Predicting nucleosome positioning using statistical equilibrium models in budding yeast.

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Hungyo Kharerin, Lu Bai

Author Information

Hungyo Kharerin: Department 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. Electronic address: kzh359@psu.edu.
Lu Bai: Department 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; Department of Physics, The Pennsylvania State University, University Park, PA, USA. Electronic address: lub15@psu.edu.

PMID: 36520634 DOI: 10.1016/j.xpro.2022.101926

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)..

Bioinformatics Biophysics Computer sciences Genomics Model Organisms Molecular Biology

R35 GM139654/NIGMS NIH HHS

Nucleosomes

Saccharomycetales

Chromatin

Transcription Factors

Base Sequence

Nucleosomes

Chromatin

Transcription Factors

Journal Article Research Support, N.I.H., Extramural

Assays for nucleosome positioning in yeast.Perfect and imperfect nucleosome positioning in yeast.Predicting nucleosome positioning using a duration Hidden Markov Model.Predicting nucleosome positions in yeast: using the absolute frequency.Systematic Study of Nucleosome-Displacing Factors in Budding Yeast.Cse4 is part of an octameric nucleosome in budding yeast.A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome.A statistical thermodynamic approach for predicting the sequence-dependent nucleosome positioning along genomes.Predicting protein localization in budding yeast.Predicting 22 protein localizations in budding yeast.

Interpretable deep residual network uncovers nucleosome positioning and associated features.

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