{"id":2796,"date":"2020-08-04T03:43:44","date_gmt":"2020-08-04T03:43:44","guid":{"rendered":"http:\/\/sites.rutgers.edu\/nb-senior-exhibits\/?page_id=2796"},"modified":"2020-08-05T03:31:39","modified_gmt":"2020-08-05T03:31:39","slug":"li-zeyue","status":"publish","type":"page","link":"https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/partners\/aresty-research-virtual-symposium-2020\/li-zeyue\/","title":{"rendered":"Li, Zeyue: Investigating Binding Site Ratios of Transcription Factors"},"content":{"rendered":"<p><a href=\"http:\/\/sites.rutgers.edu\/nb-senior-exhibits\/wp-content\/uploads\/sites\/442\/2020\/08\/ZeyueLiposter.pdf\" target=\"_blank\" rel=\"noopener noreferrer\"><img loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-2849 alignleft\" src=\"http:\/\/sites.rutgers.edu\/nb-senior-exhibits\/wp-content\/uploads\/sites\/442\/2020\/08\/ZeyueLiposter_thumbnail-300x225.png\" alt=\"\" width=\"300\" height=\"225\" srcset=\"https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/wp-content\/uploads\/sites\/442\/2020\/08\/ZeyueLiposter_thumbnail-300x225.png 300w, https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/wp-content\/uploads\/sites\/442\/2020\/08\/ZeyueLiposter_thumbnail-1024x768.png 1024w, https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/wp-content\/uploads\/sites\/442\/2020\/08\/ZeyueLiposter_thumbnail-768x576.png 768w, https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/wp-content\/uploads\/sites\/442\/2020\/08\/ZeyueLiposter_thumbnail.png 1067w\" sizes=\"(max-width: 300px) 100vw, 300px\" \/><\/a><br \/>\n<strong>Title:<\/strong> Investigating Binding Site Ratios of Transcription Factors<\/p>\n<p><strong>Name:<\/strong> Zeyue Li<\/p>\n<p><strong>Major:<\/strong> Biological Sciences<\/p>\n<p><strong>School affiliation:<\/strong> School of Environmental and Biological Sciences<\/p>\n<p><strong>Programs:<\/strong> Aresty Summer Science Program<\/p>\n<p><strong>Other contributors:<\/strong> Ann Stock, Rong Gao<\/p>\n<p><strong>Abstract:<\/strong> Bacterial signal transduction is controlled by transcription factors (TFs), which bind to specific binding sites on bacterial chromosomes. Expression levels of TFs are often presumed to be in great excess to their binding sites, leading to high ratios of TF concentrations to the numbers of TF binding sites. Previous studies have suggested a median ratio of 10. Here we used the updated binding data from regulonDB and multiple protein abundance databases to reexamine the ratios for E. coli TFs. We discovered that TFs are unlikely to be in great excess to their binding sites. Further, we believe that the binding site data from regulonDB is biased toward the intergenic promoter regions and there are more binding sites that have not been discovered, especially those within open reading frames. To better estimate the number of binding sites, we took a bioinformatics direction, using multiple sources, including high-throughput data, gSELEX data, and computational predictions using FIMO scan of the bacterial genome. Although different sources vary in their reports of the number of binding sites, all indicated at least two fold higher numbers of binding sites than those from regulonDB. Overall, we found that repressors tend to have a higher ratio compared to activators and dual function TFs, and we found that the originally reported ratio is higher than what studies with newer technology suggests.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Title: Investigating Binding Site Ratios of Transcription Factors Name: Zeyue Li Major: Biological Sciences School affiliation: School of Environmental and Biological Sciences Programs: Aresty Summer Science Program Other contributors: Ann &hellip; <a href=\"https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/partners\/aresty-research-virtual-symposium-2020\/li-zeyue\/\" class=\"\">Read More<\/a><\/p>\n","protected":false},"author":970,"featured_media":0,"parent":441,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"template-custom.php","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-2796","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v23.5 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Li, Zeyue: Investigating Binding Site Ratios of Transcription Factors - Senior Exhibits<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/partners\/aresty-research-virtual-symposium-2020\/li-zeyue\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Li, Zeyue: Investigating Binding Site Ratios of Transcription Factors - Senior Exhibits\" \/>\n<meta property=\"og:description\" content=\"Title: Investigating Binding Site Ratios of Transcription Factors Name: Zeyue Li Major: Biological Sciences School affiliation: School of Environmental and Biological Sciences Programs: Aresty Summer Science Program Other contributors: Ann &hellip; Read More\" \/>\n<meta property=\"og:url\" content=\"https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/partners\/aresty-research-virtual-symposium-2020\/li-zeyue\/\" \/>\n<meta property=\"og:site_name\" content=\"Senior Exhibits\" \/>\n<meta property=\"article:modified_time\" content=\"2020-08-05T03:31:39+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/sites.rutgers.edu\/nb-senior-exhibits\/wp-content\/uploads\/sites\/442\/2020\/08\/ZeyueLiposter_thumbnail-300x225.png\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/partners\/aresty-research-virtual-symposium-2020\/li-zeyue\/\",\"url\":\"https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/partners\/aresty-research-virtual-symposium-2020\/li-zeyue\/\",\"name\":\"Li, Zeyue: Investigating Binding Site Ratios of Transcription Factors - Senior Exhibits\",\"isPartOf\":{\"@id\":\"https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/partners\/aresty-research-virtual-symposium-2020\/li-zeyue\/#primaryimage\"},\"image\":{\"@id\":\"https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/partners\/aresty-research-virtual-symposium-2020\/li-zeyue\/#primaryimage\"},\"thumbnailUrl\":\"http:\/\/sites.rutgers.edu\/nb-senior-exhibits\/wp-content\/uploads\/sites\/442\/2020\/08\/ZeyueLiposter_thumbnail-300x225.png\",\"datePublished\":\"2020-08-04T03:43:44+00:00\",\"dateModified\":\"2020-08-05T03:31:39+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/partners\/aresty-research-virtual-symposium-2020\/li-zeyue\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/partners\/aresty-research-virtual-symposium-2020\/li-zeyue\/\"]}]},{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/partners\/aresty-research-virtual-symposium-2020\/li-zeyue\/#primaryimage\",\"url\":\"https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/wp-content\/uploads\/sites\/442\/2020\/08\/ZeyueLiposter_thumbnail.png\",\"contentUrl\":\"https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/wp-content\/uploads\/sites\/442\/2020\/08\/ZeyueLiposter_thumbnail.png\",\"width\":1067,\"height\":800},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/partners\/aresty-research-virtual-symposium-2020\/li-zeyue\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Our Symposium Partners\",\"item\":\"https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/partners\/\"},{\"@type\":\"ListItem\",\"position\":3,\"name\":\"Aresty Research Center\",\"item\":\"https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/partners\/aresty-research-virtual-symposium-2020\/\"},{\"@type\":\"ListItem\",\"position\":4,\"name\":\"Li, Zeyue: Investigating Binding Site Ratios of Transcription Factors\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/#website\",\"url\":\"https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/\",\"name\":\"Senior Exhibits\",\"description\":\"\",\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/?s={search_term_string}\"},\"query-input\":{\"@type\":\"PropertyValueSpecification\",\"valueRequired\":true,\"valueName\":\"search_term_string\"}}],\"inLanguage\":\"en-US\"}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Li, Zeyue: Investigating Binding Site Ratios of Transcription Factors - Senior Exhibits","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/sites.rutgers.edu\/nb-senior-exhibits\/partners\/aresty-research-virtual-symposium-2020\/li-zeyue\/","og_locale":"en_US","og_type":"article","og_title":"Li, Zeyue: Investigating Binding Site Ratios of Transcription Factors - Senior Exhibits","og_description":"Title: Investigating Binding Site Ratios of Transcription Factors Name: Zeyue Li Major: Biological Sciences School affiliation: School of Environmental and Biological Sciences Programs: Aresty Summer Science Program Other contributors: Ann &hellip; 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