Dataset Information

The developmental proteome of Drosophila melanogaster (embryogenesis)

ABSTRACT: Drosophila melanogaster is a well-studied genetic model organism with several large-scale transcriptome resources. Here we investigate 7,952 proteins during the fly life cycle from embryo to adult and also provide a high-resolution temporal time course proteome of 5,458 proteins during embryogenesis. We use our large scale data set to compare transcript/protein expression, uncovering examples of extreme differences between mRNA and protein abundance. In the embryogenesis proteome, the time delay in protein synthesis after transcript expression was determined. For some proteins, including the transcription factor lola, we monitor isoform specific expression levels during early fly development. Furthermore, we obtained firm evidence of 268 small proteins, which are hard to predict by bioinformatics. We observe peptides originating from non-coding regions of the genome and identified Cyp9f3psi as a protein-coding gene. As a powerful resource to the community, we additionally created an interactive web interface (http://www.butterlab.org) advancing the access to our data.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Drosophila Melanogaster (fruit Fly)

SUBMITTER: F Butter

LAB HEAD: Falk Butter

PROVIDER: PXD005713 | Pride | 2017-04-07

REPOSITORIES: Pride

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			Action	DRS
	20150513_QEP2_FBU_AB_3D_set1_10h_01.raw	Raw
	20150513_QEP2_FBU_AB_3D_set1_10h_02.raw	Raw
	20150513_QEP2_FBU_AB_3D_set1_10h_03.raw	Raw
	20150513_QEP2_FBU_AB_3D_set1_10h_04.raw	Raw
	20150513_QEP2_FBU_AB_3D_set1_12h_01.raw	Raw

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The developmental proteome of Drosophila melanogaster.

Casas-Vila Nuria N Bluhm Alina A Sayols Sergi S Dinges Nadja N Dejung Mario M Altenhein Tina T Kappei Dennis D Altenhein Benjamin B Roignant Jean-Yves JY Butter Falk F

Genome research 20170405 7

Drosophila melanogaster is a widely used genetic model organism in developmental biology. While this model organism has been intensively studied at the 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 7952 proteins, and provide a high temporal-resolved embryogenesis proteome of 5458 proteins. Our proteome data ena ...[more]

PMID: 28381612

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Project description:Long non-coding RNAs (lncRNAs) comprise a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins. Recent genome-wide studies in human and mouse have annotated lncRNAs expressed in cell lines and adult tissues, but a systematic analysis of lncRNAs expressed during vertebrate embryogenesis has been elusive. To identify lncRNAs with potential functions in vertebrate embryogenesis, we performed a time series of RNA-Seq experiments at eight stages during early zebrafish development. We reconstructed 56,535 high-confidence transcripts in 28,912 loci, recovering the vast majority of expressed RefSeq transcripts, while identifying thousands of novel isoforms and expressed loci. We defined a stringent set of 1,133 non-coding multi-exonic transcripts expressed during embryogenesis. These include long intergenic ncRNAs (lincRNAs), intronic overlapping lncRNAs, exonic antisense overlapping lncRNAs, and precursors for small RNAs (sRNAs). Zebrafish lncRNAs share many of the characteristics of their mammalian counterparts: relatively short length, low exon number, low expression, and conservation levels comparable to introns. Subsets of lncRNAs carry chromatin signatures characteristic of genes with developmental functions. The temporal expression profile of lncRNAs revealed two novel properties: lncRNAs are expressed in narrower time windows than protein-coding genes and are specifically enriched in early-stage embryos. In addition, several lncRNAs show tissue-specific expression and distinct subcellular localization patterns. Integrative computational analyses associated individual lncRNAs with specific pathways and functions, ranging from cell cycle regulation to morphogenesis. Our study provides the first comprehensive identification of lncRNAs in a vertebrate embryo and forms the foundation for future genetic, genomic and evolutionary studies. RNA-Seq for 8 zebrafish developmental stages, 2 lanes for each stage (3 for shield).

Dataset Information

The developmental proteome of Drosophila melanogaster (embryogenesis)

Dataset's files

Publications

The developmental proteome of <i>Drosophila melanogaster</i>.

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