Predicting nucleosome positioning using statistical equilibrium models in budding yeast

Hungyo Kharerin, Lu Bai

Research output: Contribution to journalArticlepeer-review


We present a protocol using thermodynamic models to predict nucleosome positioning with transcription factors (TFs) and chromatin remodelers. We describe step-by-step approaches to annotate genome-wide nucleosome-depleted regions (NDRs), compute nucleosome and TF occupancy, optimize parameters, and evaluate model performance. These models identify nucleosome-displacing TFs in the budding yeast genome and predict the locations and sizes of NDRs solely based on DNA sequence and TF motifs. The protocol can be applied to all organisms with prior knowledge of TF motifs. For complete details on the use and execution of this protocol, please refer to Kharerin and Bai (2021).1

Original languageEnglish (US)
Article number101926
JournalSTAR Protocols
Issue number1
StatePublished - Mar 17 2023

All Science Journal Classification (ASJC) codes

  • General Neuroscience
  • General Biochemistry, Genetics and Molecular Biology
  • General Immunology and Microbiology


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