摘要
嵌合RNA(chimeric RNA)是由来自不同基因的外显子片段组成的融合转录本.传统的嵌合RNA检测方法有染色体核型分析、荧光原位杂交(FISH)等,但这些技术的特异性、灵敏性和准确性较差.随着测序技术的发展,二代测序技术展现出强大的数据处理能力,可以通过高通量序列分析来检测嵌合RNA,目前基于高通量测序的检测方法有FusionCatcher、SOAPfuse、EricScript等.目前较为常用的对检测到的嵌合RNA的验证方法有聚合酶链反应(PCR)、核糖核酸酶保护实验(RPA)、琼脂糖凝胶电泳、Sanger测序等.多种检测技术的开发使得越来越多的嵌合RNA被发现,但现有的检测技术各有优劣,主要体现于检测成本、假阳性率、检测时间等方面的差异.本文对嵌合RNA的检测方法、验证方法及各方法的优劣性进行阐述.
Abstract
Chimeric RNA is a fusion transcript comprising of exon fragments from different genes.There are three splicing types:chromosome rearrangements,trans-splicing,cis-splicing,and the recently mentioned circular chimeric RNA.The traditional methods for the detection of chimeric RNA includes chromosome karyotype analysis,FISH,DNA microarray,etc.,but their specificity,sensitivity and accuracy for the detection of chimeric RNA are poorly understood.With the development of sequencing technology,second-generation sequencing technology has shown strong data processing capabilities and can detect chimeric RNA through high-throughput sequence analysis.Currently,detection methods making use of high-throughput sequencing datasets includes FusionCatcher,SOAPfuse,EricScript,etc.For validation of the detected chimeric RNA,the commonly used methods include PCR,RPA,agarose gel electrophoresis,sanger sequencing,etc.The development of newly introduced techniques has led to the discovery of different novel chimeric RNA,the third and fourth generation sequencing has also been developed and nearly mature,and the sequencing technology taking PacBio as an example has also brought a new dawn to the discovery of chimeric RNA,but each of them has its advantages and disadvantages,mainly focusing on its cost,false positive rate,detection time,etc.This paper basically describes various different techniques that can be utilized for the detection and validation of chimeric RNA.
基金项目
国家自然科学基金(81972421)
国家自然科学基金-河南联合项目(U2004135)
郑州大学高层次人才启动项目(32340177)
河南省高等学校大学生创新创业训练计划(202210459126)
河南省高等学校大学生创新创业训练计划(202210459161)
郑州大学教育教学改革研究与实验项目(2022ZZUJGXMLXS-017)
NETL
NSTL
万方数据