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2021 Journal Article Genetic and epigenetic variation in transposable element expression responses to abiotic stress in maizeLiang, 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 |
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2021 Journal Article Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposonsNoshay, 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 |
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2020 Journal Article Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomesCrisp, 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 |
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2020 Journal Article Optimization of multiplexed CRISPR/Cas9 system for highly efficient genome editing in Setaria viridisWeiss, 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 |
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2020 Journal Article Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory InteractionsZhou, 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 |
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2020 Journal Article Epigenetic regulation of ABA-induced transcriptional responses in maizeVendramin, 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 |
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2020 Journal Article Molecular and physiological responses during thermal acclimation of leaf photosynthesis and respiration in riceRashid, 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 |
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2020 Journal Article Variation and inheritance of small RNAs in maize inbreds and F1 hybridsCrisp, 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 |
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2019 Journal Article Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maizeXu, 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 |
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2019 Journal Article Monitoring the interplay between transposable element families and DNA methylation in maizeNoshay, 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 |
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2019 Journal Article Opportunities to Use DNA methylation to distil functional elements in large crop genomesCrisp, 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 |
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2019 Journal Article Hybrid decay: A transgenerational epigenetic decline in vigor and viability triggered in backcross populations of teosinte with maizeXue, 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 |
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2018 Journal Article RNA polymerase II read-through promotes expression of neighboring genes in SAL1-PAP-XRN retrograde signalingCrisp, 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 |
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2018 Journal Article Heritable epigenomic changes to the maize methylome resulting from tissue cultureHan, 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 |
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2018 Journal Article Maintenance of pre-existing DNA methylation states through recurring excess-light stressGanguly, 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 |
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2018 Book Chapter The maize methylomeNoshay, 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 |
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2017 Journal Article The arabidopsis DNA methylome is stable under transgenerational drought stressGanguly, 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 |
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2017 Journal Article Rapid recovery gene downregulation during excess-light stress and recovery in arabidopsisCrisp, 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 |
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2017 Journal Article A chloroplast retrograde signal, 3’phosphoadenosine 5’-phosphate, acts as a secondary messenger in abscisic acid signaling in stomatal closure and germinationPornsiriwong, 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 |
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2016 Journal Article Uncoupling high light responses from singlet oxygen retrograde signaling and spatial-temporal systemic acquired acclimationCarmody, 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 |
