Global assessment of organ specific basal gene expression over a diurnal cycle with analyses of gene copies exhibiting cyclic expression patterns
| Autor: | Yuan Lu, Sean M. Walter, Markita G. Savage, Mikki Boswell, Geraldo Medrano, Rebecca Marks, Jose Reyes, Raquel Salinas, Ronald B. Walter, Wesley C. Warren, Trevor J. Gonzalez, Manfred Schartl, William T. Boswell |
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| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
lcsh:QH426-470
Evolution lcsh:Biotechnology Gene Expression Biology Genome Evolution Molecular 03 medical and health sciences 0302 clinical medicine Molecular evolution Genes Duplicate Gene Duplication Basal level gene expression lcsh:TP248.13-248.65 Gene expression Gene duplication Genetics Animals Gene Phylogeny 030304 developmental biology 0303 health sciences Light response Paralog Profiling Fishes Xiphophorus Gene expression profiling lcsh:Genetics Evolutionary biology Organ Genome duplication DNA microarray 030217 neurology & neurosurgery Functional divergence Biotechnology Research Article |
| Zdroj: | BMC Genomics, Vol 21, Iss 1, Pp 1-14 (2020) BMC Genomics |
| ISSN: | 1471-2164 |
| DOI: | 10.1186/s12864-020-07202-9 |
| Popis: | BackgroundStudying functional divergences between paralogs that originated from genome duplication is a significant topic in investigating molecular evolution. Genes that exhibit basal level cyclic expression patterns including circadian and light responsive genes are important physiological regulators. Temporal shifts in basal gene expression patterns are important factors to be considered when studying genetic functions. However, adequate efforts have not been applied to studying basal gene expression variation on a global scale to establish transcriptional activity baselines for each organ. Furthermore, the investigation of cyclic expression pattern comparisons between genome duplication created paralogs, and potential functional divergence between them has been neglected. To address these questions, we utilized a teleost fish species,Xiphophorus maculatus,and profiled gene expression within 9 organs at 3-h intervals throughout a 24-h diurnal period.ResultsOur results showed 1.3–21.9% of genes in different organs exhibited cyclic expression patterns, with eye showing the highest fraction of cycling genes while gonads yielded the lowest. A majority of the duplicated gene pairs exhibited divergences in their basal level expression patterns wherein only one paralog exhibited an oscillating expression pattern, or both paralogs exhibit oscillating expression patterns, but each gene duplicate showed a different peak expression time, and/or in different organs.ConclusionsThese observations suggest cyclic genes experienced significant sub-, neo-, or non-functionalization following the teleost genome duplication event. In addition, we developed a customized, web-accessible, gene expression browser to facilitate data mining and data visualization for the scientific community. |
| Databáze: | OpenAIRE |
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