Molecular analysis of transcription start sites of separate copies of the suffix short retroelement in genome of Drosophila.

In order to study TSS in the suffix element, we used total RNA isolated from ovaries of Drosophila melanogaster. Using a 5'-RACE System (Invitrogen) and 454 sequencing, we found the full-length suffix sense transcripts. However, most 5'-RACE reads (>70%) correspond to 5'-truncated transcripts lacking the first 33-39 nucleotides. The data may indicate that these RNAs are products of the RNAi-related silencing mech-anism producing small RNAs that are larger than piRNAs. The full-length suffix transcripts could arise either from the F element or from active separate copies of suffix.