Consecutive low-frequency shifts in A/T content denote nucleosome positions across microeukaryotes
Nucleosomes are the basic repeating unit, each spanning ≈150bp, that structures DNA in the nucleus and their positions have major consequences on gene activity. Here, through analyzing DNA signatures across 1117 microeukaryote genomes, we discovered ≈150bp shifts in A/T content associated with nucleosome organization. Often consecutively arrayed across the genome, A/T peaks were enriched surrounding transcriptional start sites in specific clades. Most nucleosomes (both <i>in vitro</i> and <i>in vivo</i>) across eukaryotes aligned with A/T peaks, even in the presence of DNA modifications. Using artificial intelligence-based approaches, we describe DNA features associated with nucleosomes and construct a deep learning (DL) model for improved nucleosome occupancy prediction. Using this model, we found that ≈70% of "random" transfer DNA inserts from an <i>in vivo</i> fungal RB-TDNAseq library avoided DL predicted nucleosome-bound regions. This study reveals a eukaryote-wide strategy for generating cassettes of nucleosome-favorable DNAs that has a profound impact on nucleosome organization.
Authors
- Igor V. Grigoriev (ORCID: https://orcid.org/0000-0002-3136-8903)
- Stephen J. Mondo (ORCID: https://orcid.org/0000-0001-5797-0647)
- M. Catherine Aime (ORCID: https://orcid.org/0000-0001-8742-6685)
- Anna Lipzen (ORCID: https://orcid.org/0000-0003-2293-9329)
- Ronan C. O’Malley (ORCID: https://orcid.org/0000-0002-4907-0339)
- Lei Shu
- Doina Ciobanu (ORCID: https://orcid.org/0000-0002-3569-4079)
- Alan Kuo (ORCID: https://orcid.org/0000-0003-3514-3530)
- Aditi Sharma (ORCID: https://orcid.org/0000-0002-5364-8420)
- Robert Riley (ORCID: https://orcid.org/0000-0003-0224-0975)
- Jon Magnuson (ORCID: https://orcid.org/0000-0001-7712-7024)
- William Andreopoulos (ORCID: https://orcid.org/0000-0001-9097-1123)
- Jasmyn Pangilinan (ORCID: https://orcid.org/0000-0001-7966-3496)
- Kurt LaButti (ORCID: https://orcid.org/0000-0002-5838-1972)
- Guifen He
- Asaf Salamov
- John Gladden
- Hugh Salamon
Institutions
- Shenyang Agricultural University (CN)
- Pacific Northwest National Laboratory (US)
- Lawrence Berkeley National Laboratory (US)
- Joint Genome Institute (US)
- Purdue University West Lafayette (US)
- Ministry of Education and Child Care (CA)
- Joint BioEnergy Institute (US)
- Colorado State University (US)
- University of California, Berkeley (US)
Publication Details
- Journal
- iScience
- Published
- 2025-04-18
- DOI
- https://doi.org/10.1016/j.isci.2025.112472
- Citations
- 3
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 2.42
Funders
- Biological and Environmental Research