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Abstract:

Drosophila melanogaster is a widely used genetic model organism in developmental biology. While this model organism has been intensively studied at RNA level, a comprehensive proteomic study covering the complete life cycle is still missing. Here, we apply label-free quantitative proteomics to explore proteome remodeling across Drosophila's life cycle, resulting in 7,952 proteins, and provide a high temporal-resolved embryogenesis proteome of 5,458 proteins. Our proteome data enabled us to monitor isoform-specific expression of 34 genes during development, to identify the pseudogene Cyp9fpsi as a protein-coding gene and to obtain evidence of 268 small proteins. Moreover, the comparison with available transcriptomic data uncovered examples of poor correlation between mRNA and protein, underscoring the importance of proteomics to study developmental progression. Data integration of our embryogenesis proteome with tissue-specific data revealed spatial and temporal information for further functional studies of yet uncharacterized proteins. Overall, our high resolution proteomes provide a powerful resource and can be explored in detail in our interactive web interface.

Please cite:

Casas-Vila N.*, Bluhm A.*, Sayols S.*, Dinges N., Dejung M., Altenhein T., Kappei D., Altenhein B., Roignant J.-Y. and Butter F.
The developmental proteome of Drosophila melanogaster. Genome Res. (2017) 27, 1273-1285

How To

A how to for this webinterface is available for download:
How To

Additional Data:

Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, Tuch BB, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green RE, Hammonds A, Jiang L, Kapranov P, Langton L, Perrimon N, Sandler JE, Wan KH, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel PJ, Brenner SE, Brent MR, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Oliver B, Celniker SE. 2011. The developmental transcriptome of Drosophila melanogaster. Nature 471:473-479.

Sury MD, Chen JX, Selbach M. 2010. The SILAC fly allows for accurate protein quantification in vivo. Mol Cell Proteomics 9:2173-2183.

Lécuyer E, Yoshida H, Parthasarathy N, Alm C, Babak T, Cerovina T, Hughes TR, Tomancak P, Krause HM. 2007. Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Cell 131:174-187.

Acknowledgements:

Hosting of this webpage is supported by Zentrum für Datenverarbeitung (ZDV), University of Mainz.

Selected proteins:

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* Hover over the points to get the gene names.

* Hover over the lines to get the gene names.

Selected proteins:

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* Hover over the lines to get the gene names.

* Hover over the lines to get the gene names.

Impressum/Contact

AG Butter
Ackermannweg 4
55129 Mainz
Germany