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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. 2 — A Integrated Genomics Viewer (IGV) screenshots showing OsCLSY3 promoter derived sRNA levels (16–35 nt) in osnrpd1-kd panicle. B Northern blot showing sRNA levels in osnrpd1-kd panicle. C IGV screenshots showing enrichment of OsCLSY3 promoter derived sRNAs (16–35 nt) in RIP of different AGOs in rice (GSE18250 and GSE20748). D Barplots showing OsCLSY3 level in osnrpd1-kd panicles (top) and osnrpd1-kd anther (bottom). OsActin served as internal control. Data represents mean ± SE of 2 independent biological replicates with 3 technical replicates each (n = 6). Comparisons were made with paired two-tailed Student’s t-tests (P < 0.05 considered as significant). E IGV screenshots showing status of MITE derived sRNAs among RdDM mutants of rice (GSE130166, GSE158709, Nip—Japonica cultivar Nipponbare) (PRJNA758109, Hwa—Japonica cultivar Hwayoung). F Northern blots showing MITE derived sRNA level in osclsy4-kd and osnrpd1-kd (left panels) and analysis of DNA methylation in OsCLSY3 promoter in osclsy4-kd leaf by BS-PCR (right panel). U6 served as loading control. G IGV screenshots showing methylation status of 800 bp MITE TE region in OsCLSY3 promoter in osrdr2 seedlings (GSE130168). H IGV screenshot showing methylation status in leaves of ddccc mutant (GSE138705). ddccc is osdrm2/osdrm1/oscmt2a/oscmt2b/oscmt3 (Nip—Japonica cultivar Nipponbare). Source data are provided as a Source Data file. (B), (D) and (F) were repeated at least twice with consistent results.