title: Highly constrained intergenic Drosophila ultraconserved elements are candidate ncRNAs.
abstract: Eukaryotes contain short (∼80-200 bp) regions that have few or no substitutions among species that represent hundreds of millions of years of evolutionary divergence. These ultraconserved elements (UCEs) are candidates for containing essential functions, but their biological roles remain largely unknown. Here, we report the discovery and characterization of UCEs from 12 sequenced Drosophila species. We identified 98 elements ≥80 bp long with very high conservation across the Drosophila phylogeny. Population genetic analyses reveal that these UCEs are not present in mutational cold spots. Instead we infer that they experience a level of selective constraint almost 10-fold higher compared with missense mutations in protein-coding sequences, which is substantially higher than that observed previously for human UCEs. About one-half of these Drosophila UCEs overlap the transcribed portion of genes, with many of those that are within coding sequences likely to correspond to sites of ADAR-dependent RNA editing. For the remaining UCEs that are in nongenic regions, we find that many are potentially capable of forming RNA secondary structures. Among ten chosen for further analysis, we discovered that the majority are transcribed in multiple tissues of Drosophila melanogaster. We conclude that Drosophila species are rich with UCEs and that many of them may correspond to novel noncoding RNAs.
authors.affiliation: Department of Genetics, Rutgers University kern@biology.rutgers.edu.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Kern
authors.affiliation: Department of Molecular Biology and Genetics, Cornell University.
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Barbash
authors.affiliation: Department of Microbiology and Immunology, Drexel University College of Medicine.
authors.forename: Joshua
authors.initials: J
authors.lastname: Chang Mell
authors.affiliation: Department of Biology, Dartmouth College, Hanover, New Hampshire.
authors.forename: Daniel
authors.initials: D
authors.lastname: Hupalo
authors.affiliation: Department of Biology, Dartmouth College, Hanover, New Hampshire.
authors.forename: Amanda
authors.initials: A
authors.lastname: Jensen
mesh_terms: D000818:Animals; D001483:Base Sequence; D017124:Conserved Sequence; D004331:Drosophila melanogaster / Q000235:genetics*; D023281:Genomics; D058977:Molecular Sequence Annotation; D022661:RNA, Untranslated / Q000096:biosynthesis / Q000737:chemistry / Q000235:genetics*; D012641:Selection, Genetic
chemical_list: D022661:RNA, Untranslated
keywords: comparative genomics; natural selection; ncRNAs; ultraconserved elements