Literature DB >> 21460824

A genome-scale shRNA resource for transgenic RNAi in Drosophila.

Jian-Quan Ni1, Rui Zhou, Benjamin Czech, Lu-Ping Liu, Laura Holderbaum, Donghui Yang-Zhou, Hye-Seok Shim, Rong Tao, Dominik Handler, Phillip Karpowicz, Richard Binari, Matthew Booker, Julius Brennecke, Lizabeth A Perkins, Gregory J Hannon, Norbert Perrimon.   

Abstract

Existing transgenic RNAi resources in Drosophila melanogaster based on long double-stranded hairpin RNAs are powerful tools for functional studies, but they are ineffective in gene knockdown during oogenesis, an important model system for the study of many biological questions. We show that shRNAs, modeled on an endogenous microRNA, are extremely effective at silencing gene expression during oogenesis. We also describe our progress toward building a genome-wide shRNA resource.

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Year:  2011        PMID: 21460824      PMCID: PMC3489273          DOI: 10.1038/nmeth.1592

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  26 in total

1.  Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

Authors:  K J Livak; T D Schmittgen
Journal:  Methods       Date:  2001-12       Impact factor: 3.608

2.  The Drosophila SDE3 homolog armitage is required for oskar mRNA silencing and embryonic axis specification.

Authors:  Heather A Cook; Birgit S Koppetsch; Jing Wu; William E Theurkauf
Journal:  Cell       Date:  2004-03-19       Impact factor: 41.582

3.  A distinct small RNA pathway silences selfish genetic elements in the germline.

Authors:  Vasily V Vagin; Alla Sigova; Chengjian Li; Hervé Seitz; Vladimir Gvozdev; Phillip D Zamore
Journal:  Science       Date:  2006-06-29       Impact factor: 47.728

4.  3' UTR seed matches, but not overall identity, are associated with RNAi off-targets.

Authors:  Amanda Birmingham; Emily M Anderson; Angela Reynolds; Diane Ilsley-Tyree; Devin Leake; Yuriy Fedorov; Scott Baskerville; Elena Maksimova; Kathryn Robinson; Jon Karpilow; William S Marshall; Anastasia Khvorova
Journal:  Nat Methods       Date:  2006-03       Impact factor: 28.547

5.  Gal4 in the Drosophila female germline.

Authors:  P Rørth
Journal:  Mech Dev       Date:  1998-11       Impact factor: 1.882

6.  Zygotic lethals with specific maternal effect phenotypes in Drosophila melanogaster. I. Loci on the X chromosome.

Authors:  N Perrimon; L Engstrom; A P Mahowald
Journal:  Genetics       Date:  1989-02       Impact factor: 4.562

Review 7.  Small RNA sorting: matchmaking for Argonautes.

Authors:  Benjamin Czech; Gregory J Hannon
Journal:  Nat Rev Genet       Date:  2010-11-30       Impact factor: 53.242

8.  Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis.

Authors:  Michele A Cleary; Kristopher Kilian; Yanqun Wang; Jeff Bradshaw; Guy Cavet; Wei Ge; Amit Kulkarni; Patrick J Paddison; Kenneth Chang; Nihar Sheth; Eric Leproust; Ernest M Coffey; Julja Burchard; W Richard McCombie; Peter Linsley; Gregory J Hannon
Journal:  Nat Methods       Date:  2004-11-18       Impact factor: 28.547

9.  Regulation of zygotic gene expression in Drosophila primordial germ cells.

Authors:  M Van Doren; A L Williamson; R Lehmann
Journal:  Curr Biol       Date:  1998-02-12       Impact factor: 10.834

10.  A synthetic maternal-effect selfish genetic element drives population replacement in Drosophila.

Authors:  Chun-Hong Chen; Haixia Huang; Catherine M Ward; Jessica T Su; Lorian V Schaeffer; Ming Guo; Bruce A Hay
Journal:  Science       Date:  2007-03-29       Impact factor: 47.728

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  412 in total

1.  Genetic dissection of leukemia-associated IDH1 and IDH2 mutants and D-2-hydroxyglutarate in Drosophila.

Authors:  Zachary J Reitman; Sergey A Sinenko; Eric P Spana; Hai Yan
Journal:  Blood       Date:  2014-11-14       Impact factor: 22.113

2.  Stringent analysis of gene function and protein-protein interactions using fluorescently tagged genes.

Authors:  Ralph A Neumüller; Frederik Wirtz-Peitz; Stella Lee; Young Kwon; Michael Buckner; Roger A Hoskins; Koen J T Venken; Hugo J Bellen; Stephanie E Mohr; Norbert Perrimon
Journal:  Genetics       Date:  2011-12-14       Impact factor: 4.562

3.  Exciting times: bountiful data to facilitate studies of cis-regulatory control.

Authors:  Anil Ozdemir; Angelike Stathopoulos
Journal:  Nat Methods       Date:  2011-11-29       Impact factor: 28.547

Review 4.  RNAi screening: new approaches, understandings, and organisms.

Authors:  Stephanie E Mohr; Norbert Perrimon
Journal:  Wiley Interdiscip Rev RNA       Date:  2011-09-22       Impact factor: 9.957

5.  In Vivo Transcriptional Activation Using CRISPR/Cas9 in Drosophila.

Authors:  Shuailiang Lin; Ben Ewen-Campen; Xiaochun Ni; Benjamin E Housden; Norbert Perrimon
Journal:  Genetics       Date:  2015-08-05       Impact factor: 4.562

6.  The Transgenic RNAi Project at Harvard Medical School: Resources and Validation.

Authors:  Lizabeth A Perkins; Laura Holderbaum; Rong Tao; Yanhui Hu; Richelle Sopko; Kim McCall; Donghui Yang-Zhou; Ian Flockhart; Richard Binari; Hye-Seok Shim; Audrey Miller; Amy Housden; Marianna Foos; Sakara Randkelv; Colleen Kelley; Pema Namgyal; Christians Villalta; Lu-Ping Liu; Xia Jiang; Qiao Huan-Huan; Xia Wang; Asao Fujiyama; Atsushi Toyoda; Kathleen Ayers; Allison Blum; Benjamin Czech; Ralph Neumuller; Dong Yan; Amanda Cavallaro; Karen Hibbard; Don Hall; Lynn Cooley; Gregory J Hannon; Ruth Lehmann; Annette Parks; Stephanie E Mohr; Ryu Ueda; Shu Kondo; Jian-Quan Ni; Norbert Perrimon
Journal:  Genetics       Date:  2015-08-28       Impact factor: 4.562

7.  Cap-n-Collar Promotes Tissue Regeneration by Regulating ROS and JNK Signaling in the Drosophila melanogaster Wing Imaginal Disc.

Authors:  Amanda R Brock; Mabel Seto; Rachel K Smith-Bolton
Journal:  Genetics       Date:  2017-05-16       Impact factor: 4.562

8.  Actin Cytoskeletal Organization in Drosophila Germline Ring Canals Depends on Kelch Function in a Cullin-RING E3 Ligase.

Authors:  Andrew M Hudson; Katelynn M Mannix; Lynn Cooley
Journal:  Genetics       Date:  2015-09-16       Impact factor: 4.562

9.  HITS-CLIP reveals sex-differential RNA binding and alterative splicing regulation of SRm160 in Drosophila.

Authors:  Chen Qiu; Yu Zhang; Yu-Jie Fan; Ting-Lin Pang; Yan Su; Shuai Zhan; Yong-Zhen Xu
Journal:  J Mol Cell Biol       Date:  2019-02-01       Impact factor: 6.216

10.  A Regulatory Response to Ribosomal Protein Mutations Controls Translation, Growth, and Cell Competition.

Authors:  Chang-Hyun Lee; Marianthi Kiparaki; Jorge Blanco; Virginia Folgado; Zhejun Ji; Amit Kumar; Gerard Rimesso; Nicholas E Baker
Journal:  Dev Cell       Date:  2018-08-02       Impact factor: 12.270

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