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Sense transgene-induced post-transcriptional gene silencing (S-PTGS) is thought to be a type of RNA silencing in which ARGONAUTE1 directs the small interfering RNA (siRNA)-mediated cleavage of a target mRNA in the cytoplasm. Here, we report that the altered splicing of endogenous counterpart genes is a main cause for the reduction of their mature mRNA levels. After the S-PTGS of a tobacco endoplasmic reticulum ω-3 fatty acid desaturase ( NtFAD3 ) gene, 3′-truncated, polyadenylated  endo-NtFAD3  transcripts and 5′-truncated, intron-containing  endo-NtFAD3  transcripts were detected in the total RNA fraction. Although transcription proceeded until the last exon of the endogenous  NtFAD3  gene, intron-containing  NtFAD3  transcripts accumulated in the nucleus of the S-PTGS plants. Several intron-containing  NtFAD3  transcripts harboring most of the exon sequences were generated when an endogenous silencing suppressor gene,  rgs-CaM , was overexpressed in the S-PTGS plants. These intron-containing  NtFAD3  splice variants were generated in the presence of  NtFAD3  siRNAs that are homologous to the nucleotide sequences of these splice variants. The results of this study indicate that the inhibition of  endo-NtFAD3  gene expression is primarily directed via the alteration of splicing and not by cytoplasmic slicer activity. Our results suggest that the transgene and intron-containing endogenous counterpart genes are differentially suppressed in S-PTGS plants.

Sense Transgene-Induced Post-Transcriptional Gene Silencing in Tobacco Compromises the Splicing of Endogenous Counterpart Genes