A transcriptional analysis of the S1(Bn), (Brassica napus) family of SINE retroposons

S1(Bn) is a plant short interspersed element (SINE) whose amplification probably involves the reverse transcription of an RNA intermediate. In this report, we identified and characterized S1(Bn) transcripts from different Brassica napus tissues. Despite the presence of a consensus internal POL III promoter in a large number of genomic S1(Bn) elements, we observed that S1(Bn) transcripts are rare in B. napus cells. The use of two very sensitive methods (RT-PCR and RACE PCR) allowed the characterization of 102 independent S1(Bn) cDNA clones from three different tissues (shoot, root and callus). From this analysis, we conclude that the majority of S1(Bn) transcripts probably result from a small number of cotranscriptional events where an S1(Bn) element is transcribed due to its presence in a POL II transcriptional unit. Specific POL III RNA transcripts, initiating at the first 5' nucleotide of the DNA element, are also present in the tested tissues and possibly result from the transcriptional activity of as few as three genomic elements. Two of these transcripts could represent master transcripts responsible for the amplification of S1(Bn) subfamilies. We also observed that the population of specific POL III transcripts varies among the three tested tissues and that some transcripts appear completely tissue-specific.