Global assessment of organ specific basal gene expression over a diurnal cycle with analyses of gene copies exhibiting cyclic expression patterns.
Global assessment of organ specific basal gene expression over a diurnal cycle with analyses of gene copies exhibiting cyclic expression patterns.
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DOI：
10.1186/s12864-020-07202-9
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发表时间：
2020-11-11
期刊：
影响因子：
4.4
通讯作者：
Walter RB
中科院分区：
文献类型：
--
作者：
Lu Y;Boswell M;Boswell W;Salinas RY;Savage M;Reyes J;Walter S;Marks R;Gonzalez T;Medrano G;Warren WC;Schartl M;Walter RB
研究起源于基因组复制的旁系同源物之间的功能差异是分子进化研究中的一个重要课题。表现出基础水平循环表达模式的基因包括昼夜节律和光响应基因是重要的生理调节因子。基础基因表达模式的时间变化是研究遗传功能时需要考虑的重要因素。然而，还没有足够的努力来研究全球范围内的基础基因表达变异，以建立每个器官的转录活性基线。此外，基因组复制产生的旁系同源物之间的循环表达模式比较的研究，以及它们之间潜在的功能分歧被忽视了。为了解决这些问题，我们利用了硬骨鱼种，剑尾鱼斑，并在9个器官内的基因表达谱在3小时的时间间隔，在整个24小时的昼夜周期。结果表明，1.3-21.9%的基因在不同器官中表现出循环表达模式，其中眼睛中循环基因的比例最高，而性腺中的比例最低。大多数重复的基因对在其基础水平表达模式中表现出分歧，其中仅一个旁系同源物表现出振荡表达模式，或两个旁系同源物都表现出振荡表达模式，但每个基因重复物表现出不同的峰值表达时间，和/或在不同的器官中。这些观察结果表明，循环基因经历了显着的亚，新，或非功能化的硬骨鱼基因组复制事件。此外，我们还开发了一个定制的、可通过网络访问的基因表达浏览器，以促进科学界的数据挖掘和数据可视化。
Studying 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. Our 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. These 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.
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DOI：
10.1016/j.cbpc.2017.10.003
发表时间：
2018-06
期刊：
Comparative biochemistry and physiology. Toxicology & pharmacology : CBP
影响因子：
--
作者：
Boswell M;Boswell W;Lu Y;Savage M;Mazurek Z;Chang J;Muster J;Walter R
通讯作者：
Walter R
进食期限制改变了外周三昼夜节律基因的表达，而无需改变小鼠体重。
影响因子：
3.7
作者：
Jang H;Lee G;Kong J;Choi G;Park YJ;Kim JB
通讯作者：
Kim JB
影响因子：
9.8
作者：
Kaneko M;Cahill GM
通讯作者：
Cahill GM
DOI：
10.1016/j.cbpc.2017.09.009
发表时间：
2018-06
期刊：
Comparative biochemistry and physiology. Toxicology & pharmacology : CBP
影响因子：
--
作者：
Gonzalez TJ;Lu Y;Boswell M;Boswell W;Medrano G;Walter S;Ellis S;Savage M;Varga ZM;Lawrence C;Sanders G;Walter RB
通讯作者：
Walter RB
影响因子：
9.8
作者：
Giglia-Mari G;Theil AF;Mari PO;Mourgues S;Nonnekens J;Andrieux LO;de Wit J;Miquel C;Wijgers N;Maas A;Fousteri M;Hoeijmakers JH;Vermeulen W
通讯作者：
Vermeulen W