功能性微肽通量发现和功能验证的研究进展

doi:10.16288/j.yczz.22-007

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Hereditas(Beijing) ›› 2022, Vol. 44 ›› Issue (6): 478-490.doi: 10.16288/j.yczz.22-007

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Research progress on high throughput discovery and functional verification of functional micropeptides

Xue Lv(), Bangjie Li, Hanmei Xu()

Engineering Research Center of Synthetic Peptide Drug Discovery and Evaluation of Jiangsu Province, China Pharmaceutical University, Nanjing 211198, China

Received:2022-02-28 Revised:2022-04-02 Online:2022-06-20 Published:2022-04-14
Contact: Xu Hanmei E-mail:13837189145@163.com;xuhanmei6688@126.com
Supported by:
Supported by the National Science and Technology Major Projects No(2019ZX09301-124);the Project Program of State Key Laboratory of Natural Medicines No(SKLNMZZ202028);China Postdoctoral Science Foundation No(2020M681787);the Natural Science Foundation of Jiangsu Province No(BK20210418)

Abstract

Abstract:

With the rapid development of computational biology and deep sequencing technology, more and more studies have shown that a large number of non-classical open reading frames that have not been annotated and hidden in non-coding RNA can encode functional micropeptide. This article reviewed the current research status and technology strategy of gene sources, biological properties, predicted methods and functional verification of micropeptide, providing theoretical and reference basis for the subsequent discovery of micropeptides, research on regulatory mechanisms and development of novel targets and biomarkers.

Key words: noncoding RNA, sORFs, functional micropeptides

Xue Lv, Bangjie Li, Hanmei Xu. Research progress on high throughput discovery and functional verification of functional micropeptides[J]. Hereditas(Beijing), 2022, 44(6): 478-490.

Figures/Tables 3

Fig. 1

Table 1

The prediction algorithm for novel micropeptides"

技术名称	算法特征描述	参考文献
uPEPperoni	一种通过检测mRNA中5′-UTR保守性sORF预测潜在微肽的计算方法	[82]
PhyloCSF	一种检测跨物种sORF的进化特征和密码子替换频率作为评分以筛选潜在微肽的方法	[83]
Ribosome releasing scores (RRS)	一种基于总Ribo-Seq读段数在开放阅读框和3′-UTR之间的比例作为潜在微肽评分指标的计算方法	[84]
Fragment length organisation similarity score (FLOSS)	一种基于编码基因和非编码RNA之间核糖体片段RPF长度分布差异以预测微肽的方法	[85]
ORF regression algorithm for translational evaluation of RPFs (ORF-RATER)	一种基于比较核糖体占据的模式来量化翻译的回归算法以预测潜在微肽的方法	[86]
Ribo taper	一种采用多锥光谱分析方法从原始数据中获得具有3-nt周期性特征的序列预测微肽的的计算方法	[87]
Translated ORF classifier (TOC)	一种评估转录本中ORF编码潜力的随机森林分类器以预测潜在微肽的方法	[88]
ORFScore	一种分析跨ORF翻译核糖体的3碱基周期性预测微肽的评分方法	[25]
RiboHMM	一种测定核糖体保护片段丰度及其周期性概率模型预测微肽的计算方法	[89]
SPECtre	一种基于光谱相干性分类器对核糖体覆盖的整体周期性进行建模分析预测微肽的计算方法	[90]
RibORF	一种基于三碱基周期性和密码子间一致性的支持向量机分类器以预测ORF序列	[91]
RB-BP	一种采用无监督的贝叶斯方法从核糖体谱中预测翻译的ORF的方法	[92]
RiboCode	一种基于全翻译组从头注释的三核苷酸周期性定量分析方法	[93]
PhastCons	一种基于多序列比对的方法结合了系统发育距离和碱基替代率模型以预测潜在微肽的方法	[94]
Coding region identification tool invoking comparative analysis (CRITICA)	一种成对比对同源区域的纯化选择分析与核苷酸序列组成分析相结合预测微肽的算法	[95]
Coding potential calculator (CPC)	一种支持向量学习机分类器且结合六个序列特征以区分编码与非编码ORF预测微肽的计算方法	[96]

Table 1

Fig. 2

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Research progress on high throughput discovery and functional verification of functional micropeptides

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