PMID- 34083408 OWN - NLM STAT- PubMed-not-MEDLINE VI - 31 IP - 7 TI - Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis. PG - 1230-1244 CI - © 2021 Huang et al.; Published by Cold Spring Harbor Laboratory Press. LA - eng PT - Journal Article PL - United States TA - Genome Res JT - Genome research JID - 9518021 IS - 1549-5469 (Electronic) LID - 10.1101/gr.273771.120 [doi] FAU - Huang, Ying AU - Huang Y AD - Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France. FAU - Sicar, Sanchari AU - Sicar S AD - Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France. FAU - Ramirez-Prado, Juan S AU - Ramirez-Prado JS AD - Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France. FAU - Manza-Mianza, Deborah AU - Manza-Mianza D AD - Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France. FAU - Antunez-Sanchez, Javier AU - Antunez-Sanchez J AD - School of Life Science, University of Warwick, Coventry CV4 7AL, United Kingdom. FAU - Brik-Chaouche, Rim AU - Brik-Chaouche R AD - Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France. FAU - Rodriguez-Granados, Natalia Y AU - Rodriguez-Granados NY AD - Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France. FAU - An, Jing AU - An J AD - Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France. FAU - Bergounioux, Catherine AU - Bergounioux C AD - Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France. FAU - Mahfouz, Magdy M AU - Mahfouz MM AD - Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia. FAU - Hirt, Heribert AU - Hirt H AD - Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France. AD - Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia. FAU - Crespi, Martin AU - Crespi M AUID- ORCID: http://orcid.org/0000-0002-5698-9482 AD - Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France. FAU - Concia, Lorenzo AU - Concia L AD - Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France. AD - Institut de Biologie de l'Ecole Normale Supérieure (IBENS), ENS, CNRS UMR8197, INSERM U1024, PSL Research University, 75005, Paris, France. FAU - Barneche, Fredy AU - Barneche F AUID- ORCID: http://orcid.org/0000-0002-7014-7097 AD - Institut de Biologie de l'Ecole Normale Supérieure (IBENS), ENS, CNRS UMR8197, INSERM U1024, PSL Research University, 75005, Paris, France. FAU - Amiard, Simon AU - Amiard S AD - GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France. FAU - Probst, Aline V AU - Probst AV AD - GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France. FAU - Gutierrez-Marcos, Jose AU - Gutierrez-Marcos J AD - School of Life Science, University of Warwick, Coventry CV4 7AL, United Kingdom. FAU - Ariel, Federico AU - Ariel F AD - Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina. FAU - Raynaud, Cécile AU - Raynaud C AD - Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France. FAU - Latrasse, David AU - Latrasse D AD - Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France. FAU - Benhamed, Moussa AU - Benhamed M AD - Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France. AD - Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), F-75006 Paris, France. AD - Institut Universitaire de France (IUF). IS - 1088-9051 (Linking) SB - IM PMC - PMC8256866 LR - 20231120 DP - 2021 Jul DEP - 20210603 AB - In animals, distant H3K27me3-marked Polycomb targets can establish physical interactions forming repressive chromatin hubs. In plants, growing evidence suggests that H3K27me3 acts directly or indirectly to regulate chromatin interactions, although how this histone modification modulates 3D chromatin architecture remains elusive. To decipher the impact of the dynamic deposition of H3K27me3 on the Arabidopsis thaliana nuclear interactome, we combined genetics, transcriptomics, and several 3D epigenomic approaches. By analyzing mutants defective for histone H3K27 methylation or demethylation, we uncovered the crucial role of this chromatin mark in short- and previously unnoticed long-range chromatin loop formation. We found that a reduction in H3K27me3 levels led to a decrease in the interactions within Polycomb-associated repressive domains. Regions with lower H3K27me3 levels in the H3K27 methyltransferase clf mutant established new interactions with regions marked with H3K9ac, a histone modification associated with active transcription, indicating that a reduction in H3K27me3 levels induces a global reconfiguration of chromatin architecture. Altogether, our results reveal that the 3D genome organization is tightly linked to reversible histone modifications that govern chromatin interactions. Consequently, nuclear organization dynamics shapes the transcriptional reprogramming during plant development and places H3K27me3 as a key feature in the coregulation of distant genes.