Retroelements
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It has been proposed that oxidative stress, elicited by high levels of reactive oxygen species, accelerates telomere shortening by erosion of telomeric DNA repeats. While most eukaryotes counteract telomere shortening by telomerase-driven addition of these repeats, telomeric loss in Drosophila is compensated by retrotransposition of the telomeric retroelements HeT-A, TART and TAHRE to chromosome ends. In this study we tested the effect of chronic exposure of flies to non-/sub-lethal doses of paraquat, which is a redox cycling compound widely used to induce oxidative stress in various experimental paradigms including telomere length analyses. Indeed, chronic paraquat exposure for five generations resulted in elevated transcriptional activity of both telomeric and non-telomeric transposable elements, and extended telomeric length in the tested fly lines. We propose that low oxidative stress leads to increased telomere length within Drosophila populations. For a mechanistic understanding of the observed phenomenon we discuss two scenarios: adaption, acting through a direct stimulation of telomere extension, or positive selection favoring individuals with longer telomeres within the population.
- Klíčová slova
- Drosophila, Hormesis, Hydrogen peroxide, Oxidative stress, Paraquat, Retroelements, Telomeres,
- MeSH
- Drosophila melanogaster účinky léků genetika MeSH
- genetická transkripce účinky léků MeSH
- homeostáza telomer účinky léků MeSH
- hormeze * MeSH
- paraquat farmakologie MeSH
- reaktivní formy kyslíku farmakologie MeSH
- retroelementy účinky léků MeSH
- telomery účinky léků fyziologie MeSH
- vztah mezi dávkou a účinkem léčiva MeSH
- zkracování telomer účinky léků MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
- Názvy látek
- paraquat MeSH
- reaktivní formy kyslíku MeSH
- retroelementy MeSH
- MeSH
- genetická terapie * MeSH
- genetické nemoci vrozené genetika MeSH
- lidé MeSH
- modely genetické * MeSH
- nemoc * MeSH
- onkogeny MeSH
- retroelementy * MeSH
- Retroviridae * MeSH
- technika přenosu genů MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
- Názvy látek
- retroelementy * MeSH
Retrotransposable elements are widely distributed and diverse in eukaryotes. Their copy number increases through reverse-transcription-mediated propagation, while they can be lost through recombinational processes, generating genomic rearrangements. We previously identified extensive structurally uniform retrotransposon groups in which no member contains the gag, pol, or env internal domains. Because of the lack of protein-coding capacity, these groups are non-autonomous in replication, even if transcriptionally active. The Cassandra element belongs to the non-autonomous group called terminal-repeat retrotransposons in miniature (TRIM). It carries 5S RNA sequences with conserved RNA polymerase (pol) III promoters and terminators in its long terminal repeats (LTRs). Here, we identified multiple extended tandem arrays of Cassandra retrotransposons within different plant species, including ferns. At least 12 copies of repeated LTRs (as the tandem unit) and internal domain (as a spacer), giving a pattern that resembles the cellular 5S rRNA genes, were identified. A cytogenetic analysis revealed the specific chromosomal pattern of the Cassandra retrotransposon with prominent clustering at and around 5S rDNA loci. The secondary structure of the Cassandra retroelement RNA is predicted to form super-loops, in which the two LTRs are complementary to each other and can initiate local recombination, leading to the tandem arrays of Cassandra elements. The array structures are conserved for Cassandra retroelements of different species. We speculate that recombination events similar to those of 5S rRNA genes may explain the wide variation in Cassandra copy number. Likewise, the organization of 5S rRNA gene sequences is very variable in flowering plants; part of what is taken for 5S gene copy variation may be variation in Cassandra number. The role of the Cassandra 5S sequences remains to be established.
- Klíčová slova
- 5S RNA gene, Cassandra TRIM, ectopic recombination, genome evolution, long tandem array, retrotransposon,
- MeSH
- chromozomy hmyzu MeSH
- fylogeneze MeSH
- genom rostlinný MeSH
- genomika metody MeSH
- interakce hostitele a parazita genetika MeSH
- koncové repetice * MeSH
- konformace nukleové kyseliny MeSH
- molekulární evoluce MeSH
- můry genetika MeSH
- rekombinace genetická MeSH
- retroelementy * MeSH
- RNA ribozomální 5S genetika MeSH
- rostliny genetika parazitologie MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- retroelementy * MeSH
- RNA ribozomální 5S MeSH
The past 15 years opened new avenues for retrovirus and retroelement research. Not surprisingly, they stemmed from essential knowledge collected in the past, which remains the ground of the present and therefore should be remembered. However, a short supplement of new break-through discoveries and ideas should be recollected. Using selected examples of recent works, I tried to extend and supplement my original article published in Folia Biologica (1996).
- Publikační typ
- časopisecké články MeSH
Retroelements (RE) have been proposed as important players in cancerogenesis. Different cancer types are characterized by a different level of tumor-specific RE insertions. In previous studies, small cohorts of hematological malignancies, such as acute myeloid leukemia, multiple myeloma, and chronic lymphocytic leukemia have been characterized by a low level of RE insertional activity. Acute lymphoblastic leukemia (ALL) in adults and childhood acute leukemias have not been studied in this context. We performed a search for new RE insertions (Alu and L1) in 44 childhood ALL, 14 childhood acute myeloid leukemia, and 14 adult ALL samples using a highly sensitive NGS-based approach. First, we evaluated the method sensitivity revealing the 1% detection threshold for the proportion of cells with specific RE insertion. Following this result, we did not identify new tumor-specific RE insertions in the tested cohort of acute leukemia samples at the established level of sensitivity. Additionally, we analyzed the transcription levels of active L1 copies and found them increased. Thus, the increased transcription of active L1 copies is not sufficient for overt elevation of L1 retrotranspositional activity in leukemia.
- Klíčová slova
- acute leukemia, mobile elements, retroelements, tumor-specific insertions,
- MeSH
- akutní lymfatická leukemie genetika MeSH
- akutní myeloidní leukemie genetika MeSH
- dítě MeSH
- DNA nádorová genetika MeSH
- dospělí MeSH
- genetická transkripce MeSH
- kojenec MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladiství MeSH
- mladý dospělý MeSH
- předškolní dítě MeSH
- regulace genové exprese u leukemie MeSH
- reprodukovatelnost výsledků MeSH
- retroelementy genetika MeSH
- senioři MeSH
- Check Tag
- dítě MeSH
- dospělí MeSH
- kojenec MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladiství MeSH
- mladý dospělý MeSH
- mužské pohlaví MeSH
- předškolní dítě MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- DNA nádorová MeSH
- retroelementy MeSH
Truncated copy of reverse transcriptase of Ty1/copia retroelement (Purcopia) was found as part of the species-specific RAPD 257(540) marker of Claviceps purpurea. A region of 94 bp with 78.9% identity to an unannotated region of the genomic clone of the rice blast fungus Pyricularia grisea (accession no. AQ162050) was found at the 5' end of the pseudogene. Comparison with database sequences revealed that Purcopia is close to the plant retroelements represented by Tto1, Ta1-3 and Bare-1, whereas the other fungal elements of the Ty1/copia type grouped with Hopscotch elements. Restriction patterns obtained by hybridization of the labeled marker to HindIII digested genomic DNA of various C. purpurea isolates contained multiple bands. The banding was individual and did not yield any species- or population-specific fragments or patterns.
- MeSH
- Claviceps genetika MeSH
- DNA fungální chemie genetika MeSH
- fylogeneze MeSH
- genom fungální MeSH
- klonování DNA MeSH
- molekulární sekvence - údaje MeSH
- polymerázová řetězová reakce MeSH
- retroelementy genetika MeSH
- sekvence aminokyselin MeSH
- sekvence nukleotidů MeSH
- sekvenční seřazení MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- DNA fungální MeSH
- retroelementy MeSH
BACKGROUND: Retroelements (REs) occupy a significant part of all eukaryotic genomes including humans. The majority of retroelements in the human genome are inactive and unable to retrotranspose. Dozens of active copies are repressed in most normal tissues by various cellular mechanisms. These copies can become active in normal germline and brain tissues or in cancer, leading to new retroposition events. The consequences of such events and their role in normal cell functioning and carcinogenesis are not yet fully understood. If new insertions occur in a small portion of cells they can be found only with the use of specific methods based on RE enrichment and high-throughput sequencing. The downside of the high sensitivity of such methods is the presence of various artifacts imitating real insertions, which in many cases cannot be validated due to lack of the initial template DNA. For this reason, adequate assessment of rare (< 1%) subclonal cancer specific RE insertions is complicated. RESULTS: Here we describe a new copy-capture technique which we implemented in a method called SeqURE for Sequencing Unknown of Retroposition Events that allows for efficient and reliable identification of new genomic RE insertions. The method is based on the capture of copies of target molecules (copy-capture), selective amplification and sequencing of genomic regions adjacent to active RE insertions from both sides. Importantly, the template genomic DNA remains intact and can be used for validation experiments. In addition, we applied a novel system for testing method sensitivity and precisely showed the ability of the developed method to reliably detect insertions present in 1 out of 100 cells and a substantial portion of insertions present in 1 out of 1000 cells. Using advantages of the method we showed the absence of somatic Alu insertions in colorectal cancer samples bearing tumor-specific L1HS insertions. CONCLUSIONS: This study presents the first description and implementation of the copy-capture technique and provides the first methodological basis for the quantitative assessment of RE insertions present in a small portion of cells.
- Klíčová slova
- Copy capture, High-throughput sequencing, Human genome, Insertional polymorphism, Retroelements,
- Publikační typ
- časopisecké články MeSH
Improved knowledge of genome composition, especially of its repetitive component, generates important information for both theoretical and applied research. The olive repetitive component is made up of two main classes of sequences: tandem repeats and retrotransposons (REs). In this study, we provide characterization of a sample of 254 unique full-length long terminal repeat (LTR) REs. In the sample, Ty1-Copia elements were more numerous than Ty3-Gypsy elements. Mapping a large set of Illumina whole-genome shotgun reads onto the identified retroelement set revealed that Gypsy elements are more redundant than Copia elements. The insertion time of intact retroelements was estimated based on sister LTR's divergence. Although some elements inserted relatively recently, the mean insertion age of the isolated retroelements is around 18 million yrs. Gypsy and Copia retroelements showed different waves of transposition, with Gypsy elements especially active between 10 and 25 million yrs ago and nearly inactive in the last 7 million yrs. The occurrence of numerous solo-LTRs related to isolated full-length retroelements was ascertained for two Gypsy elements and one Copia element. Overall, the results reported in this study show that RE activity (both retrotransposition and DNA loss) has impacted the olive genome structure in more ancient times than in other angiosperms.
- Klíčová slova
- BAC sequencing, LTR retrotransposons, insertion age, next-generation sequencing, olive,
- MeSH
- celogenomová asociační studie * MeSH
- koncové repetice * MeSH
- mapování chromozomů * MeSH
- Olea genetika MeSH
- retroelementy * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- retroelementy * MeSH
Repetitive DNA contributes significantly to plant genome size, adaptation, and evolution. However, little is understood about the transcription of repeats. This is addressed here in the plant green foxtail millet (Setaria viridis). First, we used RepeatExplorer2 to calculate the genome proportion (GP) of all repeat types and compared the GP of long terminal repeat (LTR) retroelements against annotated complete and incomplete LTR retroelements (Ty1/copia and Ty3/gypsy) identified by DANTE in a whole genome assembly. We show that DANTE-identified LTR retroelements can comprise ∼0.75% of the inflorescence poly-A transcriptome and ∼0.24% of the stem ribo-depleted transcriptome. In the RNA libraries from inflorescence tissue, both LTR retroelements and DNA transposons identified by RepeatExplorer2 were highly abundant, where they may be taking advantage of the reduced epigenetic silencing in the germ line to amplify. Typically, there was a higher representation of DANTE-identified LTR retroelements in the transcriptome than RepeatExplorer2-identified LTR retroelements, potentially reflecting the transcription of elements that have insufficient genomic copy numbers to be detected by RepeatExplorer2. In contrast, for ribo-depleted libraries of stem tissues, the reverse was observed, with a higher transcriptome representation of RepeatExplorer2-identified LTR retroelements. For RepeatExplorer2-identified repeats, we show that the GP of most Ty1/copia and Ty3/gypsy families were positively correlated with their transcript proportion. In addition, guanine- and cytosine-rich repeats with high sequence similarity were also the most abundant in the transcriptome, and these likely represent young elements that are most capable of amplification due to their ability to evade epigenetic silencing.
Amplification and eventual elimination of dispersed repeats, especially those of the retroelement origin, account for most of the profound size variability observed among plant genomes. In most higher plants investigated so far, differential accumulation of various families of elements contributes to these differences. Here we report the identification of giant Ty3/gypsy-like retrotransposons from the legume plant Vicia pannonica, which alone make up approximately 38% of the genome of this species. These retrotransposons have structural features of the Ogre elements previously identified in the genomes of pea and Medicago. These features include extreme size (25 kb), the presence of an extra ORF upstream of the gag-pol region, and a putative intron dividing the prot and rt coding sequences. The Ogre elements are evenly dispersed on V. pannonica chromosomes except for terminal regions containing satellite repeats, their individual copies show extraordinary sequence similarity, and at least part of them are transcriptionally active, which suggests their recent amplification. Similar elements were also detected in several other Vicia species but in most cases in significantly lower numbers. However, there was no obvious correlation of the abundance of Ogre sequences with the genome size of these species.
- MeSH
- amplifikace genu MeSH
- DNA rostlinná genetika MeSH
- druhová specificita MeSH
- Fabaceae genetika MeSH
- genom rostlinný * MeSH
- genová dávka MeSH
- hybridizace in situ fluorescenční MeSH
- introny MeSH
- konzervovaná sekvence MeSH
- molekulární sekvence - údaje MeSH
- otevřené čtecí rámce MeSH
- retroelementy genetika MeSH
- rostlinné proteiny genetika MeSH
- sekvence nukleotidů MeSH
- vikev genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
- Názvy látek
- DNA rostlinná MeSH
- retroelementy MeSH
- rostlinné proteiny MeSH
