Comparison of ultra-conserved elements in drosophilids and vertebrates

Makunin, Igor V., Shloma, Viktor V., Stephen, Stuart J., Pheasant, Michael and Belyakin, Stepan N. (2013) Comparison of ultra-conserved elements in drosophilids and vertebrates. PLoS One, 8 12: e82362.1-e82362.12. doi:10.1371/journal.pone.0082362


Author Makunin, Igor V.
Shloma, Viktor V.
Stephen, Stuart J.
Pheasant, Michael
Belyakin, Stepan N.
Title Comparison of ultra-conserved elements in drosophilids and vertebrates
Journal name PLoS One   Check publisher's open access policy
ISSN 1932-6203
Publication date 2013-12-01
Sub-type Article (original research)
DOI 10.1371/journal.pone.0082362
Open Access Status DOI
Volume 8
Issue 12
Start page e82362.1
End page e82362.12
Total pages 12
Place of publication San Francisco, United States
Publisher Public Library of Science
Language eng
Formatted abstract
Metazoan genomes contain many ultra-conserved elements (UCEs), long sequences identical between distant species. In this study we identified UCEs in drosophilid and vertebrate species with a similar level of phylogenetic divergence measured at protein-coding regions, and demonstrated that both the length and number of UCEs are larger in vertebrates. The proportion of non-exonic UCEs declines in distant drosophilids whilst an opposite trend was observed in vertebrates. We generated a set of 2,126 Sophophora UCEs by merging elements identified in several drosophila species and compared these to the eutherian UCEs identified in placental mammals. In contrast to vertebrates, the Sophophora UCEs are depleted around transcription start sites. Analysis of 52,954 P-element, piggyBac and Minos insertions in the D. melanogaster genome revealed depletion of the P-element and piggyBac insertions in and around the Sophophora UCEs. We examined eleven fly strains with transposon insertions into the intergenic UCEs and identified associated phenotypes in five strains. Four insertions behave as recessive lethals, and in one case we observed a suppression of the marker gene within the transgene, presumably by silenced chromatin around the integration site. To confirm the lethality is caused by integration of transposons we performed a phenotype rescue experiment for two stocks and demonstrated that the excision of the transposons from the intergenic UCEs restores viability. Sequencing of DNA after the transposon excision in one fly strain with the restored viability revealed a 47 bp insertion at the original transposon integration site suggesting that the nature of the mutation is important for the appearance of the phenotype. Our results suggest that the UCEs in flies and vertebrates have both common and distinct features, and demonstrate that a significant proportion of intergenic drosophila UCEs are sensitive to disruption.
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2014 Collection
Institute for Molecular Bioscience - Publications
 
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Citation counts: TR Web of Science Citation Count  Cited 6 times in Thomson Reuters Web of Science Article | Citations
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