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 of Genetics, University of Georgia, Athens, GA, USA, 4 Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA, USA
Abstract
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 (“nascent”) 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 “distal” 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 “enhancers” 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.
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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