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Arabidopsis AGO3 predominantly recruits 24-nt small RNAs to regulate epigenetic silencing

Nature Plants volume 2, Article number: 16049 (2016) Cite this article

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Abstract

Argonaute (AGO) proteins recruit 21–24-nucleotide (nt) small RNAs (sRNAs) to constitute RNA-induced silencing complexes (RISCs) to regulate gene expression at transcriptional or posttranscriptional levels1–3. Arabidopsis encodes nine functional AGO proteins. These proteins are classified into three clusters, AGO1/5/10, AGO2/3/7 and AGO4/6/9, based on their sequence similarity, functional redundancy, as well as species and features of AGO-bound sRNAs4–7. Although most Arabidopsis AGO proteins have been studied well, AGO3-bound sRNAs and their basic function remain unknown. Here we observed that AGO3 could not complement the signature function of AGO2, the closest genetic paralog of AGO3, in host antiviral defence. We also found, surprisingly, that AGO3 predominantly bound 24-nt sRNAs with 5′-terminal adenine. The spectrum of AGO3-associated sRNAs was different from those bound to AGO2, further indicating their functional divergence. By contrast, approximately 30% of AGO3-bound 24-nt sRNAs overlapped with those bound to AGO4, and over 60% of AGO3-associated 24-nt sRNA-enriched loci were identical to those of AGO4. Moreover, the redundancy of AGO3- and AGO4-bound sRNAs is much more than that of AGO6- and AGO4-recruited sRNAs. In addition, expression of AGO3 driven by the AGO4 promoter partially complemented AGO4 function and rescued a DNA methylation defect in the ago4-1 background. Together, our results indicated that AGO3, similarly to AGO4, is a component in the epigenetic pathway.

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Figure 1: AGO3 could not complement AGO2 function in antiviral defence.
Figure 2: Purification of Arabidopsis AGO2/3-containing RISCs.
Figure 3: Characterization of AGO2/3-associated sRNAs.
Figure 4: AGO3 driven by the AGO4 promoter could partially complement ago4-1 mutant.

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Acknowledgements

We thank L.Y. Zeng for imaging facilities. This work was supported in part by the National Natural Science Foundation of China (NSFC 30725014 and 30621001) to X.-J.W., an National Science Foundation (NSF) grant (NSF CAREER MCB-1253369) and the Welch foundation (A-1777) to X.Z. and a collaborative research grant program NSFC-Texas A&M (02-230204) to X.-J.W. and X.Z.

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  1. Zhonghui Zhang and Xiuying Liu: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biochemistry and Biophysics, Texas A&M University, College Station, 77843, Texas, USA

    Zhonghui Zhang, Xinwei Guo & Xiuren Zhang

  2. Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, 77843, Texas, USA

    Zhonghui Zhang, Xinwei Guo & Xiuren Zhang

  3. State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China

    Xiuying Liu & Xiu-Jie Wang

  4. College of Horticulture, China Agricultural University, 100193, Beijing, China

    Xinwei Guo

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  1. Zhonghui Zhang
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Contributions

Z.Z., X.-J.W. and X.Z. designed the research; Z.Z., X.G. and X.Z. performed the research; X.L. and Z.Z. performed bioinformatics analysis of small RNA libraries and DNA methylation; Z.Z., X.L., X.-J.W. and X.Z. wrote the paper.

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Correspondence to Xiu-Jie Wang or Xiuren Zhang.

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Zhang, Z., Liu, X., Guo, X. et al. Arabidopsis AGO3 predominantly recruits 24-nt small RNAs to regulate epigenetic silencing. Nature Plants 2, 16049 (2016). https://doi.org/10.1038/nplants.2016.49

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