http://www.mobilednajournal.com The latest research articles published by Mobile DNA 2013-06-05T00:00:00Z Group I introns are a distinct class of RNA self-splicing introns with an ancient origin. All known group I introns present in eukaryote nuclei interrupt functional ribosomal RNA genes located in ribosomal DNA loci. The discovery of the Tetrahymena intron more than 30 years ago has been essential to our understanding of group I intron catalysis, higher-order RNA structure, and RNA folding, but other intron models have provided information about the biological role. Nuclear group I introns appear widespread among eukaryotic microorganisms, and the plasmodial slime molds (myxomycetes) contain an abundance of self-splicing introns. Here, we summarize the main conclusions from previous work on the Tetrahymena intron on RNA self-splicing catalysis as well as more recent work on myxomycete intron biology. Group I introns in myxomycetes that represent different evolutionary stages, biological roles, and functional settings are discussed. http://www.mobilednajournal.com/content/4/1/17 Annica Hedberg Steinar Johansen Mobile DNA 2013, null:17 2013-06-05T00:00:00Z doi:10.1186/1759-8753-4-17 Nuclear group I introns in self-splicing and beyond <p class="authors">Group I introns are a distinct class of RNA self-splicing introns with an ancient origin. Annica Hedberg and Steinar Johansen review their catalysis, and recent findings in plasmodial slime mould intron biology.</p> /content/figures/1759-8753-4-17-toc.gif Mobile DNA 1759-8753 ${item.volume} 17 2013-06-05T00:00:00Z XML Background: The non-long terminal repeat (non-LTR) retrotransposons, long interspersed element-1 (LINE-1) and Alu are currently active retroelements in humans. We, and others, have observed that different populations of HeLa cells from different laboratories support retrotransposition of LINE-1 and Alu to varying degrees. We therefore tested whether individual cell clones of HeLa and HCT116 cell lines supported different levels of LINE-1 and Alu retrotransposition, and whether these variations were stable upon re-cloning.FindingsStandard retrotransposition tissue culture assays were used to measure a cell's ability to support LINE-1 and Alu retrotransposition in clonal HeLa and HCT116 cell lines. We observed that both LINE-1 and Alu retrotransposition exhibited clonal variation in HeLa cells, with certain HeLa cell clones supporting high levels of LINE-1 and Alu retrotransposition and other cell clones being essentially retrotransposition-dead. This clonal variation was similarly observed in HCT116 cells, although possibly not to the same extent. These patterns of clonal variation are relatively consistent upon re-cloning. Conclusions: Observations of the variability of LINE-1 and Alu retrotransposition in different populations of the same cell line are supported by our results that indicate in some cell types, individual cell clones can have dramatically differing capacity for retrotransposition. The mixed populations of cells commonly used in laboratories have often been passaged for many generations and accumulated significant genetic and epigenetic diversity. Our results suggest that the clonal variability observed by our cloning experiments may lead to a homogenization of retrotransposition capacity, with the resulting mixed population of cells being composed of individual variants having either increased or decreased retrotransposition potential compared to the starting population. http://www.mobilednajournal.com/content/4/1/16 Vincent Streva Zachary Faber Prescott Deininger Mobile DNA 2013, null:16 2013-06-03T00:00:00Z doi:10.1186/1759-8753-4-16 /content/figures/1759-8753-4-16-toc.gif Mobile DNA 1759-8753 ${item.volume} 16 2013-06-03T00:00:00Z PDF Background: The activity of transposable elements can be regulated by different means. DNA CpG methylation is known to decrease or inhibit transpositional activity of diverse transposons. However, very surprisingly, it was previously shown that CpG methylation of the Sleeping Beauty (SB) transposon significantly enhanced transposition in mouse embryonic stem cells. Results: In order to investigate the unexpected response of SB transposition to CpG methylation, related transposons from the Tc1/mariner superfamily, that is, Tc1, Himar1, Hsmar1, Frog Prince (FP) and Minos were tested to see how transposition was affected by CpG methylation. A significant increase of >20-fold in transposition of SB, FP and Minos was seen, whereas Tc1, Himar1 and Hsmar1 showed no difference in transposition upon CpG-methylation. The terminal inverted repeats (TIRs) of the SB, FP and Minos elements share a common structure, in which each TIR contains two functionally important binding sites for the transposase (termed the IR/DR structure). The group of IR/DR elements showed increased excision after CpG methylation compared to untreated transposon donor plasmids. We found that de novo CpG methylation is not required for transposition. A mutated FP donor plasmid with depleted CpG sites in both TIRs was as efficient in transposition as the wild-type transposon, indicating that CpG sites inside the TIRs are not responsible for altered binding of factors potentially modulating transposition. By using an in vivo one-hybrid DNA-binding assay in cultured human cells we found that CpG methylation had no appreciable effect on the affinity of SB transposase to its binding sites. However, chromatin immunoprecipitation indicated that CpG-methylated transposon donor plasmids are associated with a condensed chromatin structure characterized by trimethylated histone H3K9. Finally, DNA compaction by protamine was found to enhance SB transposition. Conclusions: We have shown that DNA CpG methylation upregulates transposition of IR/DR elements in the Tc1/mariner superfamily. CpG methylation provokes the formation of a tight chromatin structure at the transposon DNA, likely aiding the formation of a catalytically active complex by facilitating synapsis of sites bound by the transposase. http://www.mobilednajournal.com/content/4/1/15 Tobias Jursch Zsuzsanna Izsvák Zoltán Ivics Mobile DNA 2013, null:15 2013-05-15T00:00:00Z doi:10.1186/1759-8753-4-15 /content/figures/1759-8753-4-15-toc.gif Mobile DNA 1759-8753 ${item.volume} 15 2013-05-15T00:00:00Z XML Group II introns are mobile genetic elements that self-splice and retrotranspose into DNA and RNA. They are considered evolutionary ancestors of the spliceosome, the ribonucleoprotein complex essential for pre-mRNA processing in higher eukaryotes. Over a 20-year period, group II introns have been characterized first genetically, then biochemically, and finally by means of X-ray crystallography. To date, 17 crystal structures of a group II intron are available, representing five different stages of the splicing cycle. This review provides a framework for classifying and understanding these new structures in the context of the splicing cycle. Structural and functional implications for the spliceosome are also discussed. http://www.mobilednajournal.com/content/4/1/14 Marco Marcia Srinivas Somarowthu Anna Pyle Mobile DNA 2013, null:14 2013-05-01T00:00:00Z doi:10.1186/1759-8753-4-14 Group II intron stuctures <p>This review by Anna Pyle and colleagues provides a framework for classifying and understanding new crystal structures of these mobile genetic elements.</p> /content/figures/1759-8753-4-14-toc.gif Mobile DNA 1759-8753 ${item.volume} 14 2013-05-01T00:00:00Z XML Background: Transposable elements (TEs) are a very dynamic component of eukaryotic genomes with important implications (e.g., in evolution) and applications (e.g., as transgenic tools). They also represent a major challenge for the assembly and annotation of genomic sequences. However, they are still largely unknown in non-model species. Results: Here, we have annotated the repeats and transposable elements present in a 600 kb genomic region of the blowfly Calliphora vicina (Diptera: Calliphoridae) which contains most of the achaete-scute gene complex of this species. This is the largest genomic region to be sequenced and analyzed in higher flies outside the Drosophila genus. We find that the repeat content spans at least 24% of the sequence. It includes 318 insertions classified as 3 LTR retrotransposons, 21 LINEs, 14 cut-and-paste DNA transposons, 4 helitrons and 33 unclassified repeats. Conclusions: This is the most detailed description of TEs and repeats in the Calliphoridae to date. This contribution not only adds to our knowledge about TE evolution but will also help in the annotation of repeats on Dipteran whole genome sequences. http://www.mobilednajournal.com/content/4/1/13 Bárbara Negre Pat Simpson Mobile DNA 2013, null:13 2013-04-03T00:00:00Z doi:10.1186/1759-8753-4-13 /content/figures/1759-8753-4-13-toc.gif Mobile DNA 1759-8753 ${item.volume} 13 2013-04-03T00:00:00Z XML Background: Bacterial insertion sequences (IS) of IS200/IS605 and IS607 family often encode a transposase (TnpA) and a protein of unknown function, TnpB. Results: Here we report two groups of TnpB-like proteins (Fanzor1 and Fanzor2) that are widespread in diverse eukaryotic transposable elements (TEs), and in large double-stranded DNA (dsDNA) viruses infecting eukaryotes. Fanzor and TnpB proteins share the same conserved amino acid motif in their C-terminal half regions: D-X(125, 275)-[TS]-[TS]-X-X-[C4 zinc finger]-X(5,50)-RD, but are highly variable in their N-terminal regions. Fanzor1 proteins are frequently captured by DNA transposons from different superfamilies including Helitron, Mariner, IS4-like, Sola and MuDr. In contrast, Fanzor2 proteins appear only in some IS607-type elements. We also analyze a new Helitron2 group from the Helitron superfamily, which contains elements with hairpin structures on both ends. Non-autonomous Helitron2 elements (CRe-1, 2, 3) in the genome of green alga Chlamydomonas reinhardtii are flanked by target site duplications (TSDs) of variable length (approximately 7 to 19 bp). Conclusions: The phylogeny and distribution of the TnpB/Fanzor proteins indicate that they may be disseminated among eukaryotic species by viruses. We hypothesize that TnpB/Fanzor proteins may act as methyltransferases. http://www.mobilednajournal.com/content/4/1/12 Weidong Bao Jerzy Jurka Mobile DNA 2013, null:12 2013-04-01T00:00:00Z doi:10.1186/1759-8753-4-12 /content/figures/1759-8753-4-12-toc.gif Mobile DNA 1759-8753 ${item.volume} 12 2013-04-01T00:00:00Z XML n/a http://www.mobilednajournal.com/content/4/1/11 Orsolya Kolacsek Virág Krízsik Anita Schamberger Zsuzsa Erdei Ágota Apáti György Várady Lajos Mátés Zsuzsanna Izsvák Zoltán Ivics Balázs Sarkadi Tamás Orbán Mobile DNA 2013, null:11 2013-03-15T00:00:00Z doi:10.1186/1759-8753-4-11 /content/figures/1759-8753-4-11-toc.gif Mobile DNA 1759-8753 ${item.volume} 11 2013-03-15T00:00:00Z XML Background: Long interspersed element type one (L1) actively modifies the human genome by inserting new copies of itself. This process, termed retrotransposition, requires the formation of an L1 ribonucleoprotein (RNP) complex, which must enter the nucleus before retrotransposition can proceed. Thus, the nuclear import of L1 RNP presents an opportunity for cells to regulate L1 retrotransposition post-translationally. The effect of cell division on L1 retrotransposition has been investigated by two previous studies, which observed varied degrees of inhibition in retrotransposition when primary cell strains or cancer cell lines were experimentally arrested in different stages of the cell cycle. However, seemingly divergent conclusions were reached. The role of cell division on retrotransposition remains highly debated.FindingsTo monitor both L1 expression and retrotransposition quantitatively, we developed a stable dual-luciferase L1 reporter cell line, in which a bi-directional tetracycline-inducible promoter drives the expression of both a firefly luciferase-tagged L1 element and a Renilla luciferase, the latter indicative of the level of promoter induction. We observed an additional 10-fold reduction in retrotransposition in cell-cycle arrested cells even after retrotransposition had been normalized to Renilla luciferase or L1 ORF1 protein levels. In synchronized cells, cells undergoing two mitoses showed 2.6-fold higher retrotransposition than those undergoing one mitosis although L1 expression was induced for the same amount of time. Conclusions: Our data provide additional support for an important role of cell division in retrotransposition and argue that restricting the accessibility of L1 RNP to nuclear DNA could be a post-translational regulatory mechanism for retrotransposition. http://www.mobilednajournal.com/content/4/1/10 Yi Xie Lajos Mates Zoltán Ivics Zsuzsanna Izsvák Sandra Martin Wenfeng An Mobile DNA 2013, null:10 2013-03-06T00:00:00Z doi:10.1186/1759-8753-4-10 /content/figures/1759-8753-4-10-toc.gif Mobile DNA 1759-8753 ${item.volume} 10 2013-03-06T00:00:00Z XML Sireviruses are an ancient and plant-specific LTR retrotransposon genus. They possess a unique genome structure that is characterized by a plethora of highly conserved sequence motifs in key domains of the non-coding genome, and often, by the presence of an envelope-like gene. Recently, their crucial role in the organization of the maize genome, where Sireviruses occupy approximately 21% of its nuclear content, was revealed, followed by an analysis of their distribution across the plant kingdom. It is now suggested that Sireviruses have been a major mediator of the evolution of many plant genomes. However, the name ‘Sirevirus’ has caused confusion in the scientific community in regards to their classification within the LTR retrotransposon order and their relationship with viruses - a situation that is not unique to Sireviruses, but also affects other LTR retrotransposon genera. Here, we clarify the phylogenetic position of Sireviruses as typical LTR retrotransposons of the Copia superfamily and explain that the confusion stems from the discrepancy in the categorization of LTR retrotransposons by the two main classification systems: the International Committee on the Taxonomy of Viruses (ICTV) system and the unified classification system for eukaryotic transposable elements. While the name ‘Sirevirus’ has been given by ICTV, we show that the transposable element system, which is more suitable for eukaryotic genome studies, lacks an appropriate taxonomic level for describing them. We urge for this inconsistency to be addressed. Finally, we provide data suggesting that of the three ICTV-proposed genera of the Pseudoviridae (that is, Copia) family, only Sireviruses form a monophyletic group, while the phylogenetic distinction between Pseudoviruses and Hemiviruses is unclear. We conclude that because of their ongoing important contribution to the classification of transposable elements, these schemes need to be frequently revisited and revised - as shown by the example of the Sirevirus LTR retrotransposon genus. http://www.mobilednajournal.com/content/4/1/9 Alexandros Bousios Nikos Darzentas Mobile DNA 2013, null:9 2013-03-04T00:00:00Z doi:10.1186/1759-8753-4-9 /content/figures/1759-8753-4-9-toc.gif Mobile DNA 1759-8753 ${item.volume} 9 2013-03-04T00:00:00Z XML Background: Chromoviruses are one of the three genera of Ty3-gypsy long terminal repeat (LTR) retrotransposons, and are present in high copy numbers in plant genomes. They are widely distributed within the plant kingdom, with representatives even in lower plants such as green and red algae. Their hallmark is the presence of a chromodomain at the C-terminus of the integrase. The chromodomain exhibits structural characteristics similar to proteins of the heterochromatin protein 1 (HP1) family, which mediate the binding of each chromovirus type to specific histone variants. A specific integration via the chromodomain has been shown for only a few chromoviruses. However, a detailed study of different chromoviral clades populating a single plant genome has not yet been carried out. Results: We conducted a comprehensive survey of chromoviruses within the Beta vulgaris (sugar beet) genome, and found a highly diverse chromovirus population, with significant differences in element size, primarily caused by their flanking LTRs. In total, we identified and annotated full-length members of 16 families belonging to the four plant chromoviral clades: CRM, Tekay, Reina, and Galadriel. The families within each clade are structurally highly conserved; in particular, the position of the chromodomain coding region relative to the polypurine tract is clade-specific. Two distinct groups of chromodomains were identified. The group II chromodomain was present in three chromoviral clades, whereas families of the CRM clade contained a more divergent motif. Physical mapping using representatives of all four clades identified a clade-specific integration pattern. For some chromoviral families, we detected the presence of expressed sequence tags, indicating transcriptional activity. Conclusions: We present a detailed study of chromoviruses, belonging to the four major clades, which populate a single plant genome. Our results illustrate the diversity and family structure of B. vulgaris chromoviruses, and emphasize the role of chromodomains in the targeted integration of these viruses. We suggest that the diverse sets of plant chromoviruses with their different localization patterns might help to facilitate plant-genome organization in a structural and functional manner. http://www.mobilednajournal.com/content/4/1/8 Beatrice Weber Tony Heitkam Daniela Holtgräwe Bernd Weisshaar André Minoche Juliane Dohm Heinz Himmelbauer Thomas Schmidt Mobile DNA 2013, null:8 2013-03-01T00:00:00Z doi:10.1186/1759-8753-4-8 /content/figures/1759-8753-4-8-toc.gif Mobile DNA 1759-8753 ${item.volume} 8 2013-03-01T00:00:00Z XML