Transcriptional inactivity of Alu repeats in HeLa cells

The in vivo transcription of human Alu family members has been investigated by a sensitive primer extension method. The selected primers represent various regions of the Alu family consensus sequence, thus assaying the transcriptional activity of the entire family rather than the activity of an individual member sequence. Using this method, a very small number of RNA molecules per HeLa cell is found to have a distribution of 5' ends centered on the in vitro Alu transcription start site. The distribution of these 5' ends suggests that they are more likely the result of hnRNA degradation rather than transcription start sites. Therefore, despite their great numerical abundance, Alu family members are transcriptionally silent in HeLa cells.