Literature DB >> 21610038

A versatile strategy for gene trapping and trap conversion in emerging model organisms.

Zacharias Kontarakis1, Anastasios Pavlopoulos, Alexandros Kiupakis, Nikolaos Konstantinides, Vassilis Douris, Michalis Averof.   

Abstract

Genetic model organisms such as Drosophila, C. elegans and the mouse provide formidable tools for studying mechanisms of development, physiology and behaviour. Established models alone, however, allow us to survey only a tiny fraction of the morphological and functional diversity present in the animal kingdom. Here, we present iTRAC, a versatile gene-trapping approach that combines the implementation of unbiased genetic screens with the generation of sophisticated genetic tools both in established and emerging model organisms. The approach utilises an exon-trapping transposon vector that carries an integrase docking site, allowing the targeted integration of new constructs into trapped loci. We provide proof of principle for iTRAC in the emerging model crustacean Parhyale hawaiensis: we generate traps that allow specific developmental and physiological processes to be visualised in unparalleled detail, we show that trapped genes can be easily cloned from an unsequenced genome, and we demonstrate targeting of new constructs into a trapped locus. Using this approach, gene traps can serve as platforms for generating diverse reporters, drivers for tissue-specific expression, gene knockdown and other genetic tools not yet imagined.

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Year:  2011        PMID: 21610038     DOI: 10.1242/dev.066324

Source DB:  PubMed          Journal:  Development        ISSN: 0950-1991            Impact factor:   6.868


  16 in total

1.  Reconfiguring gene traps for new tasks using iTRAC.

Authors:  Zacharias Kontarakis; Nikolaos Konstantinides; Anastasios Pavlopoulos; Michalis Averof
Journal:  Fly (Austin)       Date:  2011-10-01       Impact factor: 2.160

2.  Ablation of a single cell from eight-cell embryos of the amphipod crustacean Parhyale hawaiensis.

Authors:  Anastasia R Nast; Cassandra G Extavour
Journal:  J Vis Exp       Date:  2014-03-16       Impact factor: 1.355

Review 3.  Protein trap: a new Swiss army knife for geneticists?

Authors:  Svetlana A Fedorova; Natalya V Dorogova
Journal:  Mol Biol Rep       Date:  2019-11-14       Impact factor: 2.316

4.  Distinct gene expression dynamics in developing and regenerating crustacean limbs.

Authors:  Chiara Sinigaglia; Alba Almazán; Marie Lebel; Marie Sémon; Benjamin Gillet; Sandrine Hughes; Eric Edsinger; Michalis Averof; Mathilde Paris
Journal:  Proc Natl Acad Sci U S A       Date:  2022-07-01       Impact factor: 12.779

5.  The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion.

Authors:  Damian Kao; Alvina G Lai; Evangelia Stamataki; Silvana Rosic; Nikolaos Konstantinides; Erin Jarvis; Alessia Di Donfrancesco; Natalia Pouchkina-Stancheva; Marie Sémon; Marco Grillo; Heather Bruce; Suyash Kumar; Igor Siwanowicz; Andy Le; Andrew Lemire; Michael B Eisen; Cassandra Extavour; William E Browne; Carsten Wolff; Michalis Averof; Nipam H Patel; Peter Sarkies; Anastasios Pavlopoulos; Aziz Aboobaker
Journal:  Elife       Date:  2016-11-16       Impact factor: 8.140

6.  De novo assembly and characterization of a maternal and developmental transcriptome for the emerging model crustacean Parhyale hawaiensis.

Authors:  Victor Zeng; Karina E Villanueva; Ben S Ewen-Campen; Frederike Alwes; William E Browne; Cassandra G Extavour
Journal:  BMC Genomics       Date:  2011-11-25       Impact factor: 3.969

7.  High through-put sequencing of the Parhyale hawaiensis mRNAs and microRNAs to aid comparative developmental studies.

Authors:  Martin J Blythe; Sunir Malla; Richard Everall; Yu-huan Shih; Virginie Lemay; Joanna Moreton; Raymond Wilson; A Aziz Aboobaker
Journal:  PLoS One       Date:  2012-03-20       Impact factor: 3.240

8.  Gal4-based enhancer-trapping in the malaria mosquito Anopheles stephensi.

Authors:  David A O'Brochta; Kristina L Pilitt; Robert A Harrell; Channa Aluvihare; Robert T Alford
Journal:  G3 (Bethesda)       Date:  2012-11-01       Impact factor: 3.154

9.  ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species.

Authors:  Victor Zeng; Cassandra G Extavour
Journal:  Database (Oxford)       Date:  2012-11-23       Impact factor: 3.451

10.  Codon and Amino Acid Usage Are Shaped by Selection Across Divergent Model Organisms of the Pancrustacea.

Authors:  Carrie A Whittle; Cassandra G Extavour
Journal:  G3 (Bethesda)       Date:  2015-09-17       Impact factor: 3.154

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