Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus
In eukaryotes, DNA-associated protein complexes coevolve with genomic sequences to orchestrate chromatin folding. We investigate the relationship between DNA sequence and the spontaneous loading and activity of chromatin components in the absence of coevolution. Using bacterial genomes integrated into <i>Saccharomyces cerevisiae</i>, which diverged from yeast more than 2 billion years ago, we show that nucleosomes, cohesins, and associated transcriptional machinery can lead to the formation of two different chromatin archetypes, one transcribed and the other silent, independently of heterochromatin formation. These two archetypes also form on eukaryotic exogenous sequences, depend on sequence composition, and can be predicted using neural networks trained on the native genome. They do not mix in the nucleus, leading to a bipartite nuclear compartmentalization, reminiscent of the organization of vertebrate nuclei.
Authors
- Fabien Girard
- Etienne Routhier
- Julien Mozziconacci (ORCID: https://orcid.org/0000-0001-5652-0302)
- Angela Taddei (ORCID: https://orcid.org/0000-0002-3217-0739)
- Romain Koszul (ORCID: https://orcid.org/0000-0002-3086-1173)
- Domenico Libri (ORCID: https://orcid.org/0000-0001-6728-0594)
- Frédéric Beckouët (ORCID: https://orcid.org/0000-0002-9009-1852)
- Aurèle Piazza (ORCID: https://orcid.org/0000-0002-7722-0955)
- Jacques Serizay (ORCID: https://orcid.org/0000-0002-4295-0624)
- Léa Meneu (ORCID: https://orcid.org/0000-0003-4245-6762)
- Manon Perrot
- Carole Lartigue (ORCID: https://orcid.org/0000-0001-5550-7579)
- Christophe Chapard (ORCID: https://orcid.org/0000-0003-4342-6012)
- Antoine Even
- Amaury Bignaud (ORCID: https://orcid.org/0000-0003-4480-920X)
- Agnès Thierry (ORCID: https://orcid.org/0000-0002-1566-0664)
- Myriam Ruault (ORCID: https://orcid.org/0000-0003-2990-4794)
- Géraldine Gourgues
- Alex Westbrook (ORCID: https://orcid.org/0009-0002-1771-7617)
- Alexandros Minakakis
Institutions
- Centre National de la Recherche Scientifique (FR)
- Université Toulouse III - Paul Sabatier (FR)
- Université de Bordeaux (FR)
- Institut Pasteur (FR)
- Université de Montpellier (FR)
- Université Paris Cité (FR)
- Université Paris Sciences et Lettres (FR)
- Sorbonne Université (FR)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- Biologie du Fruit et Pathologie (FR)
- Centre de Biologie du Développement (FR)
- Institut de Génétique Moléculaire de Montpellier (FR)
- Muséum national d'Histoire naturelle (FR)
- Laboratoire de Physique Théorique de la Matière Condensée (FR)
- Dynamique du noyau (FR)
- Structure et Instabilité des Génomes (FR)
Publication Details
- Journal
- Science
- Published
- 2025-02-06
- DOI
- https://doi.org/10.1126/science.adm9466
- Citations
- 24
- Primary Topic
- Genomics and Chromatin Dynamics
- Type
- article
- Field-Weighted Citation Impact
- 19.34