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Updated: Aug 17, 2025

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
Published on: May 2, 2025
Predicting nucleosome positioning using statistical equilibrium models in budding yeast
1Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA.
Abstract:
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.
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