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Nascent transcription and the associated cis-regulatory landscape in rice

Background Plant genomes encode transcripts that require spatio-temporal regulation for proper cellular function, and a large fraction of the regulators can be found in intergenic regions. In animals, distal intergenic regions described as enhancer regions are actively transcribed as enhancer RNAs (eRNAs); the existence of eRNAs in plants has only been fairly recently documented. In this study, we evaluated with high sensitivity the synthesis of eRNAs that arise at genomic elements both distal and proximal to genes by combining PRO-seq with chromatin accessibility, histone modification, and methylation profiles in rice. Results We found that regions defined as transcribed intergenic regions are widespread in the rice genome, and many likely harbor transcribed regulatory elements. In addition to displaying evidence of selective constraint, the presence of these transcribed regulatory elements are correlated with an increase in nearby gene expression. We further identified molecular interactions between genic regions and intergenic transcribed regulatory elements using 3D chromosomal contact data, and found that these interactions were both associated with eQTLs as well as promoting transcription. We also compared the profile of accessible chromatin regions to our identified transcribed regulatory elements, and found less overlap than expected. Finally, we also observed that transcribed intergenic regions that overlapped partially or entirely with repetitive elements had a propensity to be enriched for cytosine methylation, and were likely involved in TE silencing rather than promoting gene transcription. Conclusion The characterization of eRNAs in the rice genome reveals that many share features of enhancers and are associated with transcription regulation, which could make them compelling candidate enhancer elements.