Biotechnology Bulletin ›› 2023, Vol. 39 ›› Issue (4): 157-165.doi: 10.13560/j.cnki.biotech.bull.1985.2022-0832
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XUE Jiao ZHU Qing-feng FENG Yan-zhao CHEN Pei LIU Wen-hua ZHANG Ai-xia LIU Qin-jian ZHANG Qi YU Yang()
Received:
2022-07-05
Online:
2023-04-26
Published:
2023-05-16
XUE Jiao ZHU Qing-feng FENG Yan-zhao CHEN Pei LIU Wen-hua ZHANG Ai-xia LIU Qin-jian ZHANG Qi YU Yang. Advances in Upstream Open Reading Frame in Plant Genes[J]. Biotechnology Bulletin, 2023, 39(4): 157-165.
Fig. 1 Upstream open reading frame(uORF)classifica-tions in plant A: The location of the stop codon of the uORF is independent of the mORF. B: The stop codon of the uORF overlaps with the mORF. C: The stop codon of the uORF is the same as that of the stop codon of the mORF. D: Multiple uORFs
Fig. 2 Regulatory mechanisms of uORF to mORF A: Leaky scanning by 40S ribosome subnit. B: Translational reinitiation at mORF. C: Ribosome dissociates from the mRNA; D: Trigger nonsense-mediated mRNA decay(NMD)
方法比较 Comparison of methods | 多聚核糖体分析技术 Polysome profiling | 核糖体-新生肽链复合物测序 RNC-Seq | 核糖体图谱分析技术 Ribo-seq | 核糖体亲和纯化技术 RAP |
---|---|---|---|---|
分离原理 | 蔗糖密度梯度离心 | 单一浓度蔗糖溶液离心 | RNA酶降解未被核糖体覆盖的mRNA后经蔗糖梯度离心 | 亲和标签免疫沉淀 |
分离对象 | 多聚核糖体复合物 | 核糖体-新生肽链复合物 | 被核糖体覆盖保护的RNA小片段 | 核糖体大亚基及其结合的mRNA |
优点 | 可对核糖体数分组进行收集分析 | RNA回收容易,得率高 | 准确度高,通量大 | 可组织特异性检测 |
检测方法 | 高通量测序或芯片技术 | 高通量测序或芯片技术 | 高通量测序 | 高通量测序或芯片技术 |
检测的mRNA长度 | 全长 | 全长 | 被核糖体覆盖的约30 nt | 全长 |
缺点 | 仪器贵重、操作繁琐、RNA回收难度大、纯度低 | 仪器贵重、无法分析结合不同数量核糖体的 mRNA | 操作复杂、酶切条件难控制 | 需构建转基因植株 |
Table 1 Comparison of the methods for predicting uORFs
方法比较 Comparison of methods | 多聚核糖体分析技术 Polysome profiling | 核糖体-新生肽链复合物测序 RNC-Seq | 核糖体图谱分析技术 Ribo-seq | 核糖体亲和纯化技术 RAP |
---|---|---|---|---|
分离原理 | 蔗糖密度梯度离心 | 单一浓度蔗糖溶液离心 | RNA酶降解未被核糖体覆盖的mRNA后经蔗糖梯度离心 | 亲和标签免疫沉淀 |
分离对象 | 多聚核糖体复合物 | 核糖体-新生肽链复合物 | 被核糖体覆盖保护的RNA小片段 | 核糖体大亚基及其结合的mRNA |
优点 | 可对核糖体数分组进行收集分析 | RNA回收容易,得率高 | 准确度高,通量大 | 可组织特异性检测 |
检测方法 | 高通量测序或芯片技术 | 高通量测序或芯片技术 | 高通量测序 | 高通量测序或芯片技术 |
检测的mRNA长度 | 全长 | 全长 | 被核糖体覆盖的约30 nt | 全长 |
缺点 | 仪器贵重、操作繁琐、RNA回收难度大、纯度低 | 仪器贵重、无法分析结合不同数量核糖体的 mRNA | 操作复杂、酶切条件难控制 | 需构建转基因植株 |
Fig. 3 Mechanisms for evading uORF-mediated regulation A: Alternative transcription start site(TSS)selection. B: Processing uORF by alternative splicing. C: Cap-independent translational initiation
Fig. 4 Manipulation of gene translation by editing uORFs A: Involved the deletion of uORF upstream sequence and initiation codon. B: Involved the mutation of uORF initiation codon. C: Utilized uORF sequence by genetic engineering
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