Diversity and dynamics of the Drosophila transcriptome

By James B. Brown, Nathan Boley, R. Eisman, Gemma E. May, M. Stoiber, M. Duff, Benjamin W. Booth, Jiayu Wen, Soo Park, A. Suzuki and 31 more. Nature, 2014

685 citations recorded by the source corpus.

Animal transcriptomes are dynamic, with each cell type, tissue and organ system expressing an ensemble of transcript isoforms that give rise to substantial diversity. Here we have identified new genes, transcripts and proteins using poly(A)+ RNA sequencing from Drosophila melanogaster in cultured cell lines, dissected organ systems and under environmental perturbations. We found that a small set of mostly neural-specific genes has the potential to encode thousands of transcripts each through extensive alternative promoter usage and RNA splicing. The magnitudes of splicing changes are larger between tissues than between developmental stages, and most sex-specific splicing is gonad-specific. Gonads express hundreds of previously unknown coding and long non-coding RNAs (lncRNAs), some of which are antisense to protein-coding genes and produce short regulatory RNAs. Furthermore, previously identified pervasive intergenic transcription occurs primarily within newly identified introns. The fly transcriptome is substantially more complex than previously recognized, with this complexity arising from combinatorial usage of promoters, splice sites and polyadenylation sites.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a1d82ee3e7b172d621b894c5862756eec87abbcd

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Cancer Research

In Molecular Biology

Citations in the corpus

FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome (2017, background): “The development of high-throughput RNA sequencing (RNA-seq) has revealed the presence of many RNAs in different organisms such as mammals (1–3), insects (4,5) and plants (6,7).”
Araport11: a complete reannotation of the Arabidopsis thaliana reference genome (2016, background): “The preferential expression of noncoding genes in reproductive organs was also observed in Drosophila (Brown et al. 2014).”
Circular RNAs are long-lived and display only minimal early alterations in response to a growth factor (2015, background): “The low abundance of circRNAs found in our cultured mammary cell model and the contrasting high abundance found in neuronal tissues might be due to frequent exon skipping events (57,59) and resulting exon circularization (29) in neuronal tissues.”
Genomewide analysis of Drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation (2014, positive): “Annotation of Circular RNAs fromDrosophila Tissue and Cell Line Total RNA-Seq Data We recently annotated the Drosophila melanogaster transcriptome using stranded, poly(A), RNA data from diverse developmental stages, tissues, and cell lines (Brown et al., 2014).”
FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations (2014, background): “org/celniker) has also provided FlyBase with de novo alignments of modENCODE RNA-Seq coverage data to the Release 6 genome, including the original developmental profile (18) and the most recent profiles for tissues, treatments and cell lines (19).”
Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution. (2019, background): “(2017), which required detection of the same peptide at least twice in two or more independent datasets, are heavily biased against detection of differentially regulated alternative splicing events even though their functionality is supported by enrichment for frame preservation and evolutionary con”
FlyBase: a guided tour of highlighted features (2022, methodology): “RNA-seq genomic coverage profiles are displayed in JBrowse using our novel “TopoView” visualization, a compact presentation of RNA-seq profiles that facilitates comparison between samples of a set (see below for details on the development and implementation of this novel display).”
Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila (2015, neutral): “Most, but not all, UCGs are expressed principally in neural tissue (Brown et al. 2014).”
Spatial expression of transcription factors in Drosophila embryonic organ development (2013, methodology): “For comparison of the mRNA in situ pattern annotations and other transcriptional profiling platforms, we utilized two large-scale studies, including an RNA-seq developmental time-course with 30 sample points [28], and 29 dissected tissues from larval, pupal, and adult stages [56].”