FlyBase: integration and improvements to query tools

Wilson, Royce J; Goodman, Joshua L.; Strelets, Victor B.

doi:10.1093/nar/gkm930

Cited by 129 publications

(147 citation statements)

References 6 publications

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“…The genes tan, ebony, Dopa-decarboxylase and yellow all affect both body color and behavior [54]. These genes are expressed in epidermal cells, where they are used to synthesize pigments (Fig.…”

Section: Pigmentation and Behaviormentioning

confidence: 99%

“…An effect on lifespan has also been described for genes involved in pteridine synthesis [83]. Descriptions of mutant phenotypes in FlyBase, the online collection of data from Drosophila genetics [54], provide many more examples of pleiotropy for pigmentation genes. (When evaluating the extent of pleiotropy, it is important to note that the definition of a phenotype is subjective.…”

Section: Pigmentation and Other Traitsmentioning

confidence: 99%

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Development and evolution of insect pigmentation: Genetic mechanisms and the potential consequences of pleiotropy

Wittkopp

Beldade

2009

Seminars in Cell & Developmental Biology

290

291

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a b s t r a c tInsect pigmentation is a premier model system in evolutionary and developmental biology. It has been at the heart of classical studies as well as recent breakthroughs. In insects, pigments are produced by epidermal cells through a developmental process that includes pigment patterning and synthesis. Many aspects of this process also impact other phenotypes, including behavior and immunity. This review discusses recent work on the development and evolution of insect pigmentation, with a focus on pleiotropy and its effects on color pattern diversification.

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Section: Pigmentation and Behaviormentioning

confidence: 99%

Section: Pigmentation and Other Traitsmentioning

confidence: 99%

Development and evolution of insect pigmentation: Genetic mechanisms and the potential consequences of pleiotropy

Wittkopp

Beldade

2009

Seminars in Cell & Developmental Biology

290

291

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“…The affinity of GST-VCP binding to the RNA probes was comparable with that of full-length GST-Vas to probes that did not contain To gain some insight into the potential number of Vas target mRNAs, we investigated the frequency of polyuridine tracts in the 39 UTRs of Drosophila melanogaster mRNAs. We obtained the sequences of 17,887 predicted 39 UTRs, totaling 8,326,756 nt from FlyBase (Wilson et al 2008), and searched for instances of seven or more consecutive U residues. Such U-motifs are quite frequent in 39 UTRs: (U) 7 or greater appeared 4030 times, or once every 2066 nt; (U) 8 or greater appeared 2419 times, or once every 3422 nt; (U) 9 or greater appeared 1622 times, or once every 5134 nt; and (U) 10 or greater appeared 998 times, or once every 8343 nt.…”

Section: Vas Activates Mei-p26 Translationmentioning

confidence: 99%

Vasa promotes Drosophila germline stem cell differentiation by activating mei-P26 translation by directly interacting with a (U)-rich motif in its 3′ UTR

Liu

Han²,

Lasko³

2009

Genes Dev.

104

105

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Vasa (Vas) is a DEAD-box RNA-binding protein required in Drosophila at several steps of oogenesis and for primordial germ cell (PGC) specification. Vas associates with eukaryotic initiation factor 5B (eIF5B), and this interaction has been implicated in translational activation of gurken mRNA in the oocyte. Vas is expressed in all ovarian germline cells, and aspects of the vas-null phenotype suggest a function in regulating the balance between germline stem cells (GSCs) and their fate-restricted descendants. We used a biochemical approach to recover Vas-associated mRNAs and obtained mei-P26, whose product represses microRNA activity and promotes GSC differentiation. We found that vas and mei-P26 mutants interact, and that mei-P26 translation is substantially reduced in vas mutant cells. In vitro, Vas protein bound specifically to a (U)-rich motif in the mei-P26 39 untranslated region (UTR), and Vas-dependent regulation of GFP-mei-P26 transgenes in vivo was dependent on the same (U)-rich 39 UTR domain. The ability of Vas to activate mei-P26 expression in vivo was abrogated by a mutation that greatly reduces its interaction with eIF5B. Taken together, our data support the conclusion that Vas promotes germ cell differentiation by directly activating mei-P26 translation in early-stage committed cells.[Keywords: Oogenesis; RNA-binding protein; DEAD-box; patterning; development] Supplemental material is available at http://www.genesdev.org.

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“…The l(3)psg7 14144 mutation is a 236-bp deletion that shifts the reading frame after codon 242, changing amino acids 243-253 from GAG-SATLSMAY to EGQEEHPEGHX. Deficiency maps and gene structures are derived from FlyBase (Wilson et al 2008). death. These screens thus provide a new direction for defining the regulation of this critical biological pathway.…”

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confidence: 99%

A Genetic Screen Identifies New Regulators of Steroid-Triggered Programmed Cell Death in Drosophila

et al. 2008

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The steroid hormone ecdysone triggers the rapid and massive destruction of larval tissues through transcriptional cascades that culminate in rpr and hid expression and caspase activation. Here we describe the use of genetic screens to further our understanding of this steroid-triggered programmed cell death response. Pupal lethal mutants were screened for specific defects in larval salivary gland destruction. A pilot screen using existing P-element collections resulted in the identification of mutations in known cell death regulators, E74 and hid, as well as multiple alleles in CBP (nejire) and dTrf2. A large-scale EMS mutagenesis screen on the third chromosome resulted in the recovery of 48 mutants. These include seven multiallelic complementation groups, at least five of which do not map to regions or genes previously associated with cell death. Five mutants display defects in the transcriptional induction of rpr and hid, and all display a penetrant block in caspase activation. Three were mapped to specific genes: CG5146, which encodes a protein of unknown function, Med24, which encodes a component of the RNA polymerase II mediator complex, and CG7998, which encodes a putative mitochondrial malate dehydrogenase. These genetic screens provide new directions for understanding the regulation of programmed cell death during development.

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FlyBase: integration and improvements to query tools

Cited by 129 publications

References 6 publications

Development and evolution of insect pigmentation: Genetic mechanisms and the potential consequences of pleiotropy

Development and evolution of insect pigmentation: Genetic mechanisms and the potential consequences of pleiotropy

Vasa promotes Drosophila germline stem cell differentiation by activating mei-P26 translation by directly interacting with a (U)-rich motif in its 3′ UTR

A Genetic Screen Identifies New Regulators of Steroid-Triggered Programmed Cell Death in Drosophila

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