Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus

• 成果类型: Article
• 署名作者: Meneu, Lea; Chapard, Christophe; Serizay, Jacques; Westbrook, Alex; Routhier, Etienne; Ruault, Myriam; Perrot, Manon; Minakakis, Alexandros; Girard, Fabien; Bignaud, Amaury; Even, Antoine; Gourgues, Geraldine; Libri, Domenico; Lartigue, Carole; Piazza, Aurele; Thierry, Agnes; Taddei, Angela; Beckouet, Frederic; Mozziconacci, Julien; Koszul, Romain
• 署名单位: Centre National de la Recherche Scientifique (CNRS); CNRS - National Institute for Biology (INSB); Pasteur Network; Universite Paris Cite; Institut Pasteur Paris; Sorbonne Universite; Centre National de la Recherche Scientifique (CNRS); CNRS - Institute of Chemistry (INC); Museum National d'Histoire Naturelle (MNHN); Centre National de la Recherche Scientifique (CNRS); Sorbonne Universite; UNICANCER; Universite PSL; Institut Curie; Centre National de la Recherche Scientifique (CNRS); CNRS - National Institute for Biology (INSB); Sorbonne Universite; Universite de Montpellier; Centre National de la Recherche Scientifique (CNRS); Universite de Bordeaux; INRAE; Universite de Toulouse; Universite Toulouse III - Paul Sabatier; Centre National de la Recherche Scientifique (CNRS); Museum National d'Histoire Naturelle (MNHN)
• 刊物名称: SCIENCE
• ISSN/ISSBN: 0036-13392
• DOI: 10.1126/science.adm9466
• 发表日期: 2025-02-07
• 关键词: yeast; genome; chromatin; ORGANIZATION; chromosomes; cohesins; cloning; transcription; determinants; principles

摘要

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 Saccharomyces cerevisiae, 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.