Genetic–epigenetic interplay in the determination of plant 3D genome organization
The 3D chromatin organization plays a major role in the control of gene expression. However, our comprehension of the governing principles behind nuclear organization remains incomplete. Particularly, the spatial segregation of loci with similar repressive transcriptional states in plants poses a significant yet poorly understood puzzle. In this study, employing a combination of genetics and advanced 3D genomics approaches, we demonstrated that a redistribution of facultative heterochromatin marks in regions usually occupied by constitutive heterochromatin marks disrupts the 3D genome compartmentalisation. This disturbance, in turn, triggers novel chromatin interactions between genic and transposable element (TE) regions. Interestingly, our results imply that epigenetic features, constrained by genetic factors, intricately mold the landscape of 3D genome organisation. This study sheds light on the profound genetic-epigenetic interplay that underlies the regulation of gene expression within the intricate framework of the 3D genome. Our findings highlight the complexity of the relationships between genetic determinants and epigenetic features in shaping the dynamic configuration of the 3D genome.
Authors
- Cécile Raynaud (ORCID: https://orcid.org/0000-0002-5231-8120)
- Javier Antúnez-Sánchez (ORCID: https://orcid.org/0000-0002-7485-7061)
- Xiaoe He (ORCID: https://orcid.org/0000-0002-4323-1381)
- Olivier Mathieu (ORCID: https://orcid.org/0000-0001-5302-1102)
- Martín Crespi (ORCID: https://orcid.org/0000-0002-5698-9482)
- Chloé Dias Lopes
- David Latrasse (ORCID: https://orcid.org/0000-0003-2149-0128)
- Jose Gutierrez‐Marcos (ORCID: https://orcid.org/0000-0002-5441-9080)
- Moussa Benhamed (ORCID: https://orcid.org/0000-0002-2716-748X)
- Magdy M. Mahfouz (ORCID: https://orcid.org/0000-0002-0616-6365)
- Catherine Bergounioux (ORCID: https://orcid.org/0000-0002-0764-2220)
- Federico Ariel (ORCID: https://orcid.org/0000-0001-8478-8808)
- Sotirios Fragkostefanakis (ORCID: https://orcid.org/0000-0001-5311-7868)
- Jing An (ORCID: https://orcid.org/0000-0003-4150-1787)
- Sophie J. M. Piquerez
- Shao Jian Zheng (ORCID: https://orcid.org/0000-0002-3336-8165)
- Rim Brik Chaouche
- Leonardo I. Pereyra-Bistraín (ORCID: https://orcid.org/0000-0003-0881-6146)
- Hugo Zalzalé
- Qingyi Wang (ORCID: https://orcid.org/0000-0003-3013-5267)
- Yijing Zhang
- Xing Ma (ORCID: https://orcid.org/0000-0001-6914-0173)
- Xingwang Li
- Ying Huang (ORCID: https://orcid.org/0000-0002-9154-5991)
- Nicolas Bouché (ORCID: https://orcid.org/0000-0002-3800-2613)
Institutions
- Goethe University Frankfurt (DE)
- Centre National de la Recherche Scientifique (FR)
- Inserm (FR)
- Institut Universitaire de France (FR)
- Université Clermont Auvergne (FR)
- Université Paris Cité (FR)
- Huazhong Agricultural University (CN)
- AgroParisTech (FR)
- Universidad de Buenos Aires (AR)
- Fudan University (CN)
- Université Paris-Saclay (FR)
- University of Warwick (GB)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- Institut des Sciences des Plantes de Paris Saclay (FR)
- Institut Jean-Pierre Bourgin (FR)
- Institute of Astronomy and Space Physics (AR)
- Institut Génétique, Reproduction et Développement (FR)
- State Key Laboratory of Plant Physiology and Biochemistry
- Fundación Ciencias Exactas y Naturales (AR)
- King Abdullah University of Science and Technology (SA)
Publication Details
- Journal
- Nucleic Acids Research
- Published
- 2024-08-16
- DOI
- https://doi.org/10.1093/nar/gkae690
- Citations
- 9
- Primary Topic
- Genomics and Chromatin Dynamics
- Type
- article
- Field-Weighted Citation Impact
- 2.10
Funders
- Agence Nationale de la Recherche
- China Scholarship Council
- Institut Universitaire de France
- Biotechnology and Biological Sciences Research Council
- H2020 European Research Council