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Research: A low-abundance class of Dicer-dependent siRNAs produced from a variety of features in C. elegans
- Thiago L. Knittel,
- Brooke E. Montgomery,
- Alex J. Tate,
- Ennis W. Deihl,
- Anastasia S. Nawrocki,
- Frederic J. Hoerndli,
- and Taiowa A. Montgomery
Genome Res. December 2024 34: 2203-2216; Published in Advance December 2, 2024, doi:10.1101/gr.279083.124
...that under optimal growth conditions, RDE-1 is not important for development. The lack of a clear phenotype in rde-1 mutants is reminiscent of the mild phenotypes originally observed in Drosophila AGO2 mutants, which appear superficially wild-type but have nonessential roles in germ cell development and male...
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Research: Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary
- Satyam P. Srivastav,
- Cédric Feschotte,
- and Andrew G. Clark
Genome Res. May 2024 34: 711-724; Published in Advance May 15, 2024, doi:10.1101/gr.278062.123
...in Drosophila melanogaster, much less is known about the origin and evolution of piCs in this or any other species. To investigate piC origin and evolution, we use a population genomic approach to compare piC activity and sequence composition across eight geographically distant strains of D. melanogaster...
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Research: Experimentally evolving Drosophila erecta populations may fail to establish an effective piRNA-based host defense against invading P-elements
- Divya Selvaraju,
- Filip Wierzbicki,
- and Robert Kofler
Genome Res. March 2024 34: 410-425; Published in Advance March 15, 2024, doi:10.1101/gr.278706.123
...(20–22 nt) may also contribute to the silencing of TEs (Chung et al. 2008; Czech et al. 2008; Barckmann et al. 2018). In contrast to piRNAs, which are solely found in the germline of most Drosophila species, siRNAs are found both in the germline and the somatic cells (Lewis et al. 2018). The siRNA...
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Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
- Junling Shi,
- Jiaqi Xu,
- Jun Ma,
- and Feng He
Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
...relative to miRNAs. This distinction may be reflective of the differences in size, abundance, modifications, and associated Argonaute proteins between tsRNAs and miRNAs. In Drosophila, miRNAs, siRNAs, and piRNAs execute post-transcriptional regulation by primarily binding to AGO1, AGO2, and AGO3/PIWI...
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Resource: Dynamic regulation of gonadal transposon control across the lifespan of the naturally short-lived African turquoise killifish
- Bryan B. Teefy,
- Ari Adler,
- Alan Xu,
- Katelyn Hsu,
- Param Priya Singh,
- and Bérénice A. Benayoun
Genome Res. January 2023 33: 141-153; Published in Advance December 28, 2022, doi:10.1101/gr.277301.122
...trajectories in addition to just gonadal aging end points. Indeed, we found that many key events, including those relating to TE regulation and piRNA pathway regulation, are most salient in middle-aged ovaries, rather than undergoing linear changes with age. Our observations differ from reports in Drosophila...
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Research: Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus
- Jaaved Mohammed,
- Alex S. Flynt,
- Alexandra M. Panzarino,
- Md Mosharrof Hossain Mondal,
- Matthew DeCruz,
- Adam Siepel,
- and Eric C. Lai
Genome Res. January 2018 28: 52-65; Published in Advance December 12, 2017, doi:10.1101/gr.226068.117
..., University of Southern Mississippi, Hattiesburg, Mississippi 39406, USA ↵6 These authors contributed equally to this work. Corresponding author: laie@mskcc.orgAbstractTo assess miRNA evolution across the Drosophila genus, we analyzed several billion small RNA reads across 12 fruit fly species. These data...
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Letter: Abundant primary piRNAs, endo-siRNAs, and microRNAs in a Drosophila ovary cell line
- Nelson C. Lau,
- Nicolas Robine,
- Raquel Martin,
- Wei-Jen Chung,
- Yuzo Niki,
- Eugene Berezikov,
- and Eric C. Lai
Genome Res. October 2009 19: 1776-1785; Published in Advance June 18, 2009, doi:10.1101/gr.094896.109
...elements (TEs). We analyzed the Drosophila ovary somatic sheet (OSS) cell line and found that it expresses miRNAs, endogenous small interfering RNAs (endo-siRNAs), and piRNAs in abundance. In contrast to intact gonads, which contain mixtures of germline and somatic cell types that express different Piwi...
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Letter: Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila
- Jian Lu and
- Andrew G. Clark
Genome Res. February 2010 20: 212-227; Published in Advance November 30, 2009, doi:10.1101/gr.095406.109
...Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila Jian Lu and Andrew G. Clark 1 Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA Abstract Transposable elements (TEs...
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Research: Small RNA profiling of Xenopus embryos reveals novel miRNAs and a new class of small RNAs derived from intronic transposable elements
- Joanne L. Harding,
- Stuart Horswell,
- Claire Heliot,
- Javier Armisen,
- Lyle B. Zimmerman,
- Nicholas M. Luscombe,
- Eric A. Miska,
- and Caroline S. Hill
Genome Res. January 2014 24: 96-106; Published in Advance September 24, 2013, doi:10.1101/gr.144469.112
.... 2008). Vertebrate piRNAs are 25- to 30-nt small RNAs that function via interaction with Piwi proteins of the Argonaute family and were initially discovered in Drosophila (Aravin et al. 2003). piRNAs are complementary to intergenic repeats and mediate silencing of 2014 Harding et al. This article...
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Research: Transposable element dynamics and PIWI regulation impacts lncRNA and gene expression diversity in Drosophila ovarian cell cultures
- Yuliya A. Sytnikova,
- Reazur Rahman,
- Gung-wei Chirn,
- Josef P. Clark,
- and Nelson C. Lau
Genome Res. December 2014 24: 1977-1990; Published in Advance September 29, 2014, doi:10.1101/gr.178129.114
...-interacting RNAs (piRNAs) repress transposable elements (TEs) from mobilizing in gonadal cells. To determine the spectrum of piRNA-regulated targets that may extend beyond TEs, we conducted a genome-wide survey for transcripts associated with PIWI and for transcripts affected by PIWI knockdown in Drosophila...

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