Publications
(* correspondence; § equal contribution )
Nan Wang, Chang Liu*. (2025) Simultaneous visualization of protein and genomic regions in plant nuclei. Methods in Molecular Biology 2025:2873:205-222. doi: 10.1007/978-1-0716-4228-3_12
Anna-Maria Göbel§, Sida Zhou§, Zhidan Wang, Sofia Tzourtzou, Axel Himmelbach, Shiwei Zheng, Mónica Pradillo, Chang Liu*, and Hua Jiang* Mutations of PDS5 genes enhance TAD-like domain formation in Arabidopsis thaliana. (2024) Nature Communications doi:10.1038/s41467-024-53760-x
Pengfei Liu, Jeromine Vigneau, Rory Craig, Josue Barrera-Redondo, Elena Avdievich, Claudia Mar-tinho, Michael Borg, Fabian B. Haas, Chang Liu, Susana M Coelho*. (2024) 3D chromatin maps of a brown alga reveal U/V sex chromosome spatial organization. Nature Communications doi:10.1038/s41467-024-53453-5
Junbin Chen§, Lei Li§, Benjamin Neuhäuser§, Mingyu Wang, Michael Thelen, Richard Hilleary, Luyang Wei, Kavita Venkataramani, Moises Exposito-Alonso, Chang Liu, Jakob Keck, A. Cristina Barragan, Rebecca Schwab, Ulrich Lutz, Sheng-Yang He, Uwe Ludewig, Detlef Weigel*, and Wangsheng Zhu*. (2023) Small proteins modulate ion channel-like ACD6 to regulate immunity in Arabidopsis thaliana. Molecular Cell doi: 10.1016/j.molcel.2023.10.030
Nan Wang§, Zhidan Wang§, Sofia Tzourtzou, Xu Wang, Xiuli Bi, Julia Leimeister, Linhao Xu, Takuya Sakamoto, Sachihiro Matsunaga, Andreas Schaller, Hua Jiang, and Chang Liu*. (2023) The plant nuclear lamina disassembles to regulate plant genome folding in stress conditions. Nature Plants doi: 10.1038/s41477-023-01457-2
Evelien Waegneer, Stéphane Rombauts, Joost Baert, Nicolas Dauchot, Annick De Keyser, Tom Eeckhaut, Annelies haegeman, Chang Liu, Olivier Maudoux, Christine Notté, Ariane Staelens, Jeroen Van der Veken, Katrijn Van Laere, and Tom Ruttink*. (2023) Industrial chicory genome gives insight into the molecular time table of flower development and male sterility. Frontiers in Plant Science doi: 10.3389/fpls.2023.1181529
Agustin L. Arce§, Regina Mencia§, Damian A. Cambiagno, Patricia L. Lang, Chang Liu, Hernán A. Burbano, Detlef Weigel, Pablo A. Manavella*. (2023) Polymorphic Inverted Repeats near coding genes impact chromatin topology and phenotypic traits in Arabidopsis thaliana. Cell Reports doi:10.1016/j.celrep.2023.112029
Fubo Cheng*, Wenxu Zheng, Chang Liu, Peter Antony Barbuti, Libo Yu-Taeger, Nicolas Casadei, Jeannette Huebener-Schmid, Jakob Admard, Karsten Boldt, Katrin Junger, Marius Ueffing, Henry Houlden, Manu Sharma, Rejko Krueger, Kathrin Grundmann-Hauser, Thomas Ott, Olaf Riess*. (2022) Intronic enhancers of the human SNCA gene predominantly regulate its expression in brain in vivo. Science Advances Vol 8, Issue 47 doi: 10.1126/sciadv.abq6324
Sean A. Montgomery, Tetsuya Hisanaga, Nan Wang, Elin Axelsson, Svetlana Akimcheva, Milos Sramek, Chang Liu, Frédéric Berger*. (2022) Polycomb-mediated repression of paternal chromosomes maintains haploid dosage in diploid embryos of Marchantia. eLife 11:e79258. doi: 10.7554/eLife.79258
Istvan Nagy, Elisabeth Veeckman, Chang Liu, Michiel van Bel, Klaas Vandepoele, Christian Sig Jensen, Tom Ruttink, Torben Asp. (2022) Chromosome-scale assembly and annotation of the perennial ryegrass genome. BMC Genomics 23(1):505, doi:10.1186/s12864-022-08697-0
Guillaume Hummel*, Chang Liu*. (2022) Organization and epigenomic control of RNA polymerase III-transcribed genes in plants. Current Opinion in Plant Biology. doi:10.1016/j.pbi.2022.102199
Cláudia Martinho, Zhengming Wang, Andrea Ghigi, Sarah Buddle, Felix Barbour, Antonia Yarur, Quentin Gouil, Sebastian Müller, Maike Stam, Chang Liu and David Baulcombe* (2022). CHROMOMETHYLTRANSFERASE3/KRYPTONITE maintains the sulfurea paramutation in Solanum lycopersicum. PNAS. doi:10.1073/pnas.2112240119
Katherine Domb§, Nan Wang§, Guillaume Hummel§, and Chang Liu* (2022). Spatial features and functional implications of plant 3D genomes organization. Annual Review of Plant Biology doi: 10.1146/annurev-arplant-102720-022810
Fubo Cheng*, Wenxu Zheng, Peter Barbuti, Paola Bonsi, Chang Liu, Nicolas Casadei, Giulia Ponterio, Maria Meringolo, Jakob Admard, Claire Dording, Libo Yu-Taeger, Huu Phuc Nguyen, Kathrin Grundmann-Hauser, Thomas Ott, Henry Houlden, Antonio Pisani, Rejko Krüger, Olaf Riess* (2022). DYT6 mutated THAP1 is a cell type dependent regulator of the SP1 family. Brain doi:10.1093/brain/awac001
Huawei Liu, Li Jiang, Zhifeng Wen, Yingjun Yang, Stacy D. Singer, Dennis Bennett, Wenying Xu, Zhen Su, Zhifang Yu, Josh Cohn, Hyunsook Chae, Qiudeng Que, Yue Liu, Chang Liu, Zongrang Liu* (2022). Rice RS2-9, which is bound by transcription factor OSH1, blocks enhancer-promoter interactions in plants. The Plant Journal, 109(3):541-554 doi:10.1111/tpj.15574
Jinping Cheng, Guiqian Zhang, Linhao Xu, Chang Liu, and Hua Jiang*. (2021) Altered H3K27 trimethylation contributes to flowering time variations in polyploid Arabidopsis thaliana ecotypes. Journal of Experimental Botany doi:10.1093/jxb/erab470
Miyuki Iwasaki, Tomoaki Kajiwara, Yukiko Yasui, Yoshihiro Yoshitake, Motoki Miyazaki, Shogo Kawamura, Noriyuki Suetsugu, Ryuichi Nishihama, Shohei Yamaoka, Dierk Wanke, Kenji Hashimoto, Kazuyuki Kuchitsu, Sean A. Montgomery, Shilpi Singh, Yasuhiro Tanizawa, Masaru Yagura, Takako Mochizuki, Mika Sakamoto, Yasukazu Nakamura, Chang Liu, Frederic Berger, Katsuyuki T. Yamato, John L. Bowman*, and Takayuki Kohchi* (2021). Identification of the sex-determining factor in the liverwort Marchantia polymorpha revealed unique evolution of sex chromosomes in a haploid system. Current Biology 10.1016/j.cub.2021.10.023
Pingtao Ding*, Toshiyuki Sakai, Ram Krishna Shrestha, Nicolas Manosalva Perez, Wenbin Guo, Bruno Pok Man Ngou, Shengbo He, Chang Liu, Xiaoqi Feng, Runxuan Zhang, Klaas Vandepoele, Dan MacLean, and Jonathan DG Jones* (2021). Chromatin accessibility landscapes activated by plant cell-surface and intracellular immune receptors. Journal of Experimental Botany doi: 10.1093/jxb/erab373
Robin Burns, Terezie Mandáková, Joanna Jagoda, Luz Mayela Soto-Jiménez, Chang Liu, Martin A. Lysak, Polina Yu. Novikova* and Magnus Nordborg*. (2021) Gradual evolution of allopolyploidy in Arabidopsis suecica. Nature Ecology & Evolution doi: 10.1038/s41559-021-01525-w
Nan Wang, Ezgi Süheyla Karaaslan, Natalie Faiss, Kenneth Wayne Berendzen and Chang Liu*. (2021) Characterization of a plant nuclear matrix constituent protein in liverwort. Frontiers in Plant Science. 12:670306 doi:10.3389/fpls.2021.670306
José A. Campoy§, Hequan Sun§, Manish Goel, Wen-Biao Jiao, Kat Folz-Donahue, Nan Wang, Manuel Rubio, Chang Liu, Christian Kukat, David Ruiz, Bruno Huettel and Korbinian Schneeberger*. (2020) Chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes. Genome Biology 21:306
Ezgi Süheyla Karaaslan, Natalie Faiß, Chang Liu*, and Kenneth Wayne Berendzen*. (2020) Isolation of lineage specific nuclei based on distinct endoreduplication levels and tissue-specific markers to study chromatin accessibility landscapes. Plants 9(11), 1478 doi:10.3390/plants9111478
Ezgi Süheyla Karaaslan, Nan Wang, Natalie Faiß, Yuyu Liang, Sean A. Montgomery, Sascha Laubinger, Kenneth Wayne Berendzen, Frédéric Berger, Holger Breuninger, and Chang Liu*. (2020) Three-dimensional chromatin structure shapes Marchantia TCP transcription factor activity. Nature Plants 6(10):1250-1261. doi:10.1038/s41477-020-00766-0
Bonnie A. Fraser*, James R. Whiting, Josephine R. Paris, Cameron J. Weadick, Paul J. Parsons, Deborah Charlesworth, Roberta Bergero, Felix Bemm, Margarete Hoffmann, Verena Kottler, Chang Liu, Christine Dreyer, and Detlef Weigel. (2020) Improved reference genome uncovers novel sex-linked regions in the guppy (Poecilia reticulata). Genome Biology and Evolution doi:10.1093/gbe/evaa187
Ana Paula Santos, Valérie Gaudin, Iva Mozgová, Frédéric Pontvianne, Daniel Schubert, Ahmet Tek, Martina Dvořáčková, Chang Liu, Paul Fransz, Stefanie Rosa*, and Sara Farrona*. (2020) Tiding-up the plant nuclear space: domains, function and dynamics. Journal of Experimental Botany 71:5160-5178. doi:10.1093/jxb/eraa282
Lorenzo Concia, Alaguraj Veluchamy, Juan S. Ramirez-Prado, Azahara Martin Ramirez, Ying Huang, Magali Perez, Severine Domenichini, Natalia Y. Rodriguez-Granados, Soonkap Kim, Thomas Blein, Susan Duncan, Clement Pichot, Deborah Manza-Mianza, Caroline Juery, Etienne Paux, Graham Moore, Heribert Hirt, Catherine Bergounioux, Martin Crespi, Magdy M Mahfouz, Abdelhafid Bendahmane, Chang Liu, Anthony Hall, Cécile Raynaud, David Latrasse and Moussa Benhamed*. (2020) Wheat chromatin architecture is organized in genome territories and transcription factories. Genome Biology 21:104
Sean A. Montgomery§, Yasuhiro Tanizawa§, Bence Galik, Nan Wang, Tasuku Ito, Takako Mochizuki, Svetlana Akimcheva, John L. Bowman, Valérie Cognat, Laurence Maréchal-Drouard, Heinz Ekker, Syuan-Fei Hong, Takayuki Kohchi, Shih-Shun Lin, Li-Yu Daisy Liu, Yasukazu Nakamura, Lia R. Valeeva, Eugene V. Shakirov, Dorothy E. Shippen, Wei-Lun Wei, Masaru Yagura, Shohei Yamaoka, Katsuyuki T. Yamato, Chang Liu*, and Frédéric Berger*. (2020) Chromatin Organization in Early Land Plants Reveals an Ancestral Association between H3K27me3, Transposons, and Constitutive Heterochromatin. Current Biology 30:573-588. doi:10.1016/j.cub.2019.12.015
Nan Wang and Chang Liu*. (2020) Study cell-type-specific chromatin organization: in situ Hi-C library preparation for low-input plant materials. Methods in Molecular Biology 2093, 115-127.
Federico Ariel*, Leandro Lucero, Aurelie Christ, Maria Florencia Mammarella, Teddy Jegu, Alaguraj Veluchamy, Kiruthiga Mariappan, David Latrasse, Thomas Blein, Chang Liu, Moussa Benhamed, Martin Crespi*. (2020) R-Loop Mediated trans Action of the APOLO Long Noncoding RNA. Molecular Cell 77:1055-1065. doi:10.1016/j.molcel.2019.12.015
Frédéric Pontvianne* and Chang Liu*. (2020) Chromatin domains in space and their functional implications. Current Opinion in Plant Biology 54:1-10.
Gareth Linsmith, Stephane Rombauts, Sara Montanari, Cecilia H Deng, Jean-Marc Celton, Philippe Guerif, Chang Liu, Rolf Lohaus, Jason D Zurn, Alessandro Cestaro, Nahla V Bassil, Linda V Bakker, Elio Schijlen, Susan E Gardiner, Yves Lespinasse, Charles-Eric Durel, Ricardo Velasco, David B Neale, David Chagne, Yves Van de Peer*, Michela Troggio*, and ProfileLuca Bianco*. (2019) Pseudo-chromosome length genome assembly of a double haploid 'Bartlett' pear (Pyrus communis L.). GigaScience Dec 1;8(12). pii: giz138. doi: 10.1093/gigascience/giz138.
Nan Wang and Chang Liu*. (2019) Implications of liquid-liquid phase separation in plant chromatin organization and transcriptional control. Current Opinion in Genetics and Development 55:59-65.
Bo Hu§, Nan Wang§, Xiuli Bi§, Ezgi Süheyla Karaaslan, Anna-Lena Weber, Kenneth Wayne Berendzen and Chang Liu*. (2019) Plant Lamin-like Proteins Mediate Chromatin Tethering at the Nuclear Periphery. Genome Biology 20:87.
Long Wang, Chuan-Miao Zhou, Yan-Xia Mai, Ling-Zi Li, Jian Gao, Heng lian, Lin Han, Tian-Qi Zhang, Hong-Bo Tang, Hang Ren, Fu-Xiang Wang, Lian-Yu Wu, Xiao-Li Liu, Chang-Sheng Wang, Er-Wang Chen, Xue-Ning Zhang, Chang Liu and Jia-Wei Wang. (2019) A Spatiotemporal Transcriptional Complex Underlies Heteroblastic Development of Leaf Hairs in Arabidopsis thaliana. The EMBO Journal e100063.
Corinna Speth, Emese Xochitl Szabo, Cláudia Martinho, Silvio Collani, Sven zur Oven-Krockhaus, Sandra Richter, Irina Droste-Borel, Boris Maček, York-Dieter Stierhof, Markus Schmid, Chang Liu and Sascha Laubinger*. (2018) Arabidopsis RNA processing factor SERRATE regulates the transcription of intronless genes. eLife 7:e37078.
Ezgi Süheyla Doğan and Chang Liu*. (2018) Three-dimensional chromatin packing and positioning of plant genomes. Nature Plants 4, 521-229.
Xiuli Bi and Chang Liu*. (2018) Genome-wide identification of chromatin domains anchored at the nuclear periphery in plants. Methods in Molecular Biology 1830, 381-393.
Olivier Raymond§, Jérôme Gouzy§, Jérémy Just§, Hélène Badouin§, Marion Verdenaud§, Arnaud Lemainque, Philippe Vergne, Sandrine Moja, Nathalie Choisne, Caroline Pont, Sébastien Carrère, Jean-Claude Caissard, Arnaud Couloux, Ludovic Cottret, Jean-Marc Aury, Judit Szecsi, David Latrasse, Mohammed-Amin Madoui, Léa François, Xiaopeng Fu, Shu-Hua Yang, Annick Dubois, Florence Piola, Antoine Larrieu, Magali Perez, Karine Labadie, Lauriane Perrier, Benjamin Govetto, Yoan Labrousse, Priscilla Villand, Claudia Bardoux, Véronique Boltz, Céline Lopez-Roques, Pascal Heitzler, Téva Vernoux, Michiel Vandenbussche, Hadi Quesneville, Adnane Boualem, Abdelhafid Bendahmane, Chang Liu, Manuel Lebris, Jérôme Salse, Sylvie Baudino, Moussa Benhamed, Patrick Wincker, Mohammed Bendahmane*. (2018) The Rosa genome provides new insights into the design of modern roses. Nature Genetics 50, 772-777.
Stefanie Dukowic-Schulze, Chang Liu and Changbin Chen* (2018) Not just gene expression: 3D implications of chromatin modifications during sexual plant reproduction. Plant Cell Reports 37, 11-16.
Wangsheng Zhu§, Bo Hu, Claude Becker, Ezgi Süheyla Doğan, Kenneth Wayne Berendzen, Detlef Weigel* and Chang Liu§*. (2017) Altered chromatin compaction and histone methylation drive non-additive gene expression in an interspecific Arabidopsis hybrid. Genome Biology 18:157.
Chang Liu*, Ying-Juan Cheng, Jia-Wei Wang, and Detlef Weigel*. (2017) Prominent topologically associated domains differentiate global chromatin packing in rice from Arabidopsis. Nature Plants 3, 742–748.
Chang Liu*. (2017) In situ Hi-C library preparation for plants to study their three-dimensional chromatin interactions on a genome-wide scale. Methods in Molecular Biology 1629, 155-166.
Xiuli Bi§, Ying-Juan Cheng§, Bo Hu, Xiaoli Ma, Rui Wu, Jia-Wei Wang and Chang Liu*. (2017) Non-random domain organization of the Arabidopsis genome at the nuclear periphery. Genome Research 27, 1162-1173.
Dominik G. Grimm*, Damian Roqueiro, Patrice A. Salomé, Stefan Kleeberger, Bastian Greshake, Wangsheng Zhu, Chang Liu, Christoph Lippert, Oliver Stegle, Bernhard Schölkopf, Detlef Weigel and Karsten M. Borgwardt*. (2017) easyGWAS: A cloud-based platform for comparing the results of genome-wide association studies. The Plant Cell 29, 20-38.
Chang Liu*, Congmao Wang, George Wang, Claude Becker, Maricris Zaidem and Detlef Weigel*. (2016) Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution. Genome Research 26,1057-1068.
Chang Liu* and Detlef Weigel*. (2015) Chromatin in 3D: Progress and Prospects for Plants. Genome Biology 16:170.
Congmao Wang§, Chang Liu§*, Damian Roqueiro, Dominik Grimm, Rebecca Schwab, Claude Becker, Christa Lanz, and Detlef Weigel*. (2015) Genome-wide analysis of local chromatin packing in Arabidopsis thaliana. Genome Research 25, 246-256.
Xingliang Hou, Jiannan Zhou, Chang Liu, Lu Liu, Lisha Shen and Hao Yu*. (2014) Nuclear Factor Y-mediated H3K27me3 demethylation of the SOC1 locus orchestrates flowering responses of Arabidopsis. Nature Communications 5, 4601.
Chang Liu, Zhi Wei Norman Teo, Yang Bi, Shiyong Song, Wanyan Xi, Xiaobei Yang , Zhongchao Yin and Hao Yu*. (2013) A conserved genetic pathway determines inflorescence architecture in Arabdidopsis and rice. Developmental Cell 24, 612-622.
Zhen Tao, Lisha Shen, Chang Liu, Lu Liu, Yuanyuan Yan and Hao Yu*. (2012) Genome-wide identification of SOC1 and SVP targets during the floral transition in Arabidopsis. The Plant Journal 70, 549-561.
Lu Liu§, Chang Liu§, Xingliang Hou, Wanyan Xi, Lisha Shen, Zhen Tao, Yue Wang, Hao Yu*. (2012) FTIP1 is an essential regulator required for florigen transport. PLoS Biology 10(4): e1001313.
Wanyan Xi§, Chang Liu§, Xingliang Hou and Hao Yu*. (2010) Mother of FT and TFL1 regulates seed germination through constituting a negative feedback loop of ABA signaling. The Plant Cell 22, 1733-1748.
Yu Wang, Chang Liu, Daiwen Yang, Hao Yu* and Yih-Cherng Liou*. (2010) Pin1At encoding a peptidyl-prolyl cis/trans isomerase regulates flowering time in Arabidopsis. Molecular Cell 37, 112-122.
Chang Liu, Zhonghui Thong and Hao Yu*. (2009) Coming into bloom: the specification of floral meristems. Development 136, 3379-3391.
Chang Liu, Wanyan Xi, Lisha Shen, Caiping Tan and Hao Yu*. (2009) Regulation of floral patterning by flowering time genes. Developmental Cell 16, 711-722.
Dan Li§, Chang Liu§, Lisha Shen§, Yang Wu, Hongyan Chen, Chris A. Helliwell, Toshiro Ito, Elliot M. Meyerowitz and Hao Yu*. (2008) A repressor complex governs the integration of flowering signals in Arabidopsis. Developmental Cell 15, 110-120.
Chang Liu, Hongyan Chen, Hong Ling Er, Hui Meng Soo, Prakash P. Kumar, Jin-Hua Han, Yih-Cherng Liou, and Hao Yu*. (2008) Direct interaction of AGL24 and SOC1 integrates flowering signals in Arabidopsis. Development 135, 1481-1491.
Chang Liu§, Jing Zhou§, Keren Bracha-Drori, Shaul Yalovsky, Toshiro Ito and Hao Yu*. (2007) Specification of Arabidopsis floral meristem identity by repressing flowering time genes. Development 134, 1901-1910.
Yinbo Gan, Chang Liu, Hao Yu and Pierre Broun*. (2007) Integration of cytokinin and gibberellin signaling by Arabidopsis transcription factors GIS, GIS2 and GIS3 in the regulation of epidermal cell fate. Development 134, 2073-2081.
Yinbo Gan, Rod Kuminoto, Chang Liua, Oliver Ratcliffe, Hao Yu and Pierre Broun*. (2006) GLABROUS INFLORESCENCE STEMS modulates gibberellin signaling in the regulation of epidermal differentiation and shoot maturation in Arabidopsis. The Plant Cell 18, 1383-1395.