An atlas of the tomato epigenome reveals that KRYPTONITE shapes TAD- like boundaries through the control of H3K9ac distribution

• 成果类型: Article
• 署名作者: An, Jing; Chaouche, Rim Brik; Bistrain, Leonardo I. Pereyra-; Zalzale, Hugo; Wang, Qingyi; Huang, Ying; He, Xiaoning; Lopes, Chloe Dias; Sanchez, Javier Antunez-; Bergounioux, Catherine; Boulogne, Claire; Dupas, Cynthia; Gillet, Cynthia; Perez-Perez, Jose Manuel; Mathieu, Olivier; Bouche, Nicolas; Fragkostefanakis, Sotirios; Zhang, Yijing; Zheng, Shaojian; Crespi, Martin; Mahfouz, Magdy M.; Ariel, Federico; Marcos, Jose Gutierrez-; Raynaud, Cecile; Latrasse, David; Benhamed, Moussa
• 署名单位: Universite Paris Cite; Universite Paris Saclay; Centre National de la Recherche Scientifique (CNRS); INRAE; Universite Paris Saclay; Universite Paris Cite; University of Warwick; CEA; Centre National de la Recherche Scientifique (CNRS); Universite Paris Saclay; Universidad Miguel Hernandez de Elche; Centre National de la Recherche Scientifique (CNRS); Institut National de la Sante et de la Recherche Medicale (Inserm); Universite Clermont Auvergne (UCA); AgroParisTech; INRAE; Universite Paris Saclay; Centre National de la Recherche Scientifique (CNRS); Goethe University Frankfurt; Fudan University; Zhejiang University; King Abdullah University of Science & Technology; National University of the Littoral; Institut Universitaire de France
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-13030
• DOI: 10.1073/pnas.2400737121
• 发表日期: 2024-07-09
• 关键词: chromatin-state discovery; dna methylation; ORGANIZATION; ELEMENTS; architecture; locus; plant

摘要

In recent years, the exploration of genome three- dimensional (3D) conformation has yielded profound insights into the regulation of gene expression and cellular functions in both animals and plants. While animals exhibit a characteristic genome topology defined by topologically associating domains (TADs), plants display similar features with a more diverse conformation across species. Employing advanced high- throughput sequencing and microscopy techniques, we investigated the landscape of 26 histone modifications and RNA polymerase II distribution in tomato (Solanum lycopersicum). Our study unveiled a rich and nuanced epigenetic landscape, shedding light on distinct chromatin states associated with heterochromatin formation and gene silencing. Moreover, we elucidated the intricate interplay between these chromatin states and the overall topology of the genome. Employing a genetic approach, we delved into the role of the histone modification H3K9ac in genome topology. Notably, our investigation revealed that the ectopic deposition of this chromatin mark triggered a reorganization of the 3D chromatin structure, defining different TAD- like borders. Our work emphasizes the critical role of H3K9ac in shaping the topology of the tomato genome, providing valuable insights into the epigenetic landscape of this agriculturally significant crop species.