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Function of ARGONAUTE proteins in the Arabidopsis shoot apical meristem (SAM) [RIP-seq]

ABSTRACT: In sexually propagating organisms, genetic and epigenetic mutations are evolutionarily relevant only if they occur in the germline and provide inherited information to the next generation. In contrast to most animals, plants are thought to lack an early segregating germline, implying that somatic cells can contribute genetic information to the progeny if they differentiate into meiocytes. Here we demonstrate that two ARGONAUTE proteins, AGO5 and AGO9, are expressed in the reproductive lineage throughout development and mark an early-segregating germline. Furthermore, both AGOs are loaded with dynamic populations of small RNAs derived from highly methylated, pericentromeric, long transposons. Sequencing single nuclei revealed that many of these transposons are highly expressed within a central stem cell domain. This indicates a host-parasite tug of war and specific silencing pathways in plant shoot apical meristems (SAMs). Our results open the path to investigate transposon biology and epigenome dynamics at cellular resolution in the SAM stem cell niche.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE192607 | GEO | 2023/09/30

REPOSITORIES: GEO

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Function of ARGONAUTE proteins in the Arabidopsis shoot apical meristem (SAM) [RNA-seq]

Project description:In sexually propagating organisms, genetic and epigenetic mutations are evolutionarily relevant only if they occur in the germline and provide inherited information to the next generation. In contrast to most animals, plants are thought to lack an early segregating germline, implying that somatic cells can contribute genetic information to the progeny if they differentiate into meiocytes. Here we demonstrate that two ARGONAUTE proteins, AGO5 and AGO9, are expressed in the reproductive lineage throughout development and mark an early-segregating germline. Furthermore, both AGOs are loaded with dynamic populations of small RNAs derived from highly methylated, pericentromeric, long transposons. Sequencing single nuclei revealed that many of these transposons are highly expressed within a central stem cell domain. This indicates a host-parasite tug of war and specific silencing pathways in plant shoot apical meristems (SAMs). Our results open the path to investigate transposon biology and epigenome dynamics at cellular resolution in the SAM stem cell niche.

2023-09-30 | GSE192608 | GEO

Function of ARGONAUTE proteins in the Arabidopsis shoot apical meristem (SAM).

2023-10-31 | GSE239462 | GEO

Function of ARGONAUTE proteins in the Arabidopsis shoot apical meristem (SAM) [Bisulfite-Seq]

2023-09-30 | GSE192606 | GEO

Function of ARGONAUTE proteins in the Arabidopsis shoot apical meristem (SAM) [seedling RNA-seq]

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Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis

Project description:We report here that gentic methylation in the male germline, from meiocytes to sperm, is established by siRNAs transcribed from transposons with imperfect sequence homology. These siRNAs are synthesized by meiocyte nurse cells (tapetum) via activity of the chromatin remodeler CLASSY3, which is specifically expressed in tapetal cells. Plants that produce siRNAs only in the tapetum have broadly normal DNA methylation of the entire germline. Finally, we also report that these nurse cell-derived siRNAs (niRNAs) silence germline transposons, thereby safeguarding genome integrity. Our results reveal the crucial role of tapetal niRNAs in germline methylation reprogramming, which is remarkably analogous to piRNA-mediated reprogramming in animal germlines.

2021-07-01 | GSE161625 | GEO

Arabidopsis AGO1 N-terminal extension acts as an essential hub for PRMT5 interaction and post-translational modifications

Project description:Plant ARGONAUTE (AGO) proteins play pivotal roles in gene expression regulation through small (s)RNA-guided mechanisms. Among the ten AGO proteins in Arabidopsis thaliana, AGO1 stands out as the main effector of post-transcriptional gene silencing. Intriguingly, a specific region of AGO1, its N-terminal extension (NTE), has gained prominence in recent studies linked to diverse regulatory functions, including subcellular localization, sRNA loading, and interactions with regulatory factors. In the realm of post-translational modifications (PTMs), little is known about arginine methylation in Arabidopsis AGOs. This study reveals a novel and intricate landscape of AGO1 methylation. Here, we have elucidated that NTEAGO1 undergoes symmetric arginine dimethylation on specific residues, and interacts with the methyltransferase PRMT5, which catalyzes its methylation. Notably, we observed that the lack of symmetric dimethylarginine has no discernible impact on AGO1's subcellular localization or miRNA loading capabilities. However, the absence of PRMT5 significantly alters the loading of a subgroup of sRNAs into AGO1 and reshapes the NTEAGO1 interactome. Importantly, our research extends beyond AGO1, illustrating that symmetric arginine dimethylation of NTEs is a common process across Arabidopsis AGOs, taking place in AGO1, AGO2, AGO3, and AGO5, deepening our understanding of PTMs in the intricate landscape of RNA-associated gene regulation.

2024-05-22 | PXD049971 | Pride

Arabidopsis AGO5 contributes to a POL II-based RNA silencing pathway directing epigenetic marks

Project description:To characterise the Arabidopsis AGO5 protein, we report the AGO5 associated sRNAs, ago5 mutant total sRNAs and digital gene indexing tags with altered abundance in the ago5 mutant. Examination of AGO5 associated sRNAs, population of total sRNAs in the ago5 mutant and characterisation of RNA transcripts with altered abundance in the ago5 mutant.

2014-07-27 | E-GEOD-30970 | biostudies-arrayexpress

Small RNAs in four Argonaute complexes in Arabidopsis

Project description:The core components of RNA silencing effector complexes include small RNAs and members of the Argonaute (AGO) protein family. Arabidopsis encodes ten AGOs and complex population of small RNAs. It remains largely unknown how these small RNAs are recognized and recruited by each AGO complex. Here we purified four AGO complexes and identified small RNAs in each complex by deep sequencing. Keywords: Small RNA sorting Small RNAs were prepared from Arabidopsis AGO1, AGO2, AGO4 and AGO5 complexes, ligated to a 3' adaptor and a 5' acceptor sequentially, and then RT-PCR amplified. PCR products were reamplified using a pair of solexa cloning primers and then provided for sequencing. For technical details, see Qi, Y., He, X., Wang, X.J., Kohany, O., Jurka, J., and Hannon, G.J. 2006. Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature 443(7114): 1008-1012.

2008-04-05 | E-GEOD-10036 | biostudies-arrayexpress

Genome-wide identification of Argonautes in Solanaceae with emphasis on potato

Project description:Regulatory small RNAs (sRNAs) play important roles in many fundamental processes in plant biology such as development, fertilization and stress responses. The AGO protein family has here a central importance in gene regulation based on their capacity to associate with sRNAs followed by mRNA targeting in a sequence-complementary manner. The present study explored Argonautes (AGOs) in the Solanaceae family, with emphasis on potato, Solanum tuberosum (St). A genome-wide monitoring was performed to provide a deeper insight into gene families, genomic localization, gene structure and expression profile against the potato late blight pathogen Phytophthora infestans. Among 15 species in the Solanaceae family we found a variation from ten AGOs in Nicotiana obtusifolia to 17 in N. tabacum. Comprehensive analyses of AGO phylogeny revealed duplication of AGO1, AGO10 and AGO4 paralogs during early radiation of Solanaceae. Fourteen AGOs were identified in potato. Orthologs of AGO8 and AGO9 were missing in the potato genome. However, AGO15 earlier annotated in tomato was identified. StAGO15 differs from the other paralogs having residues of different physico-chemical properties at functionally important amino acid positions. Upon pathogen challenge StAGO15 was significantly activated and hence may play a prominent role in sRNA-based regulation of potato defense.

2020-12-01 | GSE159015 | GEO

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