Phylogenetic and Genomewide Analyses Suggest a Functional Relationship Betweenkayak, the Drosophila Fos Homolog, andfig, a Predicted Protein Phosphatase 2C Nested Within akayakIntron

Hudson, S; Garrett, Matthew; Carlson, Joseph W.; Micklem, Gos; Celniker, S; Goldstein, Elliott S.; Newfeld, Stuart J.

doi:10.1534/genetics.107.071670

Cited by 7 publications

(10 citation statements)

References 29 publications

(21 reference statements)

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“…This two gene complex has five promoters and 6 transcripts. This nested arrangement is maintained in 11 other Drosophila species (Hudson et al, 2007). The kay gene is also an unusually large gene (~27 kb) for invertebrates; Drosophila has an average gene size of about 5 kb.…”

Section: Discussionmentioning

confidence: 95%

“…kay-γ, the putative original first exon (Hudson et al, 2007), has a 5′ UTR of 416 bp, which is large for a Drosophila gene. A large 5′UTR could be regulatory, containing motifs that could act at the transcription or translational level.…”

Section: Discussionmentioning

confidence: 99%

“…The predicted amino acid sequence of this exon of kayak and of kay sro has no homology to any of the currently sequenced organisms other than Drosophila species (Hudson et al, 2007) at this time. This coding region contains a high concentration of glutamate codons but they are scattered in clusters from 1 to 12, unlike the CAG/A repeat diseases where the cluster copy number is 30 or greater.…”

Section: Determination Of the 3′ Ends Of The Kayak-α Transcription Unitmentioning

confidence: 94%

“…5). The predicted amino acid sequence of this exon has no homology to any of the currently completely sequenced organisms other than Drosophila species (Hudson et al, 2007). …”

Section: Determination Of the 3′ Ends Of The Kayak-α Transcription Unitmentioning

confidence: 99%

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The gene structure of the Drosophila melanogaster proto-oncogene, kayak, and its nested gene, fos-intronic gene

Hudson

Goldstein

2008

Gene

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Section: Discussionmentioning

confidence: 95%

Section: Discussionmentioning

confidence: 99%

Section: Determination Of the 3′ Ends Of The Kayak-α Transcription Unitmentioning

confidence: 94%

“…5). The predicted amino acid sequence of this exon has no homology to any of the currently completely sequenced organisms other than Drosophila species (Hudson et al, 2007). …”

Section: Determination Of the 3′ Ends Of The Kayak-α Transcription Unitmentioning

confidence: 99%

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The gene structure of the Drosophila melanogaster proto-oncogene, kayak, and its nested gene, fos-intronic gene

Hudson

Goldstein

2008

Gene

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“…Additionally, we analyzed embedded gene relationships where a surrounding gene has another gene contained within its extent. This is synonymous with the term "nested genes" used elsewhere in the literature (Moriyama and Gojobori 1989;Rao and Sodja 1992;Kurzik-Dumke and Zengerle 1996;Kaymer et al 1997;Pohar et al 1999;Laundrie et al 2003;Hudson et al 2007). Studying the creation of embedded relationships, their conservation or loss, and their overlap with the set of PRGs shows this as an additional means to identify relocated genes.…”

mentioning

confidence: 99%

Genome-scale analysis of positionally relocated genes

Bhutkar¹,

Russo²,

Smith³

et al. 2007

Genome Res.

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During evolution, genome reorganization includes large-scale events such as inversions, translocations, and segmental or even whole-genome duplications, as well as fine-scale events such as the relocation of individual genes. This latter category, which we will refer to as positionally relocated genes (PRGs), is the subject of this report. Assessment of the magnitude of such PRGs and of possible contributing mechanisms is aided by a comparative analysis of related genomes, where conserved chromosomal organization can aid in identifying genes that have acquired a new location in a lineage of these genomes. Here we utilize two methods to comprehensively identify relocated protein-coding genes in the recently sequenced genomes of 12 species of genus Drosophila. We use exceptions to the general rule of maintenance of chromosome arm (Muller element) association for most Drosophila genes to identify one major class of PRGs. We also identify a partially overlapping set of PRGs among “embedded genes,” located within the extents of other surrounding genes. We provide evidence that PRG movements have at least two different origins: Some events occur via retrotransposition of processed RNAs and others via a DNA-based transposition mechanism. Overall, we identify several hundred PRGs that arose within a lineage of the genus Drosophila phylogeny and provide suggestive evidence that a few thousand such events have occurred within the radiation of the insect order Diptera, thereby illustrating the magnitude of the contribution of PRG movement to chromosomal reorganization during evolution.

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Fos metamorphoses: Lessons from mutants in model organisms

Alfonso-Gonzalez

Riesgo-Escovar

2018

Mechanisms of Development

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The Fos oncogene gene family is evolutionarily conserved throughout Eukarya. Fos proteins characteristically have a leucine zipper and a basic region with a helix-turn-helix motif that binds DNA. In vertebrates, there are several Fos homologs. They can homo- or hetero-dimerize via the leucine zipper domain. Fos homologs coupled with other transcription factors, like Jun oncoproteins, constitute the Activator Protein 1 (AP-1) complex. From its original inception as an oncogene, the subsequent finding that they act as transcription factors binding DNA sequences known as TRE, to the realization that they are activated in many different scenarios, and to loss-of-function analysis, the Fos proteins have traversed a multifarious path in development and physiology. They are instrumental in 'immediate early genes' responses, and activated by a seemingly myriad assemblage of different stimuli. Yet, the majority of these studies were basically gain-of-function studies, since it was thought that Fos genes would be cell lethal. Loss-of-function mutations in vertebrates were recovered later, and were not cell lethal. In fact, c-fos null mutations are viable with developmental defects (osteopetrosis and myeloid lineage abnormalities). It was then hypothesized that vertebrate genomes exhibit partial redundancy, explaining the 'mild' phenotypes, and complicating assessment of complete loss-of-function phenotypes. Due to its promiscuous activation, fos genes (especially c-fos) are now commonly used as markers for cellular responses to stimuli. fos homologs high sequence conservation (including Drosophila) is advantageous as it allows critical assessment of fos genes functions in this genetic model. Drosophila melanogaster contains only one fos homolog, the gene kayak. kayak mutations are lethal, and allow study of all the processes where fos is required. The kayak locus encodes several different isoforms, and is a pleiotropic gene variously required for development involving cell shape changes. In general, fos genes seem to primarily activate programs involved in cellular architectural rearrangements and cell shape changes.

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Phylogenetic and Genomewide Analyses Suggest a Functional Relationship Betweenkayak, the Drosophila Fos Homolog, andfig, a Predicted Protein Phosphatase 2C Nested Within akayakIntron

Cited by 7 publications

References 29 publications

The gene structure of the Drosophila melanogaster proto-oncogene, kayak, and its nested gene, fos-intronic gene

The gene structure of the Drosophila melanogaster proto-oncogene, kayak, and its nested gene, fos-intronic gene

Genome-scale analysis of positionally relocated genes

Fos metamorphoses: Lessons from mutants in model organisms

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