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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

Comparison of gene sets involved in embryonic versus postembryonic development.(a) The gene sets required for cuticle morphology (that is, epidermal patterning) during embryogenesis and typical insect metamorphosis are largely non-overlapping. This indicates that patterning principles may differ to quite some extent between these two stages of major morphological change. (b,c) This observation also holds true for the subsets affecting leg morphology (b) and GFP marked somatic muscles (c) indicating that both ectodermal and other patterning processes differ. (d) Gene sets required for ovary function. Many genes required for egg production in the pupal injection screen (green circle) were lethal in the larval injection screen. Hence, reduced egg production for these genes was probably due to starvation (green area outside hatched line). When comparing the non-lethal treatments (blue circle and green circle with hatched blue outline) the number of genes with an ovary phenotype in the pupal and larval injection screen are more similar. Insets: relations to the entire data set.
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f3: Comparison of gene sets involved in embryonic versus postembryonic development.(a) The gene sets required for cuticle morphology (that is, epidermal patterning) during embryogenesis and typical insect metamorphosis are largely non-overlapping. This indicates that patterning principles may differ to quite some extent between these two stages of major morphological change. (b,c) This observation also holds true for the subsets affecting leg morphology (b) and GFP marked somatic muscles (c) indicating that both ectodermal and other patterning processes differ. (d) Gene sets required for ovary function. Many genes required for egg production in the pupal injection screen (green circle) were lethal in the larval injection screen. Hence, reduced egg production for these genes was probably due to starvation (green area outside hatched line). When comparing the non-lethal treatments (blue circle and green circle with hatched blue outline) the number of genes with an ovary phenotype in the pupal and larval injection screen are more similar. Insets: relations to the entire data set.

Mentions: For the first time our data allow the systematic comparison of the gene sets required for embryonic and postembryonic development in an insect with typical metamorphosis. Importantly, larval cells are largely re-used to form the adult epidermis in most insects, instead of being replaced by imaginal cells as is the case in Drosophila24. Nevertheless, the gene sets involved in embryonic and postembryonic patterning turned out to be largely non-overlapping (Fig. 3a). This is true for processes as different as leg or muscle development (Fig. 3b,c). In the case of oogenesis, the respective numbers are probably an overestimation because most genes leading to reduced egg production in the pupal screen were lethal in the larval screen (Fig. 3d). We assume that many of these apparent oogenesis phenotypes reflect incomplete knockdown of genes with basic physiological function because we found that many animals with reduced oogenesis showed a strongly reduced fat body. Subtracting these genes (those outside the dashed line in Fig. 3d), the overlap of genes with defects in both screening parts increases substantially. Together, these data reveal that development during typical insect metamorphosis partially relies on different mechanisms than during embryogenesis.


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)

Comparison of gene sets involved in embryonic versus postembryonic development.(a) The gene sets required for cuticle morphology (that is, epidermal patterning) during embryogenesis and typical insect metamorphosis are largely non-overlapping. This indicates that patterning principles may differ to quite some extent between these two stages of major morphological change. (b,c) This observation also holds true for the subsets affecting leg morphology (b) and GFP marked somatic muscles (c) indicating that both ectodermal and other patterning processes differ. (d) Gene sets required for ovary function. Many genes required for egg production in the pupal injection screen (green circle) were lethal in the larval injection screen. Hence, reduced egg production for these genes was probably due to starvation (green area outside hatched line). When comparing the non-lethal treatments (blue circle and green circle with hatched blue outline) the number of genes with an ovary phenotype in the pupal and larval injection screen are more similar. 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

f3: Comparison of gene sets involved in embryonic versus postembryonic development.(a) The gene sets required for cuticle morphology (that is, epidermal patterning) during embryogenesis and typical insect metamorphosis are largely non-overlapping. This indicates that patterning principles may differ to quite some extent between these two stages of major morphological change. (b,c) This observation also holds true for the subsets affecting leg morphology (b) and GFP marked somatic muscles (c) indicating that both ectodermal and other patterning processes differ. (d) Gene sets required for ovary function. Many genes required for egg production in the pupal injection screen (green circle) were lethal in the larval injection screen. Hence, reduced egg production for these genes was probably due to starvation (green area outside hatched line). When comparing the non-lethal treatments (blue circle and green circle with hatched blue outline) the number of genes with an ovary phenotype in the pupal and larval injection screen are more similar. Insets: relations to the entire data set.
Mentions: For the first time our data allow the systematic comparison of the gene sets required for embryonic and postembryonic development in an insect with typical metamorphosis. Importantly, larval cells are largely re-used to form the adult epidermis in most insects, instead of being replaced by imaginal cells as is the case in Drosophila24. Nevertheless, the gene sets involved in embryonic and postembryonic patterning turned out to be largely non-overlapping (Fig. 3a). This is true for processes as different as leg or muscle development (Fig. 3b,c). In the case of oogenesis, the respective numbers are probably an overestimation because most genes leading to reduced egg production in the pupal screen were lethal in the larval screen (Fig. 3d). We assume that many of these apparent oogenesis phenotypes reflect incomplete knockdown of genes with basic physiological function because we found that many animals with reduced oogenesis showed a strongly reduced fat body. Subtracting these genes (those outside the dashed line in Fig. 3d), the overlap of genes with defects in both screening parts increases substantially. Together, these data reveal that development during typical insect metamorphosis partially relies on different mechanisms than during embryogenesis.

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