Expression of Arabidopsis LINEs from two promoters

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.

A LINE-type retrotransposon active in meristem stem cells causes heritable transpositions in the sweet potato genome

We isolated a LINE-type retrotransposon, LIb, which showed high transposition activity in sweet potato callus. A copy transposed in the callus was 6303 bp in length and showed key features of a LINE element. Apparently full-length copies sharing the 5' UTR sequence with the 6303-bp copy increased dramatically in the callus as several original copies in the sweet potato genome. These apparently full-length copies had almost identical sequences to other transposed copies, many of which were truncated at the 5' end upon transposition. These results indicate that active LIb is confined to a single LINE family, and that members containing a long functional 5' UTR are present in limited numbers in the sweet potato genome. This is despite their copy numbers being estimated at over 100. The transcription of LIb was not completely suppressed, even in wild-type plants. Spontaneous transpositions were found among local variant lines of the cultivar Koukei14, from which the callus with high LIb activity was derived. Meristem culture of this cultivar appeared to facilitate transpositions of LIb in a mericlone plant. This is the first experimental demonstration of retrotransposition in a plant species without the imposition of cell differentiation. LIb transpositions appear to occur in single founder cells in the meristem because the LIb insertion was found throughout mericlone plant tissues. Transpositional activities in meristem cells might be essential characteristics of plant retrotransposons that cause heritable changes in host plant genomes and genetic systems.

Synthesis and processing of tRNA-related SINE transcripts in Arabidopsis thaliana

Despite the ubiquitous distribution of tRNA-related short interspersed elements (SINEs) in eukaryotic species, very little is known about the synthesis and processing of their RNAs. In this work, we have characterized in detail the different RNA populations resulting from the expression of a tRNA-related SINE S1 founder copy in Arabidopsis thaliana. The main population is composed of poly(A)-ending (pa) SINE RNAs, while two minor populations correspond to full-length (fl) or poly(A) minus [small cytoplasmic (sc)] SINE RNAs. Part of the poly(A) minus RNAs is modified by 3'-terminal addition of C or CA nucleotides. All three RNA populations accumulate in the cytoplasm. Using a mutagenesis approach, we show that the poly(A) region and the 3' end unique region, present at the founder locus, are both important for the maturation and the steady-state accumulation of the different S1 RNA populations. The observation that primary SINE transcripts can be post-transcriptionally processed in vivo into a poly(A)-ending species introduces the possibility that this paRNA is used as a retroposition intermediate.