Genome-wide redistribution of 24-nt siRNAs in rice gametes
- Chenxin Li1,5,
- Hengping Xu2,5,
- Fang-Fang Fu3,
- Scott D. Russell2,
- Venkatesan Sundaresan1,4 and
- Jonathan I. Gent3
- 1Department of Plant Biology, University of California, Davis, California 95616, USA;
- 2Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, USA;
- 3Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA;
- 4Department of Plant Sciences, University of California, Davis, California 95616, USA
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↵5 These authors contributed equally to this work.
Abstract
Gametes constitute a critical stage of the plant life cycle during which the genome undergoes reprogramming in preparation for embryogenesis. Here, we examined genome-wide distributions of small RNAs in the sperm and egg cells of rice. We found that 24-nt siRNAs, which are a hallmark of RNA-directed DNA methylation (RdDM) in plants, were depleted from heterochromatin boundaries in both gametes relative to vegetative tissues, reminiscent of siRNA patterns in DDM1-type nucleosome remodeler mutants. In sperm cells, 24-nt siRNAs were spread across heterochromatic regions, while in egg cells, 24-nt siRNAs were concentrated at a smaller number of heterochromatic loci throughout the genome, especially at loci which also produced siRNAs in other tissues. In both gametes, patterns of CHH methylation, typically a strong indicator of RdDM, were similar to vegetative tissues, although lower in magnitude. These findings indicate that the small RNA transcriptome undergoes large-scale redistribution in both male and female gametes, which is not correlated with recruitment of DNA methyltransferases in gametes and suggestive of unexplored regulatory activities of gamete small RNAs.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.253674.119.
- Received June 13, 2019.
- Accepted December 23, 2019.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
