Predicting nucleosome positioning using statistical equilibrium models in budding yeast
Summary: 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 paramet...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-03-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166722008061 |
| _version_ | 1811177582665662464 |
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| author | Hungyo Kharerin Lu Bai |
| author_facet | Hungyo Kharerin Lu Bai |
| author_sort | Hungyo Kharerin |
| collection | DOAJ |
| description | Summary: 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 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-04-11T06:04:54Z |
| format | Article |
| id | doaj.art-13019608c3d84b67ab7e13e25902bf15 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-04-11T06:04:54Z |
| publishDate | 2023-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-13019608c3d84b67ab7e13e25902bf152022-12-22T04:41:32ZengElsevierSTAR Protocols2666-16672023-03-0141101926Predicting nucleosome positioning using statistical equilibrium models in budding yeastHungyo Kharerin0Lu Bai1Department 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; Corresponding authorDepartment 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; Corresponding authorSummary: 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 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166722008061BioinformaticsBiophysicsGenomicsModel OrganismsMolecular BiologyComputer sciences |
| spellingShingle | Hungyo Kharerin Lu Bai Predicting nucleosome positioning using statistical equilibrium models in budding yeast STAR Protocols Bioinformatics Biophysics Genomics Model Organisms Molecular Biology Computer sciences |
| title | Predicting nucleosome positioning using statistical equilibrium models in budding yeast |
| title_full | Predicting nucleosome positioning using statistical equilibrium models in budding yeast |
| title_fullStr | Predicting nucleosome positioning using statistical equilibrium models in budding yeast |
| title_full_unstemmed | Predicting nucleosome positioning using statistical equilibrium models in budding yeast |
| title_short | Predicting nucleosome positioning using statistical equilibrium models in budding yeast |
| title_sort | predicting nucleosome positioning using statistical equilibrium models in budding yeast |
| topic | Bioinformatics Biophysics Genomics Model Organisms Molecular Biology Computer sciences |
| url | http://www.sciencedirect.com/science/article/pii/S2666166722008061 |
| work_keys_str_mv | AT hungyokharerin predictingnucleosomepositioningusingstatisticalequilibriummodelsinbuddingyeast AT lubai predictingnucleosomepositioningusingstatisticalequilibriummodelsinbuddingyeast |