Do human transposable element small RNAs serve primarily as genome defenders or genome regulators?

Miniature inverted-repeat transposable elements (MITEs) have been associated with genic regions in plant genomes and may play important roles in the regulation of nearby genes via recruitment of small RNAs (sRNA) to the MITEs loci. We identified eight families of MITEs in the sugarcane genome assembly with MITE-Hunter pipeline. These sequences were found to be upstream, downstream or inserted into 67 genic regions in the genome. The position of the most abundant MITE (Stowaway-like) in genic regions, which we call AddIn-MITE, was confirmed in a WD40 gene. The analysis of four monocot species showed conservation of the AddIn-MITE sequence, with a large number of copies in their genomes. We also investigated the conservation of the AddIn-MITE’ position in the WD40 genes from sorghum, maize and, in sugarcane cultivars and wild Saccharum species. In all analyzed plants, AddIn-MITE has located in WD40 intronic region. Furthermore, the role of AddIn-MITE-related sRNA in WD40 genic region was investigated. We found sRNAs preferentially mapped to the AddIn-MITE than to other regions in the WD40 gene in sugarcane. In addition, the analysis of the small RNA distribution patterns in the WD40 gene and the structure of AddIn-MITE, suggests that the MITE region is a proto-miRNA locus in sugarcane. Together, these data provide insights into the AddIn-MITE role in Andropogoneae grasses.

Download Full-text

Evolutionary dynamics of piRNA clusters in Drosophila

10.1101/2021.08.20.457083 ◽

2021 ◽

Cited By ~ 1

Author(s):

Filip Wierzbicki ◽

Robert Kofler ◽

Sarah Signor

Keyword(s):

Transposable Element ◽

Small Rnas ◽

Evolutionary Dynamics ◽

Quality Metrics ◽

Selfish Dna ◽

Insertions And Deletions ◽

Multiple Alignments ◽

Pirna Cluster ◽

Crucial Component

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

Download Full-text

Rapid evolution of piRNA-mediated silencing of an invading transposable element was driven by abundant de novo mutations

10.1101/611350 ◽

2019 ◽

Cited By ~ 1

Author(s):

Shuo Zhang ◽

Erin S. Kelleher

Keyword(s):

Transposable Element ◽

Small Rnas ◽

Evolutionary Dynamics ◽

De Novo ◽

Rapid Evolution ◽

De Novo Mutations ◽

Element Insertion ◽

Pirna Cluster ◽

Genomic Regions ◽

First Time

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.

Download Full-text

Faculty Opinions recommendation of Small RNAs Are Implicated in Regulation of Gene and Transposable Element Expression in the Protist Trichomonas vaginalis.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.739326846.793582787 ◽

2021 ◽

Author(s):

David Leitsch

Keyword(s):

Transposable Element ◽

Small Rnas ◽

Trichomonas Vaginalis

Download Full-text

Transposable-Element Associated Small RNAs in Bombyx mori Genome

PLoS ONE ◽

10.1371/journal.pone.0036599 ◽

2012 ◽

Vol 7 (5) ◽

pp. e36599 ◽

Cited By ~ 17

Author(s):

Yimei Cai ◽

Qing Zhou ◽

Caixia Yu ◽

Xumin Wang ◽

Songnian Hu ◽

...

Keyword(s):

Transposable Element ◽

Bombyx Mori ◽

Small Rnas

Download Full-text

Coupled protein synthesis and ribosome-guided piRNA processing on mRNAs

Nature Communications ◽

10.1038/s41467-021-26233-8 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Yu H. Sun ◽

Ruoqiao Huiyi Wang ◽

Khai Du ◽

Jiang Zhu ◽

Jihong Zheng ◽

...

Keyword(s):

Protein Synthesis ◽

Transposable Element ◽

Small Rnas ◽

Protein Production ◽

Fine Tuning ◽

Untranslated Regions ◽

Protein Coding ◽

Rna Surveillance ◽

Non Coding Rnas ◽

Pirna Pathway

AbstractPIWI-interacting small RNAs (piRNAs) protect the germline genome and are essential for fertility. piRNAs originate from transposable element (TE) RNAs, long non-coding RNAs, or 3´ untranslated regions (3´UTRs) of protein-coding messenger genes, with the last being the least characterized of the three piRNA classes. Here, we demonstrate that the precursors of 3´UTR piRNAs are full-length mRNAs and that post-termination 80S ribosomes guide piRNA production on 3´UTRs in mice and chickens. At the pachytene stage, when other co-translational RNA surveillance pathways are sequestered, piRNA biogenesis degrades mRNAs right after pioneer rounds of translation and fine-tunes protein production from mRNAs. Although 3´UTR piRNA precursor mRNAs code for distinct proteins in mice and chickens, they all harbor embedded TEs and produce piRNAs that cleave TEs. Altogether, we discover a function of the piRNA pathway in fine-tuning protein production and reveal a conserved piRNA biogenesis mechanism that recognizes translating RNAs in amniotes.

Download Full-text

tRNA-derived small RNAs target transposable element transcripts

10.1101/085043 ◽

2016 ◽

Cited By ~ 1

Author(s):

Sarah Choudury ◽

R. Keith Slotkin ◽

German Martinez

Keyword(s):

Transposable Element ◽

Small Rnas ◽

Genome Stability ◽

Degradation Products ◽

Male Gamete ◽

Flowering Plant ◽

Wild Type Male ◽

Rna Fragments ◽

Bona Fide ◽

Flowering Plant Species

ABSTRACTtRNA-derived RNA fragments (tRFs) are 18-26 nucleotide small RNAs that are not random degradation products, but are rather specifically cleaved from mature tRNA transcripts. Abundant in stressed or viral-infected cells, the function and potential targets of tRFs are not known. We identified that in the unstressed wild-type male gamete containing pollen of flowering plants, and analogous reproductive structure in non-flowering plant species, tRFs accumulate to high levels. In the reference plant Arabidopsis thaliana, tRFs are cleaved by Dicer-like 1 and incorporated into Argonaute1 (AGO1), akin to a microRNA. We utilized the fact that many plant small RNAs direct cleavage of their target transcripts to demonstrate that where the tRF-AGO1 complex acts to specifically target and cleave endogenous transposable element (TE) mRNAs produced from transcriptionally active TEs. The data presented here demonstrate that tRFs are bona-fide regulatory microRNA-like small RNAs involved in the regulation of genome stability through the targeting of TE transcripts.

Download Full-text