Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat

• Main Authors: Chen, Y. (Author), Dong, Z. (Author), Li, Z. (Author), Liu, M. (Author), Xie, Y. (Author), Zhang, Y. (Author), Zhu, J. (Author)
• Format: Article
• Language: English
• Published: BioMed Central Ltd 2022
• Subjects: article; Bread wheat; chromatin; Enhancer; enhancer region; eRNA; gene expression; genetic transcription; Nascent RNA; nonhuman; Subgenome-bias; transcription initiation; Triticum aestivum; wheat
• Online Access: View Fulltext in Publisher
• ISBN: 14747596 (ISSN)
• DOI: 10.1186/s13059-022-02675-1

The precise spatiotemporal gene expression is orchestrated by enhancers that lack general sequence features and thus are difficult to be computationally identified. By nascent RNA sequencing combined with epigenome profiling, we detect active transcription of enhancers from the complex bread wheat genome. We find that genes associated with transcriptional enhancers are expressed at significantly higher levels, and enhancer RNA is more precise and robust in predicting enhancer activity compared to chromatin features. We demonstrate that sub-genome-biased enhancer transcription could drive sub-genome-biased gene expression. This study highlights enhancer transcription as a hallmark in regulating gene expression in wheat. © 2022, The Author(s).