{"id":{"repo_id":"buffalo","oai_identifier":"oai:ubir.buffalo.edu:10477/80839"},"canonical_url":"https://search.dev.ndltd.org/etd/buffalo/oai:ubir.buffalo.edu:10477/80839","repository":{"repo_id":"buffalo","name":"Buffalo","base_url":"https://ubir.buffalo.edu/oai/request"},"display":{"title":"Defining P53 and P63 Proteins Chromatin Interaction Capabilities","abstract":"Ph.D.","abstract_html":"Ph.D.","abstract_has_math":false,"creators":["Yu, Xinyang"],"institution":"State University of New York at Buffalo","degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":["Buck, Michael","Biochemistry"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2019,"date_issued":"2019-10-29T16:47:26Z","date_published":"2019-10-29T16:47:26Z","updated_at":"2026-07-27T19:05:25Z","subjects":["biochemistry","genetics","bioinformatics"],"languages":["eng"],"rights":["Users of works found in University at Buffalo Institutional Repository (UBIR) are responsible for identifying and contacting the copyright owner for permission to reuse. University at Buffalo Libraries do not manage rights for copyright-protected works and cannot assist with permissions.","Copyright retained by author."],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/10477/80839","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Buck, Michael","Biochemistry"]},{"key":"dc:creator","label":"Author","values":["Yu, Xinyang"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2019-10-29T16:47:26Z","2019","2019-06-23 19:02:41"]},{"key":"dc:publisher","label":"Institution","values":["State University of New York at Buffalo"]},{"key":"dc:type","label":"Dc Type","values":["Text","Dissertation"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["biochemistry","genetics","bioinformatics"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Users of works found in University at Buffalo Institutional Repository (UBIR) are responsible for identifying and contacting the copyright owner for permission to reuse. University at Buffalo Libraries do not manage rights for copyright-protected works and cannot assist with permissions.","Copyright retained by author."]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/10477/80839"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Ph.D.","Human genome is compacted into highly condensed chromatin structure with nucleosome as basic unit, but accurate gene regulation requires transcription factors (TFs) to bind their corresponding response elements (RE) usually occluded within nucleosomes. Over the last few decades, a special class of TFs has been defined as pioneer factors with the ability to bind transcription factor binding site (TFBS) buried inside nucleosomes. However, it is still not clear how these pioneer factors bind to nucleosomal DNA. In order to learn how TFBS positioning within the nucleosome and sequence characteristic of TFBS itself can affect binding, our lab developed PIONEER-seq (transcriPtIon factOr NuclEosomE binding pRotocol) combining traditional competitive TF-nucleosome binding assay with high throughput sequencing to comprehensively examine TF-nucleosome binding. This test was performed on p53 protein and its family member p63. Our results demonstrate that both factors can bind nucleosomes nucleosome edges, and the nucleotide composition of binding site also plays a role. In vivo study on p63-overepressing cell lines further proves p63 protein being able to target inaccessible chromatin with limited histone modifications. Moreover, active histone mark H3K27ac significantly increases after p63 binds to those target sites. Overall, our results suggest that p53 and p63 proteins function as pioneer factors, given the fact that both of them can bind to nucleosomal DNA, p63 can even lead to chromatin states alternation at bound site. But their pioneering ability is affected by target site location on the nucleosome and also the nucleotide composition of target sequence."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Defining P53 and P63 Proteins Chromatin Interaction Capabilities"]}]}],"canonical_facts":{"dc:contributor":["Buck, Michael","Biochemistry"],"dc:creator":["Yu, Xinyang"],"dc:date":["2019-10-29T16:47:26Z","2019","2019-06-23 19:02:41"],"dc:description":["Ph.D.","Human genome is compacted into highly condensed chromatin structure with nucleosome as basic unit, but accurate gene regulation requires transcription factors (TFs) to bind their corresponding response elements (RE) usually occluded within nucleosomes. Over the last few decades, a special class of TFs has been defined as pioneer factors with the ability to bind transcription factor binding site (TFBS) buried inside nucleosomes. However, it is still not clear how these pioneer factors bind to nucleosomal DNA. In order to learn how TFBS positioning within the nucleosome and sequence characteristic of TFBS itself can affect binding, our lab developed PIONEER-seq (transcriPtIon factOr NuclEosomE binding pRotocol) combining traditional competitive TF-nucleosome binding assay with high throughput sequencing to comprehensively examine TF-nucleosome binding. This test was performed on p53 protein and its family member p63. Our results demonstrate that both factors can bind nucleosomes nucleosome edges, and the nucleotide composition of binding site also plays a role. In vivo study on p63-overepressing cell lines further proves p63 protein being able to target inaccessible chromatin with limited histone modifications. Moreover, active histone mark H3K27ac significantly increases after p63 binds to those target sites. Overall, our results suggest that p53 and p63 proteins function as pioneer factors, given the fact that both of them can bind to nucleosomal DNA, p63 can even lead to chromatin states alternation at bound site. But their pioneering ability is affected by target site location on the nucleosome and also the nucleotide composition of target sequence."],"dc:format":["application/pdf"],"dc:identifier":["http://hdl.handle.net/10477/80839"],"dc:language":["eng"],"dc:publisher":["State University of New York at Buffalo"],"dc:rights":["Users of works found in University at Buffalo Institutional Repository (UBIR) are responsible for identifying and contacting the copyright owner for permission to reuse. University at Buffalo Libraries do not manage rights for copyright-protected works and cannot assist with permissions.","Copyright retained by author."],"dc:subject":["biochemistry","genetics","bioinformatics"],"dc:title":["Defining P53 and P63 Proteins Chromatin Interaction Capabilities"],"dc:type":["Text","Dissertation"]},"updated_at":"2026-07-27T19:05:25Z"}