Journal article
Expression profile and gene age jointly shaped the genome-wide distribution of premature termination codons in a Drosophila melanogaster population
Molecular biology and evolution, Vol.32(1), pp.216-228
01/2015
DOI: 10.1093/molbev/msu299
PMCID: PMC4271532
PMID: 25371429
Abstract
Widespread premature termination codon mutations (PTCs) were recently observed in human and fly populations. We took advantage of the population resequencing data in the Drosophila Genetic Reference Panel to investigate how the expression profile and the evolutionary age of genes shaped the allele frequency distribution of PTCs. After generating a high-quality data set of PTCs, we clustered genes harboring PTCs into three categories: genes encoding low-frequency PTCs (≤ 1.5%), moderate-frequency PTCs (1.5-10%), and high-frequency PTCs (>10%). All three groups show narrow transcription compared with PTC-free genes, with the moderate- and high-PTC frequency groups showing a pronounced pattern. Moreover, nearly half (42%) of the PTC-encoding genes are not expressed in any tissue. Interestingly, the moderate-frequency PTC group is strongly enriched for genes expressed in midgut, whereas genes harboring high-frequency PTCs tend to have sex-specific expression. We further find that although young genes born in the last 60 My compose a mere 9% of the genome, they represent 16%, 30%, and 50% of the genes containing low-, moderate-, and high-frequency PTCs, respectively. Among DNA-based and RNA-based duplicated genes, the child copy is approximately twice as likely to contain PTCs as the parent copy, whereas young de novo genes are as likely to encode PTCs as DNA-based duplicated new genes. Based on these results, we conclude that expression profile and gene age jointly shaped the landscape of PTC-mediated gene loss. Therefore, we propose that new genes may need a long time to become stably maintained after the origination.
Details
- Title: Subtitle
- Expression profile and gene age jointly shaped the genome-wide distribution of premature termination codons in a Drosophila melanogaster population
- Creators
- Haiwang Yang - Chinese Academy of SciencesBin Z He - Harvard UniversityHuijing Ma - Chinese Academy of SciencesShun-Chern Tsaur - National Taiwan Normal UniversityChenyu Ma - Chinese Academy of SciencesYing Wu - Chinese Academy of SciencesChau-Ti Ting - National Taiwan Normal UniversityYong E Zhang - Chinese Academy of Sciences
- Resource Type
- Journal article
- Publication Details
- Molecular biology and evolution, Vol.32(1), pp.216-228
- Publisher
- United States
- DOI
- 10.1093/molbev/msu299
- PMID
- 25371429
- PMCID
- PMC4271532
- ISSN
- 1537-1719
- eISSN
- 1537-1719
- Grant note
- Howard Hughes Medical Institute
- Language
- English
- Date published
- 01/2015
- Academic Unit
- Biology
- Record Identifier
- 9983991995802771
Metrics
34 Record Views