A deformation energy model reveals sequence-dependent property of nucleosome positioning
| العنوان: | A deformation energy model reveals sequence-dependent property of nucleosome positioning |
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| المؤلفون: | Hongyu Zhao, Yongqiang Xing, Lu Cai, Hu Meng, Guoqing Liu |
| المصدر: | Chromosoma |
| بيانات النشر: | Springer Science and Business Media LLC, 2021. |
| سنة النشر: | 2021 |
| مصطلحات موضوعية: | Saccharomyces cerevisiae Proteins, Transcription, Genetic, Rotational positioning, Chromatin remodeler, Saccharomyces cerevisiae, Deformation (meteorology), Biology, Nucleosome occupancy, Chromatin remodeling, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Sequence dependent, Genetics, Nucleosome, Genetics (clinical), 030304 developmental biology, Adenosine Triphosphatases, 0303 health sciences, Nucleosome free energy, Deformation energy, Chromatin Assembly and Disassembly, Budding yeast, Nucleosomes, DNA-Binding Proteins, chemistry, Biophysics, Original Article, Energy Metabolism, 030217 neurology & neurosurgery, DNA, Energy (signal processing), Transcription Factors |
| الوصف: | We present a deformation energy model for predicting nucleosome positioning, in which a position-dependent structural parameter set derived from crystal structures of nucleosomes was used to calculate the DNA deformation energy. The model is successful in predicting nucleosome occupancy genome-wide in budding yeast, nucleosome free energy, and rotational positioning of nucleosomes. Our model also indicates that the genomic regions underlying the MNase-sensitive nucleosomes in budding yeast have high deformation energy and, consequently, low nucleosome-forming ability, while the MNase-sensitive non-histone particles are characterized by much lower DNA deformation energy and high nucleosome preference. In addition, we also revealed that remodelers, SNF2 and RSC8, are likely to act in chromatin remodeling by binding to broad nucleosome-depleted regions that are intrinsically favorable for nucleosome positioning. Our data support the important role of position-dependent physical properties of DNA in nucleosome positioning. Supplementary Information The online version contains supplementary material available at 10.1007/s00412-020-00750-9. |
| تدمد: | 1432-0886 0009-5915 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bdad5a16014b624239a6ed5078b13bbeTest https://doi.org/10.1007/s00412-020-00750-9Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....bdad5a16014b624239a6ed5078b13bbe |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 14320886 00095915 |
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