Rapid evolution and conserved function of the piRNA pathway | Open Biology. 1. Introduction Single celled organisms to complex animals face the threat of pathogens, which are countered by powerful adaptive and innate immune systems [1]. However, the targets of host defence systems can mutate to evade detection or express inhibitors that suppress the host immune response [2]. Host–pathogen interactions thus lead to the positive selection of pathogen mutations that evade the host defences and allow propagation, followed by positive selection of host mutations that restore the pathogen control.
The resulting ‘Red Queen arms race’, characterized by cycles of adaptive evolution, drives rapid coevolution of interacting host and pathogen genes [3]. 1.1. Transposons were discovered by Barbara McClintock through cytogenetic analysis of mosaic pigmentation patterns in maize kernels [7,8]. Retrotransposons move by a copy–paste mechanism with an RNA intermediate [11]. 1.2. Transposons can disrupt the host genome function by a variety of mechanisms. 2. 2.1.1. 2.1.2. 2.1.3.
An ancient satellite repeat controls gene expression and embryonic development in Aedes aegypti through a highly conserved piRNA. Variation in piRNA and Transposable Element Content in Strains of Drosophila melanogaster | Genome Biology and Evolution. We use cookies to enhance your experience on our website. By clicking 'continue' or by continuing to use our website, you are agreeing to our use of cookies.
You can change your cookie settings at any time. We use cookies to enhance your experience on our website.By continuing to use our website, you are agreeing to our use of cookies. You can change your cookie settings at any time. <a href=" Find out more</a> Skip to Main Content Sign In Register Close Advanced Search Article Navigation Volume 6 Issue 10 October 2014 Article Contents Variation in piRNA and Transposable Element Content in Strains of Drosophila melanogaster Jimin Song Department of Genetics, Rutgers University BioMaPS Institute for Quantitative Biology, Rutgers University Search for other works by this author on: Oxford Academic PubMed Google Scholar Jimin Song, Jixia Liu Human Genetics Institute of New Jersey, Rutgers University Oxford Academic PubMed Google Scholar Jixia Liu, Sandra L.
PubMed PubMed Ha. Nanopore sequencing and Hi-C scaffolding provide insight into the evolutionary dynamics of transposable elements and piRNA production in wild strains of Drosophila melanogaster | Nucleic Acids Research. We use cookies to enhance your experience on our website.By continuing to use our website, you are agreeing to our use of cookies. You can change your cookie settings at any time. <a href=" Find out more</a> Skip to Main Content Sign In Register Close Advanced Search Article Navigation Article Contents Comments (0) Nanopore sequencing and Hi-C scaffolding provide insight into the evolutionary dynamics of transposable elements and piRNA production in wild strains of Drosophila melanogaster Christopher E Ellison Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey , Piscataway, NJ, To whom correspondence should be addressed.
Search for other works by this author on: Oxford Academic PubMed Google Scholar Christopher E Ellison, Weihuan Cao Oxford Academic PubMed Google Scholar Weihuan Cao Nucleic Acids Research, gkz1080, Published: 22 November 2019 Article history Received: Accepted: Untangling the web: The diverse functions of the PIWI/piRNA pathway - Mani - 2013 - Molecular Reproduction and Development. Evidence accumulated from many studies in Drosophila suggests that the PIWI/piRNA pathway functions to repress transposons in the germline (Malone et al., 2009; Lau, 2010; Saito and Siomi, 2010; Senti and Brennecke, 2010; Siomi et al., 2010b, 2011).
This is thought to occur at both the transcriptional and post‐transcriptional levels. Important clues about PIWIs, piRNAs, and their association with transposon repression were gained from pioneering work in Drosophila ovaries. piRNAs were identified in the Drosophila ovary by sequencing the small RNAs specifically associated with PIWI proteins. About 80% of the piRNAs identified from the Drosophila ovary (both germ and somatic cells) map to repeat sequences, and the vast majority of these are transposons or transposon remnants (Brennecke et al., 2007). This is a significant enrichment for transposon sequences, as only 10% of the Drosophila genome is composed of repetitive elements (Table 2; Sela et al., 2010). The emerging roles of PIWI-interacting RNA in human cancers | CMAR.
Introduction Among human genes, 70% comprise the actively transcribed genome, less than 3% are protein-coding genes, and most of them are non-coding RNAs (ncRNAs).1–3 The discovery of ncRNAs provides us with a brand new way of understanding gene expression and regulation. Unlike messenger RNA (mRNA), ncRNA functions either in the nucleus by binding to DNA to contribute to gene silencing, or in the cytoplasm by regulating mRNA to affect protein expression. The machinery of coding RNAs and ncRNAs works together to guarantee overall homeostasis. There are two kinds of ncRNA, with different functions, namely regulatory ncRNAs and housekeeper ncRNAs. Discovery of piRNAs There are three groups of piRNAs, namely lncRNA-derived, mRNA-derived, and transposon-derived piRNAs.27,28 The entire lncRNA transcript is the typical source of lncRNA-derived piRNAs. mRNA-derived piRNAs originate from the 3ʹ-untranslated regions (UTRs) of mRNAs and are sense to the mRNA from which they are processed. 1. 2.
Computational identification of piRNA targets on mouse mRNAs | Bioinformatics. Processing math: 100% We use cookies to enhance your experience on our website.By continuing to use our website, you are agreeing to our use of cookies. You can change your cookie settings at any time. <a href=" Find out more</a> Skip to Main Content Sign In Register Close Advanced Search Article Navigation Volume 32 Issue 8 15 April 2016 Article Contents Computational identification of piRNA targets on mouse mRNAs Jiao Yuan Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology and CAS Key Laboratory of Rna Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China †The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors.
Search for other works by this author on: Oxford Academic PubMed Google Scholar Jiao Yuan, Peng Zhang Oxford Academic PubMed Google Scholar Peng Zhang, Ya Cui Oxford Academic PubMed Google Scholar Ya Cui, Jiajia Wang Oxford Academic PubMed Gou. Functional specialization of Piwi proteins in Paramecium tetraurelia from post-transcriptional gene silencing to genome remodelling. - PubMed - NCBI. Phytophthora infestans Argonaute 1 binds microRNA and small RNAs from effector genes and transposable elements - Åsman - 2016.
Introduction RNA plays a central regulatory role in all cellular life forms. Not only is RNA the catalytic component of the ribosome, it also functions in defense against infectious agents and plasmids, mediates epigenetic control of gene expression and is an essential component of the pre‐mRNA splicing machinery. Eukaryotic genomes contain large amounts of nonprotein‐coding RNA (ncRNA) and it has been suggested that it is not the number of genes, but the proportion of ncRNA, that determines organismal complexity (Liu et al., 2013; Morris & Mattick, 2014). Regulatory RNAs of < 200 nucleotides (nt) in length (small RNAs (sRNAs)) act as sequence‐specific guide molecules to direct the silencing of complementary DNA and RNA.
The first RNA silencing process described in plants was double‐stranded RNA‐induced virus resistance, later termed RNA interference (RNAi; Waterhouse et al., 1998). In some species, sRNAs have the capacity to translocate between cells. Materials and Methods Results. Variable genome evolution in fungi after transposon-mediated amplification of a housekeeping gene | Mobile DNA | Full Text. Previous analyses have shown that amplification of genes or gene fragments can have huge effects on genome architecture and evolution. However, as far as we know this is the first analysis in which a housekeeping gene has been amplified to a high copy number as part of a transposable element, yet all of the copies were inactivated, except for the original. This phenomenon resulted in the genome evolving to a much larger size due to the accumulation of numerous RIP-affected copies of inactivated gene fragments. Capture and amplification of a transcript of the housekeeping gene histone H3 as part of a hAT DNA (class II) transposon was identified in six of 12 genomes tested in the family Mycosphaerellaceae, order Capnodiales of the fungal class Dothideomycetes.
In each species all copies were inactivated by RIP, except for the presumed original, leading to one active gene plus hundreds of RIP-inactivated copies scattered throughout the genome. The piRNA Pathway Guards the Germline Genome Against Transposable Elements. Transcriptional Silencing of Transposons by Piwi and Maelstrom and Its Impact on Chromatin State and Gene Expression: Cell. Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y.C., Laslo, P., Cheng, J.X., Murre, C., Singh, H., and Glass, C.K. (2010). Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589.Jayaprakash, A.D., Jabado, O., Brown, B.D., and Sachidanandam, R. (2011). Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing.
Nucleic Acids Res. 39, e141.Jurka, J. (1998). Repeats in genomic DNA: mining and meaning. Curr. Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state. The emerging role of the piRNA/piwi complex in cancer. PIWI-interacting RNAs (piRNAs) constitute a class of recently discovered small non-coding RNAs in germ- and somatic cells comprising 24–31 nucleotides (nt) with a 5′-terminal uridine or tenth position adenosine bias, lacking clear secondary structure motifs [1]. They were first described in 2001 in Drosophila testes as small RNAs derived from the Su(Ste) tandem repeats, which silence Stellate transcripts to maintain male fertility [2].
Unlike miRNAs and siRNAs, which typically rely on RNase type III enzymes to convert double-stranded RNA precursors into functional small RNAs, mature piRNAs derive from an initial transcript encompassing a piRNA cluster via a unique biosynthesis process [3]. piRNAs can bind to piwi proteins to form a piRNA/piwi complex, thereby influencing transposon silencing, spermiogenesis, genome rearrangement, epigenetic regulation, protein regulation, and germ stem-cell maintenance [4]. PiRNA/piwi protein function and mechanism in cancer piRNAs in cancer Table 1.
Decoding the 5′ nucleotide bias of PIWI-interacting RNAs. DNA constructs and transgenic flies Plasmids and oligonucleotides are listed in Supplementary Data 1. Piwi coding sequence (cds) was cloned into pENTRD/TOPO (ThermoFisher). Mutations in Piwi’s specificity loop (SL) were introduced using the Q5 Site-Directed Mutagenesis Kit (NEB), and mutagenic primers were purchased as recommended by the manufacturer (NEBuilder).
Expression vectors were generated through the LR Clonase (ThermoFisher) reaction, using the pPFHW destination vector (UASp promoter, N-terminal 3×FLAG/3×HA) (DGRC: #1125). CRISPR constructs for transgenic piwi>Gal4 flies For the sgRNA construct, oligonucleotides (piwi_sgRNA_f and piwi_sgRNA_r) were annealed and ligated into BbsI-digested U6-BbsI-chiRNA (Addgene # 45946). The CRISPR piwi>Gal4 allele was generated by co-injection of plasmids encoding the sgRNA and the donor construct for genome-editing into TH_attP2 nos-Cas9 flies (Bestgene plan Plan RI, Marker: RFP+/DsRed +).
Immunofluorescence and microscopy Molecular modeling. PIWI-piRNA pathway-mediated transposable element repression in Hydra somatic stem cells. Argonaute protein PIWI controls mobilization of retrotransposons in the Drosophila male germline | Nucleic Acids Research. We use cookies to enhance your experience on our website.By continuing to use our website, you are agreeing to our use of cookies. You can change your cookie settings at any time. <a href=" Find out more</a> Skip to Main Content Sign In Register Close Advanced Search Article Navigation Volume 33 Issue 6 1 April 2005 Article Contents Comments (0) Argonaute protein PIWI controls mobilization of retrotransposons in the Drosophila male germline Alla I.
. * To whom correspondence should be addressed. Search for other works by this author on: Oxford Academic PubMed Google Scholar Alla I. Mikhail S. Oxford Academic PubMed Google Scholar Mikhail S. Vladimir A. Oxford Academic PubMed Google Scholar Vladimir A. Nucleic Acids Research, Volume 33, Issue 6, 1 April 2005, Pages 2052–2059, Published: 01 January 2005 Article history Received: 15 January 2005 Revision received: 06 February 2005 Accepted: 07 March 2005 Abstract Issue Section: Article Figure 1 Cell. PIWI-interacting RNAs: small RNAs with big functions | Nature Reviews Genetics. Pfam: Family: Piwi (PF02171) Puccinia striiformis f. sp. tritici microRNA‐like RNA 1 (Pst‐milR1), an important pathogenicity factor of Pst, impairs wheat resistance to Pst by suppressing the wheat pathogenesis‐related 2 gene - Wang - 2017. Introduction RNA interference (RNAi) is a conserved eukaryotic mechanism in which small RNAs (sRNAs) are involved in the maintenance of RNA stability, RNA processing, biotic stress responses, and the regulation of morphological and developmental processes (Dang et al., 2011). sRNAs are produced from hairpin‐structured or double‐stranded RNA (dsRNA) by RNase III‐like endonucleases called Dicers (Bartel, 2004).
The silencing effects mediated by sRNAs in different pathways require an Argonaute/Piwi protein as the core component of the RNA‐induced silencing complex (RISC; Ghildiyal & Zamore, 2009; Kim et al., 2009). A number of sRNA classes have been described in plants and animals. Based on whether their biogenesis is dependent on Dicer, the known eukaryotic sRNAs can be classified as Dicer‐dependent or Dicer‐independent (Lee et al., 2010). The Dicer‐dependent group of sRNAs includes various small interfering RNAs (siRNAs) and microRNAs (miRNAs; Ghildiyal & Zamore, 2009).
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