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Background  Intergenic splicing resulting in the combination of mRNAs sequences from distinct genes is a newly identified mechanism likely to contribute to protein diversity. Few cases have been described, most of them involving neighboring genes and thus suggesting a cotranscription event presumably due to transcriptional termination bypass.    Results  We identified bovine chimeric transcripts resulting from cotranscription and intergenic splicing of two neighboring genes,  PPARG  and  TSEN2 . These two genes encode the Peroxisome Proliferator Activated Receptors γ1 and γ2 and the tRNA Splicing Endonuclease 2 homolog and are situated in the same orientation about 50 kb apart on bovine chromosome 22q24. Their relative position is conserved in human and mouse. We identified two types of chimeric transcripts containing all but the last exon of the  PPARG  gene followed by all but the first exon of the  TSEN2  gene. The two chimers differ by the presence/absence of an intermediate exon resulting from transcription of a LINE L2 sequence situated between the two genes. Both transcripts use canonical splice sites for all exons coming from both genes, as well as for the LINE L2 sequence. One of these transcripts harbors a premature STOP codon and the other encodes a putative chimeric protein combining most of the PPARγ protein and the entire TSEN2 protein, but we could not establish the existence of this protein.    Conclusion  By showing that both individual and chimeric transcripts are transcribed from  PPARG  and  TSEN2 , we demonstrated regulation of transcription termination. Further, the existence and functionality of a chimeric protein harboring active motifs that are  a priori  unrelated is hypothesized.

Cotranscription and intergenic splicing of the PPARG and TSEN2 genes in cattle