One chimeric RNA contains two-partner-genes’ sequences indicated by a striped bar and a black bar, respectively. Illustration of how RNA protection assay, in situ hybridization or Northern blotting may produce a false signal by detecting only one of the two partner sequences. RNA deep sequencing chimeric RNA expression sequence tag polymerase chain reactions reverse transcription trans-splicing. In today's chimeric RNA research, there are still several key flaws, technical constraints and understudied tasks, which are also described in this perspective essay. Many RNAs containing sequences of two neighboring genes may be transcribed via a readthrough mechanism, and thus are actually RNAs of unannotated genes or RNA variants of known genes, but not chimeras. We propose that only those RNAs that are formed by joining two RNA transcripts together without a fusion gene as a genomic basis should be regarded as authentic chimeras, whereas those RNAs transcribed as, and cis-spliced from, single transcripts should not be deemed as chimeras. Otherwise, not only will chimeric RNA studies be misled but also characterization of fusion genes and unannotated genes will be hindered. Since the number of putative chimeras is soaring, it is imperative to establish a pellucid definition for it, in order to differentiate chimeras from regular RNAs. However, "chimeric RNA" has never been lucidly defined, partly because "gene" itself is still ill-defined and because the means of production for many RNAs is unclear. have been tens of thousands of RNAs deposited in different databases that contain sequences of two genes and are coined chimeric RNAs, or chimeras. 11 Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang 550004, China. 10 Department of Pathology, Guizhou Medical University Hospital, Guiyang 550004, China. 9 Hormel Institute, University of Minnesota, Austin, MN 55912, USA. 8 Department of Biochemistry, China Three Gorges University, Yichang 443002, China. 7 School of Clinical Laboratory Science, Guizhou Medical University, Guiyang 550004, China. 6 Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang 550004, China. 5 Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang 550004, China. 4 Department of Pathology, Guizhou Medical University Hospital, Guiyang 550004, China. 3 Hormel Institute, University of Minnesota, Austin, MN 55912, USA. 2 Hormel Institute, University of Minnesota, Austin, MN 55912, USA. 1 Department of Biochemistry, China Three Gorges University, Yichang 443002, China.
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