[1] Xu Yuming, Qi Ting, Gu Wanjun, Lu Zuhong, et al. Evolutionary selection on synonymous codons in RNAG-quadruplex structural region [J]. Journal of Southeast University (English Edition), 2021, 37 (2): 177-183. [doi:10.3969/j.issn.1003-7985.2021.02.007]
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Evolutionary selection on synonymous codons in RNAG-quadruplex structural region(
)
RNA G-四联体结构区的同义密码子进化选择
)Journal of Southeast University (English Edition)[ISSN:1003-7985/CN:32-1325/N]
- Volumn:
- 37
- Issue:
- 2021 2
- Page:
- 177-183
- Research Field:
- Biological Science and Medical Engineering
- Publishing date:
- 2021-06-20
Info
- Title:
- Evolutionary selection on synonymous codons in RNAG-quadruplex structural region
- RNA G-四联体结构区的同义密码子进化选择
- Author(s):
- Xu Yuming; Qi Ting; Gu Wanjun; Lu Zuhong
- School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
- PACS:
- Q311
- DOI:
- 10.3969/j.issn.1003-7985.2021.02.007
- Abstract:
- To investigate how synonymous codons have been adapted to the formation of ribonucleic acid(RNA)G-quadruplex(rG4)structure, a computational searching algorithm G4Hunter was applied to detect rG4 structures in protein-coding sequences of mRNAs in five eukaryotic species. The native sequences forming rG4s were then compared with randomized sequences to evaluate selection on synonymous codons. Factors that may influence the formation of rG4 were also investigated, and the selection pressures of rG4 in different gene regions were compared to explore its potential roles in gene regulation. The results show universal selective pressure acts on synonymous codons in rG4 regions to facilitate rG4 formation in five eukaryotic organisms. While G-rich codon combinations are preferred in the rG4 structural region, C-rich codon combinations are selectively unfavorable for rG4 formation. Gene’s codon usage bias, nucleotide composition, and evolutionary rate can account for the selective variations on synonymous codons among rG4 structures within a species. Moreover, rG4 structures in the translational initiation region showed significantly higher selective pressures than those in the translational elongation region.
- 为探索同义密码子对RNA G-四联体(rG4)形成的适应效应, 利用G4Hunter算法搜寻5类真核生物mRNA蛋白编码区的rG4结构.通过对比天然序列和随机序列, 评估rG4结构对同义密码子的选择偏好, 分析影响rG4形成的因素, 检验基因特定区域rG4结构的选择压力, 以揭示rG4在基因调控中的潜在作用.结果表明, 在5类真核生物中, rG4结构区内的同义密码子普遍受到促使rG4形成的选择压力.在rG4结构区内的蛋白编码序列倾向于使用富含鸟嘌呤的密码子组合, 不倾向于选择富含胞嘧啶的密码子组合.密码子使用偏好、碱基成分以及进化速率等因素和rG4对同义密码子的选择压力具有相关性.基因翻译起始区的序列受到更强的促使rG4结构形成的选择压力.
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Memo
- Memo:
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Biographies: Xu Yuming(1988—), male, Ph.D. candidate; Lu Zuhong(corresponding author), male, doctor, professor, zhlu@seu.edu.cn.
Foundation items: The National Key Research and Development Program of China(No. 2018YFC1314900, 2018YFC1314902), the National Natural Science Foundation of China(No. 61571109), the Fundamental Research Funds for the Central Universities(No. 2242017K3DN04).
Citation: Xu Yuming, Qi Ting, Gu Wanjun, et al.Evolutionary selection on synonymous codons in RNA G-quadruplex structural region[J].Journal of Southeast University(English Edition), 2021, 37(2):177-183.DOI:10.3969/j.issn.1003-7985.2021.02.007.