OMEGA基因编辑系统：结构、功能及其优化方案的研究进展

doi:10.11843/j.issn.0366-6964.2025.11.001

畜牧兽医学报 ›› 2025, Vol. 56 ›› Issue (11): 5335-5351.doi: 10.11843/j.issn.0366-6964.2025.11.001

OMEGA基因编辑系统：结构、功能及其优化方案的研究进展

岳怡冰¹^,²(), 李俊良¹(), 包斌武¹^,³, 高晨¹, 陈燕¹, 朱波¹, 张路培¹, 王泽昭¹, 高会江¹, 高雪¹^,*(), 黄永震²^,*(), 李俊雅¹^,*()

1. 中国农业科学院北京畜牧兽医研究所, 北京 100193
2. 西北农林科技大学动物科技学院, 杨凌 712100
3. 宁夏大学动物科技学院, 银川 750021

收稿日期:2025-04-16 出版日期:2025-11-23 发布日期:2025-11-27
通讯作者: 高雪,黄永震,李俊雅 E-mail:yueyibing2023@163.com;lijunliang@caas.cn;gaoxue@caas.cn;hyzsci@nwafu.edu.cn;lijunya@caas.cn
作者简介:岳怡冰(2001-)，女，河南洛阳人，硕士生，主要从事动物遗传育种与繁殖研究，E-mail: yueyibing2023@163.com
李俊良(1992-)，男，河南济源人，博士，主要从事基因编辑与动物遗传育种研究，E-mail：lijunliang@caas.cn
第一联系人：
岳怡冰和李俊良为同等贡献作者
基金资助:
内蒙古肉牛经济性状遗传解析与创新利用(2023KJHZ0028);科技创新2030—重大项目(2023ZD04048；2023ZD0404801)

Research Progress on OMEGA Gene Editing System: Structure, Function, and Optimization Strategies

YUE Yibing¹^,²(), LI Junliang¹(), BAO Binwu¹^,³, GAO Chen¹, CHEN Yan¹, ZHU Bo¹, ZHANG Lupei¹, WANG Zezhao¹, GAO Huijiang¹, GAO Xue¹^,*(), HUANG Yongzhen²^,*(), LI Junya¹^,*()

1. Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
2. College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
3. College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China

Received:2025-04-16 Online:2025-11-23 Published:2025-11-27
Contact: GAO Xue, HUANG Yongzhen, LI Junya E-mail:yueyibing2023@163.com;lijunliang@caas.cn;gaoxue@caas.cn;hyzsci@nwafu.edu.cn;lijunya@caas.cn

摘要/Abstract

摘要：

OMEGA编辑系统被认为是CRISPR-Cas系统的祖先，因其较小的尺寸和RNA引导的DNA切割能力成为基因编辑工具研究的热点。本文详细介绍了OMEGA编辑系统的基本结构和功能，并综述了通过对OMEGA系统核酸酶进行优化设计和引导RNA工程化改造等策略来提高其编辑效率和特异性；或通过融合脱氨酶实现碱基编辑，拓展其应用范围，为新工具的开发和优化提供参考。

关键词: OMEGA系统, 基因编辑工具优化, OMEGA系统核酸酶优化设计, 引导RNA工程, 融合脱氨酶

Abstract:

The OMEGA editing system is considered the ancestor to the CRISPR-Cas system and has become a hotspot in gene editing tool research due to its compact size and RNA-guided DNA cleavage capability. This article provides a detailed introduction to the basic structure and function of the OMEGA editing system, and reviews the strategies for improving the editing efficiency and specificity of the OMEGA system nuclease through optimized design and engineered modification of guide RNA. By fusing deaminases to achieve base editing, it expands its application scope, providing references for the development and optimization of new tools.

Key words: OMEGA system, gene editing tool optimization, optimized design of OMEGA system nucleases, guide RNA engineering, fusion deaminase

中图分类号:

S813

岳怡冰, 李俊良, 包斌武, 高晨, 陈燕, 朱波, 张路培, 王泽昭, 高会江, 高雪, 黄永震, 李俊雅. OMEGA基因编辑系统：结构、功能及其优化方案的研究进展[J]. 畜牧兽医学报, 2025, 56(11): 5335-5351.

YUE Yibing, LI Junliang, BAO Binwu, GAO Chen, CHEN Yan, ZHU Bo, ZHANG Lupei, WANG Zezhao, GAO Huijiang, GAO Xue, HUANG Yongzhen, LI Junya. Research Progress on OMEGA Gene Editing System: Structure, Function, and Optimization Strategies[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(11): 5335-5351.

图/表 5

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表 1

OMEGA编辑系统的优化策略及进展"

时间 Date	优化系统 Optimization system	蛋白大小/aa Protein size	ωRNA长度/nt ωRNA length	编辑对象 Editing target	优化方案 Optimization strategies			优化后编辑效率 Optimized editing efficiency	优化后碱基编辑器编辑效率 Optimized base editor efficiency	参考文献 Reference
时间 Date	优化系统 Optimization system	蛋白大小/aa Protein size	ωRNA长度/nt ωRNA length	编辑对象 Editing target	OMEGA系统核酸酶设计 The OMEGA system nuclease design	ωRNA工程化改造 ωRNA engineering	融合脱氨酶 Fusion deaminase for base editing	优化后编辑效率 Optimized editing efficiency	优化后碱基编辑器编辑效率 Optimized base editor efficiency	参考文献 Reference
2023/5/25	OgeuIscB-ωRNA系统	496	222	HEK293T细胞	1.氨基酸替换：E85R、H369R、S387R和S457R得到IscB*；2.融合T5核酸外切酶(T5E)：基于enIscB将T5E融合到IscB蛋白C端得到enIscB-T5E	R1茎环截短15 bp(M3)、R2茎环第10碱基对被G-C碱基对独立替换，得到ωRNA^*	miABE和miCBE	enIscB-T5E(60.61%±27.43%)在23个目标位点显示出与SpG Cas9(53.25%±30.92%)相当的编辑效率	miABE编辑效率可达52.37%~60.06%；miCBE编辑效率可达50.17±2.49%~66.42%±1.13%。	[36]
2024/7/8	OgeuIscB-ωRNA系统	496	222	HEK293T、A549 and HeLa细胞	氨基酸替换：M102R、F137K、V159K、N281R、Q324R、Y327K、H368R和L393K得到enOgeuIscB	将茎环中的无序区域使用更稳定的四环“GAAA”取代，并恢复茎环2中的错配，得到ωRNA-v2；在ωRNA-v2的基础上恢复茎环1中的错配得到ωRNA-v13	enOgeuIscB BE	在6个基因组位点上观察到64.5%~87.3%的编辑效率	优化后的编辑效率达到36.1%±21.1%，野生型OgeuIscB-ωRNA的编辑率为20.3%±21.2%	[41]
2024/7/8	OgeuIscB-ωRNA系统	496	222	HEK293T细胞	氨基酸替换：D97K、F138N、S431K、S457R得到IscBnQM	删除了ωRNA的部分茎环1和3′末端生成了优化的ωRNA变体	SIminiBEs	与野生型IscBn相比，IscBnQM编辑效率从3.16%~10.13%提高到70.85%~84.60%，优化的ωRNA变体比野生型编辑效率提高了约2倍	编辑效率可达50%~60%，提高约2~3倍	[69]
2024/8/15	IscB.m16系统	400左右	200~300	HEK293T细胞	氨基酸替换：E326R、P460S、T462H和T459E得到IscB.m16^RESH	R1茎环截短13 bp、R5茎环截短10 bp、第24、25、57、79、117和189 bp的碱基对替换为G-C，将其命名为enωRNA	IscB.m16-ABE和IscB.m16-CBE	工程化的IscB.m16*编辑效率在多个位点都超过了40%，比野生型提高2~9倍	IscB.m16-ABE(46.15%±4.08%)显示出显著高于IscB.m16-ABE(9.19%± 2.34%)；IscB.m16-CBE编辑效率显著高于SpG-CBE	[42]
2024/8/22	OgeuIscB-ωRNA系统	496	222	HEK293T细胞	1.氨基酸替换：D96R、E84R、V159R，融合HMG-D结构域；得到IscB-DIscB-D2.核定位信号优化：进行了SV40 NLS融合，优化后的变体被命名为eIscB-D	P1茎环截短15 bp、P2茎环截短4 bp、P5茎环截短4 bp、末端发夹截断、在第11位用G-C配对替换A-U配对和在第103位用A替换C以形成A-U配对，命名为eωRNA	eiABE，eiCBE	eIscB-D编辑效率最高可达91.3%；与原始IscB相比，工程化的eIscB-D/eωRNA系统的活性平均增加了20.2倍	eiABE效率高达58.3%，eiCBE效率为35.7%~79.2%(平均61.9%)	[37]
2024/11/26	enIscB系统	496	163	HEK293T细胞	无	茎环2的完全去除、茎环3中88号位置的A: U配对替换以及3′尾序列的14个核苷酸缺失，最终长度为163 nt，命名为ωRNA*-v2	对miABE、miCBE进行AAV包装，在酪氨酸血症小鼠模型中实现了疾病纠正	编辑效率可达87.3%	碱基编辑效率可达62.2%	[68]
2024/1/27	ISDra2 TnpB系统	408	231	HEK293T、小鼠N2a细胞、植物细胞(nicotiana benthamiana，本氏烟草)	无	S1、S2和S3的同时缺失并用5′-GAAA-3′环序列替换SL3亚结构域的序列得到ωRNA*变体(99nt)	无	与野生型ωRNA相比，ωRNA*的基因编辑效率提高了两倍(70%左右)，与SaCas9效率相当	无	[70]
2024/3/19	ISDra2 TnpB系统	408	231	HEK293T和HeLa细胞，小鼠NIH/3T3细胞	蛋白结构域截短：截短CTD结构域，TnpB379	无	无	TnpB379(29.0%±12.3%)编辑效率高于TnpB(26.4%±10.7%)	无	[47]
2024/6/28	ISDra2 TnpB系统	408	231	水稻、拟南芥	1.密码子优化：将ISDra2 TnpB基因的密码子替换为植物细胞偏好的密码子；2.启动子优化：使用Pol-II启动子(ZmUbi)替代Pol-III(RNA聚合酶Ⅲ)启动子(OsU3)得到TnpB2	无	D191A突变，得到TnpB-ABE	在植物基因组中实现了平均高达33.58% 的编辑效率	编辑效率只有0.42%~1.12%	[62]
2024/8/7	TnpB系统	408	231	水稻、拟南芥、青蒿、丹参、黄芩、靛蓝和党参	1.核定位信号优化：TnpB载体的两个末端融合了真核核定位信号，将TnpB与黄色荧光蛋白(YFP)融合生成了YFP-TnpB构建体；2.启动子优化：由U6和UBQ1启动子驱动reRNA和TnpB载体	无	无	编辑效率最高达30%	无	[58]
2024/8/21	IsDge10 TnpB系统	400左右	200~300	水稻	启动子优化：IsDge10蛋白在ZmUbi1启动子下表达，7个sgRNA在OsUbi启动子下表达并融合了HH-HDV双核酶系统	无	无	在水稻原生质体中的效率为4.3% 至18.2%	无	[66]
2024/9/23	ISDra2 TnpB系统	408	231	HEK293T细胞、小鼠肝脏、大脑	1.氨基酸替换：蛋白第76位引入氨基酸替换(K76A、K76C和K76S)；2.核定位信号优化：ARC13设计(在C端包含额外的GS接头和二分NLS序列)；3.密码子优化：对TnpBmax系统进行了哺乳动物密码子优化	利用TEEP将原始的ωRNA支架缩短至117个核苷酸，在ωRNA的3′端融合HDV核酶得到mini-ωRNA	TnpBmax系统的RuvC结构域中引入了突变(D191A)并融合了TadA8e16生成碱基编辑器	编辑率比野生型提高了1.3倍；在小鼠肝脏中实现了高达75.3%的编辑效率，在小鼠脑中实现了高达65.9%的编辑效率	编辑效率可达16.6%	[25]
2025/2/16	ISDra2 TnpB系统	408	231	HEK293T；本氏烟草	1.氨基酸替换：P282I单点突变使效率提升四倍；深度突变扫描(DMS)筛选到6个组合突变的变体(eTnpB1a-eTnpB1f)，eTnpB1e效率最高；2.蛋白结构域截短：C端截短至376 aa，是最小活性TnpB截断变体	茎2区域的“铰链”区域(rA-37-rU-44)发生的碱基缺失和替换编辑效率最高	无	eTnpB1e在PDS1-1位点编辑效率为33%，与WT ISDra2 TnpB (< 1%)相比增加了50倍以上	无	[43]

表 1

图 4

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OMEGA基因编辑系统：结构、功能及其优化方案的研究进展

Research Progress on OMEGA Gene Editing System: Structure, Function, and Optimization Strategies

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