scholarly journals Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements

2017 ◽  
Author(s):  
Samuel H. Lewis ◽  
Kaycee A. Quarles ◽  
Yujing Yang ◽  
Melanie Tanguy ◽  
Lise Frézal ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Small Rna ◽  
Rna Silencing ◽  
Individual Species ◽  
Rna Molecules ◽  
Horseshoe Crabs ◽  
Silencing Pathways ◽  
Pirna Pathway ◽  
Interference Mechanism

AbstractIn animals, small RNA molecules termed PIWI-interacting RNAs (piRNAs) silence transposable elements (TEs), protecting the germline from genomic instability and mutation. piRNAs have been detected in the soma in a few animals, but these are believed to be specific adaptations of individual species. Here, we report that somatic piRNAs were likely present in the ancestral arthropod more than 500 million years ago. Analysis of 20 species across the arthropod phylum suggests that somatic piRNAs targeting TEs and mRNAs are common among arthropods. The presence of an RNA-dependent RNA polymerase in chelicerates (horseshoe crabs, spiders, scorpions) suggests that arthropods originally used a plant-like RNA interference mechanism to silence TEs. Our results call into question the view that the ancestral role of the piRNA pathway was to protect the germline and demonstrate that small RNA silencing pathways have been repurposed for both somatic and germline functions throughout arthropod evolution.

scholarly journals Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin

2021 ◽  
Author(s):  
Jaemyung Choi ◽  
David Bruce Lyons ◽  
Daniel Zilberman
Keyword(s):  
Dna Methylation ◽  
Transposable Elements ◽  
Small Rna ◽  
Histone H3 ◽  
Histone H1 ◽  
Dna Methyltransferases ◽  
Flowering Plants ◽  
Genomic Sequences ◽  
Rna Molecules ◽  
Rna Biogenesis

Flowering plants utilize small RNA molecules to guide DNA methyltransferases to genomic sequences. This RNA-directed DNA methylation (RdDM) pathway preferentially targets euchromatic transposable elements. However, RdDM is thought to be recruited by methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin. How RdDM is targeted to euchromatin despite an affinity for H3K9me is unclear. Here we show that loss of histone H1 enhances heterochromatic RdDM, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically required for small RNA biogenesis, and without H1 small RNA production quantitatively expands to non-CG methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the small RNA-generating branch of RdDM from non-CG methylated heterochromatin.

scholarly journals Multiple roles of PIWIL1 in mouse neocorticogenesis

2017 ◽  
Author(s):  
Barbara Viljetic ◽  
Liyang Diao ◽  
Jixia Liu ◽  
Zeljka Krsnik ◽  
Sagara H.R. Wijeratne ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Small Rna ◽  
Radial Glia ◽  
Multiple Roles ◽  
Small Rna Sequencing ◽  
Knock Out ◽  
Deep Layers ◽  
Pirna Pathway ◽  
The Brain

AbstractPIWI-interacting RNAs (piRNAs) and their associated PIWI proteins play an important role in repressing transposable elements in animal germlines. However, little is known about the function of PIWI proteins and piRNAs in the developing brain. Here, we investigated the role of an important PIWI family member, Piwi-like protein 1 (Piwil1; also known as Miwi in mouse) in the developing mouse neocortex. Using a Piwil1 knock-out (Piwil1 KO) mouse strain, we found that Piwil1 is essential for several steps of neocorticogenesis, including neocortical cell cycle, neuron migration and dendritogenesis. Piwil1 deletion resulted in increased cell cycle re-entry at embryonic day 17 (E17) when predominantly intracortically projecting neurons are being produced. Prenatal Piwil1 deletion increased the number of Pax6+ radial glia at postnatal day 0 (P0). Furthermore, Piwil1 deletion disrupted migration of Satb2+ neurons within deep layers at E17, P0 and P7. Satb2+ neurons showed increased co-localization with Bcl11b (also known as Ctip2), marker of subcortically projecting neurons. Piwil1 knockouts had disrupted neocortical circuitry represented by thinning of the corpus callosum and altered dendritogenesis. We further investigated if Piwil1 deletion disrupted expression levels of neocortical piRNAs by small RNA-sequencing in neocortex. We did not find differential expression of piRNAs in the neocortices of Piwil1 KO, while differences were observed in other Piwil1 KO tissues. This result suggests that Piwil1 may act independently of piRNAs and have novel roles in higher cognitive centers, such as neocortex. In addition, we report a screen of piRNAs derived from tRNA fragments in developing neocortices. Our result is the first report of selective subsets of piRNAs and tRNA fragments in developing prenatal neocortices and helps clarify some outstanding questions about the role of the piRNA pathway in the brain.

scholarly journals tRNA 2′-O-methylation by a duo of TRM7/FTSJ1 proteins modulates small RNA silencing in Drosophila

2020 ◽  
Vol 48 (4) ◽  
pp. 2050-2072 ◽  
Author(s):  
Margarita T Angelova ◽  
Dilyana G Dimitrova ◽  
Bruno Da Silva ◽  
Virginie Marchand ◽  
Caroline Jacquier ◽  
...  
Keyword(s):  
Small Rna ◽  
Rna Structure ◽  
Rna Silencing ◽  
Defense Mechanisms ◽  
Rna Virus ◽  
Virus Infections ◽  
Self Recognition ◽  
Silencing Pathways ◽  
Rna Pathways ◽  
And Function

Abstract 2′-O-Methylation (Nm) represents one of the most common RNA modifications. Nm affects RNA structure and function with crucial roles in various RNA-mediated processes ranging from RNA silencing, translation, self versus non-self recognition to viral defense mechanisms. Here, we identify two Nm methyltransferases (Nm-MTases) in Drosophila melanogaster (CG7009 and CG5220) as functional orthologs of yeast TRM7 and human FTSJ1. Genetic knockout studies together with MALDI-TOF mass spectrometry and RiboMethSeq mapping revealed that CG7009 is responsible for methylating the wobble position in tRNAPhe, tRNATrp and tRNALeu, while CG5220 methylates position C32 in the same tRNAs and also targets additional tRNAs. CG7009 or CG5220 mutant animals were viable and fertile but exhibited various phenotypes such as lifespan reduction, small RNA pathways dysfunction and increased sensitivity to RNA virus infections. Our results provide the first detailed characterization of two TRM7 family members in Drosophila and uncover a molecular link between enzymes catalyzing Nm at specific tRNAs and small RNA-induced gene silencing pathways.

scholarly journals Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

Cell ◽  
2009 ◽  
Vol 136 (3) ◽  
pp. 461-472 ◽  
Author(s):  
R. Keith Slotkin ◽  
Matthew Vaughn ◽  
Filipe Borges ◽  
Miloš Tanurdžić ◽  
Jörg D. Becker ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Small Rna ◽  
Rna Silencing ◽  
Epigenetic Reprogramming

scholarly journals Small RNA Silencing Pathways in Germ and Stem Cells

2008 ◽  
Vol 73 (0) ◽  
pp. 283-290 ◽  
Author(s):  
A.A. Aravin ◽  
G.J. Hannon
Keyword(s):  
Stem Cells ◽  
Small Rna ◽  
Rna Silencing ◽  
Silencing Pathways

scholarly journals Adaptive role of tmRNA

2005 ◽  
Vol 3 (3) ◽  
pp. 12-18
Author(s):  
Galina A Zhouravleva ◽  
Nikolay S Rovinski
Keyword(s):  
Small Rna ◽  
Rna Molecules ◽  
Translation Error ◽  
Adaptive Role

тmRNA is a small RNA molecule, found only in bacteria, that exhibits properties of tRNA and mRNA. TmRNA involved in process of «trans-translation» when protein translates from two different RNA molecules and one of them is tmRNA. Its function is decreasing of translation error amount by releasing of stalled ribosomes and degradation of incorrect proteins.

scholarly journals The Etiological Agent of Lyme Disease, Borrelia burgdorferi, Appears To Contain Only a Few Small RNA Molecules

2004 ◽  
Vol 186 (24) ◽  
pp. 8472-8477 ◽  
Author(s):  
Yngve Östberg ◽  
Ignas Bunikis ◽  
Sven Bergström ◽  
Jörgen Johansson
Keyword(s):  
Borrelia Burgdorferi ◽  
Small Rna ◽  
Rna Binding ◽  
Rna Binding Protein ◽  
Rnase E ◽  
Regulatory Pathways ◽  
Rna Molecules ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas

ABSTRACT Small regulatory RNAs (sRNAs) have recently been shown to be the main controllers of several regulatory pathways. The function of sRNAs depends in many cases on the RNA-binding protein Hfq, especially for sRNAs with an antisense function. In this study, the genome of Borrelia burgdorferi was subjected to different searches for sRNAs, including direct homology and comparative genomics searches and ortholog- and annotation-based search strategies. Two new sRNAs were found, one of which showed complementarity to the rpoS region, which it possibly controls by an antisense mechanism. The role of the other sRNA is unknown, although observed complementarities against particular mRNA sequences suggest an antisense mechanism. We suggest that the low level of sRNAs observed in B. burgdorferi is at least partly due to the presumed lack of both functional Hfq protein and RNase E activity.

scholarly journals The Role of Small RNA-Based Epigenetic Silencing for Purifying Selection on Transposable Elements in Capsella grandiflora

2017 ◽  
Vol 9 (10) ◽  
pp. 2911-2920 ◽  
Author(s):  
Robert Horvath ◽  
Tanja Slotte
Keyword(s):  
Transposable Elements ◽  
Small Rna ◽  
Purifying Selection ◽  
Epigenetic Silencing

Analysis of CACTA transposase genes unveils the mechanism of intron loss and distinct small RNA silencing pathways underlying divergent evolution of Brassica genomes

2020 ◽  
Author(s):  
Beibei Liu ◽  
Aiko Iwata‐Otsubo ◽  
Diya Yang ◽  
Robert L. Baker ◽  
Chun Liang ◽  
...  
Keyword(s):  
Small Rna ◽  
Rna Silencing ◽  
Intron Loss ◽  
Divergent Evolution ◽  
Silencing Pathways
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