Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline

article Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline published yes Jincheng Long author Chao Yang author 082e3e6e-8069-11ed-8390-c8cce7b1aaca Shujuan Xu author 9724dd9d-f591-11ee-bd51-e97ed0652286 Joke G De Jaeger-Braet author 26bd38d3-c59a-11ee-a1af-d7a988cafcc5 Wenjing She author Seijiro Ono author James Walker author Ygor de Souza Vieira author af019b77-d2a9-11f1-9e65-c47a5932b764 Arp Schnittger author Xiaoqi Feng author e0164712-22ee-11ed-b12a-d80fcdf359580000-0002-4008-1234 XiFe department The moleculaR mEchAnismS Of dNa methylatIon reprogrammiNg in Arabidopsis sexual lineaGe project IST-BRIDGE: International postdoctoral program project Establishment, modulation and inheritance of sexual lineage specific DNA methylation in plants project Mechanisms and biological functions of H3K27me3 reprogramming in plant microspores project Small RNAs (sRNAs) are widespread across diverse flowering plant species and play important roles regulating reproduction and environmental responses. However, how sRNAs exert their function is largely unknown, likely due to their typical origin in non-genic regions, the lack of distinct gene targets, and the sparse characterization of their associated Argonaute (AGO) effector proteins. Here we show that Arabidopsis male reproductive sRNAs associate with AGO4, 5, 6 and 9, all of which are enriched in meiocytes along with RNA Polymerase V (Pol V). This enables these sRNAs to methylate loci with imperfect sequence homology. AGO4, AGO6 and AGO9 predominantly load 24-nucleotide (nt) Pol IV-derived sRNAs and mediate DNA methylation in meiocytes in a dosage-dependent manner. Despite closer homology to microRNA-associated AGO1 and AGO10, AGO5 primarily binds CLSY3- and Pol IV-derived 21-24 nt sRNAs. Transcriptomic and methylomic analyses of meiocytes from single and compound ago mutants demonstrate distinct yet complementary roles of AGO4/6/9 and AGO5 in regulating protein-coding genes and silencing transposons in the germline. These molecular disruptions are accompanied by significant meiotic defects. Together, our findings reveal how AGO4/6/9-mediated DNA methylation and AGO5, likely acting through post-transcriptional gene silencing, work together to promote male germline development. https://research-explorer.ista.ac.at/download/23198/23204/2026_NatureComm_Long.pdf application/pdfno Springer Nature2026 eng Nature Communications 2041-1723 4286990410.1038/s41467-026-77326-1 17 J. Long et al., “Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline,” Nature Communications, vol. 17. Springer Nature, 2026. J. Long, C. Yang, S. Xu, J.G. De Jaeger-Braet, W. She, S. Ono, J. Walker, Y. de Souza Vieira, A. Schnittger, X. Feng, Nature Communications 17 (2026). Long, Jincheng, Chao Yang, Shujuan Xu, Joke G De Jaeger-Braet, Wenjing She, Seijiro Ono, James Walker, Ygor de Souza Vieira, Arp Schnittger, and Xiaoqi Feng. “Multiple Argonaute Complexes Orchestrate Epigenetic Silencing in the Arabidopsis Germline.” Nature Communications. Springer Nature, 2026. <a href="https://doi.org/10.1038/s41467-026-77326-1">https://doi.org/10.1038/s41467-026-77326-1</a>. Long, J., Yang, C., Xu, S., De Jaeger-Braet, J. G., She, W., Ono, S., … Feng, X. (2026). Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline. Nature Communications. Springer Nature. <a href="https://doi.org/10.1038/s41467-026-77326-1">https://doi.org/10.1038/s41467-026-77326-1</a> Long J, Yang C, Xu S, et al. Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline. Nature Communications. 2026;17. doi:<a href="https://doi.org/10.1038/s41467-026-77326-1">10.1038/s41467-026-77326-1</a> Long, Jincheng, et al. “Multiple Argonaute Complexes Orchestrate Epigenetic Silencing in the Arabidopsis Germline.” Nature Communications, vol. 17, 10758, Springer Nature, 2026, doi:<a href="https://doi.org/10.1038/s41467-026-77326-1">10.1038/s41467-026-77326-1</a>. Long J, Yang C, Xu S, De Jaeger-Braet JG, She W, Ono S, Walker J, de Souza Vieira Y, Schnittger A, Feng X. 2026. Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline. Nature Communications. 17, 10758. 231982026-10-27T10:38:56Z2026-10-28T08:43:20Z