Predicting nucleosome positioning using statistical equilibrium models in budding yeast.
Predicting nucleosome positioning using statistical equilibrium models in budding yeast.
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DOI：
10.1016/j.xpro.2022.101926
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发表时间：
2023-03-17
期刊：
影响因子：
--
通讯作者：
Bai, Lu
中科院分区：
文献类型：
--
作者：
Kharerin, Hungyo;Bai, Lu
我们提出了一个协议，使用热力学模型来预测核小体定位与转录因子（TF）和染色质重塑。我们描述了一步一步的方法来注释全基因组核小体耗尽区（NDRs），计算核小体和TF占用，优化参数，并评估模型的性能。这些模型识别核小体置换TF在芽殖酵母基因组和预测的位置和大小的NDRs仅基于DNA序列和TF基序。该协议可以适用于所有生物体的TF基序的先验知识。有关本方案使用和执行的完整详细信息，请参阅Kharerin和Bai（2021）。基于酵母中的序列和TF基序预测核小体定位的模型进行NDR注释、统计建模、拟合和评估的步骤识别和整合对NDR形成至关重要的TF子集整合核小体重塑剂以更好地预测NDR大小出版商注：进行任何实验方案都需要遵守当地机构的实验室安全和伦理指南。我们提出了一个协议，使用热力学模型来预测核小体定位与转录因子（TF）和染色质重塑。我们描述了一步一步的方法来注释全基因组核小体耗尽区（NDRs），计算核小体和TF占用，优化参数，并评估模型的性能。这些模型识别核小体置换TF在芽殖酵母基因组和预测的位置和大小的NDRs仅基于DNA序列和TF基序。该协议可以适用于所有生物体的TF基序的先验知识。
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). Models to predict nucleosome positioning based on sequence and TF motifs in yeast Steps to perform NDR annotation, statistical modeling, fitting, and evaluation Identification and incorporation of a subset of TFs crucial for NDR formation Incorporation of nucleosome remodelers for better prediction of NDR sizes Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. 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.
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