Diversity and dynamics of the Drosophila transcriptome

Abstract

Animal transcriptomes are dynamic, each cell type, tissue and organ system expressing an ensemble of transcript isoforms that give rise to substantial diversity. We identified new genes, transcripts, and proteins using poly(A)+ RNA sequence from Drosophila melanogaster cultured cell lines, dissected organ systems, and environmental perturbations. We found 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 noncoding 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 arising from combinatorial usage of promoters, splice sites, and polyadenylation sites.

Comparative validation of the D. melanogaster modENCODE transcriptome annotation

“…Therefore, as a cost-effective sampling strategy, we performed RNA-seq on poly(A) + RNA (Supplemental Table S3) from adult whole females and males (34-172 million mapped reads for each sex) of all eight of the newly assembled and six of the previously assembled genomes (D. simulans, D. yakuba, D. ananassae, D. pseudoobscura, D. virilis, and D. mojavensis), as well as previously published RNA-seq data for D. pseudoobscura and D. mojavensis head samples (Graveley et al 2011). D. melanogaster reads reported here are independent from those used for the annotation (Brown et al 2014). To assay stage-and tissue-biased expression, we also performed poly(A) + RNA-seq on samples from mixed-sex embryos or several dissected tissues from the 14 non-melanogaster species (Supplemental Table S4).…”

“…Although we chose to use a conservative neutral model incorporating both expressed and nonexpressed intergenic space, the rare aligned and transcribed intergenic regions will be of special interest in future rounds of annotation. Indeed many have already been incorporated as UTR exons in the working draft of the modENCODE version 3 annotation (MDv3) (Brown et al 2014).…”

“…Importantly, the splice junction spanning reads in those RNA-seq profiles revealed a much richer set of processed transcripts. Additional RNA-seq data sets, along with cap analysis of gene expression (CAGE-seq) and full-insert cDNA sequencing, have been used to generate the modENCODE D. melanogaster transcriptome annotation version 2 (MDv2), including MDv3 (Brown et al 2014). This modENCODE annotation was used to support analysis in the current set of publications from the Consortium.…”

Critical roles of long noncoding RNAs in Drosophila spermatogenesis

“…In multiple species, the largest repertoire of lncRNAs is expressed in the testis, as revealed by genome-wide transcriptome analyses (Djebali et al 2012;Nam and Bartel 2012;Brown et al 2014;Morris and Mattick 2014). Moreover, lncRNAs participate with protein-coding genes in evolutionarily conserved coexpression networks during spermatogenesis (Necsulea et al 2014), the process by which male germline stem cells (GSCs) divide and differentiate into mature sperm in sexual organisms.…”

The Y Chromosome Modulates Splicing and Sex-Biased Intron Retention Rates in Drosophila

“…First, ovaries, testes and accessory glands from 4-day-old flies, as well as whole body of adult flies of different ages (1,5 and 30 days old) were downloaded from the modENCODE project (GRAVELEY et al 2011;BROWN et al 2014). Second, gonad tissues (ovaries and testes) of genotypes with wild type chromosome numbers and gonad tissues of genotypes with Y chromosome aneuploidy (females:…”