title: Possible formation of mitochondrial-RNA containing chimeric or trimeric RNA implies a post-transcriptional and post-splicing mechanism for RNA fusion.
abstract: Human cells are known to express many chimeric RNAs, i.e. RNAs containing two genes' sequences. Wondering whether there also is trimeric RNA, i.e. an RNA containing three genes' sequences, we wrote simple computer code to screen human expression sequence tags (ESTs) deposited in different public databases, and obtained hundreds of putative trimeric ESTs. We then used NCBI Blast and UCSC Blat browsers to further analyze their sequences, and identified 61 trimeric and two tetrameric ESTs (one EST containing four different sequences). We also identified 57 chimeric, trimeric or teterameric ESTs that contained both mitochondrial (mt) RNA and nuclear RNA (nRNA), i.e. were mtRNA-nRNA fusions. In some trimeric ESTs, the downstream partner was fused to the poly-A tail of the upstream partner, which, together with the mtRNA-nRNA fusions, suggests a possible new mechanism for RNA fusion that occurs after both transcription and splicing have been terminated, and possibly outside the nucleus, in contrast to the two current hypothetical mechanisms, trans-splicing and transcriptional-slippage, that occur in the nucleus. The mt-sequences in the mtRNA-nRNA fusions had pseudogenes in the nucleus but, surprisingly, localized mainly in chromosomes 1 and 5. In some mtRNA-nRNA fusions, as well as in some ESTs that were derived only from mtRNA, the mt-sequences might be cis- or trans-spliced. Actually, we cloned a new cis-spliced mtRNA, coined as 16SrRNA-s. Hence, mtDNA may not always be intron-less. Fusion of three or more RNAs to one, fusion of nRNA to mtRNA, and cis- or trans-splicing of mtRNA should all enlarge the cellular RNA repertoire, in turn enlarging the cellular functions. Therefore, future experimental verification of the existence of these novel classes of fusion RNAs and spliced mtRNAs in human cells should significantly advance our understanding of biology and medicine.
authors.affiliation: Guangxi Veterinary Research Institute, Nanning, Guangxi, P.R. China.
authors.forename: Wei
authors.initials: W
authors.lastname: Yang
authors.forename: Jian-min
authors.initials: JM
authors.lastname: Wu
authors.forename: An-ding
authors.initials: AD
authors.lastname: Bi
authors.forename: Yong-chang
authors.initials: YC
authors.lastname: Ou-Yang
authors.forename: Hai-hong
authors.initials: HH
authors.lastname: Shen
authors.forename: Gung-wei
authors.initials: GW
authors.lastname: Chirn
authors.forename: Jian-hua
authors.initials: JH
authors.lastname: Zhou
authors.forename: Emily
authors.initials: E
authors.lastname: Weiss
authors.forename: Emily Pauline
authors.initials: EP
authors.lastname: Holman
authors.forename: D Joshua
authors.initials: DJ
authors.lastname: Liao
mesh_terms: D001483:Base Sequence; D002467:Cell Nucleus / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D020224:Expressed Sequence Tags / Q000737:chemistry; D015870:Gene Expression; D057809:HEK293 Cells; D006367:HeLa Cells; D006801:Humans; D007438:Introns / Q000235:genetics; D008957:Models, Genetic; D008969:Molecular Sequence Data; D012313:RNA / Q000235:genetics*; D012322:RNA Precursors / Q000235:genetics*; D012323:RNA Processing, Post-Transcriptional; D012333:RNA, Messenger / Q000235:genetics; D000077278:RNA, Mitochondrial; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D020040:Trans-Splicing
chemical_list: D004272:DNA, Mitochondrial; D012322:RNA Precursors; D012333:RNA, Messenger; D000077278:RNA, Mitochondrial; D012336:RNA, Ribosomal, 16S; D012313:RNA