title: A candidate chimeric mammalian mRNA transcript is derived from distinct chromosomes and is associated with nonconsensus splice junction motifs.
abstract: The process of creating chimeric mRNA transcripts derived from separately transcribed genes via known spliceosome mechanisms is termed trans-splicing, and has been primarily described in lower eukaryotes. Isolation of cDNA clones containing sequences from distinct genes has raised the possibility of trans-splicing across distinct genes in mammalian systems; however, the possibility of cloning artifacts or splicing via nonspliceosome mechanisms has been difficult to rule out. In most cases, the absence of corresponding genomic clones has limited assessment of splice donor and acceptance sites and associated intronic elements that would be expected to participate in spliceosome-based reactions. We have previously reported a cDNA clone encoding the rat Leukocyte Common Antigen-Related (LAR) tyrosine phosphatase receptor that contains an alternative 3' UTR. In the present study Northern, RT-PCR and RNase protection assays verified the existence of developmentally regulated 3' UTR alternative splicing of LAR transcripts in vivo. FISH and radiation hybrid mapping demonstrated that loci encoding LAR and its alternative 3' UTR are present on distinct chromosomes, raising the possibility that alternatively spliced transcripts resulted from trans-splicing. Exon/intron analysis of corresponding genomic clones revealed nonconsensus splice junctions along with elements known to promote both cis- and trans-splicing. Verification in a mammalian in vivo system of chimeric transcripts derived from distinct genes along with identification of atypical nonconsensus-associated genomic elements points to the novel possibilities of atypical spliceosome-based trans-splicing or nonconventional, nonspliceosome-based mechanisms leading to chimeric transcripts.
authors.affiliation: Department of Neurology, University of California at San Francisco, San Francisco, California, USA.
authors.forename: Cheng
authors.initials: C
authors.lastname: Zhang
authors.forename: Youmei
authors.initials: Y
authors.lastname: Xie
authors.forename: John A
authors.initials: JA
authors.lastname: Martignetti
authors.forename: Tracy T
authors.initials: TT
authors.lastname: Yeo
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Massa
authors.forename: Frank M
authors.initials: FM
authors.lastname: Longo
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics*; D017398:Alternative Splicing; D000818:Animals; D001483:Base Sequence; D015152:Blotting, Northern; D002678:Chimera; D002875:Chromosomes / Q000235:genetics*; D017124:Conserved Sequence; D017931:DNA Primers; D018076:DNA, Complementary; D005091:Exons; D018507:Gene Expression Regulation, Developmental; D016678:Genome; D007438:Introns; D008969:Molecular Sequence Data; D009419:Nerve Tissue Proteins / Q000235:genetics* / Q000378:metabolism; D017027:Protein Tyrosine Phosphatases / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D021101:Radiation Hybrid Mapping; D051381:Rats; D017207:Rats, Sprague-Dawley; D054623:Receptor-Like Protein Tyrosine Phosphatases, Class 2; D011956:Receptors, Cell Surface / Q000235:genetics* / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012259:Ribonuclease, Pancreatic / Q000378:metabolism; D020040:Trans-Splicing
chemical_list: D020413:3' Untranslated Regions; D017931:DNA Primers; D018076:DNA, Complementary; D009419:Nerve Tissue Proteins; D012333:RNA, Messenger; D011956:Receptors, Cell Surface; D012259:Ribonuclease, Pancreatic; D017027:Protein Tyrosine Phosphatases; C516774:Ptprf protein, rat; D054623:Receptor-Like Protein Tyrosine Phosphatases, Class 2