A Framework for piRNA Cluster Manipulation

Author(s):  
Ivan Olovnikov ◽  
Adrien Le Thomas ◽  
Alexei A. Aravin
Keyword(s):  
Genes ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 209 ◽  
Author(s):  
Elizaveta Radion ◽  
Olesya Sokolova ◽  
Sergei Ryazansky ◽  
Pavel Komarov ◽  
Yuri Abramov ◽  
...  

Piwi-interacting RNAs (piRNAs) control transposable element (TE) activity in the germline. piRNAs are produced from single-stranded precursors transcribed from distinct genomic loci, enriched by TE fragments and termed piRNA clusters. The specific chromatin organization and transcriptional regulation of Drosophila germline-specific piRNA clusters ensure transcription and processing of piRNA precursors. TEs harbour various regulatory elements that could affect piRNA cluster integrity. One of such elements is the suppressor-of-hairy-wing (Su(Hw))-mediated insulator, which is harboured in the retrotransposon gypsy. To understand how insulators contribute to piRNA cluster activity, we studied the effects of transgenes containing gypsy insulators on local organization of endogenous piRNA clusters. We show that transgene insertions interfere with piRNA precursor transcription, small RNA production and the formation of piRNA cluster-specific chromatin, a hallmark of which is Rhino, the germline homolog of the heterochromatin protein 1 (HP1). The mutations of Su(Hw) restored the integrity of piRNA clusters in transgenic strains. Surprisingly, Su(Hw) depletion enhanced the production of piRNAs by the domesticated telomeric retrotransposon TART, indicating that Su(Hw)-dependent elements protect TART transcripts from piRNA processing machinery in telomeres. A genome-wide analysis revealed that Su(Hw)-binding sites are depleted in endogenous germline piRNA clusters, suggesting that their functional integrity is under strict evolutionary constraints.


2015 ◽  
Vol 44 (D1) ◽  
pp. D223-D230 ◽  
Author(s):  
David Rosenkranz

2018 ◽  
Author(s):  
Gen Zhang ◽  
Shikui Tu ◽  
Tianxiong Yu ◽  
Xiaoou Zhang ◽  
Swapnil S. Parhad ◽  
...  
Keyword(s):  

2013 ◽  
Vol 41 (11) ◽  
pp. 5757-5768 ◽  
Author(s):  
Ivan Olovnikov ◽  
Sergei Ryazansky ◽  
Sergey Shpiz ◽  
Sergey Lavrov ◽  
Yuri Abramov ◽  
...  

PLoS Genetics ◽  
2015 ◽  
Vol 11 (11) ◽  
pp. e1005652 ◽  
Author(s):  
Gung-wei Chirn ◽  
Reazur Rahman ◽  
Yuliya A. Sytnikova ◽  
Jessica A. Matts ◽  
Mei Zeng ◽  
...  
Keyword(s):  

2017 ◽  
Author(s):  
Patrick Schreiner ◽  
Peter W. Atkinson

AbstractBackgroundPiwi-interacting RNAs (piRNAs) are sRNAs that have a distinct biogenesis and molecular function from siRNAs and miRNAs. The piRNA pathway is well-conserved and shown to play an important role in the regulatory capacity of germline cells in Metazoans. Significant subsets of piRNAs are generated from discrete genomic loci referred to as piRNA clusters. Given that the contents of piRNA clusters dictate the target specificity of primary piRNAs, and therefore the generation of secondary piRNAs, they are of great significance when considering transcriptional and post-transcriptional regulation on a genomic scale. A quantitative comparison of top piRNA cluster composition can provide further insight into piRNA cluster biogenesis and function.ResultsWe have developed software for general use, piClusterBusteR, which performs nested annotation of piRNA cluster contents to ensure high-quality characterization, provides a quantitative representation of piRNA cluster composition by feature, and makes available annotated and unannotated piRNA cluster sequences that can be utilized for downstream analysis. The data necessary to run piClusterBusteR and the skills necessary to execute this software on any species of interest are not overly burdensome for biological researchers.piClusterBusteR has been utilized to compare the composition of top piRNA generating loci amongst 13 Metazoan species. Characterization and quantification of cluster composition allows for comparison within piRNA clusters of the same species and between piRNA clusters of different species.ConclusionsWe have developed a tool that accurately, automatically, and efficiently describes the contents of piRNA clusters in any biological system that utilizes the piRNA pathway. The results from piClusterBusteR have provided an in-depth description and comparison of the architecture of top piRNA clusters within and between 13 species, as well as a description of annotated and unannotated sequences from top piRNA cluster loci in these Metazoans.piClusterBusteR is available for download on GitHub: https://github.com/pschreiner/piClusterBuster


Author(s):  
Filip Wierzbicki ◽  
Robert Kofler ◽  
Sarah Signor

AbstractSmall RNAs produced from transposable element (TE) rich sections of the genome, termed piRNA clusters, are a crucial component in the genomic defense against selfish DNA. In animals it is thought the invasion of a TE is stopped when a copy of the TE inserts into a piRNA cluster, triggering the production of cognate small RNAs that silence the TE. Despite this importance for TE control, little is known about the evolutionary dynamics of piRNA clusters, mostly because these repeat rich regions are difficult to assemble and compare. Here we establish a framework for studying the evolution of piRNA clusters quantitatively. Previously introduced quality metrics and a newly developed software for multiple alignments of repeat annotations (Manna) allow us to estimate the level of polymorphism segregating in piRNA clusters and the divergence among homologous piRNA clusters. By studying 20 conserved piRNA clusters in multiple assemblies of four Drosophila species we show that piRNA clusters are evolving rapidly. While 70-80% of the clusters are conserved within species, the clusters share almost no similarity between species as closely related as D. melanogaster and D. simulans. Furthermore, abundant insertions and deletions are segregating within the Drosophila species. We show that the evolution of clusters is mainly driven by large insertions of recently active TEs, and smaller deletions mostly in older TEs. The effect of these forces is so rapid that homologous clusters often do not contain insertions from the same TE families.x


2018 ◽  
Author(s):  
Karine Casier ◽  
Valérie Delmarre ◽  
Nathalie Gueguen ◽  
Catherine Hermant ◽  
Elise Viodé ◽  
...  

ABSTRACTTransposable element (TE) activity is repressed in animal gonads by PIWI-interacting RNAs (piRNAs), a class of small RNAs produced by specific loci made of TEs insertions and fragments. Current models propose that these loci are functionally defined by the maternal inheritance of piRNAs produced during the previous generation, raising the question of their first activation in the absence of piRNAs. Taking advantage of an inactive cluster of P-element derived transgene insertions, we show here that raising flies at high temperature (29°C) instead of 25°C results in a rare but invasive epigenetic conversion of this locus into an active piRNAs producing one. The newly acquired epigenetic state is stable over many generations even when flies are switch back to 25°C. The silencing capacities, piRNA production and chromatin modifications of the cluster are all identical whether conversion occurred by maternal piRNA inheritance or by high temperature. We also demonstrate that in addition to high temperature, a single homologous transgene inserted elsewhere in the genome is required to activate the locus. We thus have identified a minimal system of three components to create a stable piRNA producing locus: 1) a locus with multiple TE derived sequences; 2) an euchromatic copy of these sequences and 3) elevated temperature. Altogether, these data report the first case of the establishment of an active piRNA cluster by environmental changes. It highlights how such variations of species natural habitat can become heritable and shape their epigenome.SIGNIFICANCE STATEMENTRecently, we have witnessed great progress in our understanding of the silencing of Transposable Elements (TEs) by piRNAs, a class of small RNAs produced by piRNA clusters. At each generation, piRNA clusters are supposed to be activated by homologous piRNAs inherited from the mother raising the question of the making of the first piRNAs. Here, we report the birth of a stable and functional piRNA cluster induced by high temperature without maternal inheritance of homologous piRNAs. We propose a minimal system to create a piRNA cluster: a sufficient number of repeated sequences, a euchromatic copy of these sequences and an increase in the production of antisense RNA.


2019 ◽  
Author(s):  
Shuo Zhang ◽  
Erin S. Kelleher

ABSTRACTThe regulation of transposable element (TE) activity by small RNAs is a ubiquitous feature of germlines. However, despite the obvious benefits to the host in terms of ensuring the production of viable gametes and maintaining the integrity of the genomes they carry, it remains controversial whether TE regulation evolves adaptively. We examined the emergence and evolutionary dynamics of repressor alleles after P-elements invaded the Drosophila melanogaster genome in the mid 20th century. In many animals including Drosophila, repressor alleles are produced by transpositional insertions into piRNA clusters, genomic regions encoding the Piwi-interacting RNAs (piRNAs) that regulate TEs. We discovered that ∼94% of recently collected isofemale lines in the Drosophila Genetic Reference Panel (DGRP) contain at least one P-element insertion in a piRNA cluster, indicating that repressor alleles are produced by de novo insertion at an exceptional rate. Furthermore, in our sample of ∼200 genomes, we uncovered no fewer than 80 unique P-element insertion alleles in at least 15 different piRNA clusters. Finally, we observe no footprint of positive selection on P-element insertions in piRNA clusters, suggesting that the rapid evolution of piRNA-mediated repression in D. melanogaster was driven primarily by mutation. Our results reveal for the first time how the unique genetic architecture of piRNA production, in which numerous piRNA clusters can encode regulatory small RNAs upon transpositional insertion, facilitates the non-adaptive rapid evolution of repression.


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