Expression Profile and Gene Age Jointly Shaped the Genome-Wide Distribution of Premature Termination Codons in a Drosophila melanogaster Population
| Autor: | Chenyu Ma, Shun-Chern Tsaur, Chau-Ti Ting, Bin Z. He, Haiwang Yang, Huijing Ma, Yong Zhang, Ying Wu |
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| Rok vydání: | 2014 |
| Předmět: |
endocrine system diseases
Population midgut Biology young gene Genome Chromosomes Evolution Molecular Transcription (biology) Gene duplication Genetics Animals Drosophila Proteins Tissue Distribution education Molecular Biology Allele frequency Gene Discoveries Ecology Evolution Behavior and Systematics education.field_of_study Gene Expression Profiling gene duplication Computational Biology Sequence Analysis DNA gene loss premature termination codon biology.organism_classification humanities Gene expression profiling Drosophila melanogaster Codon Nonsense |
| Zdroj: | Molecular Biology and Evolution |
| ISSN: | 1537-1719 0737-4038 |
| DOI: | 10.1093/molbev/msu299 |
| Popis: | 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 (410%). 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 highfrequency 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 youn gd e 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 prop ose that new genes may need al ong time to become stably maintained after the origination. |
| Databáze: | OpenAIRE |
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