Global assessment of organ specific basal gene expression over a diurnal cycle with analyses of gene copies exhibiting cyclic expression patterns

BMC Genomics

Wesley C. Warren¹  Mikki Boswell²  Ronald B. Walter²  Rebecca Marks²  Markita Savage²  Geraldo Medrano²  Jose Reyes²  Sean Walter²  Yuan Lu²  Trevor Gonzalez²  William Boswell²  Manfred Schartl³  Raquel Ybanez Salinas⁴ 

[1] Bond Life Sciences Center, University of Missouri, Columbia, MO, USA;The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, 78666, San Marcos, TX, USA;The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, 78666, San Marcos, TX, USA;Developmental Biochemistry, Theodor-Boveri-Institute, Biozentrum, University of Würzburg, Würzburg, Germany;The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, 78666, San Marcos, TX, USA;The University of Texas MD Anderson Cancer Center, Graduate School of Biomedical Sciences, Houston, TX, USA;

关键词: Xiphophorus;    Organ;    Gene expression profiling;    Profiling;    Light response;    Basal level gene expression;    Paralog;    Genome duplication;    Evolution;   

DOI  :  10.1186/s12864-020-07202-9

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY