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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
...-induced misincorporation tRNA sequencing), an RNA-seq pipeline designed for tRNA analysis (Behrens et al. 2021), in our study of tsRNAs in Drosophila melanogaster. The library construction step of this pipeline includes necessary measures to minimize tRNA modifications that can hinder effective detection and quantitation...
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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
...′ uridylation.DiscussionA deep and broad empirical analysis of miRNA flux across the Drosophila genusIn this study, we extended our previous deep curation of D. melanogaster miRNAs (Berezikov et al. 2011) with largescale empirical analysis of sRNA data across the Drosophila genus, first yielding cloning...
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Resource: Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines
- Jiayu Wen,
- Jaaved Mohammed,
- Diane Bortolamiol-Becet,
- Harrison Tsai,
- Nicolas Robine,
- Jakub O. Westholm,
- Erik Ladewig,
- Qi Dai,
- Katsutomo Okamura,
- Alex S. Flynt,
- Dayu Zhang,
- Justen Andrews,
- Lucy Cherbas,
- Thomas C. Kaufman,
- Peter Cherbas,
- Adam Siepel,
- and Eric C. Lai
Genome Res. July 2014 24: 1236-1250; Published in Advance July 1, 2014, doi:10.1101/gr.161554.113
...and relate these properties back to the animal. Altogether, the deep profiling of small RNAs and mRNAs across this set of cell lines provides a valuable foundation for their study. Results Overview of the Drosophila cell line small RNA data sets We deeply sequenced total small RNAs from 25 cell lines...
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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
...pathways in vertebrates may also regulate TE-associated lncRNAs. Deep-sequencing of inbred fly lines from the Drosophila Genetic Reference Panel has also revealed extensive diversity in de novo TE insertions, with multiple insertions detected per fly line and in all the inbred lines (Linheiro...
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Research: MicroRNA evolution, expression, and function during short germband development in Tribolium castaneum
- Maria Ninova,
- Matthew Ronshaugen,
- and Sam Griffiths-Jones
Genome Res. January 2016 26: 85-96; Published in Advance October 30, 2015, doi:10.1101/gr.193367.115
...and vertebrates (for review, see Kloosterman and Plasterk 2006). Most of our understanding of microRNA function in the development of arthropods comes from studies in the classical model organism Drosophila melanogaster, where they control essential developmental processes suchas...
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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
.... Science 318: 271–274. Creighton CJ, Reid JG, Gunaratne PH. 2009. Expression profiling of microRNAs by deep sequencing. Brief Bioinform 10: 490–497. Czech B,Malone CD, Zhou R, Stark A, Schlingeheyde C, DusM, PerrimonN, Kellis M, Wohlschlegel JA, Sachidanandam R, et al. 2008. An endogenous small interfering...
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Research: Discovery of hundreds of mirtrons in mouse and human small RNA data
- Erik Ladewig,
- Katsutomo Okamura,
- Alex S. Flynt,
- Jakub O. Westholm,
- and Eric C. Lai
Genome Res. September 2012 22: 1634-1645; doi:10.1101/gr.133553.111
...additional splicingderived miRNAs have mostly been incidental, and adjunct to efforts to annotate canonical miRNAs. However, algorithms that identify miRNAs from deep sequence data do not necessarily identify mirtrons, owing to their distinct properties. We recently compiled >100–200 small RNAdata sets from...
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Resource: Synthetic spike-in standards for RNA-seq experiments
- Lichun Jiang,
- Felix Schlesinger,
- Carrie A. Davis,
- Yu Zhang,
- Renhua Li,
- Marc Salit,
- Thomas R. Gingeras,
- and Brian Oliver
Genome Res. September 2011 21: 1543-1551; Published in Advance August 4, 2011, doi:10.1101/gr.121095.111
...aligned (for parameters, see Methods) to the Drosophila melanogaster , and the vastmajority of these readswere due to polyA/T alignments to unassembled portions of the . Less than 0.01% of reads in the library mapped to the human (hg19). Any spurious alignments of the ERCC reads to genes result in density...
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Research: Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality
- Daniel F. Simola,
- Lothar Wissler,
- Greg Donahue,
- Robert M. Waterhouse,
- Martin Helmkampf,
- Julien Roux,
- Sanne Nygaard,
- Karl M. Glastad,
- Darren E. Hagen,
- Lumi Viljakainen,
- Justin T. Reese,
- Brendan G. Hunt,
- Dan Graur,
- Eran Elhaik,
- Evgenia V. Kriventseva,
- Jiayu Wen,
- Brian J. Parker,
- Elizabeth Cash,
- Eyal Privman,
- Christopher P. Childers,
- Monica C. Muñoz-Torres,
- Jacobus J. Boomsma,
- Erich Bornberg-Bauer,
- Cameron R. Currie,
- Christine G. Elsik,
- Garret Suen,
- Michael A.D. Goodisman,
- Laurent Keller,
- Jürgen Liebig,
- Alan Rawls,
- Danny Reinberg,
- Chris D. Smith,
- Chris R. Smith,
- Neil Tsutsui,
- Yannick Wurm,
- Evgeny M. Zdobnov,
- Shelley L. Berger,
- and Jürgen Gadau
Genome Res. August 2013 23: 1235-1247; Published in Advance May 1, 2013, doi:10.1101/gr.155408.113
..., which have comparable divergence time to the 12 sequenced Drosophila species, and to 86% between the two leaf-cutter ants (Supplemental Fig. 12A). Thus, despite fragmented assemblies and deep evolutionary history, ant s show moderate to strong genomic synteny, especially in gene-rich, euchromatic...
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Research: Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity
- Stacia K. Wyman,
- Emily C. Knouf,
- Rachael K. Parkin,
- Brian R. Fritz,
- Daniel W. Lin,
- Lucas M. Dennis,
- Michael A. Krouse,
- Philippa J. Webster,
- and Muneesh Tewari
Genome Res. September 2011 21: 1450-1461; Published in Advance August 3, 2011, doi:10.1101/gr.118059.110
...; 8Department of Medicine, University of Washington, Seattle, Washington 98195, USA ↵ 9 These authors contributed equally to this work. ↵ 10 Present address: Illumina, Inc., 9865 Towne Centre Drive, San Diego, CA 92121, USA. Abstract Modification of microRNA...

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