Nurse cell­–derived small RNAs define paternal epigenetic inheritance in <em>Arabidopsis</em>

doi:10.1126/science.abh0556

GSTDTAP > 气候变化

DOI	10.1126/science.abh0556
	Nurse cell–derived small RNAs define paternal epigenetic inheritance in Arabidopsis
	Jincheng Long; James Walker; Wenjing She; Billy Aldridge; Hongbo Gao; Samuel Deans; Martin Vickers; Xiaoqi Feng
	2021-07-02
发表期刊	Science
出版年	2021
英文摘要	Genomes of germ cells present an existential vulnerability to organisms because germ cell mutations will propagate to future generations. Transposable elements are one source of such mutations. In the small flowering plant Arabidopsis , Long et al. found that genome methylation in the male germline is directed by small interfering RNAs (siRNAs) imperfectly transcribed from transposons (see the Perspective by Mosher). These germline siRNAs silence germline transposons and establish inherited methylation patterns in sperm, thus maintaining the integrity of the plant genome across generations. Science , abh0556, this issue p. [eabh0556][1]; see also abj5020, p. [26][2] ### INTRODUCTION Epigenetic modifications to chromatin, such as the methylation of DNA cytosines, carry regulatory information across the generations in plants and animals. Epigenetic marks are inherited through germlines, which can undergo epigenetic reprogramming that affects germline function. Mammalian germlines undergo genome-wide demethylation and remethylation, which resets epigenetic marks and restores cellular pluripotency. Germlines of flowering plants differentiate later than those of mammals and undergo distinct DNA methylation reprogramming. Global methylation level changes have been observed in plant germ cells, as well as local de novo methylation that regulates germline gene expression. However, the reprogramming mechanism remains unclear, which limits the understanding of tissue-specific and transgenerational epigenetic inheritance in plants. ### RATIONALE De novo methylation of genes in the Arabidopsis male germline is catalyzed by the small RNA-directed DNA methylation pathway (RdDM). RdDM uses 24-nucleotide (nt) small interfering RNAs (siRNAs) transcribed from a source locus, typically a transposon, to guide methyltransferases to methylate the cognate region. RdDM is ubiquitous among cells and normally methylates transposons. We investigated how RdDM targets genes in the germline, how such reprogramming is limited to the germline, and how the hundreds of target genes are selected. ### RESULTS We show that in Arabidopsis , germline-specific methylation at hundreds of genes is established by 24-nt siRNAs transcribed from hypermethylated transposons with imperfect sequence homology. CRISPR deletion of siRNA source transposons abolishes DNA methylation at corresponding genes in male meiocytes, demonstrating the ability of these siRNAs to target methylation in trans with mismatches. Furthermore, we found that meiocytes are quiescent in 24-nt siRNA biogenesis, and the gene targeting siRNAs are produced in tapetal nurse cells and transported into meiocytes. The siRNA profile of tapetal cells resembles that of meiocytes, suggesting bulk siRNA movement through the cytoplasmic channels (known as plasmodesmata) that connect these cells during early meiosis. Although gene-targeting siRNAs accumulate to levels in the tapetum comparable with those in meiocytes, the target genes are not methylated in the tapetum, showing that meiocytes can use imperfectly matching siRNAs to target DNA methylation. We also show that the biogenesis of gene-targeting siRNAs in the tapetum is driven by a putative chromatin remodeler, CLASSY3 (CLSY3). CLSY3 is absent in vegetative tissues but enriched in female and male organs. In male organs, CLSY3 is specifically expressed in tapetal cells. The clsy3 mutation eliminates de novo methylation at genes in male meiocytes as well as sperm, revealing the role of tapetal siRNAs in driving methylation reprogramming throughout the male germline. This conclusion was reinforced with experiments with a genetic mosaic system that restricted siRNA biogenesis to the tapetum. In the mosaic lines, tapetal siRNAs restore methylation in the male germline at genes specifically methylated in the germline and at transposons targeted by RdDM in all tissues. This shows that tapetal siRNAs shape the full spectrum of RNA-directed DNA methylation throughout the male germline, from meiocytes to sperm. As tapetal siRNAs induce methylation at transposons in the male germline, we investigated whether these siRNAs serve to silence germline transposons in addition to their gene regulatory function. We found that tapetal siRNAs methylate and prevent the expression of a Gypsy retrotransposon ( GP1 ) that is specifically active in reproductive cells, demonstrating that tapetal siRNAs ensure germline genome integrity by suppressing transposons. ### CONCLUSION Our work reveals the role of tapetum-derived 24-nt siRNAs in determining the paternal methylome. Tapetal siRNAs drive de novo methylation at genes in the germline and safeguard genome integrity by silencing transposons. The ability of meiocytes to use mismatched 24-nt siRNAs to induce methylation allows RdDM to target sequences similar to those of transposons that produce siRNAs in the tapetum. This should facilitate recognition and silencing of new transposons, indicating that meiosis is a key stage for genome surveillance and allows RdDM to specifically regulate germline gene expression. The broad targeting competence of tapetal siRNAs resembles that of metazoan gonad-expressed Piwi-interacting RNAs (piRNAs), suggesting convergent evolution of specialized small RNA pathways to control transposons and genes in plant and animal germlines. ![Figure][3] Tapetal siRNAs shape germline DNA methylation. RNA polymerase IV (Pol IV) transcripts are processed by RNA-dependent RNA polymerase 2 (RDR2) and Dicer-Like 3 (DCL3) into 24-nt siRNAs. Tapetal siRNAs are transcribed from transposons, enabled by CLSY3 expression. Tapetal siRNAs move to meiocytes and induce methylation at corresponding transposons and genes with similar sequences. This genic methylation is germline-specific, indicating that the siRNA-targeted de novo methylation pathway is hypersensitive in meiocytes. TE, transposable element. CREDIT: ADAPTED BY N. CARY/ SCIENCE The plant male germline undergoes DNA methylation reprogramming, which methylates genes de novo and thereby alters gene expression and regulates meiosis. Here, we reveal the molecular mechanism underlying this reprogramming. We demonstrate that genic methylation in the male germline, from meiocytes to sperm, is established by 24-nucleotide small interfering RNAs (siRNAs) transcribed from transposons with imperfect sequence homology. These siRNAs are synthesized by meiocyte nurse cells (tapetum) through activity of CLSY3, a chromatin remodeler absent in other anther cells. Tapetal siRNAs govern germline methylation throughout the genome, including the inherited methylation patterns in sperm. Tapetum-derived siRNAs also silence germline transposons, safeguarding genome integrity. Our results reveal that tapetal siRNAs are sufficient to reconstitute germline methylation patterns and drive functional methylation reprogramming throughout the male germline. [1]: /lookup/doi/10.1126/science.abh0556 [2]: /lookup/doi/10.1126/science.abj5020 [3]: pending:yes
领域	气候变化 ; 资源环境
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文献类型	期刊论文
条目标识符	http://119.78.100.173/C666/handle/2XK7JSWQ/334178
专题	气候变化资源环境科学
推荐引用方式 GB/T 7714	Jincheng Long,James Walker,Wenjing She,等. Nurse cell–derived small RNAs define paternal epigenetic inheritance in Arabidopsis[J]. Science,2021.
APA	Jincheng Long.,James Walker.,Wenjing She.,Billy Aldridge.,Hongbo Gao.,...&Xiaoqi Feng.(2021).Nurse cell–derived small RNAs define paternal epigenetic inheritance in Arabidopsis.Science.
MLA	Jincheng Long,et al."Nurse cell–derived small RNAs define paternal epigenetic inheritance in Arabidopsis".Science (2021).