{"doi":"10.1007/s00412-020-00750-9","title":"A deformation energy model reveals sequence-dependent property of nucleosome positioning","abstract":"<jats:title>Abstract</jats:title><jats:p>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.</jats:p>","journal":"Chromosoma","year":2021,"id":47195,"datarank":0.48043895659941477,"base_score":2.1972245773362196,"endowment":2.1972245773362196,"self_citation_contribution":0.32958368660043297,"citation_network_contribution":0.1508552699989818,"self_endowment_contribution":0.32958368660043297,"citer_contribution":0.1508552699989818,"corpus_percentile":null,"corpus_rank":null,"citation_count":8,"citer_count":8,"citers_with_citation_signal":7,"citers_with_endowment":7,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":217784,"name":"Hongyu Zhao","orcid":null,"position":1,"is_corresponding":false},{"id":217785,"name":"Hu Meng","orcid":null,"position":2,"is_corresponding":false},{"id":217786,"name":"Yongqiang Xing","orcid":null,"position":3,"is_corresponding":false},{"id":217787,"name":"Lu Cai","orcid":null,"position":4,"is_corresponding":false},{"id":217783,"name":"Guoqing Liu","orcid":"0000-0001-5190-4614","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"A deformation energy model reveals sequence-dependent property of nucleosome positioning","abstract":"<jats:title>Abstract</jats:title><jats:p>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.</jats:p>","is_dataset_classified":null,"base_score":2.1972245773362196,"endowment":2.1972245773362196,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"33452566","pmcid":"PMC7889546","openalex_id":"https://openalex.org/W3124098632","authors":[],"funders":[{"funder_name":"National Natural Science Foundation of China","grant_id":"31660322","title":null},{"funder_name":"National Natural Science Foundation of China","grant_id":"31760247","title":null},{"funder_name":"Natural Science Foundation of Inner Mongolia","grant_id":"2018LH03023","title":null},{"funder_name":"Natural Science Foundation of Inner Mongolia","grant_id":"2019BS03024","title":null}],"total_grants":4,"fwci":0.5551,"citation_percentile":0.62411144,"influential_citations":3,"citation_trend":[{"year":2021,"count":3},{"year":2022,"count":3},{"year":2023,"count":1},{"year":2026,"count":1}],"oa_status":"hybrid","license":"cc-by","oa_locations":[{"url":"https://link.springer.com/content/pdf/10.1007/s00412-020-00750-9.pdf","host_type":"journal"},{"url":"https://link.springer.com/content/pdf/10.1007/s00412-020-00750-9.pdf","host_type":"HYBRID"},{"url":"https://link.springer.com/content/pdf/10.1007/s00412-020-00750-9.pdf","host_type":"publisher"},{"url":"https://link.springer.com/article/10.1007/s00412-020-00750-9/fulltext.html","host_type":"publisher"},{"url":"https://doi.org/10.1007/s00412-020-00750-9","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/33452566","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7889546","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC7889546","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC7889546?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["Genomics and Chromatin Dynamics","RNA and protein synthesis mechanisms","DNA Repair Mechanisms","Medicine","Biology","Adenosine Triphosphatases","Chromatin Assembly and Disassembly","DNA-Binding Proteins","Energy Metabolism","Nucleosomes","Saccharomyces cerevisiae","Saccharomyces cerevisiae Proteins","Transcription Factors","Transcription, Genetic"],"mesh_terms":["Adenosine Triphosphatases","DNA-Binding Proteins","Energy Metabolism","Nucleosomes","Saccharomyces cerevisiae","Transcription Factors","Transcription, Genetic","Saccharomyces cerevisiae Proteins","Chromatin Assembly and Disassembly"],"keywords":["Nucleosome","Histone","SWI/SNF","Biology","Chromatin","Linker DNA","Chromatosome","Deformation (meteorology)","DNA","Position (finance)","Biophysics","Genetics","Physics","Nucleosome Occupancy","Rotational Positioning","Chromatin Remodeler","Deformation Energy","Nucleosome Free Energy"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Affordable and clean energy"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"pdb"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-17T15:09:17.768686Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}