Fig. 1: Ea-IR methylation affects EFR expression.
From: Transposon-triggered epigenetic chromatin dynamics modulate EFR-related pathogen response
a, Diagram of the EFR and Xl-k region on chromosome 5 (yellow bars, exons; blue bars, untranslated regions). The LIMPET1 transposon and the transposon-derived Ea-IR IR are indicated by purple bars. The T-DNA insertion disrupting Ea-IR in the eair-1 mutant is also indicated. Numbers indicate chromosome 5 coordinates. b, The 24-nt siRNAs mapping Ea-IR in Col-0 wild-type, dcl234 and ddc plants. For each genotype, the results from three replicates are shown with different shading. c, Left, cytosine methylation in the CHH, CHG and CG contexts at Ea-IR (delimited by vertical gray lines) and flanking regions (700 bp) in Col-0 wild-type, dcl234 and ddc plants. The average of three individual BS-seq replicates is plotted for each genotype. Right, the average percentage of cytosine methylation in the CG, CHG and CG for each region and the same genotypes. d, Chromatin contacts from CaptureC in the EFR and Xl-k region in Col-0 wild-type, ddc and dcl234 plants. LoopEFR, which includes Ea-IR, is marked in cyan, LoopXl-k is marked in green and all other interactions are marked in purple. The region targeted by CaptureC is indicated, with all potential restriction fragments below. Fragments diagnostic for the Ea-IR region are indicated in cyan. e, Top, purple pins indicate XbaI sites used for 3C experiments. Given the resolution of 3C experiments, the anchor points for the two loops, which are also indicated, can be located anywhere within each of the ligated restriction fragments (green arrow). Bottom, quantification of LoopEFR (blue rings) and LoopXl-k (gray rings) by 3C–qPCR in Col-0 wild-type, eair-1, ddc and dcl234 plants. f, Expression of EFR (blue rings) and Xl-k (gray rings) as measured by quantitative PCR with reverse transcription (RT–qPCR) and normalized against ACT2. In e,f, values of n = 3 biologically independent mutant samples are expressed relative to the average values of Col-0 wild-type plants. Data are presented as the mean values ± s.d. P values were calculated with a two-tailed unpaired t-test with Welch’s correction.
