The developmental transcriptome of Drosophila melanogaster

Graveley, Brenton R.; Brooks, Angela N.; Carlson, Joseph W.; Duff, Michael O.; Landolin, Jane M.; Yang, Li; Artieri, Carlo G.; Baren, Marijke J. van; Boley, Nathan; Booth, Benjamin W.; Brown, James B.; Cherbas, Lucy; Davis, Carrie A.; Dobin, Alexander; Li, Renhua; Lin, Wei; Malone, John H.; Mattiuzzo, Nicolas R.; Miller, David S.; Sturgill, David; Tuch, Brian B.; Zaleski, Chris; Zhang, Dayu; Blanchette, Marco; Dudoit, Sandrine; Eads, Brian D.; Green, Edward; Hammonds, Ann S.; Jiang, Lichun; Kapranov, Phil; Langton, Laura; Perrimon, Norbert; Sandler, Jeremy E.; Wan, Kenneth H.; Willingham, Aarron; Zhang, Yu; Zou, Yi; Andrews, Justen; Bickel, Peter J.; Brenner, Steven E.; Brent, Michael R.; Cherbas, Peter; Gingeras, T; Hoskins, Roger A.; Kaufman, Thomas C.; Oliver, Brian; Celniker, S

doi:10.1038/nature09715

Cited by 1,393 publications

(1,528 citation statements)

References 48 publications

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“…Retained intron, in which a single intron is alternatively included or spliced out of the mature mRNA via an intron-definition splicing mechanism, was the most prevalent type of AS event (30.4%; Fig. 3C), consistent with previous studies in plants (Black, 2003;Wang and Brendel, 2006;Barbazuk et al, 2008;Filichkin et al, 2010;Li et al, 2010;Lu et al, 2010;Zhang et al, 2010;Marquez et al, 2012) but in contrast to animal AS events, where exon skipping (cassette exons or coordinate cassette exons) is the predominant mechanism (Sultan et al, 2008;Wang et al, 2008;Daines et al, 2011;Graveley et al, 2011). Furthermore, alternative 39 splice sites (A3SS; 21.0%) or alternative last exons (ALE; 11.5%) and alternative 59 splice sites (A5SS; 12.2%) or alternative first exons (AFE; 11.7%) were other types of common AS events observed in our data (Fig.…”

Section: As Is Differentially Regulated Between Embryo and Endospermsupporting

confidence: 79%

“…Previous studies have shown that NTRs have fewer and shorter exons, less protein-coding potential, and less tissue-specific expression than annotated protein-coding genes (Bruno et al, 2010;Lu et al, 2010;Wetterbom et al, 2010;Zhang et al, 2010;Aanes et al, 2011;Graveley et al, 2011). To determine whether endospermic and embryonic NTRs have similar features, we analyzed the structure, coding potentials, and expression levels of the NTRs.…”

Section: Discovery Of Ntrsmentioning

confidence: 99%

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The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

Chen

Shu

et al. 2013

Plant Physiology

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Transcriptome analysis of early-developing maize (Zea mays) seed was conducted using Illumina sequencing. We mapped 11,074,508 and 11,495,788 paired-end reads from endosperm and embryo, respectively, at 9 d after pollination to define gene structure and alternative splicing events as well as transcriptional regulators of gene expression to quantify transcript abundance in both embryo and endosperm. We identified a large number of novel transcribed regions that did not fall within maize annotated regions, and many of the novel transcribed regions were tissue-specifically expressed. We found that 50.7% (8,556 of 16,878) of multiexonic genes were alternatively spliced, and some transcript isoforms were specifically expressed either in endosperm or in embryo. In addition, a total of 46 trans-splicing events, with nine intrachromosomal events and 37 interchromosomal events, were found in our data set. Many metabolic activities were specifically assigned to endosperm and embryo, such as starch biosynthesis in endosperm and lipid biosynthesis in embryo. Finally, a number of transcription factors and imprinting genes were found to be specifically expressed in embryo or endosperm. This data set will aid in understanding how embryo/endosperm development in maize is differentially regulated.Maize (Zea mays) seeds are one of the most important crop materials that provide resources for food, feed, biofuel, and raw material for processing. Maize seed development initiates from double fertilization, in which two of the pollen sperms fuse with an egg cell and a central cell to produce embryo and endosperm, respectively (Randolph, 1936;Chaudhury et al., 2001). The main function of endosperm is to provide nutrient for the developing embryo and germinating embryo.After fertilization, the zygote undergoes an asymmetric division into a small apical cell and a large basal cell, giving rise to the embryo proper and the suspensor, respectively. The radial symmetry of the proembryo is shifted to a bilateral symmetry at the transition stage, which is characterized by protoderm formation. The shoot apical meristem and the root apical meristem can be distinguished at the onset of the coleoptile stage, and then the position of the future coleoptile is marked by a small protuberance. The mature embryo is composed of the embryo axis, which is formed by the plumule with five or six short internodes, and leaf primordia and primary root surrounded by the coleoptile and the coleorhiza, respectively, and the scutellum (Randolph, 1936;Abbe and Stein, 1954;Diboll, 1968;Lammeren, 1986;Vernoud et al., 2005).Maize endosperm follows the nucleus-type endosperm development, where the fertilized central cell undergoes several rounds of synchronous division in the absence of cell wall formation and cytokinesis to produce a syncytium (Lopes and Larkins, 1993;Olsen, 2004). Cellularization allows the formation of the internuclear radial microtubule systems and open-ended alveolation from the periphery of the endosperm toward the central vacuole (Olsen et al., ...

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Section: As Is Differentially Regulated Between Embryo and Endospermsupporting

confidence: 79%

Section: Discovery Of Ntrsmentioning

confidence: 99%

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

Chen

Shu

et al. 2013

Plant Physiology

View full text Add to dashboard Cite

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“…RNAseq datasets represent another avenue to identify novel immune-regulated genes through their association with known immune genes in co-regulated clusters [67]. Finally, the Drosophila Genetic Reference Panel (DGRP) represents a unique asset for population genomics and genome-wide association studies (GWAS) based on 168 fully sequenced strains that can be subjected to any number of infectious challenges [68].…”

Section: Methods For Identifying Novel Immune Genes Based On Large Scmentioning

confidence: 99%

Methods to study Drosophila immunity

Neyen

Bretscher

Binggeli

et al. 2014

Methods

132

127

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a b s t r a c tInnate immune mechanisms are well conserved throughout evolution, and many theoretical concepts, molecular pathways and gene networks are applicable to invertebrate model organisms as much as vertebrate ones. Drosophila immunity research benefits from an easily manipulated genome, a fantastic international resource of transgenic tools and over a quarter century of accumulated techniques and approaches to study innate immunity. Here we present a short collection of ways to challenge the fruit fly immune system with various pathogens and parasites, as well as read-outs to assess its functions, including cellular and humoral immune responses. Our review covers techniques for assessing the kinetics and efficiency of immune responses quantitatively and qualitatively, such as survival analysis, bacterial persistence, antimicrobial peptide gene expression, phagocytosis and melanisation assays. Finally, we offer a toolkit of Drosophila strains available to the research community for current and future research.

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“…CG8949 codes for several protein isoforms, the longest one consisting of 876 amino acids, and shows the highest expression in adult ovaries and the larval central nervous system. 29,30 WAC is 26% identical and 39% conserved over the C-terminal 588 amino acids of the fly protein, with sequence similarity distributed over the whole protein, further characterized by clusters of short sequences of high conservation for the important functional motifs of the protein. 13 We investigated the role of the Drosophila WAC orthologue in lightoff jump reflex habituation paradigm.…”

Section: Panneuronal Knockdown Of the Drosophila Wac Orthologue Resulmentioning

confidence: 99%

De novo loss-of-function mutations in WAC cause a recognizable intellectual disability syndrome and learning deficits in Drosophila

et al. 2016

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Recently WAC was reported as a candidate gene for intellectual disability (ID) based on the identification of a de novo mutation in an individual with severe ID. WAC regulates transcription-coupled histone H2B ubiquitination and has previously been implicated in the 10p12p11 contiguous gene deletion syndrome. In this study, we report on 10 individuals with de novo WAC mutations which we identified through routine (diagnostic) exome sequencing and targeted resequencing of WAC in 2326 individuals with unexplained ID. All but one mutation was expected to lead to a loss-of-function of WAC. Clinical evaluation of all individuals revealed phenotypic overlap for mild ID, hypotonia, behavioral problems and distinctive facial dysmorphisms, including a square-shaped face, deep set eyes, long palpebral fissures, and a broad mouth and chin. These clinical features were also previously reported in individuals with 10p12p11 microdeletion syndrome. To investigate the role of WAC in ID, we studied the importance of the Drosophila WAC orthologue (CG8949) in habituation, a non-associative learning paradigm. Neuronal knockdown of Drosophila CG8949 resulted in impaired learning, suggesting that WAC is required in neurons for normal cognitive performance. In conclusion, we defined a clinically recognizable ID syndrome, caused by de novo loss-of-function mutations in WAC. Independent functional evidence in Drosophila further supported the role of WAC in ID. On the basis of our data WAC can be added to the list of ID genes with a role in transcription regulation through histone modification.

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The developmental transcriptome of Drosophila melanogaster

Cited by 1,393 publications

References 48 publications

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

Methods to study Drosophila immunity

De novo loss-of-function mutations in WAC cause a recognizable intellectual disability syndrome and learning deficits in Drosophila

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