Detection and Validation of Chimeric RNA
10.16476/j.pibb.2023.0234
- VernacularTitle:嵌合RNA检测和验证技术
- Author:
Guang-Fu WANG
1
;
Yong-Wei DING
2
;
Yue TANG
1
;
Fu-Jun QIN
1
Author Information
1. Department of Microbiology and Immunology, School of Basic Science, Zhengzhou University, Zhengzhou 450001, China
2. Department of Pathology and Pathophysiology, School of Basic Medicine, Zhengzhou University, Zhengzhou 450001, China
- Publication Type:Journal Article
- Keywords:
chimeric RNA;
detection techniques;
validation techniques;
RNA-Seq;
bioinformatics
- From:
Progress in Biochemistry and Biophysics
2024;51(4):797-808
- CountryChina
- Language:Chinese
-
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.
