The University of Queensland

The maize methylome

Noshay, Jaclyn M., Crisp, Peter A. and Springer, Nathan M. (2018). The maize methylome. The Maize Genome. (pp. 81-96) edited by Jeffrey Bennetzen, Sherry Flint-Garcia, Candice Hirsch and Roberto Tuberosa. Cham, Switzerland: Springer. doi: 10.1007/978-3-319-97427-9_6

Grafting in Arabidopsis

Bainbridge, Katherine, Bennett, Tom, Crisp, Peter, Leyser, Ottoline and Turnbull, Colin (2014). Grafting in Arabidopsis. Arabidopsis Protocols. (pp. 155-163) edited by SanchezSerrano, JJ and Salinas, J. New York, NY, United States: Humana Press. doi: 10.1007/978-1-62703-580-4_7

Dynamics of <scp>mRNA</scp> fate during light stress and recovery: from transcription to stability and translation

Smith, Aaron B., Ganguly, Diep R., Moore, Marten, Bowerman, Andrew F., Janapala, Yoshika, Shirokikh, Nikolay E., Pogson, Barry J. and Crisp, Peter A. (2023). Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translation. The Plant Journal, 117 (3), 818-839. doi: 10.1111/tpj.16531

Genetic mapping, candidate gene identification and marker validation for host plant resistance to the race 4 of Fusarium oxysporum f. sp. cubense using Musa acuminata ssp. malaccensis

Chen, Andrew, Sun, Jiaman, Viljoen, Altus, Mostert, Diane, Xie, Yucong, Mangila, Leroy, Bothma, Sheryl, Lyons, Rebecca, Hřibová, Eva, Christelová, Pavla, Uwimana, Brigitte, Amah, Delphine, Pearce, Stephen, Chen, Ning, Batley, Jacqueline, Edwards, David, Doležel, Jaroslav, Crisp, Peter, Brown, Allan F., Martin, Guillaume, Yahiaoui, Nabila, D’Hont, Angelique, Coin, Lachlan, Swennen, Rony and Aitken, Elizabeth A. B. (2023). Genetic mapping, candidate gene identification and marker validation for host plant resistance to the race 4 of Fusarium oxysporum f. sp. cubense using Musa acuminata ssp. malaccensis. Pathogens, 12 (6) 820, 820. doi: 10.3390/pathogens12060820

Epigenetic features drastically impact CRISPR–Cas9 efficacy in plants

Weiss, Trevor, Crisp, Peter A., Rai, Krishan M., Song, Meredith, Springer, Nathan M. and Zhang, Feng (2022). Epigenetic features drastically impact CRISPR–Cas9 efficacy in plants. Plant Physiology, 190 (2), 1153-1164. doi: 10.1093/plphys/kiac285

Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks

Wrightsman, Travis, Marand, Alexandre P., Crisp, Peter A., Springer, Nathan M. and Buckler, Edward S. (2022). Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks. The Plant Genome, 15 (3) e20249, 1-13. doi: 10.1002/tpg2.20249

Identifying transcription factor-DNA interactions using machine learning

Bang, Sohyun, Galli, Mary, Crisp, Peter A., Gallavotti, Andrea and Schmitz, Robert J. (2022). Identifying transcription factor-DNA interactions using machine learning. In Silico Plants, 4 (2) diac014, 1-15. doi: 10.1093/insilicoplants/diac014

Enzymes degraded under high light maintain proteostasis by transcriptional regulation in Arabidopsis

Li, Lei, Duncan, Owen, Ganguly, Diep R., Lee, Chun Pong, Crisp, Peter A., Wijerathna-Yapa, Akila, Salih, Karzan, Trösch, Josua, Pogson, Barry J. and Millar, A. Harvey (2022). Enzymes degraded under high light maintain proteostasis by transcriptional regulation in Arabidopsis. Proceedings of the National Academy of Sciences, 119 (20) e2121362119, 1-11. doi: 10.1073/pnas.2121362119

Genome‐wide loss of CHH methylation with limited transcriptome changes in Setaria viridis DOMAINS REARRANGED METHYLTRANSFERASE (DRM) mutants

Read, Andrew, Weiss, Trevor, Crisp, Peter A, Liang, Zhikai, Noshay, Jaclyn, Menard, Claire C, Wang, Chunfang, Song, Meredith, Hirsch, Candice N, Springer, Nathan M and Zhang, Feng (2022). Genome‐wide loss of CHH methylation with limited transcriptome changes in Setaria viridis DOMAINS REARRANGED METHYLTRANSFERASE (DRM) mutants. The Plant Journal, 111 (1), 103-116. doi: 10.1111/tpj.15781

Decoding the sorghum methylome: understanding epigenetic contributions to agronomic traits

Vafadarshamasbi, Ulduz, Mace, Emma, Jordan, David and Crisp, Peter A. (2022). Decoding the sorghum methylome: understanding epigenetic contributions to agronomic traits. Biochemical Society Transactions, 50 (1), 583-596. doi: 10.1042/bst20210908

Harnessing genetic variation at regulatory regions to fine-tune traits for climate resilient crops

Ganguly, Diep R., Hickey, Lee T. and Crisp, Peter A. (2022). Harnessing genetic variation at regulatory regions to fine-tune traits for climate resilient crops. Molecular Plant, 15 (2), 222-224. doi: 10.1016/j.molp.2021.12.011

Beyond the gene: epigenetic and cis-regulatory targets offer new breeding potential for the future

Crisp, Peter A., Bhatnagar-Mathur, Pooja, Hundleby, Penny, Godwin, Ian D., Waterhouse, Peter M. and Hickey, Lee T. (2022). Beyond the gene: epigenetic and cis-regulatory targets offer new breeding potential for the future. Current Opinion in Biotechnology, 73, 88-94. doi: 10.1016/j.copbio.2021.07.008

Epigenome guided crop improvement: current progress and future opportunities

Zhang, Yan, Andrews, Haylie, Eglitis-Sexton, Judith, Godwin, Ian, Tanurdžić, Miloš and Crisp, Peter A. (2022). Epigenome guided crop improvement: current progress and future opportunities. Emerging Topics in Life Sciences, 6 (2), 141-151. doi: 10.1042/etls20210258

Prediction of conserved and variable heat and cold stress response in maize using cis-regulatory information

Zhou, Peng, Enders, Tara A., Myers, Zachary A., Magnusson, Erika, Crisp, Peter A., Noshay, Jaclyn M., Gomez-Cano, Fabio, Liang, Zhikai, Grotewold, Erich, Greenham, Kathleen and Springer, Nathan M. (2022). Prediction of conserved and variable heat and cold stress response in maize using cis-regulatory information. The Plant Cell, 34 (1), 514-534. doi: 10.1093/plcell/koab267

Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes

Noshay, Jaclyn M., Liang, Zhikai, Zhou, Peng, Crisp, Peter A., Marand, Alexandre P., Hirsch, Candice N., Schmitz, Robert J. and Springer, Nathan M. (2021). Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes. G3: Genes, Genomes, Genetics, 11 (8) jkab190. doi: 10.1093/g3journal/jkab190

Science forum: a community-led initiative for training in reproducible research

Auer, Susann, Haelterman, Nele A., Weissgerber, Tracey L., Erlich, Jeffrey C., Susilaradeya, Damar, Julkowska, Magdalena, Gazda, Małgorzata Anna, Schwessinger, Benjamin, Jadavji, Nafisa M., Abitua, Angela, Niraulu, Anzela, Shahb, Aparna, Clyburne-Sherinb, April, Guiquel, Benoit, Alicea, Bradly, Lamanna, Caroline, Ganguly, Diep, Perkins, Eric, Jambor, Helena, Li, Ian Man Ho, Tsang, Jennifer, Kamens, Joanne, Teytelman, Lenny, Paul, Mariella, Cronin, Michelle, Schmelling, Nicolas, Crisp, Peter, Kutum, Rintu, Phuyal, Santosh ... Bachle, Susanna (2021). Science forum: a community-led initiative for training in reproducible research. eLife, 10 e64719. doi: 10.7554/eLife.64719

Current status and prospects of plant genome editing in Australia

Zhang, Yan, Restall, Jemma, Crisp, Peter, Godwin, Ian and Liu, Guoquan (2021). Current status and prospects of plant genome editing in Australia. In Vitro Cellular & Developmental Biology - Plant, 57 (4), 1-10. doi: 10.1007/s11627-021-10188-y

Genetic and epigenetic variation in transposable element expression responses to abiotic stress in maize

Liang, Zhikai, Anderson, Sarah N., Noshay, Jaclyn M., Crisp, Peter A., Enders, Tara A. and Springer, Nathan M. (2021). Genetic and epigenetic variation in transposable element expression responses to abiotic stress in maize. Plant Physiology, 186 (1), 1-14. doi: 10.1093/plphys/kiab073

Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons

Noshay, Jaclyn M., Marand, Alexandre P., Anderson, Sarah N., Zhou, Peng, Mejia Guerra, Maria Katherine, Lu, Zefu, O’Connor, Christine H., Crisp, Peter A., Hirsch, Candice N., Schmitz, Robert J. and Springer, Nathan M. (2021). Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons. Genetics, 217 (1) iyaa003, 1-13. doi: 10.1093/genetics/iyaa003

Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

Crisp, Peter A., Marand, Alexandre P., Noshay, Jaclyn M., Zhou, Peng, Lu, Zefu, Schmitz, Robert J. and Springer, Nathan M. (2020). Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes. Proceedings of the National Academy of Sciences, 117 (38), 202010250-24000. doi: 10.1073/pnas.2010250117

Optimization of multiplexed CRISPR/Cas9 system for highly efficient genome editing in Setaria viridis

Weiss, Trevor, Wang, Chunfang, Kang, Xiaojun, Zhao, Hui, Elena Gamo, Maria, Starker, Colby G., Crisp, Peter A., Zhou, Peng, Springer, Nathan M., Voytas, Daniel F. and Zhang, Feng (2020). Optimization of multiplexed CRISPR/Cas9 system for highly efficient genome editing in Setaria viridis. Plant Journal, 104 (3) tpj.14949, 828-838. doi: 10.1111/tpj.14949

Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions

Zhou, Peng, Li, Zhi, Magnusson, Erika, Gomez Cano, Fabio, Crisp, Peter A., Noshay, Jaclyn M., Grotewold, Erich, Hirsch, Candice N., Briggs, Steven P. and Springer, Nathan M. (2020). Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions. The Plant Cell, 32 (5), 1377-1396. doi: 10.1105/tpc.20.00080

Epigenetic regulation of ABA-induced transcriptional responses in maize

Vendramin, Stefania, Huang, Ji, Crisp, Peter A., Madzima, Thelma F. and McGinnis, Karen M. (2020). Epigenetic regulation of ABA-induced transcriptional responses in maize. G3: Genes, Genomes, Genetics, 10 (5), 1727-1743. doi: 10.1534/g3.119.400993

Molecular and physiological responses during thermal acclimation of leaf photosynthesis and respiration in rice

Rashid, Fatimah Azzahra Ahmad, Crisp, Peter A., Zhang, You, Berkowitz, Oliver, Pogson, Barry J., Day, David A., Masle, Josette, Dewar, Roderick C., Whelan, James, Atkin, Owen K. and Scafaro, Andrew P. (2020). Molecular and physiological responses during thermal acclimation of leaf photosynthesis and respiration in rice. Plant Cell and Environment, 43 (3), 594-610. doi: 10.1111/pce.13706

Variation and inheritance of small RNAs in maize inbreds and F1 hybrids

Crisp, Peter A., Hammond, Reza, Zhou, Peng, Vaillancourt, Brieanne, Lipzen, Anna, Daum, Chris, Barry, Kerrie, de Leon, Natalia, Buell, C Robin, Kaeppler, Shawn M., Meyers, Blake C., Hirsch, Candice N. and Springer, Nathan M. (2020). Variation and inheritance of small RNAs in maize inbreds and F1 hybrids. Plant Physiology, 182 (1), 318-331. doi: 10.1104/pp.19.00817

Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize

Xu, Jing, Chen, Guo, Hermanson, Peter J., Xu, Qiang, Sun, Changshuo, Chen, Wenqing, Kan, Qiuxin, Li, Minqi, Crisp, Peter A., Yan, Jianbing, Li, Lin, Springer, Nathan M. and Li, Qing (2019). Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize. Genome Biology, 20 (1) 243. doi: 10.1186/s13059-019-1859-0

Monitoring the interplay between transposable element families and DNA methylation in maize

Noshay, Jaclyn M., Anderson, Sarah N., Zhou, Peng, Ji, Lexiang, Ricci, William, Lu, Zefu, Stitzer, Michelle C., Crisp, Peter A., Hirsch, Candice N., Zhang, Xiaoyu, Schmitz, Robert J. and Springer, Nathan M. (2019). Monitoring the interplay between transposable element families and DNA methylation in maize. PLOS Genetics, 15 (9) e1008291, e1008291. doi: 10.1371/journal.pgen.1008291

Opportunities to Use DNA methylation to distil functional elements in large crop genomes

Crisp, Peter A., Noshay, Jaclyn M., Anderson, Sarah N. and Springer, Nathan M. (2019). Opportunities to Use DNA methylation to distil functional elements in large crop genomes. Molecular Plant, 12 (3), 282-284. doi: 10.1016/j.molp.2019.02.006

Hybrid decay: A transgenerational epigenetic decline in vigor and viability triggered in backcross populations of teosinte with maize

Xue, Wei, Anderson, Sarah N., Wang, Xufeng, Yang, Liyan, Crisp, Peter A., Li, Qing, Noshay, Jaclyn, Albert, Patrice S., Birchler, James A., Bilinski, Paul, Stitzer, Michelle C., Ross-Ibarra, Jeffrey, Flint-Garcia, Sherry, Chen, Xuemei, Springer, Nathan M. and Doebley, John F. (2019). Hybrid decay: A transgenerational epigenetic decline in vigor and viability triggered in backcross populations of teosinte with maize. Genetics, 213 (1), 143-160. doi: 10.1534/genetics.119.302378

RNA polymerase II read-through promotes expression of neighboring genes in SAL1-PAP-XRN retrograde signaling

Crisp, Peter A., Smith, Aaron B., Ganguly, Diep R., Murray, Kevin D., Eichten, Steven R., Millar, Anthony A. and Pogson, Barry J. (2018). RNA polymerase II read-through promotes expression of neighboring genes in SAL1-PAP-XRN retrograde signaling. Plant Physiology, 178 (4), 1614-1630. doi: 10.1104/pp.18.00758

Heritable epigenomic changes to the maize methylome resulting from tissue culture

Han, Zhaoxue, Crisp, Peter A., Stelpflug, Scott, Kaeppler, Shawn M., Li, Qing and Springer, Nathan M. (2018). Heritable epigenomic changes to the maize methylome resulting from tissue culture. Genetics, 209 (4), 983-995. doi: 10.1534/genetics.118.300987

Maintenance of pre-existing DNA methylation states through recurring excess-light stress

Ganguly, Diep R., Crisp, Peter A., Eichten, Steven R. and Pogson, Barry J. (2018). Maintenance of pre-existing DNA methylation states through recurring excess-light stress. Plant Cell and Environment, 41 (7), 1657-1672. doi: 10.1111/pce.13324

The arabidopsis DNA methylome is stable under transgenerational drought stress

Ganguly, Diep R., Crisp, Peter A., Eichten, Steven R. and Pogson, Barry J. (2017). The arabidopsis DNA methylome is stable under transgenerational drought stress. Plant Physiology, 175 (4), 1893-1912. doi: 10.1104/pp.17.00744

Rapid recovery gene downregulation during excess-light stress and recovery in arabidopsis

Crisp, Peter A., Ganguly, Diep R., Smith, Aaron B., Murray, Kevin D., Estavillo, Gonzalo M., Searle, Iain, Ford, Ethan, Bogdanović, Ozren, Lister, Ryan, Borevitz, Justin O., Eichten, Steven R. and Pogson, Barry J. (2017). Rapid recovery gene downregulation during excess-light stress and recovery in arabidopsis. Plant Cell, 29 (8), 1836-1863. doi: 10.1105/tpc.16.00828

A chloroplast retrograde signal, 3’phosphoadenosine 5’-phosphate, acts as a secondary messenger in abscisic acid signaling in stomatal closure and germination

Pornsiriwong, Wannarat, Estavillo, Gonzalo M., Chan, Kai Xun, Tee, Estee E., Ganguly, Diep, Crisp, Peter A., Phua, Su Yin, Zhao, Chenchen, Qiu, Jiaen, Park, Jiyoung, Yong, Miing Tiem, Nisar, Nazia, Yadav, Arun Kumar, Schwessinger, Benjamin, Rathjen, John, Cazzonelli, Christopher I., Wilson, Philippa B., Gilliham, Matthew, Chen, Zhong-Hua and Pogson, Barry J. (2017). A chloroplast retrograde signal, 3’phosphoadenosine 5’-phosphate, acts as a secondary messenger in abscisic acid signaling in stomatal closure and germination. eLife, 6 e23361, e23361. doi: 10.7554/eLife.23361

Uncoupling high light responses from singlet oxygen retrograde signaling and spatial-temporal systemic acquired acclimation

Carmody, Melanie, Crisp, Peter A., d’Alessandro, Stefano, Ganguly, Diep, Gordon, Matthew, Havaux, Michel, Albrecht-Borth, Verónica and Pogson, Barry J. (2016). Uncoupling high light responses from singlet oxygen retrograde signaling and spatial-temporal systemic acquired acclimation. Plant Physiology, 171 (3), 1734-1749. doi: 10.1104/pp.16.00404

Reconsidering plant memory: intersections between stress recovery, RNA turnover, and epigenetics

Crisp, Peter A., Ganguly, Diep, Eichten, Steven R., Borevitz, Justin O. and Pogson, Barry J. (2016). Reconsidering plant memory: intersections between stress recovery, RNA turnover, and epigenetics. Science Advances, 2 (2) e1501340, e1501340. doi: 10.1126/sciadv.1501340

Learning the languages of the chloroplast: retrograde signaling and beyond

Chan, Kai Xun, Phua, Su Yin, Crisp, Peter, McQuinn, Ryan and Pogson, Barry J. (2016). Learning the languages of the chloroplast: retrograde signaling and beyond. Annual Review of Plant Biology, 67 (1), 25-53. doi: 10.1146/annurev-arplant-043015-111854

Genetic suppression of plant development and chloroplast biogenesis via the Snowy Cotyledon 3 and Phytochrome B pathways

Ganguly, Diep, Crisp, Peter, Harter, Klaus, Pogson, Barry J. and Albrecht-Borth, Veronica (2015). Genetic suppression of plant development and chloroplast biogenesis via the Snowy Cotyledon 3 and Phytochrome B pathways. Functional Plant Biology, 42 (7), 676-686. doi: 10.1071/fp15026

Subset of heat-shock transcription factors required for the early response of Arabidopsis to excess light

Jung, Hou-Sung, Crisp, Peter A., Estavillo, Gonzalo M., Cole, Benjamin, Hong, Fangxin, Mockler, Todd C., Pogson, Barry J. and Chory, Joanne (2013). Subset of heat-shock transcription factors required for the early response of Arabidopsis to excess light. Proceedings of the National Academy of Sciences of the United States of America, 110 (35), 14474-14479. doi: 10.1073/pnas.1311632110

Evidence for a SAL1-PAP chloroplast retrograde pathway that functions in drought and high light signaling in Arabidopsis

Estavillo, Gonzalo M., Crisp, Peter A., Pornsiriwong, Wannarat, Wirtz, Markus, Collinge, Derek, Carrie, Chris, Giraud, Estelle, Whelan, James, David, Pascale, Javot, Helene, Brearley, Charles, Hell, Ruediger, Marin, Elena and Pogson, Barry J. (2011). Evidence for a SAL1-PAP chloroplast retrograde pathway that functions in drought and high light signaling in Arabidopsis. Plant Cell, 23 (11), 3992-4012. doi: 10.1105/tpc.111.091033

A novel fry1 allele reveals the existence of a mutant phenotype unrelated to 5 '-> 3 ' exoribonuclease (XRN) activities in Arabidopsis thaliana roots

Hirsch, Judith, Misson, Julie, Crisp, Peter A., David, Pascale, Bayle, Vincent, Estavillo, Gonzalo M., Javot, Helene, Chiarenza, Serge, Mallory, Allison C., Maizel, Alexis, Declerck, Marie, Pogson, Barry J., Vaucheret, Herve, Crespi, Martin, Desnos, Thierry, Thibaud, Marie-Christine, Nussaume, Laurent and Marin, Elena (2011). A novel fry1 allele reveals the existence of a mutant phenotype unrelated to 5 '-> 3 ' exoribonuclease (XRN) activities in Arabidopsis thaliana roots. PloS One, 6 (2) e16724, e16724. doi: 10.1371/journal.pone.0016724

Chloroplast-to-nucleus communication: current knowledge, experimental strategies and relationship to drought stress signaling

Chan, Kai Xun, Crisp, Peter Alexander, Estavillo, Gonzalo Martin and Pogson, Barry James (2010). Chloroplast-to-nucleus communication: current knowledge, experimental strategies and relationship to drought stress signaling. Plant Signaling and Behavior, 5 (12), 1575-1582. doi: 10.4161/psb.5.12.13758

Regulation of carotenoid composition and shoot branching in arabidopsis by a chromatin modifying histone methyltransferase, SDG8

Cazzonelli, Christopher I., Cuttriss, Abby J., Cossetto, Susan B., Pye, William, Crisp, Peter, Whelan, Jim, Finnegan, E. Jean, Turnbull, Colin and Pogson, Barry J. (2009). Regulation of carotenoid composition and shoot branching in arabidopsis by a chromatin modifying histone methyltransferase, SDG8. Plant Cell, 21 (1), 39-53. doi: 10.1105/tpc.108.063131

Enzymes degraded under high light maintain proteostasis by transcriptional regulation in Arabidopsis

Li, Lei, Duncan, Owen, Ganguly, Diep R., Lee, Chun Pong, Crisp, Peter A., Wijerathna-Yapa, Akila, Salih, Karzan, Trösch, Josua, Pogson, Barry J. and Millar, A. Harvey (2021). Enzymes degraded under high light maintain proteostasis by transcriptional regulation in Arabidopsis.