Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat

Abstract

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.

Characterization of Expression and Epigenetic Features of Core Genes in Common Wheat

“…For example, core genes were exclusively enriched for cell cycle phase transition/DNA replication initiation ( Figure 2 G); whereas non-core genes were enriched exclusively for the mitochondrial cell cycle ( Figure 2 H). We also compared the GRO-seq levels for different subtypes of genes, and in general, higher gene expression levels were associated with higher GRO-seq signals ( Figure 2 I–L), consistent with previous results [ 44 ].…”

“…Data Availability Statement: All data used in this study were obtained from public data. the Gene Expression Omnibus Database accession numbers are as follows: GRO-seq:GSE178276 [44]. ChIPseq and DNase-seq data and tissue development, and stress-treated RNAseq data of bread wheat were published previously under accession GSE139019 and GSE121903 [32,58].…”

Protocol for affordable and efficient profiling of nascent RNAs in bread wheat using GRO-seq

“…Recently, we optimized our previous protocol by performing rRNA depletion immediately after nuclear run-on and RNA isolation, which have been proved to be significantly more efficient and affordable during detecting enhancer transcription in bread wheat ( Xie et al., 2022 ). The protocol below provides detailed steps on how to construct rRNA removal GRO-seq libraries using 12-day-old bread wheat seedling.…”

“…The final cDNA libraries can be applied to next-generation sequencing (NGS) to generate nascent transcriptome datasets. For more details, please refer to the recent publication ( Xie et al., 2022 ).…”

“…We have successfully applied this protocol to profile enhancer transcription in allohexaploid bread wheat and increased the proportion of valid data by 20 times. For complete details on the use and execution of this protocol, please refer to Xie et al. (2022) .…”