A sensitive RNase protection assay to detect transcripts from potentially functional human endogenous L1 retrotransposons.

A high background of read-through transcripts from degenerate human L1 retrotransposons is present in almost all human cell types. This prevents the detection of RNA transcripts from potentially functional elements. To overcome this, we have developed an RNase protection assay based on the reconstructed consensus sequence for the 5' end of the major L1 family. In the human Ntera2D1 teratocarcinoma cell line, this assay readily detected L1 transcripts that were located primarily in the cytoplasm and where 20% were in filterable particles. By this assay, potentially functional L1 elements are also transcriptionally active in lymphocytes from some but not all normal individuals. Together with the full length protection product, there were three other discrete L1 RNAs, two of which (305 and 275 bases) were transcribed from the 5' end of the L1 element. These smaller L1 RNAs do not appear to be derived from transcripts from divergent L1 families but are either discrete shorter transcripts or specifically processed products from longer initial transcripts.