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The iBeetle large-scale RNAi screen reveals gene functions for insect development and physiology.

Schmitt-Engel C, Schultheis D, Schwirz J, Ströhlein N, Troelenberg N, Majumdar U, Dao VA, Grossmann D, Richter T, Tech M, Dönitz J, Gerischer L, Theis M, Schild I, Trauner J, Koniszewski ND, Küster E, Kittelmann S, Hu Y, Lehmann S, Siemanowski J, Ulrich J, Panfilio KA, Schröder R, Morgenstern B, Stanke M, Buchhholz F, Frasch M, Roth S, Wimmer EA, Schoppmeier M, Klingler M, Bucher G - Nat Commun (2015)

Bottom Line: Therefore, although deep sequencing is revealing the genes of ever more insect species, the functional studies predominantly focus on candidate genes previously identified in Drosophila, which is biasing research towards conserved gene functions.RNAi screens in other organisms promise to reduce this bias.This work transcends the restrictions of the candidate gene approach and opens fields of research not accessible in Drosophila.

View Article: PubMed Central - PubMed

Affiliation: 1] Johann-Friedrich-Blumenbach-Institut, GZMB, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany [2] Department Biologie, Entwicklungsbiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstraße 5, 91058 Erlangen, Germany.

ABSTRACT
Genetic screens are powerful tools to identify the genes required for a given biological process. However, for technical reasons, comprehensive screens have been restricted to very few model organisms. Therefore, although deep sequencing is revealing the genes of ever more insect species, the functional studies predominantly focus on candidate genes previously identified in Drosophila, which is biasing research towards conserved gene functions. RNAi screens in other organisms promise to reduce this bias. Here we present the results of the iBeetle screen, a large-scale, unbiased RNAi screen in the red flour beetle, Tribolium castaneum, which identifies gene functions in embryonic and postembryonic development, physiology and cell biology. The utility of Tribolium as a screening platform is demonstrated by the identification of genes involved in insect epithelial adhesion. This work transcends the restrictions of the candidate gene approach and opens fields of research not accessible in Drosophila.

No MeSH data available.


Related in: MedlinePlus

Essential and lethal genes.(a) For more than 56% of the injected genes, phenotypes were observed. The pupal injection screen revealed phenotypes for a larger portion of genes compared with the larval injection screen. (b) Death of the injected animals was scored 22 days post injection (larval injection; blue circle) and 11 days post injection (pupal and larval injection; dark green and hatched blue circles). Note that embryonic lethality is based on maternal and zygotic gene knockdown. ‘Parental lethal': death of the injected animal. (c) Selected phenotypic categories after pupal injection. Embryonic lethal injections are further categorized showing that more than half of the embryonic lethal genes lead to abortion of embryogenesis before cuticle secretion. (d) Phenotypic categories after larval injection. ‘Defects during the process of metamorphosis': metamorphosis not completed or entered precociously. Insets: relations to the entire data set.
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f2: Essential and lethal genes.(a) For more than 56% of the injected genes, phenotypes were observed. The pupal injection screen revealed phenotypes for a larger portion of genes compared with the larval injection screen. (b) Death of the injected animals was scored 22 days post injection (larval injection; blue circle) and 11 days post injection (pupal and larval injection; dark green and hatched blue circles). Note that embryonic lethality is based on maternal and zygotic gene knockdown. ‘Parental lethal': death of the injected animal. (c) Selected phenotypic categories after pupal injection. Embryonic lethal injections are further categorized showing that more than half of the embryonic lethal genes lead to abortion of embryogenesis before cuticle secretion. (d) Phenotypic categories after larval injection. ‘Defects during the process of metamorphosis': metamorphosis not completed or entered precociously. Insets: relations to the entire data set.

Mentions: Of the 3,400 genes tested in both the larval and pupal screens, 56.3% gave any phenotype (Fig. 2a), with 49.6% being lethal for at least one developmental stage (Fig. 2b). In all, 22.9% of the genes displayed a phenotype in both screens, while almost twice as many genes showed a phenotype exclusively in the pupal screen (21.1%) compared with phenotypes restricted to the larval screen (12.3%; Fig. 2a). Thirteen per cent of the genes showing any phenotype (including lethality) were beetle specific genes (Supplementary Table 1), illustrating the importance of screens in additional model organisms (see Supplementary Table 3 for definition of phenotype classes and Supplementary Data 2 for lists of treatments in the respective classes).


The iBeetle large-scale RNAi screen reveals gene functions for insect development and physiology.

Schmitt-Engel C, Schultheis D, Schwirz J, Ströhlein N, Troelenberg N, Majumdar U, Dao VA, Grossmann D, Richter T, Tech M, Dönitz J, Gerischer L, Theis M, Schild I, Trauner J, Koniszewski ND, Küster E, Kittelmann S, Hu Y, Lehmann S, Siemanowski J, Ulrich J, Panfilio KA, Schröder R, Morgenstern B, Stanke M, Buchhholz F, Frasch M, Roth S, Wimmer EA, Schoppmeier M, Klingler M, Bucher G - Nat Commun (2015)

Essential and lethal genes.(a) For more than 56% of the injected genes, phenotypes were observed. The pupal injection screen revealed phenotypes for a larger portion of genes compared with the larval injection screen. (b) Death of the injected animals was scored 22 days post injection (larval injection; blue circle) and 11 days post injection (pupal and larval injection; dark green and hatched blue circles). Note that embryonic lethality is based on maternal and zygotic gene knockdown. ‘Parental lethal': death of the injected animal. (c) Selected phenotypic categories after pupal injection. Embryonic lethal injections are further categorized showing that more than half of the embryonic lethal genes lead to abortion of embryogenesis before cuticle secretion. (d) Phenotypic categories after larval injection. ‘Defects during the process of metamorphosis': metamorphosis not completed or entered precociously. Insets: relations to the entire data set.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4525174&req=5

f2: Essential and lethal genes.(a) For more than 56% of the injected genes, phenotypes were observed. The pupal injection screen revealed phenotypes for a larger portion of genes compared with the larval injection screen. (b) Death of the injected animals was scored 22 days post injection (larval injection; blue circle) and 11 days post injection (pupal and larval injection; dark green and hatched blue circles). Note that embryonic lethality is based on maternal and zygotic gene knockdown. ‘Parental lethal': death of the injected animal. (c) Selected phenotypic categories after pupal injection. Embryonic lethal injections are further categorized showing that more than half of the embryonic lethal genes lead to abortion of embryogenesis before cuticle secretion. (d) Phenotypic categories after larval injection. ‘Defects during the process of metamorphosis': metamorphosis not completed or entered precociously. Insets: relations to the entire data set.
Mentions: Of the 3,400 genes tested in both the larval and pupal screens, 56.3% gave any phenotype (Fig. 2a), with 49.6% being lethal for at least one developmental stage (Fig. 2b). In all, 22.9% of the genes displayed a phenotype in both screens, while almost twice as many genes showed a phenotype exclusively in the pupal screen (21.1%) compared with phenotypes restricted to the larval screen (12.3%; Fig. 2a). Thirteen per cent of the genes showing any phenotype (including lethality) were beetle specific genes (Supplementary Table 1), illustrating the importance of screens in additional model organisms (see Supplementary Table 3 for definition of phenotype classes and Supplementary Data 2 for lists of treatments in the respective classes).

Bottom Line: Therefore, although deep sequencing is revealing the genes of ever more insect species, the functional studies predominantly focus on candidate genes previously identified in Drosophila, which is biasing research towards conserved gene functions.RNAi screens in other organisms promise to reduce this bias.This work transcends the restrictions of the candidate gene approach and opens fields of research not accessible in Drosophila.

View Article: PubMed Central - PubMed

Affiliation: 1] Johann-Friedrich-Blumenbach-Institut, GZMB, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany [2] Department Biologie, Entwicklungsbiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstraße 5, 91058 Erlangen, Germany.

ABSTRACT
Genetic screens are powerful tools to identify the genes required for a given biological process. However, for technical reasons, comprehensive screens have been restricted to very few model organisms. Therefore, although deep sequencing is revealing the genes of ever more insect species, the functional studies predominantly focus on candidate genes previously identified in Drosophila, which is biasing research towards conserved gene functions. RNAi screens in other organisms promise to reduce this bias. Here we present the results of the iBeetle screen, a large-scale, unbiased RNAi screen in the red flour beetle, Tribolium castaneum, which identifies gene functions in embryonic and postembryonic development, physiology and cell biology. The utility of Tribolium as a screening platform is demonstrated by the identification of genes involved in insect epithelial adhesion. This work transcends the restrictions of the candidate gene approach and opens fields of research not accessible in Drosophila.

No MeSH data available.


Related in: MedlinePlus