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. 2022 Jul 21;20:165. doi: 10.1186/s12915-022-01362-8

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© The Author(s) 2022

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 1 — Distal enhancer transcription were responsive to flg22 treatment in Arabidopsis. a Numbers of transcribed distal enhancer before and after flg22 signaling activation. Trans-enhancers^A, ATAC-seq-based transcribed enhancers; Trans-enhancers^D, DNase-seq-based transcribed enhancers. b Volcano Plots show differentially expressed transcribed enhancers^A and transcribed enhancers^D upon flg22 treatment. The numbers of up (x-axis > 0, warm orange) and down (x-axis < 0, blackish green) transcribed enhancers are shown, respectively. c Heatmaps of transcript levels at transcribed enhancers, transposons, promoters (proximal ATAC-seq peaks), and random sequences. Transcript level with and without flg22 treatment were calculated at and around (±0.5 kb) the sequence candidates. The color scales are in BPM for transcript level. d Distribution of the mean distance from enhancers to the nearest RNA Pol II peaks. e, f Distribution of the signals (BPM scale) derived from GRO-seq (e) and pNET-seq (f) at transcribed enhancers, nontranscribed enhancers, and random sequences. Left and right panels represent ATAC-seq-based enhancers and DNase-seq-based enhancers, respectively