Nascent transcriptomic landscape in bread wheat detected Pol II-dependent enhancer transcription

Bread wheat is the major staple food of the world with a complex hexaploidy genome. The precise spatiotemporal gene expression is orchestrated by enhancers, which lack general sequence features and thus are difficult to be located, especially in large genomes. Epigenomic architecture, including chromatin openness and active chromatin marks, has been widely used to characterize enhancers. However, an active chromatin environment does not necessarily mean an active enhancer. Recently, enhancer RNAs (eRNAs), the hallmark for active enhancers, have been detected by nascent RNA sequencing in both Drosophila and mammalian. In order to answer whether plant enhancers could be transcribed, we investigated the transcriptome of bread wheat via two nascent RNA sequencing methods, GRO-seq and pNET-seq combining with epigenome profiling. Our study demonstrates the presence and wide distribution of transcription at intergenic enhancers, which accurately reflects high enhancer activity, shedding light on the complex gene expression regulation across subgenomes in bread wheat. To elucidate the general features and functional roles of enhancer transcription in bread wheat, we modified and applied global nuclear run-on sequencing (GRO-seq) and plant native elongating transcript sequencing (pNET-seq), both methods are competent for capturing nascent transcripts regardless of the stability, thus capable of mapping the exact position, amount and orientation of transcriptionally engaged RNA polymerase II in a more complete and precise manner.