{"id":{"repo_id":"wustl","oai_identifier":"oai:openscholarship.wustl.edu:etd-1431"},"canonical_url":"https://search.dev.ndltd.org/etd/wustl/oai:openscholarship.wustl.edu:etd-1431","repository":{"repo_id":"wustl","name":"Washington University in St. Louis","base_url":"https://openscholarship.wustl.edu/do/oai/"},"display":{"title":"Calling Cards For DNA-Binding Proteins","abstract":"Organisms respond to their environment by altering patterns of gene expression. This process is orchestrated by transcription factors, which bind to specific DNA sequences near genes. In order to understand the regulatory networks that control transcription, the genomic targets of all transcription factors under various conditions and in different cell types must be identified. This remains a distant goal, mainly due to the lack of a high-throughput, in vivo method to study protein-DNA interactions. To fill this gap, I developed transposon \"Calling Cards\" for DNA-binding proteins. I endowed DNA binding proteins with the ability to direct the insertion of a transposon into the genome near to where they bind. The transposon becomes a \"Calling Card\" that marks the visit of a DNA-binding protein to the genome. I demonstrated that the Calling Card method is accurate and robust. I combined Calling Cards with \"next generation\" DNA sequencing technology to increase the sensitivity, specificity, and resolution of the method. This improved method: \"Calling Card-Seq\") allows for multiple transcription factors to be analyzed in a single experiment, greatly increasing sample throughput. I used Calling Card-Seq to study transcription factors of the yeast S. cerevisiae that have not been well-characterized, and I successfully identified DNA sequence recognition motifs and target genes for many of them. Calling Card-Seq will enable a systematic exploration of transcription factor binding under many different environments and growth conditions in a way that has heretofore not been possible. This dissertation describes my work developing this method, as well as several interesting results obtained using this method to study the gene regulatory networks of the yeast S. cerevisiae.","abstract_html":"Organisms respond to their environment by altering patterns of gene expression. This process is orchestrated by transcription factors, which bind to specific DNA sequences near genes. In order to understand the regulatory networks that control transcription, the genomic targets of all transcription factors under various conditions and in different cell types must be identified. This remains a distant goal, mainly due to the lack of a high-throughput, in vivo method to study protein-DNA interactions. To fill this gap, I developed transposon "Calling Cards" for DNA-binding proteins. I endowed DNA binding proteins with the ability to direct the insertion of a transposon into the genome near to where they bind. The transposon becomes a "Calling Card" that marks the visit of a DNA-binding protein to the genome. I demonstrated that the Calling Card method is accurate and robust. I combined Calling Cards with "next generation" DNA sequencing technology to increase the sensitivity, specificity, and resolution of the method. This improved method: "Calling Card-Seq") allows for multiple transcription factors to be analyzed in a single experiment, greatly increasing sample throughput. I used Calling Card-Seq to study transcription factors of the yeast S. cerevisiae that have not been well-characterized, and I successfully identified DNA sequence recognition motifs and target genes for many of them. Calling Card-Seq will enable a systematic exploration of transcription factor binding under many different environments and growth conditions in a way that has heretofore not been possible. This dissertation describes my work developing this method, as well as several interesting results obtained using this method to study the gene regulatory networks of the yeast S. cerevisiae.","abstract_has_math":false,"creators":["Wang, Haoyi"],"institution":null,"degree_name":"Doctor of Philosophy (PhD)","degree_level":"Dissertation","degree_discipline":"Biology and Biomedical Sciences: Molecular Cell Biology","degree_department":null,"school":null,"contributors":["Mark Johnston"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2009,"date_issued":"2009-01-01T08:00:00Z","date_published":"2009-01-01T08:00:00Z","updated_at":"2026-07-24T06:12:58Z","subjects":["Biology","Molecular","Genetics","Cell","Calling Card","DNA-binding protein","Transcription factor","Ty5"],"languages":["English (en)"],"rights":[],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier.doi","label":"DOI","values":["https://doi.org/10.7936/K7MK69XS"],"render_values":[{"text":"https://doi.org/10.7936/K7MK69XS","href":"https://doi.org/10.7936/K7MK69XS","code":true}]}]},"links":{"outbound_url":"https://openscholarship.wustl.edu/etd/432","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Mark Johnston"]},{"key":"dc:creator","label":"Author","values":["Wang, Haoyi"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.available","label":"Dc Date Available","values":["2014-05-25T07:00:00Z"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biology and Biomedical Sciences: Molecular Cell Biology"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Doctor of Philosophy (PhD)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Biology","Molecular","Genetics","Cell","Calling Card","DNA-binding protein","Transcription factor","Ty5"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["English (en)"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://openscholarship.wustl.edu/etd/432"]},{"key":"dc:identifier.doi","label":"DOI","values":["https://doi.org/10.7936/K7MK69XS"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Organisms respond to their environment by altering patterns of gene expression. This process is orchestrated by transcription factors, which bind to specific DNA sequences near genes. In order to understand the regulatory networks that control transcription, the genomic targets of all transcription factors under various conditions and in different cell types must be identified. This remains a distant goal, mainly due to the lack of a high-throughput, in vivo method to study protein-DNA interactions. To fill this gap, I developed transposon \"Calling Cards\" for DNA-binding proteins. I endowed DNA binding proteins with the ability to direct the insertion of a transposon into the genome near to where they bind. The transposon becomes a \"Calling Card\" that marks the visit of a DNA-binding protein to the genome. I demonstrated that the Calling Card method is accurate and robust. I combined Calling Cards with \"next generation\" DNA sequencing technology to increase the sensitivity, specificity, and resolution of the method. This improved method: \"Calling Card-Seq\") allows for multiple transcription factors to be analyzed in a single experiment, greatly increasing sample throughput. I used Calling Card-Seq to study transcription factors of the yeast S. cerevisiae that have not been well-characterized, and I successfully identified DNA sequence recognition motifs and target genes for many of them. Calling Card-Seq will enable a systematic exploration of transcription factor binding under many different environments and growth conditions in a way that has heretofore not been possible. This dissertation describes my work developing this method, as well as several interesting results obtained using this method to study the gene regulatory networks of the yeast S. cerevisiae."]},{"key":"dc:title","label":"Title","values":["Calling Cards For DNA-Binding Proteins"]}]}],"canonical_facts":{"dc:contributor":["Mark Johnston"],"dc:creator":["Wang, Haoyi"],"dc:date.available":["2014-05-25T07:00:00Z"],"dc:description.abstract":["Organisms respond to their environment by altering patterns of gene expression. This process is orchestrated by transcription factors, which bind to specific DNA sequences near genes. In order to understand the regulatory networks that control transcription, the genomic targets of all transcription factors under various conditions and in different cell types must be identified. This remains a distant goal, mainly due to the lack of a high-throughput, in vivo method to study protein-DNA interactions. To fill this gap, I developed transposon \"Calling Cards\" for DNA-binding proteins. I endowed DNA binding proteins with the ability to direct the insertion of a transposon into the genome near to where they bind. The transposon becomes a \"Calling Card\" that marks the visit of a DNA-binding protein to the genome. I demonstrated that the Calling Card method is accurate and robust. I combined Calling Cards with \"next generation\" DNA sequencing technology to increase the sensitivity, specificity, and resolution of the method. This improved method: \"Calling Card-Seq\") allows for multiple transcription factors to be analyzed in a single experiment, greatly increasing sample throughput. I used Calling Card-Seq to study transcription factors of the yeast S. cerevisiae that have not been well-characterized, and I successfully identified DNA sequence recognition motifs and target genes for many of them. Calling Card-Seq will enable a systematic exploration of transcription factor binding under many different environments and growth conditions in a way that has heretofore not been possible. This dissertation describes my work developing this method, as well as several interesting results obtained using this method to study the gene regulatory networks of the yeast S. cerevisiae."],"dc:identifier":["https://openscholarship.wustl.edu/etd/432"],"dc:identifier.doi":["https://doi.org/10.7936/K7MK69XS"],"dc:language":["English (en)"],"dc:subject":["Biology","Molecular","Genetics","Cell","Calling Card","DNA-binding protein","Transcription factor","Ty5"],"dc:title":["Calling Cards For DNA-Binding Proteins"],"thesis:degree_discipline":["Biology and Biomedical Sciences: Molecular Cell Biology"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Doctor of Philosophy (PhD)"]},"updated_at":"2026-07-24T06:12:58Z"}