1)Department of Microbiology and Immunology, School of Basic Science, Zhengzhou University, Zhengzhou 450001, China;2)Center for Medical Epigenetics, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China;3)Molecular Pathology Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China;4)Translational Medicine Platform, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China;5.6)Department of Pathology and Pathophysiology, School of Basic Medicine, Zhengzhou University, Zhengzhou 450001, China;6.5)State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou 450052, China
This work was supported by grants from The National Natural Science Foundation of China (81972421), Joint Program NSFC-Henan (U2004135), Zhengzhou University High-level Talent Start-up Project (32340177), Innovation and Entrepreneurship Training Program for College Students of Henan Province (202210459126, 202210459161), and Education and Teaching Reform Research and Practice Project of Zhengzhou University (2022ZZUJGXMLXS-017).
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.
WANG Guang-Fu, DING Yong-Wei, TANG Yue, QIN Fu-Jun. Detection and Validation of Chimeric RNA[J]. Progress in Biochemistry and Biophysics,2024,51(4):797-808
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