Functional and regulatory diversification of Period genes responsible for circadian rhythm in vertebrates.

IF 2.1 3区 生物学 Q3 GENETICS & HEREDITY
Jun Soung Kwak, M Ángel León-Tapia, Celian Diblasi, Domniki Manousi, Lars Grønvold, Guro Katrine Sandvik, Marie Saitou
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Abstract

The Period genes (Per) play essential roles in modulating the molecular circadian clock timing in a broad range of species, which regulates the physiological and cellular rhythms through the transcription-translation feedback loop. While the Period gene paralogs are widely observed among vertebrates, the evolutionary history and the functional diversification of Per genes across vertebrates are not well known. In this study, we comprehensively investigated the evolution of Per genes at the copy number and sequence levels, including de novo binding motif discovery by comparative genomics. We also determined the lineage-specific transcriptome landscape across tissues and developmental stages and phenotypic effects in public RNA-seq data sets of model species. We observed multiple lineage-specific gain and loss events Per genes, though no simple association was observed between ecological factors and Per gene numbers in each species. Among salmonid fish species, the per3 gene has been lost in the majority, whereas those retaining the per3 gene exhibit not a signature of relaxed selective constraint but rather a signature of intensified selection. We also determined the signature of adaptive diversification of the CRY-binding region in Per1 and Per3, which modulates the circadian rhythm. We also discovered putative regulatory sequences, which are lineage-specific, suggesting that these cis-regulatory elements may have evolved rapidly and divergently across different lineages. Collectively, our findings revealed the evolution of Per genes and their fine-tuned contribution to the plastic and precise regulation of circadian rhythms in various vertebrate taxa.

脊椎动物昼夜节律周期基因的功能和调控多样化。
昼夜节律基因(Per)在多种物种的分子昼夜节律时钟定时调节中发挥着重要作用,通过转录-翻译反馈回路调节生理和细胞节律。虽然脊椎动物中广泛存在Per基因的旁系亲属,但人们对Per基因在脊椎动物中的进化历史和功能多样性并不十分清楚。在这项研究中,我们从拷贝数和序列水平上全面研究了Per基因的进化,包括通过比较基因组学发现新的结合基序。我们还在模式物种的公共 RNA-seq 数据集中确定了不同组织和发育阶段的品系特异性转录组格局以及表型效应。我们观察到多个品系特异性的 Per 基因增益和缺失事件,尽管在每个物种中没有观察到生态因素与 Per 基因数量之间的简单关联。在鲑科鱼类中,per3 基因在大多数鱼类中丢失,而保留 per3 基因的鱼类并没有表现出选择性限制放松的特征,而是表现出选择性加强的特征。我们还确定了 Per1 和 Per3 中调节昼夜节律的 CRY 结合区的适应性多样化特征。我们还发现了具有品系特异性的推定调控序列,这表明这些顺式调控元件可能在不同品系之间发生了快速和分化进化。总之,我们的研究结果揭示了Per基因的进化及其对各种脊椎动物类群昼夜节律可塑性和精确调控的微调贡献。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
G3: Genes|Genomes|Genetics
G3: Genes|Genomes|Genetics GENETICS & HEREDITY-
CiteScore
5.10
自引率
3.80%
发文量
305
审稿时长
3-8 weeks
期刊介绍: G3: Genes, Genomes, Genetics provides a forum for the publication of high‐quality foundational research, particularly research that generates useful genetic and genomic information such as genome maps, single gene studies, genome‐wide association and QTL studies, as well as genome reports, mutant screens, and advances in methods and technology. The Editorial Board of G3 believes that rapid dissemination of these data is the necessary foundation for analysis that leads to mechanistic insights. G3, published by the Genetics Society of America, meets the critical and growing need of the genetics community for rapid review and publication of important results in all areas of genetics. G3 offers the opportunity to publish the puzzling finding or to present unpublished results that may not have been submitted for review and publication due to a perceived lack of a potential high-impact finding. G3 has earned the DOAJ Seal, which is a mark of certification for open access journals, awarded by DOAJ to journals that achieve a high level of openness, adhere to Best Practice and high publishing standards.
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