEBS Journal, 281 (1), 63-73. doi: 10.1111/febs.12601