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Evolution of genes and genomes on the Drosophila phylogeny
TLDR
These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution.
Systematic generation of high-resolution deletion coverage of the Drosophila melanogaster genome
TLDR
Two methods are described that provide for the systematic isolation of targeted deletions in the D. melanogaster genome and enable the generation of small custom deletions with predictable endpoints throughout the genome and should make their isolation a simple and routine task.
Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE
TLDR
Two studies identified regions of the nematode and fly genomes that show highly occupied targets (or HOT) regions where DNA was bound by more than 15 of the transcription factors analyzed and the expression of related genes were characterized.
The Developmental Transcriptome of Drosophila melanogaster
TLDR
111,195 new elements are identified, 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.
FlyBase 2.0: the next generation
TLDR
These major new features and functionalities of the FlyBase 2.0 site are described and how they support the use of Drosophila as a model organism for biological discovery and translational research are described.
Diversity and dynamics of the Drosophila transcriptome
TLDR
It is 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 in Drosophila melanogaster.
Hox genes and the evolution of the arthropod body plan 1
TLDR
In this review, the expression and functional data regarding the 10 arthropod Hox genes are summarized and mechanisms of developmental evolutionary change thought to be important for the emergence of novel morphological features within the arthropods are discussed.
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
TLDR
This work uses the genomes of 12 Drosophila species for the de novo discovery of functional elements in the fly, and identifies several classes of pre- and post-transcriptional regulatory motifs, and predicts individual motif instances with high confidence.
Genome-wide analysis of promoter architecture in Drosophila melanogaster.
TLDR
It is shown that TSS distributions form a complex continuum of shapes, and that promoters active in the embryo and adult have highly similar shapes in 95% of cases, which suggests that these distributions are generally determined by static elements such as local DNA sequence and are not modulated by dynamic signals such as histone modifications.
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