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

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

功能性微肽通量发现和功能验证的研究进展

吕雪(), 李帮洁, 徐寒梅()

中国药科大学,江苏省合成多肽药物发现与评价工程中心,南京 211198

收稿日期:2022-02-28 修回日期:2022-04-02 出版日期:2022-06-20 发布日期:2022-04-14
通讯作者: 徐寒梅 E-mail:13837189145@163.com;xuhanmei6688@126.com
作者简介:吕雪,在读硕士研究生,专业方向：微生物与生化药学。E-mail: 13837189145@163.com
基金资助:
国家科技重大专项编号(2019ZX09301-124);中国药科大学天然药物活性组分与药效国家重点实验编号(SKLNMZZ202028);中国博士后科学基金资助项目编号(2020M681787);江苏省自然科学基金资助编号(BK20210418)

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)

摘要/Abstract

摘要：

随着计算生物学和深度测序技术的飞速发展,愈来愈多的研究表明大量之前未被注释、隐藏在非编码RNA中的非经典开放阅读框(open reading frame, ORF)具有编码功能性微肽(micropeptide)的能力。本文对微肽的基因来源、生物性质、预测方法和功能验证的研究现状和技术策略展开综述,以期为后续开展微肽发现、研究调控机制以及新靶点、生物标志物的开发等提供理论基础和参考依据。

关键词: 非编码RNA, sORFs, 功能性微肽

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

吕雪, 李帮洁, 徐寒梅. 功能性微肽通量发现和功能验证的研究进展[J]. 遗传, 2022, 44(6): 478-490.

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.

图/表 3

图1

表1

微肽的预测算法"

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]

表1

图2

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功能性微肽通量发现和功能验证的研究进展

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

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