title: It Is Imperative to Establish a Pellucid Definition of Chimeric RNA and to Clear Up a Lot of Confusion in the Relevant Research.
abstract: There have been tens of thousands of RNAs deposited in different databases that contain sequences of two genes and are coined chimeric RNAs, or chimeras. 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. 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. Otherwise, not only will chimeric RNA studies be misled but also characterization of fusion genes and unannotated genes will be hindered. 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, andcis-spliced from, single transcripts should not be deemed as chimeras. 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. 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.
authors.affiliation: Department of Biochemistry, China Three Gorges University, Yichang 443002, China. yuancf46@ctgu.edu.cn.
authors.forename: Chengfu
authors.initials: C
authors.lastname: Yuan
authors.affiliation: Hormel Institute, University of Minnesota, Austin, MN 55912, USA. yhen@hi.umn.edu.
authors.forename: Yaping
authors.initials: Y
authors.lastname: Han
authors.affiliation: Hormel Institute, University of Minnesota, Austin, MN 55912, USA. luc.zellmer@gmail.com.
authors.forename: Lucas
authors.initials: L
authors.lastname: Zellmer
authors.affiliation: Department of Pathology, Guizhou Medical University Hospital, Guiyang 550004, China. ypq1964@163.com.
authors.forename: Wenxiu
authors.initials: W
authors.lastname: Yang
authors.affiliation: Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang 550004, China. zhizhongguan@gmc.edu.cn.
authors.forename: Zhizhong
authors.initials: Z
authors.lastname: Guan
authors.affiliation: Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang 550004, China. wenfengyu2013@126.com.
authors.forename: Wenfeng
authors.initials: W
authors.lastname: Yu
authors.affiliation: School of Clinical Laboratory Science, Guizhou Medical University, Guiyang 550004, China. huanghai828@gmc.edu.cn.
authors.forename: Hai
authors.initials: H
authors.lastname: Huang
authors.affiliation: Department of Biochemistry, China Three Gorges University, Yichang 443002, China. djliao@gmc.edu.cn.|Hormel Institute, University of Minnesota, Austin, MN 55912, USA. djliao@gmc.edu.cn.|Department of Pathology, Guizhou Medical University Hospital, Guiyang 550004, China. djliao@gmc.edu.cn.|Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang 550004, China. djliao@gmc.edu.cn.
authors.forename: D Joshua
authors.initials: DJ
authors.lastname: Liao
mesh_terms: D000818:Animals; D001483:Base Sequence; D030561:Databases, Nucleic Acid; D006801:Humans; D012313:RNA / Q000235:genetics*; D012106:Research; D009626:Terminology as Topic
chemical_list: D012313:RNA
keywords: RNA deep sequencing; chimeric RNA; expression sequence tag; polymerase chain reactions; reverse transcription; trans-splicing