Consecutive low-frequency shifts in A/T content denote nucleosome positions across microeukaryotes
Summary: 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 w...
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Elsevier
2025-05-01
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004225007333 |
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| author | Stephen J. Mondo Guifen He Aditi Sharma Doina Ciobanu Robert Riley William B. Andreopoulos Anna Lipzen Alan Kuo Kurt LaButti Jasmyn Pangilinan Asaf Salamov Hugh Salamon Lili Shu John Gladden Jon Magnuson M. Catherine Aime Ronan O’Malley Igor V. Grigoriev |
| author_facet | Stephen J. Mondo Guifen He Aditi Sharma Doina Ciobanu Robert Riley William B. Andreopoulos Anna Lipzen Alan Kuo Kurt LaButti Jasmyn Pangilinan Asaf Salamov Hugh Salamon Lili Shu John Gladden Jon Magnuson M. Catherine Aime Ronan O’Malley Igor V. Grigoriev |
| author_sort | Stephen J. Mondo |
| collection | DOAJ |
| description | Summary: 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 in vitro and in vivo) 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 in vivo 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. |
| format | Article |
| id | doaj-art-7cfec7be14be47dcace2ca79fa67c69f |
| institution | DOAJ |
| issn | 2589-0042 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj-art-7cfec7be14be47dcace2ca79fa67c69f2025-08-20T02:57:02ZengElsevieriScience2589-00422025-05-0128511247210.1016/j.isci.2025.112472Consecutive low-frequency shifts in A/T content denote nucleosome positions across microeukaryotesStephen J. Mondo0Guifen He1Aditi Sharma2Doina Ciobanu3Robert Riley4William B. Andreopoulos5Anna Lipzen6Alan Kuo7Kurt LaButti8Jasmyn Pangilinan9Asaf Salamov10Hugh Salamon11Lili Shu12John Gladden13Jon Magnuson14M. Catherine Aime15Ronan O’Malley16Igor V. Grigoriev17US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA; Corresponding authorUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USACollege of Horticulture, Shenyang Agricultural University, Shenyang 110866, P.R. China; Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, P.R. ChinaJoint BioEnergy Institute, Emeryville, CA 94608, USAPacific Northwest National Laboratory, Richland, WA 99352, USADepartment of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USASummary: 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 in vitro and in vivo) 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 in vivo 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.http://www.sciencedirect.com/science/article/pii/S2589004225007333GenomicsChromosome organizationMolecular interactionModel organismArtificial intelligence |
| spellingShingle | Stephen J. Mondo Guifen He Aditi Sharma Doina Ciobanu Robert Riley William B. Andreopoulos Anna Lipzen Alan Kuo Kurt LaButti Jasmyn Pangilinan Asaf Salamov Hugh Salamon Lili Shu John Gladden Jon Magnuson M. Catherine Aime Ronan O’Malley Igor V. Grigoriev Consecutive low-frequency shifts in A/T content denote nucleosome positions across microeukaryotes iScience Genomics Chromosome organization Molecular interaction Model organism Artificial intelligence |
| title | Consecutive low-frequency shifts in A/T content denote nucleosome positions across microeukaryotes |
| title_full | Consecutive low-frequency shifts in A/T content denote nucleosome positions across microeukaryotes |
| title_fullStr | Consecutive low-frequency shifts in A/T content denote nucleosome positions across microeukaryotes |
| title_full_unstemmed | Consecutive low-frequency shifts in A/T content denote nucleosome positions across microeukaryotes |
| title_short | Consecutive low-frequency shifts in A/T content denote nucleosome positions across microeukaryotes |
| title_sort | consecutive low frequency shifts in a t content denote nucleosome positions across microeukaryotes |
| topic | Genomics Chromosome organization Molecular interaction Model organism Artificial intelligence |
| url | http://www.sciencedirect.com/science/article/pii/S2589004225007333 |
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