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. 2020 Jun 26;11:3224. doi: 10.1038/s41467-020-16951-w

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© The Author(s) 2020

Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 5 — a Transposon families harboring the EPICATs. Shown are total numbers of TEs. All, wild-type: TEs in the A. thaliana genome and TEs harboring active TSSs in wild-type plants, respectively. *TE families enriched compared to the genome-wide average (p < 3e-04, Hypergeometric test). b Violin and/or boxplots showing the Length (left), DNA methylation (middle), and Distance to the nearest gene (right), of TEs harboring (EPICAT+), not harboring (EPICAT−) the EPICATs in ddm1, and harboring active TSSs in wild-type plants (wtACTIVE). ***p < 2.2e-16, two-sided Mann–Whitney test. c Fractions of TEs harboring consensus DNA motifs found at the ddm1-activated EPICATs. d Sequence alignment of representative LTRs of TEs belonging to the Gypsy ATGP1 sub-family. LTR sequences were aligned based on relative positions of cryptic TSSs detected by CAGE-seq. A, C, G, T nucleotides were colored in green, yellow, red, and blue. Putative TATA-box and YR-motifs are indicated by black box and red line, respectively. Relative positions and strand information of each LTRs in the genome are indicated (bottom left). Heatmaps of the normalized CAGE-seq data mapped to the LTRs using one replicate of each mutants are shown on the right side of the bottom panel. e DNA methylation of TEs in the wild-type (wt) and ddm1 backgrounds. TE lengths were normalized to 1 Kb and aligned by their two ends (indicated by TSS and TES). Methylation levels were calculated for non-overlapping 100 bp windows within TE body and surrounding region of ±2 Kb, and sorted by the average value of each row. f Chromatin accessibility at TEs in ddm1 and wild-type (wt) plants, given by DNase-seq data in flower (F) and leaf (L) tissues. Signals were calculated and presented as described in e, with the window size of 50 bp. g Ectopic recruitment of RNAPII Ser2P and Ser5P to TEs in the wild-type (wt) and ddm1 plants. Signals were calculated and presented as described in e, with the window size of 50 bp.