Natural trans-spliced mRNAs are generated from the human estrogen receptor-alpha (hER alpha) gene.

The human estrogen receptor-alpha (hER alpha) gene is a complex genomic unit exhibiting alternative splicing and promoter usage in a tissue-specific manner. During the investigation of new hER alpha mRNA variants by rapid amplification of 5' cDNA ends, we identified a cDNA in which the acceptor site of exon 1A, into which the different leader exons are normally alternatively spliced, was spliced accurately the 3' extremity of exon 1A (scrambled 1A-->1A hER alpha cDNA). Reverse transcription-PCR and S1 nuclease mapping analysis revealed that 1A-->1A hER alpha transcripts were not circular RNAs constituted by exon 1A only but corresponded to linear polyadenylated hER alpha RNAs composed of the eight coding exons of the hER alpha gene and characterized by a duplication of exon 1A. Genomic Southern blot experiments excluded the hypothesis of duplication of hER alpha exon 1A in the human genome. Therefore, these data suggested that 1A-->1A hER alpha transcripts were likely generated by trans-splicing. The production of such transcripts by trans-splicing of pre-mRNAs generated from a chimeric gene formed by a single hER alpha exon 1A, exon 2, and their flanking intronic regions was demonstrated in transient transfection experiments. Therefore, in addition to the alternative cis-splicing, the hER alpha gene is also subject to natural trans-splicing.