The Developmental Transcriptome of Drosophila melanogaster

By Brenton R. Graveley, Angela N. Brooks, Joseph W. Carlson, Michael O. Duff, J. Landolin, Li Yang, C. Artieri, M. V. van Baren, Nathan Boley, Benjamin W. Booth and 37 more. Nature, 2010

1,557 citations recorded by the source corpus.

Drosophila melanogaster is one of the most well studied genetic model organisms; nonetheless, its genome still contains unannotated coding and non-coding genes, transcripts, exons and RNA editing sites. Full discovery and annotation are pre-requisites for understanding how the regulation of transcription, splicing and RNA editing directs the development of this complex organism. Here we used RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages. We identified 111,195 new elements, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events, and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches. These data substantially expand the number of known transcribed elements in the Drosophila genome and provide a high-resolution view of transcriptome dynamics throughout development.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b92373d91798fe47b155ed649e49bf7f4307bcf8

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Citations in the corpus

RADAR: a rigorously annotated database of A-to-I RNA editing (2013, methodology): “(30) identified RNA editing sites using RNA sequencing data from the modENCODE consortium, Rodriguez et al.”
FlyBase: updates to the Drosophila melanogaster knowledge base (2020, neutral): “The data presented is derived from two sources: anatomy expression data manually curated by FlyBase from individual publications and high-throughput stage-specific RNA-seq data from the modENCODE project (17).”
Spatial reconstruction of single-cell gene expression (2015, methodology): “Seurat consists of the following steps: (1) It uses co-expression patterns across cells in the single-cell RNA-seq profiles to impute the expression of each landmark gene in each cell.”
FlyBase 102—advanced approaches to interrogating FlyBase (2013, background): “For several different RNA-Seq datasets, these bin values are displayed on Gene Reports as histograms to illustrate the pattern of expression either through developmental time, across different tissues, in different cell lines or in response to different treatments (3).”
A Protein Complex Network of Drosophila melanogaster (2011, methodology): “(B) Distribution of correlation coefficients between mRNAs corresponding to interacting proteins in the DPiM compared to all gene pairs, based on the RNA-Seq data (Graveley et al., 2011).”
Ultrasensitive proteome analysis using paramagnetic bead technology (2014, neutral): “Ultrasensitive proteome analysis Christopher S Hughes et al differential abundance in proteins such as Kugelkern, which is known to be present throughout early embryogenesis, switching from a maternally deposited isoform to a zygotic form thereafter (Guilgur et al , 2014).”
The mysterious presence of a 5-methylcytosine oxidase in the Drosophila genome (2013, background): “4).(59) This tissue specificity mirrors the expression pattern in mice, where Tet3 expression has been reported to be high in the developing brain,(60) the tissue which also has the highest reported levels of 5hmC.”
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