Uncovering Signatures of DNA Methylation in Ancient Plant Remains From Patterns of Post-mortem DNA Damage
作者： Stefanie Wagner , Christophe Plomion , Ludovic Orlando
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摘要: The ultra-short DNA molecules still preserved in archaeological remains can provide invaluable genetic information about past individuals, species and communities within the half to one-million-year time range. sequence data are, however, generally affected by post-mortem damage include specific patterns of nucleotide mis-incorporations, which help authentication. Recent work ancient mammals has shown that such also assess levels methylation CpG contexts. Despite pioneering barley sorghum, epigenetic marks have received limited attention plants it unknown whether signatures be retrieved any three main contexts (CG, CHG CHH). To address this question, we extended a statistical score originally proposed trace cytosine mammal accommodate plant-specific We applied range tissues (wood, cobs grains) (oak, maize barley), spanning both desiccated waterlogged samples. Ancient obtained for USER-treated extracts yielded scores on par with modern organellar nuclear genomes. At quantitative level, were (1) positively correlated deamination, (2) replicated relative contributions CG, CHH assessed bisulfite sequencing plant tissues. This demonstrates genuine characterized remains, opens new avenues investigating evolutionary response farming, pollution, epidemics changing environmental conditions.
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sci-hub.st 参考文章(52)
Vagheesh M Narasimhan, Nick Patterson, Priya Moorjani, Nadin Rohland, Rebecca Bernardos, Swapan Mallick, Iosif Lazaridis, Nathan Nakatsuka, Iñigo Olalde, Mark Lipson, Alexander M Kim, Luca M Olivieri, Alfredo Coppa, Massimo Vidale, James Mallory, Vyacheslav Moiseyev, Egor Kitov, Janet Monge, Nicole Adamski, Neel Alex, Nasreen Broomandkhoshbacht, Francesca Candilio, Kimberly Callan, Olivia Cheronet, Brendan J Culleton, Matthew Ferry, Daniel Fernandes, Suzanne Freilich, Beatriz Gamarra, Daniel Gaudio, Mateja Hajdinjak, Éadaoin Harney, Thomas K Harper, Denise Keating, Ann Marie Lawson, Matthew Mah, Kirsten Mandl, Megan Michel, Mario Novak, Jonas Oppenheimer, Niraj Rai, Kendra Sirak, Viviane Slon, Kristin Stewardson, Fatma Zalzala, Zhao Zhang, Gaziz Akhatov, Anatoly N Bagashev, Alessandra Bagnera, Bauryzhan Baitanayev, Julio Bendezu-Sarmiento, Arman A Bissembaev, Gian Luca Bonora, Temirlan T Chargynov, Tatiana Chikisheva, Petr K Dashkovskiy, Anatoly Derevianko, Miroslav Dobeš, Katerina Douka, Nadezhda Dubova, Meiram N Duisengali, Dmitry Enshin, Andrey Epimakhov, Alexey V Fribus, Dorian Fuller, Alexander Goryachev, Andrey Gromov, Sergey P Grushin, Bryan Hanks, Margaret Judd, Erlan Kazizov, Aleksander Khokhlov, Aleksander P Krygin, Elena Kupriyanova, Pavel Kuznetsov, Donata Luiselli, Farhod Maksudov, Aslan M Mamedov, Talgat B Mamirov, Christopher Meiklejohn, Deborah C Merrett, Roberto Micheli, Oleg Mochalov, Samariddin Mustafokulov, Ayushi Nayak, Davide Pettener, Richard Potts, Dmitry Razhev, Marina Rykun, Stefania Sarno, Tatyana M Savenkova, Kulyan Sikhymbaeva, Sergey M Slepchenko, Oroz A Soltobaev, Nadezhda Stepanova, Svetlana Svyatko, Kubatbek Tabaldiev, Maria Teschler-Nicola, Alexey A Tishkin, Vitaly V Tkachev, Sergey Vasilyev, Petr Velemínský, Dmitriy Voyakin, Antonina Yermolayeva, Muhammad Zahir, Valery S Zubkov, Alisa Zubova, Vasant S Shinde, Carles Lalueza-Fox, Matthias Meyer, David Anthony, Nicole Boivin, Kumarasamy Thangaraj, Douglas J Kennett, Michael Frachetti, Ron Pinhasi, David Reich, None, The Formation of Human Populations in South and Central Asia Science. ,vol. 365, pp. 999- 999 ,(2019) , 10.1126/SCIENCE.AAT7487
Maria A. Spyrou, Marcel Keller, Rezeda I. Tukhbatova, Christiana L. Scheib, Elizabeth A. Nelson, Aida Andrades Valtueña, Gunnar U. Neumann, Don Walker, Amelie Alterauge, Niamh Carty, Craig Cessford, Hermann Fetz, Michaël Gourvennec, Robert Hartle, Michael Henderson, Kristin von Heyking, Sarah A. Inskip, Sacha Kacki, Felix M. Key, Elizabeth L. Knox, Christian Later, Prishita Maheshwari-Aplin, Joris Peters, John E. Robb, Jürgen Schreiber, Toomas Kivisild, Dominique Castex, Sandra Lösch, Michaela Harbeck, Alexander Herbig, Kirsten I. Bos, Johannes Krause, Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes Nature Communications. ,vol. 10, pp. 4470- 4470 ,(2019) , 10.1038/S41467-019-12154-0
Rick W. A. Smith, Cara Monroe, Deborah A. Bolnick, Detection of Cytosine Methylation in Ancient DNA from Five Native American Populations Using Bisulfite Sequencing PLOS ONE. ,vol. 10, pp. e0125344- ,(2015) , 10.1371/JOURNAL.PONE.0125344
Arnaud Couloux, Corinne Da Silva, Sébastien Duplessis, François Ehrenmann, Barbara Estrada-Mairey, Stéphanie Fouteau, Nicolas Francillonne, Christine Gaspin, Cécile Guichard, Christophe Klopp, Karine Labadie, Céline Lalanne, Isabelle Le Clainche, Jean-Charles Leplé, Grégoire Le Provost, Thibault Leroy, Isabelle Lesur, Francis Martin, Jonathan Mercier, Célia Michotey, Florent Murat, Franck Salin, Delphine Steinbach, Patricia Faivre-Rampant, Patrick Wincker, Jérôme Salse, Hadi Quesneville, Antoine Kremer, Christophe Plomion, Jean-Marc Aury, Joëlle Amselem, Tina Alaeitabar, Valérie Barbe, Caroline Belser, Hélène Bergès, Catherine Bodénès, Nathalie Boudet, Christophe Boury, Aurélie Canaguier, Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies Molecular Ecology Resources. ,vol. 16, pp. 254- 265 ,(2016) , 10.1111/1755-0998.12425
B. Vernot, J. M. Akey, Resurrecting Surviving Neandertal Lineages from Modern Human Genomes Science. ,vol. 343, pp. 1017- 1021 ,(2014) , 10.1126/SCIENCE.1245938
Shawn J. Cokus, Suhua Feng, Xiaoyu Zhang, Zugen Chen, Barry Merriman, Christian D. Haudenschild, Sriharsa Pradhan, Stanley F. Nelson, Matteo Pellegrini, Steven E. Jacobsen, Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning Nature. ,vol. 452, pp. 215- 219 ,(2008) , 10.1038/NATURE06745
Adrian W. Briggs, Udo Stenzel, Matthias Meyer, Johannes Krause, Martin Kircher, Svante Pääbo, Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA Nucleic Acids Research. ,vol. 38, pp. 1- 12 ,(2010) , 10.1093/NAR/GKP1163
David Reich, Richard E. Green, Martin Kircher, Johannes Krause, Nick Patterson, Eric Y. Durand, Bence Viola, Adrian W. Briggs, Udo Stenzel, Philip L. F. Johnson, Tomislav Maricic, Jeffrey M. Good, Tomas Marques-Bonet, Can Alkan, Qiaomei Fu, Swapan Mallick, Heng Li, Matthias Meyer, Evan E. Eichler, Mark Stoneking, Michael Richards, Sahra Talamo, Michael V. Shunkov, Anatoli P. Derevianko, Jean-Jacques Hublin, Janet Kelso, Montgomery Slatkin, Svante Pääbo, Genetic history of an archaic hominin group from Denisova Cave in Siberia Nature. ,vol. 468, pp. 1053- 1060 ,(2010) , 10.1038/NATURE09710
D. Gokhman, E. Lavi, K. Prufer, M. F. Fraga, J. A. Riancho, J. Kelso, S. Paabo, E. Meshorer, L. Carmel, Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan Science. ,vol. 344, pp. 523- 527 ,(2014) , 10.1126/SCIENCE.1250368
P. S. Schnable, D. Ware, R. S. Fulton, J. C. Stein, F. Wei, S. Pasternak, C. Liang, J. Zhang, L. Fulton, T. A. Graves, P. Minx, A. D. Reily, L. Courtney, S. S. Kruchowski, C. Tomlinson, C. Strong, K. Delehaunty, C. Fronick, B. Courtney, S. M. Rock, E. Belter, F. Du, K. Kim, R. M. Abbott, M. Cotton, A. Levy, P. Marchetto, K. Ochoa, S. M. Jackson, B. Gillam, W. Chen, L. Yan, J. Higginbotham, M. Cardenas, J. Waligorski, E. Applebaum, L. Phelps, J. Falcone, K. Kanchi, T. Thane, A. Scimone, N. Thane, J. Henke, T. Wang, J. Ruppert, N. Shah, K. Rotter, J. Hodges, E. Ingenthron, M. Cordes, S. Kohlberg, J. Sgro, B. Delgado, K. Mead, A. Chinwalla, S. Leonard, K. Crouse, K. Collura, D. Kudrna, J. Currie, R. He, A. Angelova, S. Rajasekar, T. Mueller, R. Lomeli, G. Scara, A. Ko, K. Delaney, M. Wissotski, G. Lopez, D. Campos, M. Braidotti, E. Ashley, W. Golser, H. Kim, S. Lee, J. Lin, Z. Dujmic, W. Kim, J. Talag, A. Zuccolo, C. Fan, A. Sebastian, M. Kramer, L. Spiegel, L. Nascimento, T. Zutavern, B. Miller, C. Ambroise, S. Muller, W. Spooner, A. Narechania, L. Ren, S. Wei, S. Kumari, B. Faga, M. J. Levy, L. McMahan, P. Van Buren, M. W. Vaughn, K. Ying, C.-T. Yeh, S. J. Emrich, Y. Jia, A. Kalyanaraman, A.-P. Hsia, W. B. Barbazuk, R. S. Baucom, T. P. Brutnell, N. C. Carpita, C. Chaparro, J.-M. Chia, J.-M. Deragon, J. C. Estill, Y. Fu, J. A. Jeddeloh, Y. Han, H. Lee, P. Li, D. R. Lisch, S. Liu, Z. Liu, D. H. Nagel, M. C. McCann, P. SanMiguel, A. M. Myers, D. Nettleton, J. Nguyen, B. W. Penning, L. Ponnala, K. L. Schneider, D. C. Schwartz, A. Sharma, C. Soderlund, N. M. Springer, Q. Sun, H. Wang, M. Waterman, R. Westerman, T. K. Wolfgruber, L. Yang, Y. Yu, L. Zhang, S. Zhou, Q. Zhu, J. L. Bennetzen, R. K. Dawe, J. Jiang, N. Jiang, G. G. Presting, S. R. Wessler, S. Aluru, R. A. Martienssen, S. W. Clifton, W. R. McCombie, R. A. Wing, R. K. Wilson, The B73 Maize Genome: Complexity, Diversity, and Dynamics Science. ,vol. 326, pp. 1112- 1115 ,(2009) , 10.1126/SCIENCE.1178534