[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"detail-sidebar-cat-0-en-105":3,"doc-seo-290595-105":59,"doc-detail-290595-en":130},{"code":4,"msg":5,"data":6},0,"success",[7,13,18,23,28,33,38,43,48,51,55],{"id":8,"doc_module":4,"doc_module_name":9,"category_name":10,"show_sort_weight":11,"slug":12},1,"Document","Story & Novel",90,"story-novel",{"id":14,"doc_module":4,"doc_module_name":9,"category_name":15,"show_sort_weight":16,"slug":17},2,"Literature",80,"literature",{"id":19,"doc_module":4,"doc_module_name":9,"category_name":20,"show_sort_weight":21,"slug":22},4,"Exam",70,"exam",{"id":24,"doc_module":4,"doc_module_name":9,"category_name":25,"show_sort_weight":26,"slug":27},5,"Comic",60,"comic",{"id":29,"doc_module":4,"doc_module_name":9,"category_name":30,"show_sort_weight":31,"slug":32},6,"Technology",50,"technology",{"id":34,"doc_module":4,"doc_module_name":9,"category_name":35,"show_sort_weight":36,"slug":37},7,"Healthcare",40,"healthcare",{"id":39,"doc_module":4,"doc_module_name":9,"category_name":40,"show_sort_weight":41,"slug":42},8,"Research & Report",30,"research-report",{"id":44,"doc_module":4,"doc_module_name":9,"category_name":45,"show_sort_weight":46,"slug":47},9,"Religion & Spirituality",20,"religion-spirituality",{"id":46,"doc_module":4,"doc_module_name":9,"category_name":49,"show_sort_weight":46,"slug":50},"World Cup","world-cup",{"id":52,"doc_module":4,"doc_module_name":9,"category_name":53,"show_sort_weight":52,"slug":54},10,"Lifestyle","lifestyle",{"id":56,"doc_module":4,"doc_module_name":9,"category_name":57,"show_sort_weight":24,"slug":58},19,"General","general",{"code":4,"msg":60,"data":61},"ok",{"site_id":62,"language":63,"slug":64,"title":65,"keywords":66,"description":67,"schema_data":68,"social_meta":123,"head_meta":125,"extra_data":127,"updated_unix":129},105,"en","analysis-of-the-drosophila-and-human-dpr-elements-reveals-a-distinct-human-variant-whose-specificity-can-be-enhanced-by-machine-learning-290595","Analysis of the Drosophila and Human DPR elements reveals a distinct human variant whose specificity can be enhanced by machine learning","","RNA polymerase II core promoter sequences integrate multiple signals that initiate transcription. A comparative study analyzes the downstream core promoter region (DPR) in Drosophila and humans using machine learning, identifying a distinct human-specific DPR version. The work applies machine learning models to discover synthetic extreme DPR motifs that show specificity for human transcription factors versus Drosophila factors, and vice versa. More broadly, such models enable design of synthetic DNA elements with tailored functional properties for customized transcriptional behavior.",{"@graph":69,"@context":122},[70,84,105],{"@type":71,"itemListElement":72},"BreadcrumbList",[73,77,79,82],{"item":74,"name":75,"@type":76,"position":8},"https://docshare.wps.com","Home","ListItem",{"item":78,"name":9,"@type":76,"position":14},"https://docshare.wps.com/document/",{"item":80,"name":40,"@type":76,"position":81},"https://docshare.wps.com/document/research-report/",3,{"item":83,"name":65,"@type":76,"position":19},"https://docshare.wps.com/document/analysis-of-the-drosophila-and-human-dpr-elements-reveals-a-distinct-human-variant-whose-specificity-can-be-enhanced-by-machine-learning-290595/290595/",{"url":83,"name":65,"@type":85,"image":86,"author":91,"headline":65,"publisher":94,"fileFormat":97,"inLanguage":63,"description":67,"dateModified":98,"datePublished":99,"encodingFormat":97,"isAccessibleForFree":100,"interactionStatistic":101},"DigitalDocument",{"url":87,"@type":88,"width":89,"height":90},"https://docshare.wps.com/thumbnails/analysis-of-the-drosophila-and-human-dpr-elements-reveals-a-distinct-human-variant-whose-specificity-can-be-enhanced-by-machine-learning-290595/290595.png","ImageObject",300,407,{"name":92,"@type":93},"Oliver","Person",{"url":74,"name":95,"@type":96},"DocShare","Organization","application/pdf","2026-10-27","2026-09-17",true,{"@type":102,"interactionType":103,"userInteractionCount":52},"InteractionCounter",{"@type":104},"ViewAction",{"@type":106,"mainEntity":107},"FAQPage",[108,114,118],{"name":109,"@type":110,"acceptedAnswer":111},"What does the study focus on regarding transcription initiation?","Question",{"text":112,"@type":113},"It examines the RNA polymerase II core promoter, especially the downstream core promoter region (DPR), and how specific DPR motifs contribute to transcription initiation signals.","Answer",{"name":115,"@type":110,"acceptedAnswer":116},"How is machine learning used in the DPR analysis?",{"text":117,"@type":113},"Machine learning models are used to analyze comparative DPR sequences, generate quantitative predictions, and identify synthetic extreme DPR motifs with factor specificity between humans and Drosophila.",{"name":119,"@type":110,"acceptedAnswer":120},"What key finding distinguishes the human DPR from the Drosophila DPR?",{"text":121,"@type":113},"The analyses reveal a distinct human-specific DPR variant, supporting different transcription factor specificities relative to Drosophila.","https://schema.org",{"og:url":83,"og:type":124,"og:title":65,"og:site_name":95,"og:description":67},"article",{"robots":126,"canonical":83},"index,follow",{"doc_id":128,"site_id":62},290595,1789642149,{"code":4,"msg":5,"data":131},{"doc_id":128,"user_id":132,"nickname":92,"user_avatar":133,"doc_module":4,"category_id":39,"category_name":40,"doc_title":65,"doc_description":67,"doc_content":134,"file_id":135,"file_url":136,"file_type":137,"file_size":138,"view_count":52,"is_deleted":4,"is_public":8,"is_downloadable":8,"audit_status":8,"page_count":139,"language":140,"language_code":63,"site_id":62,"html_lang":63,"table_of_contents":141,"faqs":142,"seo_title":143,"seo_description":67,"update_tm":129,"read_time":144,"preview_page_count":4},8796095461610,"https://ap-avatar.wpscdn.com/davatar_276721f389ce27ea32af1340a28f341c","UC San Diego  \nUC San Diego Previously Published Works  \nTitle  \nAnalysis of the Drosophila and human DPR elements reveals a distinct human variant whose specificity can be enhanced by machine learning.  \nPermalink  \n[https://escholarship.org/uc/item/1rt3r053](https://escholarship.org/uc/item/1rt3r053)  \nJournal  \nGenes & Development, 37(9-10)  \nISSN  \n0890-9369  \nAuthors  \nVo Ngoc, Long  \nRhyne, Torrey EKadonaga, James T  \nPublication Date  \n2023-05-01  \nDOI  \n10.1101/gad.350572.123  \nCopyright Information  \nThis work is made available under the terms of a Creative Commons AttributionNonCommercial-NoDerivatives License, availalbe at [https://creativecommons.org/licenses/by-nc-nd/4.0/](https://creativecommons.org/licenses/by-nc-nd/4.0/)  \nPeer reviewed  \n[eScholarship.org](eScholarship.org) Powered by the California Digital Library  \nUniversity of California  \nVo ngoc et al. (Kadonaga) 1  \nRESEARCH COMMUNICATION  \nAnalysis of the Drosophila and Human DPR Elements Reveals a Distinct Human Variant Whose Specificity Can Be Enhanced by Machine Learning  \nLong Vo ngoc , 1,2,3 Torrey E. Rhyne , 1,3 and James T. Kadonaga 1,4  \n[Key words: Transcription, RNA Polymerase II, Core Promoter, Gene Expression , Drosophila]  \nRunning Head: Enhancing DNA element specificity by using AI  \n1 Department of Molecular Biology, University of California, San Diego, La Jolla, California 92093 , USA; 2Current address: Velia Therapeutics, San Diego, California 92130.  \n3These authors contributed equally to this work 4Corresponding author: [jkadonaga@ucsd.edu](jkadonaga@ucsd.edu)  \nVo ngoc et al. (Kadonaga) 2  \nAbstract  \nThe RNA polymerase II core promoter is the site of convergence of the signals that lead to the initiation of transcription. Here, we perform a comparative analysis of the downstream core promoter region (DPR) in Drosophila and humans by using machine learning. These studies revealed a distinct human-specific version of the DPR and led to the use of machine learning models for the identification of synthetic extreme DPR motifs with specificity for human transcription factors relative to Drosophila factors, and vice versa. More generally, machine learning models could similarly be used to design synthetic DNA elements with customized functional properties.  \nVo ngoc et al. (Kadonaga) 3  \nThe initiation of transcription by RNA polymerase II is an important step in the expression of genes (see, for example: Cramer 2019, Galouzis and Furlong 2022, Haberle et al. 2018, Roeder 2019, Schier and Taatjes 2020, Sloutskin et al. 2021, Vo ngoc et al. 2019 , Zeitlinger 2020) . Transcription initiates at the core promoter, which comprises the stretch of DNA from about −40 to +40 relative to the +1 transcription start site (TSS) . The core promoter is often referred to asthe \"gateway to transcription\", as it is the site of convergence of the signals that direct the initiation of transcription. Core promoter activity is driven by DNA sequence elements such asthe TATA box, initiator (Inr) , and downstream promoter region (DPR) , which is the revised name for the combined motif ten element (MTE; Lim et al. 2004) and downstream core promoter element (DPE; Burke and Kadonaga 1996) from +17 to +35 relative to the +1 TSS (Vo ngoc et al. 2020) . There are no universal core promoter elements. Moreover, individual core promoter motifs are involved in transcriptional regulatory functions such as enhancer-core promoter specificity (see, for example, Ohtsuki et al. 1998, Butler and Kadonaga 2001 , Zabidi et al. 2015 , Galouzis and Furlong 2022) .  \nA key challenge in the study of the core promoter has been the ability to predict the existence and activity of particular core promoter elements. In the past , the presence of core promoter motifs has been generally assessed by the similarity of the DNA sequences to consensus sequences, such as TATAAA for the TATA box. This method can lead to the incorrect assignments of motifs and also does not provide a quantitative ","cbCaiehVqloTLBh2","https://ap.wps.com/l/cbCaiehVqloTLBh2","pdf",7890542,43,"English","# Abstract\n# Introduction\n## Core promoter and DPR roles\n## Predicting core promoter elements\n# Results & Discussion\n## SVR model for DPR activity in Drosophila\n## Comparative analysis in humans and Drosophila","[{\"question\":\"What does the study focus on regarding transcription initiation?\",\"answer\":\"It examines the RNA polymerase II core promoter, especially the downstream core promoter region (DPR), and how specific DPR motifs contribute to transcription initiation signals.\"},{\"question\":\"How is machine learning used in the DPR analysis?\",\"answer\":\"Machine learning models are used to analyze comparative DPR sequences, generate quantitative predictions, and identify synthetic extreme DPR motifs with factor specificity between humans and Drosophila.\"},{\"question\":\"What key finding distinguishes the human DPR from the Drosophila DPR?\",\"answer\":\"The analyses reveal a distinct human-specific DPR variant, supporting different transcription factor specificities relative to Drosophila.\"}]","Analysis of the Drosophila and Human DPR elements reveals a distinct human variant whose specificity can be enhanced by machine learning | PDF",108]