{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/100991"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/100991","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Statistical analysis and modeling of nucleosome positioning","abstract":"Nucleosome is the fundamental building block of eukaryotic chromatin. The precise location of nucleosome along the genome plays a central role in gene regulation by controlling the accessibility of genetic information encoded in DNA. Understanding the principles underlying the establishment of genome-wide nucleosome landscape is a critical step towards understanding chromatin structure and diverse cellular processes taking place on the chromatin template. Recent studies have identified various factors that impact the nucleosome landscape in vivo, such as DNA sequence, statistical positioning, and chromatin remodelers; but the results remain largely unconnected and sometimes even provide conflicting views. A comprehensive study integrating different determinants of nucleosome landscape into one consistent framework is still missing. Taking advantage of the flourishing experimental data generated by high-throughput sequencing technology, this thesis applies novel statistical analysis methods and statistical mechanics modeling to the nucleosome positioning problem. We start from quantifying the extent of DNA-encoded sequence signatures and characterizing their respective contributions to different aspects of nucleosome landscape. We then integrate multiple determinants of nucleosome landscape into a unified computational framework and investigate how different factors work together to accurately regulate nucleosome organization.","abstract_html":"Nucleosome is the fundamental building block of eukaryotic chromatin. The precise location of nucleosome along the genome plays a central role in gene regulation by controlling the accessibility of genetic information encoded in DNA. Understanding the principles underlying the establishment of genome-wide nucleosome landscape is a critical step towards understanding chromatin structure and diverse cellular processes taking place on the chromatin template. Recent studies have identified various factors that impact the nucleosome landscape in vivo, such as DNA sequence, statistical positioning, and chromatin remodelers; but the results remain largely unconnected and sometimes even provide conflicting views. A comprehensive study integrating different determinants of nucleosome landscape into one consistent framework is still missing. Taking advantage of the flourishing experimental data generated by high-throughput sequencing technology, this thesis applies novel statistical analysis methods and statistical mechanics modeling to the nucleosome positioning problem. We start from quantifying the extent of DNA-encoded sequence signatures and characterizing their respective contributions to different aspects of nucleosome landscape. We then integrate multiple determinants of nucleosome landscape into a unified computational framework and investigate how different factors work together to accurately regulate nucleosome organization.","abstract_has_math":false,"creators":["Jin, Hu"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Physics","degree_department":null,"school":null,"contributors":["Song, Jun S.","Aksimentiev, Aleksei","Kuhlman, Thomas E.","Kuehn, Seppe"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2018,"date_issued":"2018-09-04T20:27:11Z","date_published":"2018-09-04T20:27:11Z","updated_at":"2026-07-22T22:24:38Z","subjects":["Nucleosome","Nucleosome positioning","Nucleosome occupancy","DNA sequence","Statistical mechanics","Chromatin","Cross-entropy","10-bp periodicity"],"languages":["en"],"rights":["Copyright 2018 Hu Jin"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/100991","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Song, Jun S.","Aksimentiev, Aleksei","Kuhlman, Thomas E.","Kuehn, Seppe"]},{"key":"dc:creator","label":"Author","values":["Jin, Hu"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2018-09-04T20:27:11Z","2018-04-16","2018-05"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Physics"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Nucleosome","Nucleosome positioning","Nucleosome occupancy","DNA sequence","Statistical mechanics","Chromatin","Cross-entropy","10-bp periodicity"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2018 Hu Jin"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/100991"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Nucleosome is the fundamental building block of eukaryotic chromatin. The precise location of nucleosome along the genome plays a central role in gene regulation by controlling the accessibility of genetic information encoded in DNA. Understanding the principles underlying the establishment of genome-wide nucleosome landscape is a critical step towards understanding chromatin structure and diverse cellular processes taking place on the chromatin template. Recent studies have identified various factors that impact the nucleosome landscape in vivo, such as DNA sequence, statistical positioning, and chromatin remodelers; but the results remain largely unconnected and sometimes even provide conflicting views. A comprehensive study integrating different determinants of nucleosome landscape into one consistent framework is still missing. Taking advantage of the flourishing experimental data generated by high-throughput sequencing technology, this thesis applies novel statistical analysis methods and statistical mechanics modeling to the nucleosome positioning problem. We start from quantifying the extent of DNA-encoded sequence signatures and characterizing their respective contributions to different aspects of nucleosome landscape. We then integrate multiple determinants of nucleosome landscape into a unified computational framework and investigate how different factors work together to accurately regulate nucleosome organization.","Submission original under an indefinite embargo labeled 'Open Access'. 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Understanding the principles underlying the establishment of genome-wide nucleosome landscape is a critical step towards understanding chromatin structure and diverse cellular processes taking place on the chromatin template. Recent studies have identified various factors that impact the nucleosome landscape in vivo, such as DNA sequence, statistical positioning, and chromatin remodelers; but the results remain largely unconnected and sometimes even provide conflicting views. A comprehensive study integrating different determinants of nucleosome landscape into one consistent framework is still missing. Taking advantage of the flourishing experimental data generated by high-throughput sequencing technology, this thesis applies novel statistical analysis methods and statistical mechanics modeling to the nucleosome positioning problem. We start from quantifying the extent of DNA-encoded sequence signatures and characterizing their respective contributions to different aspects of nucleosome landscape. We then integrate multiple determinants of nucleosome landscape into a unified computational framework and investigate how different factors work together to accurately regulate nucleosome organization.","Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2018-08-31 without embargo terms","The student, Hu Jin, accepted the attached license on 2018-04-16 at 14:27.","The student, Hu Jin, submitted this Dissertation for approval on 2018-04-16 at 14:40.","This Dissertation was approved for publication on 2018-04-16 at 16:42.","DSpace SAF Submission Ingestion Package generated from Vireo submission #12279 on 2018-08-31 at 17:12:54","Made available in DSpace on 2018-09-04T20:27:11Z (GMT). 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