Endogenous siRNAs Derived from Transposons and mRNAs in Drosophila Somatic Cells

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
Science (Impact Factor: 33.61). 06/2008; 320(5879):1077-81. DOI: 10.1126/science.1157396
Source: PubMed


Small interfering RNAs (siRNAs) direct RNA interference (RNAi) in eukaryotes. In flies, somatic cells produce siRNAs from
exogenous double-stranded RNA (dsRNA) as a defense against viral infection. We identified endogenous siRNAs (endo-siRNAs),
21 nucleotides in length, that correspond to transposons and heterochromatic sequences in the somatic cells of Drosophila melanogaster. We also detected endo-siRNAs complementary to messenger RNAs (mRNAs); these siRNAs disproportionately mapped to the complementary
regions of overlapping mRNAs predicted to form double-stranded RNA in vivo. Normal accumulation of somatic endo-siRNAs requires
the siRNA-generating ribonuclease Dicer-2 and the RNAi effector protein Argonaute2 (Ago2). We propose that endo-siRNAs generated
by the fly RNAi pathway silence selfish genetic elements in the soma, much as Piwi-interacting RNAs do in the germ line.

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Available from: Megha Ghildiyal, May 16, 2014
    • "Introduction to the transformative technology of RNAi: how RNAi is being used in agricultural biotechnology (Munyikwa) Many natural processes in eukaryotic organisms (plants, insects, animals, and nematodes etc.) such as the regulation of gene expression, suppression of invading viruses, and overall protection of the genome have been shown to be mediated by small RNAs. This occurs via a process now universally called RNAi (Fire et al., 1998; Brodersen and Voinnet, 2006; Ghildiyal et al., 2008; Jones-Rhoades et al., 2006; Mallory and Vaucheret, 2006; Huvenne and Smagghe, 2010). The term RNAi was popularized by Fire and Mello following their Nobel Prize winning work in Science or Medicine (2006) which demonstrated the potent effects of double stranded RNA (dsRNA) in Caenorhabditis elegans (Fire et al., 1998) and initiated intense research to understand the mechanisms underlying RNAi and its potential uses. "
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    • "Reviewing previous studies on Drosophila sRNAs we hypothesize that our conclusions drawn on the basis of the tupaia data could also be valid for sRNA silencing pathways in Drosophila. In Drosophila, siRNAs were assumed to silence TEs mainly in the soma, displaying a more or less separation of the siRNA-and piRNA-pathway into soma and germline (Ghildiyal et al. 2008). However, TE-derived si-as well as piRNAs were sequenced from the Drosophila ovary somatic sheet cell line (Lau et al. 2009). "
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    ABSTRACT: Argonaute proteins comprising Piwi-like and Argonaute-like proteins and their guiding small RNAs combat mobile DNA on the transcriptional and post-transcriptional level. While Piwi-like proteins and associated piRNAs are generally restricted to the germline, Argonaute-like proteins and siRNAs have been linked with transposon control in the germline as well as in the soma. Intriguingly, evolution has realized distinct Argonaute subfunctionalization patterns in different species but our knowledge about mammalian RNA interference pathways relies mainly on findings from the mouse model. However, mice differ from other mammals by absence of functional Piwil3 and expression of an oocyte-specific Dicer isoform. Thus, studies beyond the mouse model are required for a thorough understanding of function and evolution of mammalian RNA interference pathways. We high-throughput sequenced small RNAs from the male Tupaia belangeri germline, which represents a close outgroup to primates, hence phylogenetically links mice with humans. We identified transposon-derived piRNAs as well as siRNAs clearly contrasting the separation of piRNA- and siRNA-pathways into male and female germline as seen in mice. Genome-wide analysis of tree shrew transposons reveal that putative siRNAs map to transposon sites that form foldback secondary structures thus representing suitable Dicer substrates. In contrast piRNAs target transposon sites that remain accessible. With this we provide a basic mechanistic explanation how secondary structure of transposon transcripts influences piRNA- and siRNA-pathway utilization. Finally, our analyses of tree shrew piRNA clusters indicate A-Myb and the testis-expressed transcription factor RFX4 to be involved in the transcriptional regulation of mammalian piRNA clusters. © 2015 Rosenkranz et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
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    • "Since many endogenous cells in Drosophila (i.e., follicle, nurse, and salivary gland cells) naturally undergo polyploidization, the different ploidy in OSC and OSS cells may be a natural characteristic. Many Drosophila cell cultures are persistently infected with viruses, such as Drosophila S2 cells (Aliyari et al. 2008; Czech et al. 2008; Ghildiyal et al. 2008; Kawamura et al. 2008; Flynt et al. 2009; Goic et al. 2013) as well as OSS cells (Wu et al. 2010). Drosophila cells stem this viral overload with RNA interference (RNAi) pathways , including the Piwi pathway; however, we have frequently observed newly thawed and stressed OSS and OSC cultures succumb after a few weeks of growth as cells lose adherence to the plastic substrate and lift off in clumps. "
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