Sense transcripts originated from an internal part of the human retrotransposon LINE-1 5′ UTR

L1 (LINE-1) is one of the most abundant families of human transposable elements. Full-length human L1 has an ~ 900 bp long 5′ untranslated region (5′ UTR) which harbors an internal promoter for the RNA polymerase II. It is generally accepted that the first 100 bp of the 5′ UTR function as a “minimal promoter” which directs transcription of the entire LINE-1 unit from the extreme 5′ terminus. We re-investigated promoter activities of the different DNA fragments that cover the whole L1 5′ UTR in cultured human cells by using the luciferase reporter system. Analysis of both mRNA expression and luciferase activity levels indicated that the very important region for the effective transcription is located within the internal part of the L1 5′ UTR between nucleotide positions + 390 and + 526. 5′ RACE analysis revealed that in the context of the complete 5′ UTR, this part drives mRNA synthesis both from the canonical 5′-terminal transcription start site (TSS) and from within the internal region. In the absence of the first 100 bp, the L1 5′ UTR efficiently directed transcription from aberrant TSSs located within its 3′ proximal part or the ORF1. Finally, we analyzed transcripts originated from endogenous (genomic) L1 elements and identified two novel TSSs located at positions + 525 and + 570. We propose a model in which the internal part (390–526) of the L1 5′ UTR plays a key role for recruitment of transcription initiation complex, which then may be either positioned onto the 5′ terminally located “minimal promoter”, or used proximately to direct 5′ truncated RNA copy. Intriguingly, this internal regulatory element substantially overlaps with the region of the L1 5′ UTR that is known to drive transcription in the opposite direction suggesting the existence of a common core for the bidirectional transcription.

► 5’ UTR of the human retrotransposon L1 harbors an internal promoter for RNA pol II.
► We examined L1 promoter activity in cultured human cells using reporter constructs.
► An internal region of L1 5’ UTR was shown to be critical for transcription efficiency.
► Alternative transcription start sites were found in the internal part of L1 5’ UTR.
► We propose a new model for the mechanism of the L1 promoter action.