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Genome-wide redistribution of 24-nt siRNAs in rice gametes

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...

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Autores principales: Li, Chenxin, Xu, Hengping, Fu, Fang-Fang, Russell, Scott D., Sundaresan, Venkatesan, Gent, Jonathan I.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7050532/
https://www.ncbi.nlm.nih.gov/pubmed/31896557
http://dx.doi.org/10.1101/gr.253674.119
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author Li, Chenxin
Xu, Hengping
Fu, Fang-Fang
Russell, Scott D.
Sundaresan, Venkatesan
Gent, Jonathan I.
author_facet Li, Chenxin
Xu, Hengping
Fu, Fang-Fang
Russell, Scott D.
Sundaresan, Venkatesan
Gent, Jonathan I.
author_sort Li, Chenxin
collection PubMed
description 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.
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spelling pubmed-70505322020-08-01 Genome-wide redistribution of 24-nt siRNAs in rice gametes Li, Chenxin Xu, Hengping Fu, Fang-Fang Russell, Scott D. Sundaresan, Venkatesan Gent, Jonathan I. Genome Res Research 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. Cold Spring Harbor Laboratory Press 2020-02 /pmc/articles/PMC7050532/ /pubmed/31896557 http://dx.doi.org/10.1101/gr.253674.119 Text en © 2020 Li et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/4.0/ 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/.
spellingShingle Research
Li, Chenxin
Xu, Hengping
Fu, Fang-Fang
Russell, Scott D.
Sundaresan, Venkatesan
Gent, Jonathan I.
Genome-wide redistribution of 24-nt siRNAs in rice gametes
title Genome-wide redistribution of 24-nt siRNAs in rice gametes
title_full Genome-wide redistribution of 24-nt siRNAs in rice gametes
title_fullStr Genome-wide redistribution of 24-nt siRNAs in rice gametes
title_full_unstemmed Genome-wide redistribution of 24-nt siRNAs in rice gametes
title_short Genome-wide redistribution of 24-nt siRNAs in rice gametes
title_sort genome-wide redistribution of 24-nt sirnas in rice gametes
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7050532/
https://www.ncbi.nlm.nih.gov/pubmed/31896557
http://dx.doi.org/10.1101/gr.253674.119
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