{"id":{"repo_id":"buffalo","oai_identifier":"oai:ubir.buffalo.edu:10477/86471"},"canonical_url":"https://search.dev.ndltd.org/etd/buffalo/oai:ubir.buffalo.edu:10477/86471","repository":{"repo_id":"buffalo","name":"Buffalo","base_url":"https://ubir.buffalo.edu/oai/request"},"display":{"title":"Characterizing ΔNp63α Binding Sites Based on Nucleosome Organization and Histone Modifications","abstract":"M.S.","abstract_html":"M.S.","abstract_has_math":false,"creators":["Tabrejee, Shamira"],"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","Genetics, Genomics and Bioinformatics"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2025,"date_issued":"2025-02-21T17:22:45Z","date_published":"2025-02-21T17:22:45Z","updated_at":"2026-07-27T19:05:32Z","subjects":["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/10477/86471","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Buck, Michael","Genetics, Genomics and Bioinformatics"]},{"key":"dc:creator","label":"Author","values":["Tabrejee, Shamira"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2025-02-21T17:22:45Z","2020"]},{"key":"dc:publisher","label":"Institution","values":["State University of New York at Buffalo"]},{"key":"dc:type","label":"Dc Type","values":["Text","Thesis"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["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/10477/86471"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["M.S.","p63 is an essential transcription factor required for stratified epithelial development and also overexpressed in different squamous cell carcinomas. Our broader goal is to define the biological rules dictating p63 binding on chromosomal DNA. For approaching that we aimed to determine the nucleosome organization and histone modifications at p63 binding sites before and after p63 binding. The wild type and DNA binding mutant of predominant isoform of p63, ΔNp63α was ectopically induced in p63 naïve cells, K562. 1040 sites among 1427 common p63 binding sites identified by different p63 ChIP-seq datasets were found to contain 1214 p63 motifs using FIMO. We discovered that these p63 binding sites have higher nucleosome occupancy by assessing MNase-seq data for K562 cells. Also, before p63 binding the targeted sites lack H3K27ac signal indicating the capability of p63 to bind to unmodified chromatin. After p63 binding, regions surrounding the binding sites acquired H3K27ac, but the binding site itself lacked H3K27ac indicating the capability of p63 to recruit an enzyme responsible for acetylation and the depletion of nucleosome at the p63 binding site after binding respectively. Whereas, there was no difference in the nucleosome occupancy or H3K27ac signal at transcription start sites between before and after p63 binding. Then we found that 109 p63 binding sites among those 1040 motif containing sites are repressed or heterochromatin in K562 but enhancers in p63 native cell line NHEK indicating the ability of p63 to bind to inaccessible chromatin state. 13 among 109 sites were chosen based on ChIP-seq p-value and validated by ChIP-qPCR for characterization. All of these sites fall within or at the edges of nucleosomes, lacking H3K27ac in mutant ΔNp63α expressing K562 cell and obtaining H3K27ac on flanking regions with a depletion of signal at the motif site in wild-type ΔNp63α expressing K562 cells. We checked the nucleosome position at one individual p63 binding site using MNase digestion-qPCR in both wild-type and mutant ΔNp63α expressing K562 cells. Fold enrichment of the region covering the nucleosome center is higher in mutant cells compared to that of wild type cells indicating the displacement of nucleosome from that position. ChIP-qPCR for nucleosome subunit H4 for five p63 binding sites and two control sites positioned approximately 400 base pairs right and left to each of those five sites was performed. Two sites show lower fold enrichment for wild type K562 compared to that of the mutant K562 cells which again suggests the loss of nucleosomes from those p63 binding sites upon ΔNp63α binding, though the fold enrichment for the control sites in wild type and mutant cells did not show any consistency. ChIP-qPCR for chromatin remodeler BAF subunit brg1 for those 5 selected p63 binding sites were also executed to check the occupancy of BAF complex on those sites after p63 binding. Three sites exhibited slightly higher brg1 occupancy in wild type ΔNp63α expressing K562 compared to that of the mutant one. Finally, to know the occupancy of histone acetyl transferase on 13 p63 binding sites in K562 cells, histone acetyl transferase-p300 ChIP-qPCR was performed in wild type and mutant K562 cells. But no conclusion could be inferred from the experiment due to the unreliability of the data. In future, more comprehensive studies can be done to know the detailed mechanism of nucleosome repositioning and chromatin modification at p63 binding sites by the combinatorial actions of different factors upon p63 binding.","**To request an accessible version of the file(s) associated with this item, contact library@buffalo.edu. Please include the item's persistent URL [http://hdl.handle.net/. . .] in your request.**"]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Characterizing ΔNp63α Binding Sites Based on Nucleosome Organization and Histone Modifications"]}]}],"canonical_facts":{"dc:contributor":["Buck, Michael","Genetics, Genomics and Bioinformatics"],"dc:creator":["Tabrejee, Shamira"],"dc:date":["2025-02-21T17:22:45Z","2020"],"dc:description":["M.S.","p63 is an essential transcription factor required for stratified epithelial development and also overexpressed in different squamous cell carcinomas. Our broader goal is to define the biological rules dictating p63 binding on chromosomal DNA. For approaching that we aimed to determine the nucleosome organization and histone modifications at p63 binding sites before and after p63 binding. The wild type and DNA binding mutant of predominant isoform of p63, ΔNp63α was ectopically induced in p63 naïve cells, K562. 1040 sites among 1427 common p63 binding sites identified by different p63 ChIP-seq datasets were found to contain 1214 p63 motifs using FIMO. We discovered that these p63 binding sites have higher nucleosome occupancy by assessing MNase-seq data for K562 cells. Also, before p63 binding the targeted sites lack H3K27ac signal indicating the capability of p63 to bind to unmodified chromatin. After p63 binding, regions surrounding the binding sites acquired H3K27ac, but the binding site itself lacked H3K27ac indicating the capability of p63 to recruit an enzyme responsible for acetylation and the depletion of nucleosome at the p63 binding site after binding respectively. Whereas, there was no difference in the nucleosome occupancy or H3K27ac signal at transcription start sites between before and after p63 binding. Then we found that 109 p63 binding sites among those 1040 motif containing sites are repressed or heterochromatin in K562 but enhancers in p63 native cell line NHEK indicating the ability of p63 to bind to inaccessible chromatin state. 13 among 109 sites were chosen based on ChIP-seq p-value and validated by ChIP-qPCR for characterization. All of these sites fall within or at the edges of nucleosomes, lacking H3K27ac in mutant ΔNp63α expressing K562 cell and obtaining H3K27ac on flanking regions with a depletion of signal at the motif site in wild-type ΔNp63α expressing K562 cells. We checked the nucleosome position at one individual p63 binding site using MNase digestion-qPCR in both wild-type and mutant ΔNp63α expressing K562 cells. Fold enrichment of the region covering the nucleosome center is higher in mutant cells compared to that of wild type cells indicating the displacement of nucleosome from that position. ChIP-qPCR for nucleosome subunit H4 for five p63 binding sites and two control sites positioned approximately 400 base pairs right and left to each of those five sites was performed. Two sites show lower fold enrichment for wild type K562 compared to that of the mutant K562 cells which again suggests the loss of nucleosomes from those p63 binding sites upon ΔNp63α binding, though the fold enrichment for the control sites in wild type and mutant cells did not show any consistency. ChIP-qPCR for chromatin remodeler BAF subunit brg1 for those 5 selected p63 binding sites were also executed to check the occupancy of BAF complex on those sites after p63 binding. Three sites exhibited slightly higher brg1 occupancy in wild type ΔNp63α expressing K562 compared to that of the mutant one. Finally, to know the occupancy of histone acetyl transferase on 13 p63 binding sites in K562 cells, histone acetyl transferase-p300 ChIP-qPCR was performed in wild type and mutant K562 cells. But no conclusion could be inferred from the experiment due to the unreliability of the data. In future, more comprehensive studies can be done to know the detailed mechanism of nucleosome repositioning and chromatin modification at p63 binding sites by the combinatorial actions of different factors upon p63 binding.","**To request an accessible version of the file(s) associated with this item, contact library@buffalo.edu. Please include the item's persistent URL [http://hdl.handle.net/. . .] in your request.**"],"dc:format":["application/pdf"],"dc:identifier":["http://hdl.handle.net/10477/86471"],"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":["genetics","bioinformatics"],"dc:title":["Characterizing ΔNp63α Binding Sites Based on Nucleosome Organization and Histone Modifications"],"dc:type":["Text","Thesis"]},"updated_at":"2026-07-27T19:05:32Z"}