Profiling active regulatory elements during immunity in Arabidopsis

*This is a poster presented at ICAR 2025, Ghent, Belgium.

Transcriptional reprogramming occurs within minutes of plant perception of pathogens and continues throughout the immune response. The earliest up-regulated genes are enriched for transcription factors, suggesting the immune response necessitates a complex network of regulators to successfully activate and maintain immunity. However, our understanding of this process is limited by the current lack of nascent transcriptomic data necessary to accurately assess the impact of these regulators on transcription itself, and not the accumulation of stable protein-coding transcripts outside the nucleus. Additionally, we know little about the regulatory elements necessary for immunity and their role in gene activation. Using capped-small RNA sequencing (csRNA-seq), a method which detects nascent transcription initiation events, of flg22-treated Arabidopsis thaliana seedlings undergoing PAMP-triggered immunity (PTI), we observed widespread non-coding transcription initiation originating from active regulatory elements throughout the genome. These non-coding RNAs bear a striking resemblance to enhancer RNAs discovered in metazoans. Our analysis revealed over 1500 such regions were activated during PTI, of which nearly a third transcribed bidirectional eRNAs. These data expand our understanding of the activities of transcriptional regulators and their target cis-regulatory elements involved in PTI.