{"id":{"repo_id":"buffalo","oai_identifier":"oai:ubir.buffalo.edu:10477/79946"},"canonical_url":"https://search.dev.ndltd.org/etd/buffalo/oai:ubir.buffalo.edu:10477/79946","repository":{"repo_id":"buffalo","name":"Buffalo","base_url":"https://ubir.buffalo.edu/oai/request"},"display":{"title":"Defining Pioneering Capabilities with Pioneer-Seq","abstract":"M.S.","abstract_html":"M.S.","abstract_has_math":false,"creators":["Anandh, Swetha"],"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":2019,"date_issued":"2019-07-30T15:11:19Z","date_published":"2019-07-30T15:11:19Z","updated_at":"2026-07-27T19:05:21Z","subjects":["genetics","biochemistry"],"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/10477/79946","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":["Anandh, Swetha"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2019-07-30T15:11:19Z","2019","2019-05-15 10:49:54"]},{"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","biochemistry"]}]},{"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/10477/79946"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["M.S.","Gene expression involves the targeting of transcription factors (TFs) to regulatory sequences often occluded within nucleosomes. The ability to target a transcription factor binding site (TFBS) within a nucleosome has been the defining characteristic for a special class of TFs known as pioneer factors. Several proteins including TP53, TP63, SOX2, KLF4 and FOXA1 have been found to function as pioneer factor. These factors appear to target their TFBS within nucleosomes, but it remains unclear how positioning within the nucleosome and sequence characteristics of the TFBS affect binding. To comprehensively examine TF-nucleosome binding we developed Pioneer-Seq (transcriPtIon factOr NuclEosomE binding pRotocol). For Pioneer-seq, in vitro nucleosomes are formed from multiple DNA sequences containing a variant of the TFBS in a unique nucleosome orientation. These nucleosomes are then bound to the TF of interest and the protein-nucleosome complex is isolated and the nucleosome sequence is determined by next-generation sequencing. A nucleosome library containing 7500 different nucleosome sequences was in silico designed with various TFBS for 14 different TF families. Nucleosomes were assembled in vitro by reconstituting on the designed templates and then purified for binding assay. To examine nucleosome binding, we competitively bound TF to the in vitro formed nucleosomes. Stable TF-nucleosome complexes were isolated and quantified using next generation sequencing."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Defining Pioneering Capabilities with Pioneer-Seq"]}]}],"canonical_facts":{"dc:contributor":["Buck, Michael","Genetics, Genomics and Bioinformatics"],"dc:creator":["Anandh, Swetha"],"dc:date":["2019-07-30T15:11:19Z","2019","2019-05-15 10:49:54"],"dc:description":["M.S.","Gene expression involves the targeting of transcription factors (TFs) to regulatory sequences often occluded within nucleosomes. The ability to target a transcription factor binding site (TFBS) within a nucleosome has been the defining characteristic for a special class of TFs known as pioneer factors. Several proteins including TP53, TP63, SOX2, KLF4 and FOXA1 have been found to function as pioneer factor. These factors appear to target their TFBS within nucleosomes, but it remains unclear how positioning within the nucleosome and sequence characteristics of the TFBS affect binding. To comprehensively examine TF-nucleosome binding we developed Pioneer-Seq (transcriPtIon factOr NuclEosomE binding pRotocol). For Pioneer-seq, in vitro nucleosomes are formed from multiple DNA sequences containing a variant of the TFBS in a unique nucleosome orientation. These nucleosomes are then bound to the TF of interest and the protein-nucleosome complex is isolated and the nucleosome sequence is determined by next-generation sequencing. A nucleosome library containing 7500 different nucleosome sequences was in silico designed with various TFBS for 14 different TF families. Nucleosomes were assembled in vitro by reconstituting on the designed templates and then purified for binding assay. To examine nucleosome binding, we competitively bound TF to the in vitro formed nucleosomes. Stable TF-nucleosome complexes were isolated and quantified using next generation sequencing."],"dc:format":["application/pdf"],"dc:identifier":["http://hdl.handle.net/10477/79946"],"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","biochemistry"],"dc:title":["Defining Pioneering Capabilities with Pioneer-Seq"],"dc:type":["Text","Thesis"]},"updated_at":"2026-07-27T19:05:21Z"}