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. 2024 Sep 6;15:7807. doi: 10.1038/s41467-024-52239-z

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, 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 you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. 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-nc-nd/4.0/.

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Fig. 6 — A Boxplot showing sRNAs (23–24 nt) derived from siren loci in osnrpd1-kd EN (797 loci). ASINH converted RPKM values were used for boxplot. B Boxplot representing status of sRNAs (23–24 nt) from siren loci in osclsy3-kd EN. C Heatmap showing siren sRNAs in osclsy3-kd EN. Row Z-score was plotted. D IGV screenshot showing expression of siren loci in osclsy3-kd and osnrpd1-kd EN. VL vegetative leaf. E IGV screenshots showing expression of siren sRNAs and DNA methylation in osclsy3-kd EN. F Northern blot showing siren sRNAs in RdDM mutants. G Volcano plot representing all DEGs of osclsy3-kd. H Boxplot showing sRNA levels near DEGs. I Correlation plot showing accumulation of CLSY3-dependent sRNAs and mRNA expression of adjacent genes (RPKM). J IGV screenshots showing expression of two selected DEGs and levels of adjacent sRNA loci in osclsy3-kd EN (violet lines mark DNA hypomethylated regions). K Heatmap showing expression of genes adjacent to siren loci (510) and seed development (102) genes. Row Z-score was plotted. In (A), (B) and (H), boxes show median values and interquartile range. Whiskers shows minimum and maximum values, excluding outliers. Comparisons were made with two-sided Wilcoxon test (P < 0.01 was considered significant). Source data are provided as a Source Data file.