Consecutive low-frequency shifts in A/T content denote nucleosome positions across microeukaryotes.

Journal: iScience
Published Date: Apr 18, 2025

Abstract

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 and ) 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 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

  • Stephen J Mondo
    US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Guifen He
    US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Aditi Sharma
    Computer Science Engineering & Information Technology, Institute of Engineering & Technology, Lucknow, Uttar Pradesh, India.
  • Doina Ciobanu
    US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Robert Riley
    US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • William B Andreopoulos
    Joint Genome Institute, US Department of Energy, LBNL Berkeley, CA, USA.
  • Anna Lipzen
    US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Alan Kuo
    US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Kurt LaButti
    US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Jasmyn Pangilinan
    US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Asaf Salamov
    US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Hugh Salamon
    Knowledge Synthesis Inc., Berkeley, CA, USA. Electronic address: hugh@knowledgesynthesis.com.
  • Lili Shu
    College of Horticulture, Shenyang Agricultural University, Shenyang 110866, P.R. China.
  • John Gladden
    Joint BioEnergy Institute, Emeryville, CA 94608, USA.
  • Jon Magnuson
    Pacific Northwest National Laboratory, Richland, WA 99352, USA.
  • M Catherine Aime
    Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA.
  • Ronan O'Malley
    US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Igor V Grigoriev
    US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

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