Fig. 1

Retrotransposition competent LINE-1 RNA preferentially localizes to the nucleus in human cell lines. Transcripts expressed from retrotransposition competent L1-Hs were assayed by RT-PCR in nuclear (Nuc) and cytoplasmic (Cyt) RNA fractions from 293T, A375, HCT116, HeLa and U2OS cell lines. a Schematic depiction of LINE-1 transcription. Transcription is initiated by RNA Pol II at the internal promoter in the 5’UTR. Red arrows marked 1 and 2 indicate the position of primer sets 5pUTR P1 and 5pUTR P2 respectively. b Full-length LINE-1 transcripts are highly enriched in the nucleus. The two primer sets used, 5pUTR P1 and 5pUTR P2, indicated by the two sets of red arrows in (A), detect all expressed L1-Hs with an intact 5’UTR. c Schematic depiction of read-through transcription from a LINE-1 coding sequence. Due to a weak 3p UTR polyA signal, RNA Pol II transcription can continue beyond the non-unique L1 3’UTR into downstream unique intergenic regions. Red and blue arrows indicate the position of the constant forward and variable reverse primers that were used to uniquely detect read-through transcription from individual, identifiable L1-Hs elements. d Transcripts from three distinct and uniquely identifiable L1-Hs also show nuclear enrichment of their transcripts in all the cell lines used in our assay. Red arrow heads indicate the expected amplicon size. Unique L1 #1 and #2 refer to specific L1-Hs elements on chromosome 7, whereas unique L1 #3 refers to a target L1-Hs element on chromosome 13 (see Additional File 15 for genomic coordinates of unique L1 copies). e Malat1, a nuclear RNA, and spliced β-actin transcript, which primarily localizes to the cytoplasm, serve as fractionation controls