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Journal article
Highly Constrained Intergenic Drosophila Ultraconserved Elements Are Candidate ncRNAs
Genome biology and evolution, v 7(3), pp 689-698
01 Mar 2015
PMID: 25618141
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Eukaryotes contain short (similar to 80-200 bp) regions thathave 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 missens emutations 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.
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Details
- Title
- Highly Constrained Intergenic Drosophila Ultraconserved Elements Are Candidate ncRNAs
- Creators
- Andrew D. Kern - Rutgers, The State University of New JerseyDaniel A. Barbash - Cornell UniversityJoshua Chang Mell - Drexel UniversityDaniel Hupalo - Dartmouth CollegeAmanda Jensen - Dartmouth College
- Publication Details
- Genome biology and evolution, v 7(3), pp 689-698
- Publisher
- Oxford Univ Press
- Number of pages
- 10
- Grant note
- MCB-1052148; MCB-1050980 / NSF; National Science Foundation (NSF) 1050980 / Div Of Molecular and Cellular Bioscience; National Science Foundation (NSF); NSF - Directorate for Biological Sciences (BIO)
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Microbiology and Immunology
- Web of Science ID
- WOS:000354750300006
- Scopus ID
- 2-s2.0-84938515034
- Other Identifier
- 991019168044204721
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- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Evolutionary Biology
- Genetics & Heredity