Evidence for a reverse transcription intermediate for a marked line transposon in tumoral rat cells

L1 retrotransposition in the soma: a field jumping ahead

Retrotransposons are transposable elements (TEs) capable of "jumping" in germ, embryonic and tumor cells and, as is now clearly established, in the neuronal lineage. Mosaic TE insertions form part of a broader landscape of somatic genome variation and hold significant potential to generate phenotypic diversity, in the brain and elsewhere. At present, the LINE-1 (L1) retrotransposon family appears to be the most active autonomous TE in most mammals, based on experimental data obtained from disease-causing L1 mutations, engineered L1 reporter systems tested in cultured cells and transgenic rodents, and single-cell genomic analyses. However, the biological consequences of almost all somatic L1 insertions identified thus far remain unknown. In this review, we briefly summarize the current state-of-the-art in the field, including estimates of L1 retrotransposition rate in neurons. We bring forward the hypothesis that an extensive subset of retrotransposition-competent L1s may be de-repressed and mobile in the soma but largely inactive in the germline. We discuss recent reports of non-canonical L1-associated sequence variants in the brain and propose that the elevated L1 DNA content reported in several neurological disorders may predominantly comprise accumulated, unintegrated L1 nucleic acids, rather than somatic L1 insertions. Finally, we consider the main objectives and obstacles going forward in elucidating the biological impact of somatic retrotransposition.

Identification of the proteins specifically binding to the rat LINE1 promoter

The initial step of LINE1 retrotransposons dissemination requires transcription from species-specific promoter located within 5'-untranslated region of LINE1. Although the 5'-untranslated region of the rat LINE1 element shows promoter activity, no promoter-binding proteins have been discovered so far. Using an EMSA and Southwestern blotting methods, we identified Sp1 and Sp3 proteins, which specifically bind to the rat LINE1 promoter in vitro. The Sp1/Sp3-binding motif within rat LINE1 promoter is located downstream of the major predicted transcription initiation site.

Functional differences between the human LINE retrotransposon and retroviral reverse transcriptases for in vivo mRNA reverse transcription

We have analysed the reverse transcriptase (RT) activity of the human LINE retrotransposon and that of two retroviruses, using an in vivo assay within mammalian (murine and human) cells. The assay relies on transfection of the cells with expression vectors for the RT of the corresponding elements and PCR analysis of the DNA extracted 2-4 days post-transfection using primers bracketing the intronic domains of co-transfected reporter genes or of cellular genes. This assay revealed high levels of reverse-transcribed cDNA molecules, with the intron spliced out, with expression vectors for the LINE. Generation of cDNA molecules requires LINE ORF2, whereas ORF1 is dispensable. Deletion derivatives within the 3.8 kb LINE ORF2 allowed further delineation of the RT domain: > 0.7 kb at the 5'-end of the LINE ORF2 is dispensable for reverse transcription, consistent with this domain being an endonuclease-like domain, as well as 1 kb at the 3'-end, a putative RNase H domain. Conversely, the RT of the two retroviruses tested, Moloney murine leukemia virus and human immunodeficiency virus, failed to produce similar reverse transcripts. These experiments demonstrate a specific and high efficiency reverse transcription activity for the LINE RT, which applies to RNA with no sequence specificity, including those from cellular genes, and which might therefore be responsible for the endogenous activity that we previously detected within mammalian cells through the formation of pseudogene-like structures.

A genetically tagged, defective I element can be complemented by actively transposing I factors in the germline of I-R dysgenic females in Drosophila melanogaster

Non-LTR retrotransposons, also known as LINEs, transpose by reverse transcription of an RNA intermediate. Their mechanism of transposition is apparently different from that of retrotransposons and similar to that of proviruses of retroviruses. The I factor is responsible for the I-R system of hybrid dysgenesis in Drosophila melanogaster. Inducer strains contain several functional I factors whereas reactive strains do not. Transposition of I factors can be experimentally induced: they are stable in inducer strains, but transpose at high frequency in the germline of females, known as SF females, produced by crossing reactive females and inducer males. We have constructed an I element, called IviP2, marked with the vermilion gene, the coding sequence of which was interrupted by an intron. Splicing of the intron can only occur in the transcript initiated from the I element promoter. Transposed copies expressing a wild-type vermilion phenotype were recovered in the germline of SF females in which I factors were actively transposing. This indicates that trans-complementation of a defective I element, deficient for the second open reading frame, by functional I factors can occur in the germline of dysgenic females.

The full-length transcript of the I factor, a LINE element of Drosophila melanogaster, is a potential bicistronic RNA messenger

The I factor of Drosophila melanogaster is a retrotransposon of the LINE superfamily. The I factor displays two non-overlapping open reading frames (ORFs) that have the potential to encode for a nucleic acid-binding protein (ORF1) and a reverse transcriptase (ORF2). Retrotransposition of the I factor has been demonstrated and a putative full-length RNA intermediate has been identified. No other transcript from functional I factor has ever been described, suggesting that the full-length RNA is also used as a messenger. Here we report that a bicistronic RNA which conserves the ORF1-ORF2 organization of the I factor transcript is a template for ORF2 translation in vivo. We further demonstrate that the first AUG of ORF2 initiates translation, but efficiency of this initiation increases approximately 200 fold when ORF1 is deleted. Our results show that the I factor transcript may be used to translate both ORFs from their own initiation codons at different rates. Various mechanisms of translation are proposed.

Retrotransposition of a marked Drosophila line-like I element in cells in culture

We have marked a Drosophila transposable element--the LINE-like I element--with an intron-containing indicator gene inserted in place of a large deletion in the I element second ORF encompassing the reverse transcriptase domain, and this marked element was placed downstream to a potent actin promoter. An expression vector for the I element ORFs was also constructed, under the same heterologous promoter. The indicator gene contains a lacZ reporter gene the expression of which is conditioned by retrotransposition of the marked element, thus allowing detection of transposition events by testing for either beta-galactosidase expression or occurrence of spliced DNA molecules. The marked I element was introduced into Drosophila melanogaster cells in culture by transfection. Spliced DNA copies of the marked element and specifically stained beta-galactosidase-expressing cells were detected only upon co-transfection with the I expression vector, thus indicating that an ORF2-deleted element can be complemented in trans for transposition. This simple assay for retrotransposition in Drosophila cells in culture provides a tool for the rapid analysis of the mechanism of I transposition in its cis and trans sequence requirements.

The Doc transposable element in Drosophila melanogaster and Drosophila simulans: genomic distribution and transcription

The mobile element Doc is similar in structure and coding potential to the LINE families found in various organisms. In this paper, we analyze the insertional and structural polymorphism of this element and show that it appears to have a long evolutionary history in the genome of D. melanogaster. Like the family of I elements, the Doc family seems to display three types of elements: full length elements, defective members that have recently transposed and long since immobilized members common to each D. melanogaster strain. These three classes of Doc elements seem to be present in D. simulans, a closely related species to D. melanogaster. Furthermore, we show that Doc is transcribed as a polyadenylated RNA of about 5 kb in length, presumed to be a full length RNA. This transcript is present in different tissues and at different stages of Drosophila development. These results are compared with previous records on the chromosomal distribution of LINEs or other transposable element families. Doc transcription is analyzed in an attempt to understand the link between Doc transcription and transposition.

I factors in Drosophila melanogaster: transposition under control

I factors are responsible for the I-R system of hybrid dysgenesis in Drosophila melanogaster. They belong to the LINE class of mobile elements, which transpose via reverse transcription of a full-length RNA intermediate. I factors are active members of the I element family, which also contains defective I elements that are immobilized within peri-centromeric heterochromatin and represent very old components of the genome. Active I factors have recently invaded natural populations of Drosophila melanogaster, giving rise to inducer strains. Reactive strains, devoid of active I factors, derive from old laboratory stocks established before the invasion. Transposition of I factors is activated at very high frequencies in the germline of hybrid females issued from crosses between females from reactive strains and males from inducer strains. It results in the production of high rates of mutations and chromosomal rearrangements as well as in a particular syndrome of sterility. The frequency of transposition of I factors is dependent on the amount of full-length RNA that is synthesized from an internal promoter. This full-length RNA serves both as an intermediate of transposition and presumably as a messenger for protein synthesis. Regulators of transposition apparently affect transcription initiation from the internal promoter. The data presented here lead to the proposal of a tentative model for transposition.

Transnuclear retrotransposition of the Tad element of Neurospora

Tad is a LINE-like DNA element found in Neutrospora crassa. A Neurospora artificial intron based on the first intron of the am (glutamate dehydrogenase) gene was constructed and introduced, in the correct orientation, into a unique Nru I site in open reading frame 1 of an active Tad element, Tad1-1. Transformants containing the Tad element with the artificial intron were placed in forced heterokaryons with strains lacking Tad elements. Tad was shown to transpose between nuclei in these heterokaryons. Examination of the transposed Tad elements showed that the intron had been precisely removed in all cases. This confirms that Tad is a retrotransposon and that there is a cytoplasmic phase in these retrotransposition events.

Synchronous expression of LINE-1 RNA and protein in mouse embryonal carcinoma cells

L1, or LINE-1, is a repetitive DNA family found in all mammalian genomes that have been examined. At least a few individual members of the L1 family are functional transposable elements. Expression of these active elements leads to new insertions of L1 into the genomic DNA by the process of retrotransposition. We have detected coexpression of full-length, sense-strand L1 RNA transcripts and L1-encoded protein in mouse embryonal carcinoma cell lines. Both of these L1 expression products are candidates for intermediates in the retrotransposition process. L1 protein is found in what appear to be cytoplasmic aggregates and is not localized to any known cytoplasmic organelles. The six embryonal carcinoma cell lines tested were chosen to represent commitment to different developmental pathways in early mouse embryogenesis. The only two cell lines that express L1 are unique among the six in that they have a strong predilection to differentiate into extraembryonic endoderm. This observation is consistent with L1 expression and transposition in primordial germ cells of the mouse. An important implication of these studies is that L1 expression may provide a new marker for use in determining the origin of primordial germ cells during mouse embryogenesis.

Synchronous expression of LINE-1 RNA and protein in mouse embryonal carcinoma cells

L1, or LINE-1, is a repetitive DNA family found in all mammalian genomes that have been examined. At least a few individual members of the L1 family are functional transposable elements. Expression of these active elements leads to new insertions of L1 into the genomic DNA by the process of retrotransposition. We have detected coexpression of full-length, sense-strand L1 RNA transcripts and L1-encoded protein in mouse embryonal carcinoma cell lines. Both of these L1 expression products are candidates for intermediates in the retrotransposition process. L1 protein is found in what appear to be cytoplasmic aggregates and is not localized to any known cytoplasmic organelles. The six embryonal carcinoma cell lines tested were chosen to represent commitment to different developmental pathways in early mouse embryogenesis. The only two cell lines that express L1 are unique among the six in that they have a strong predilection to differentiate into extraembryonic endoderm. This observation is consistent with L1 expression and transposition in primordial germ cells of the mouse. An important implication of these studies is that L1 expression may provide a new marker for use in determining the origin of primordial germ cells during mouse embryogenesis.

Germ-line expression of the I factor, a functional LINE from the fruit fly Drosophila melanogaster, is positively regulated by reactivity, a peculiar cellular state

I factor is a functional LINE (long interspersed nucleotidic element) which is mobilized in the germ-line of dysgenic SF females during I-R hybrid dysgenesis. Such females are obtained when an oocyte from a reactive stock, devoid of I factors but characterized by a level of reactivity, i.e. its potential for hybrid dysgenesis, is fertilized by a spermatozoon from an I factor-containing inducer stock. In a previous paper we described the expression of an I factor-lacZ fusion. Expression was detected in the ovaries of reactive and dysgenic flies only. In this paper we show that this transgenic activity can be quantified and depends upon the maternally inherited reactivity. Reactivity is not just a permissive state and modifiers of the reactivity level such as heat treatment and ageing change the level of expression of our transgenic fusion accordingly. Moreover, ageing through generations has the same cumulative and reversible effect on both reactivity and I factor expression. Using our fusion as a test for reactivity we show that the silencing of I factor after its introduction into a reactive genome may not be established in a single generation.