{"id":336,"date":"2024-03-16T16:11:38","date_gmt":"2024-03-16T23:11:38","guid":{"rendered":"https:\/\/labs.wsu.edu\/duttke\/?page_id=336"},"modified":"2025-12-04T16:25:01","modified_gmt":"2025-12-05T00:25:01","slug":"mcdonaldbr_ernaplants_2024","status":"publish","type":"page","link":"https:\/\/labs.wsu.edu\/duttke\/mcdonaldbr_ernaplants_2024\/","title":{"rendered":"Enhancers associated with unstable RNAs are rare in plants"},"content":{"rendered":"\n

Bayley R. McDonald, Colette Picard2<\/sup>, Ian M. Brabb1<\/sup>, Marina I. Savenkova1<\/sup>, Robert J. Schmitz3<\/sup>, Steven E. Jacobsen2,4<\/sup> and Sascha H. Duttke1#<\/sup> <\/p>\n\n\n\n

1<\/sup><\/strong> School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA. 2<\/sup><\/strong> Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA. 3<\/sup><\/strong> Department of Genetics, University of Georgia, Athens, GA, USA,  4<\/sup><\/strong> Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA, USA <\/p>\n\n\n\n

Abstract<\/h2>\n\n\n\n

Unstable transcripts have emerged as markers of active enhancers in vertebrates and shown to be involved in many cellular processes and medical disorders. However, their prevalence and role in plants is largely unexplored. Here, we comprehensively captured all actively initiating (\u201cnascent\u201d) transcripts across diverse crops and other plants using capped small (cs)RNA-seq. We discovered that unstable transcripts are rare, unlike in vertebrates, and often originate from promoters. Additionally, many \u201cdistal\u201d elements in plants initiate tissue-specific stable transcripts and are likely bone fide promoters of yet-unannotated genes or non-coding RNAs, cautioning against using genome annotations to infer \u201cenhancers\u201d or transcript stability. To investigate enhancer function, we integrated STARR-seq data. We found that annotated promoters, and other regions that initiate stable transcripts rather than unstable transcripts, function as stronger enhancers in plants. Our findings underscore the blurred line between promoters and enhancers and suggest that cis-regulatory elements encompass diverse structures and mechanisms in eukaryotes.<\/p>\n\n\n\n

IGV Browser Sessions<\/h2>\n\n\n\n
Species<\/th>Sample Type(s) (if applicable)<\/th>Browser Session Link<\/th><\/tr><\/thead>
Agaricus bisporus<\/em><\/td>Duttke, et al. 2022.<\/a><\/td>Browser session of A. bisporus<\/a><\/td><\/tr>
Arabidopsis thaliana<\/em><\/td>Seedlings 6-day<\/td>Browser session of A. thaliana seedlings 6-day<\/a><\/td><\/tr>
Arabidopsis thaliana<\/em><\/td>Col-0 Cells and Mature Leaf<\/td>Browser session of A. thaliana Col-0 Cells and Mature Leaf<\/a><\/td><\/tr>
Carica papaya<\/em><\/td>Young Leaves<\/td>Browser session of Carica papaya<\/a><\/td><\/tr>
Chlamydomonas reinhardtii<\/em><\/td>Whole<\/td>Browser session of Chlamydomonas reinhardtii<\/a><\/td><\/tr>
Drosophila melanogaster<\/em><\/td>Cells<\/td>Browser session of Drosophila melanogaster<\/a><\/td><\/tr>
Homo sapiens<\/em><\/td>H9<\/td>Browser session of Homo sapiens H9 cells<\/a><\/td><\/tr>
Homo sapiens<\/em><\/td>White blood cells<\/td>Browser session of Homo sapeins white blood cells<\/a><\/td><\/tr>
Hordeum vulgare<\/em><\/td>Embryonic Tissue from Grain Tissue<\/td>Browser session of Hordeum vulgare<\/a><\/td><\/tr>
Oryza sativa<\/em><\/td>Duttke, et al. 2019.<\/a><\/td>Browser session of Oryza sativa<\/a><\/td><\/tr>
Physcomitrella patens<\/em><\/td>Whole<\/td>Browser session of Physcomitrella patens<\/a><\/td><\/tr>
Saccharomyces cerevisiae<\/em><\/td>Duttke, et al. 2022.<\/a><\/td>Browser session of saccharomyces cerevisiae<\/a><\/td><\/tr>
Selaginella moellendorffii<\/em><\/td>Stem and Leaves<\/td>Browser session of Selaginella moellendorffii<\/a><\/td><\/tr>
Zea mays<\/em><\/td>Adult Leaf and Leaves 7-day<\/td>Browser session of Zea mays adult leaf and leaves 7-day<\/a><\/td><\/tr>
Zea mays<\/em><\/td>Root 7-day and Shoot 7-day<\/td>Browser session of Zea mays root 7-day and shoot 7-day<\/a><\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n

GEOSubmit<\/h2>\n\n\n\n

All raw and processed data generated for this study can be accessed at NCBI Gene Expression Omnibus (GEO; https:\/\/www.ncbi.nlm.nih.gov\/geo\/) accession number GSE233927 <\/p>\n","protected":false},"excerpt":{"rendered":"

Bayley R. McDonald, Colette Picard2, Ian M. Brabb1, Marina I. Savenkova1, Robert J. Schmitz3, Steven E. Jacobsen2,4 and Sascha H. Duttke1#  1 School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA. 2 Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA. 3 Department […]<\/p>\n","protected":false},"author":40210,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"categories":[],"tags":[],"wsuwp_university_location":[],"wsuwp_university_org":[],"_links":{"self":[{"href":"https:\/\/labs.wsu.edu\/duttke\/wp-json\/wp\/v2\/pages\/336"}],"collection":[{"href":"https:\/\/labs.wsu.edu\/duttke\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/labs.wsu.edu\/duttke\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/labs.wsu.edu\/duttke\/wp-json\/wp\/v2\/users\/40210"}],"replies":[{"embeddable":true,"href":"https:\/\/labs.wsu.edu\/duttke\/wp-json\/wp\/v2\/comments?post=336"}],"version-history":[{"count":7,"href":"https:\/\/labs.wsu.edu\/duttke\/wp-json\/wp\/v2\/pages\/336\/revisions"}],"predecessor-version":[{"id":470,"href":"https:\/\/labs.wsu.edu\/duttke\/wp-json\/wp\/v2\/pages\/336\/revisions\/470"}],"wp:attachment":[{"href":"https:\/\/labs.wsu.edu\/duttke\/wp-json\/wp\/v2\/media?parent=336"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/labs.wsu.edu\/duttke\/wp-json\/wp\/v2\/categories?post=336"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/labs.wsu.edu\/duttke\/wp-json\/wp\/v2\/tags?post=336"},{"taxonomy":"wsuwp_university_location","embeddable":true,"href":"https:\/\/labs.wsu.edu\/duttke\/wp-json\/wp\/v2\/wsuwp_university_location?post=336"},{"taxonomy":"wsuwp_university_org","embeddable":true,"href":"https:\/\/labs.wsu.edu\/duttke\/wp-json\/wp\/v2\/wsuwp_university_org?post=336"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}