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Mobile DNA

A Herrmann, S Wittmann, D Thomas, C N Shepard, B Kim, N Ferreirós, T Gramberg
[This corrects the article DOI: 10.1186/s13100-018-0116-5.].
2018: Mobile DNA
R Keith Slotkin
In the course of analyzing whole-genome data, it is common practice to mask or filter out repetitive regions of a genome, such as transposable elements and endogenous retroviruses, in order to focus only on genes and thus simplify the results. This Commentary is a plea from one member of the Mobile DNA community to all gene-centric researchers: please do not ignore the repetitive fraction of the genome . Please stop narrowing your findings by only analyzing a minority of the genome, and instead broaden your analyses to include the rich biology of repetitive and mobile DNA...
2018: Mobile DNA
Stephanie Cheung, Savrina Manhas, Vivien Measday
Retrotransposons are genetic elements that are similar in structure and life cycle to retroviruses by replicating via an RNA intermediate and inserting into a host genome. The Saccharomyces cerevisiae ( S. cerevisiae ) Ty1-5 elements are long terminal repeat (LTR) retrotransposons that are members of the Ty1- copia ( Pseudoviridae ) or Ty3- gypsy ( Metaviridae ) families. Four of the five S. cerevisiae Ty elements are inserted into the genome upstream of RNA Polymerase (Pol) III-transcribed genes such as transfer RNA (tRNA) genes...
2018: Mobile DNA
Vallmer E Jordan, Jerilyn A Walker, Thomas O Beckstrom, Cody J Steely, Cullen L McDaniel, Corey P St Romain, Kim C Worley, Jane Phillips-Conroy, Clifford J Jolly, Jeffrey Rogers, Miriam K Konkel, Mark A Batzer
Background: Since the completion of the human genome project, the diversity of genome sequencing data produced for non-human primates has increased exponentially. Papio baboons are well-established biological models for studying human biology and evolution. Despite substantial interest in the evolution of Papio , the systematics of these species has been widely debated, and the evolutionary history of Papio diversity is not fully understood. Alu elements are primate-specific transposable elements with a well-documented mutation/insertion mechanism and the capacity for resolving controversial phylogenetic relationships...
2018: Mobile DNA
Akash Sookdeo, Crystal M Hepp, Stéphane Boissinot
Background: LINE-1 (L1) is the dominant autonomously replicating non-LTR retrotransposon in mammals. Although our knowledge of L1 evolution across the tree of life has considerably improved in recent years, what we know of L1 evolution in mammals is biased and comes mostly from studies in primates (mostly human) and rodents (mostly mouse). It is unclear if patterns of evolution that are shared between those two groups apply to other mammalian orders. Here we performed a detailed study on the evolution of L1 in perissodactyls by making use of the complete genome of the domestic horse and of the white rhinoceros...
2018: Mobile DNA
Alexandra Herrmann, Sabine Wittmann, Dominique Thomas, Caitlin N Shepard, Baek Kim, Nerea Ferreirós, Thomas Gramberg
Background: The restriction factor SAMHD1 regulates intracellular nucleotide level by degrading dNTPs and blocks the replication of retroviruses and DNA viruses in non-cycling cells, like macrophages or dendritic cells. In patients, inactivating mutations in samhd1 are associated with the autoimmune disease Aicardi-Goutières Syndrome (AGS). The accumulation of intracellular nucleic acids derived from endogenous retroelements thriving in the absence of SAMHD1 has been discussed as potential trigger of the autoimmune reaction...
2018: Mobile DNA
Cody J Steely, Jasmine N Baker, Jerilyn A Walker, Charles D Loupe, Mark A Batzer
Background: Alu elements are primate-specific retroposons that mobilize using the enzymatic machinery of L1 s. The recently completed baboon genome project found that the mobilization rate of Alu elements is higher than in the genome of any other primate studied thus far. However, the Alu subfamily structure present in and specific to baboons had not been examined yet. Results: Here we report 129 Alu subfamilies that are propagating in the genome of the olive baboon, with 127 of these subfamilies being new and specific to the baboon lineage...
2018: Mobile DNA
Jasmine N Baker, Jerilyn A Walker, Michael W Denham, Charles D Loupe, Mark A Batzer
Background: The evolution of Alu elements has been ongoing in primate lineages and Alu insertion polymorphisms are widely used in phylogenetic and population genetics studies. Alu subfamilies in the squirrel monkey ( Saimiri ), a New World Monkey (NWM), were recently reported. Squirrel monkeys are commonly used in biomedical research and often require species identification. The purpose of this study was two-fold: 1) Perform locus-specific PCR analyses on recently integrated Alu insertions in Saimiri to determine their amplification dynamics, and 2) Identify a subset of Alu insertion polymorphisms with species informative allele frequency distributions between the Saimiri sciureus and Saimiri boliviensis groups...
2018: Mobile DNA
Yabin Guo, Yin Zhang, Kaishun Hu
Background: Sleeping Beauty transposon (SB) has become an increasingly important genetic tool for generating mutations in vertebrate cells. It is widely thought that SB exclusively integrates into TA dinucleotides. However, this strict TA-preference has not been rigorously tested in large numbers of insertion sites that now can be detected with next generation sequencing. Li et al. found 71 SB insertions in non-TA dinucleotides in 2013, suggesting that TA dinucleotides are not the only sites of SB integration, yet further studies on this topic have not been carried out...
2018: Mobile DNA
Keiko Tsuji Wakisaka, Kenji Ichiyanagi, Seiko Ohno, Masanobu Itoh
Background: P -element transposition in the genome causes P-M hybrid dysgenesis in Drosophila melanogaster . Maternally deposited piRNAs suppress P -element transposition in the progeny, linking them to P-M phenotypes; however, the role of zygotic piRNAs derived from paternal P elements is poorly understood. Results: To elucidate the molecular basis of P -element suppression by zygotic factors, we investigated the genomic constitution and P -element piRNA production derived from fathers...
2018: Mobile DNA
Gabriel Luz Wallau, Cristina Vieira, Élgion Lúcio Silva Loreto
Background: All living species contain genetic information that was once shared by their common ancestor. DNA is being inherited through generations by vertical transmission (VT) from parents to offspring and from ancestor to descendant species. This process was considered the sole pathway by which biological entities exchange inheritable information. However, Horizontal Transfer (HT), the exchange of genetic information by other means than parents to offspring, was discovered in prokaryotes along with strong evidence showing that it is a very important process by which prokaryotes acquire new genes...
2018: Mobile DNA
Robin M Delahay, Nicola J Croxall, Amberley D Stephens
Background: The genome of the gastric pathogen Helicobacter pylori is characterised by considerable variation of both gene sequence and content, much of which is contained within three large genomic islands comprising the cag pathogenicity island ( cag PAI) and two mobile integrative and conjugative elements (ICEs) termed tfs3 and tfs4 . All three islands are implicated as virulence factors, although whereas the cag PAI is well characterised, understanding of how the tfs elements influence H...
2018: Mobile DNA
Cathleen M Green, Olga Novikova, Marlene Belfort
Background: Inteins are mobile, self-splicing sequences that interrupt proteins and occur across all three domains of life. Scrutiny of the intein landscape in prokaryotes led to the hypothesis that some inteins are functionally important. Our focus shifts to eukaryotic inteins to assess their diversity, distribution, and dissemination, with the aim to comprehensively evaluate the eukaryotic intein landscape, understand intein maintenance, and dissect evolutionary relationships. Results: This bioinformatics study reveals that eukaryotic inteins are scarce, but present in nuclear genomes of fungi, chloroplast genomes of algae, and within some eukaryotic viruses...
2018: Mobile DNA
Liangliang Wang, Wei Si, Huping Xue, Xin Zhao
Background: IS Sau2 has been suggested as a member of the IS 150 f subgroup in the IS3 family. It encodes a fusion transposase OrfAB produced by programmed - 1 translational frameshifting with two overlapping reading frames orfA and orfB . To better characterize IS Sau2 , the binding and cleaving activities of the IS Sau2 transposase and its transposition frequency were studied. Results: The purified IS Sau2 transposase OrfAB was a functional protein in vitro since it bound specifically to IS Sau2 terminal inverted repeat sequences (IRs) and cleaved the transposon ends at the artificial mini-transposon pUC19-IRL-gfp-IRR...
2018: Mobile DNA
Kenji K Kojima
Repbase is a comprehensive database of eukaryotic transposable elements (TEs) and repeat sequences, containing over 1300 human repeat sequences. Recent analyses of these repeat sequences have accumulated evidences for their contribution to human evolution through becoming functional elements, such as protein-coding regions or binding sites of transcriptional regulators. However, resolving the origins of repeat sequences is a challenge, due to their age, divergence, and degradation. Ancient repeats have been continuously classified as TEs by finding similar TEs from other organisms...
2018: Mobile DNA
Erica M Briggs, Susan Ha, Paolo Mita, Gregory Brittingham, Ilaria Sciamanna, Corrado Spadafora, Susan K Logan
Background: Long Interspersed Nuclear Element-1 (LINE-1) is an autonomous retrotransposon that generates new genomic insertions through the retrotransposition of a RNA intermediate. Expression of LINE-1 is tightly repressed in most somatic tissues to prevent DNA damage and ensure genomic integrity. However, the reactivation of LINE-1 has been documented in cancer and the role of LINE-1 protein expression and retrotransposition has become of interest in the development, progression, and adaptation of many epithelial neoplasms, including prostate cancer...
2018: Mobile DNA
Thomas Wicker, Alan H Schulman, Jaakko Tanskanen, Manuel Spannagl, Sven Twardziok, Martin Mascher, Nathan M Springer, Qing Li, Robbie Waugh, Chengdao Li, Guoping Zhang, Nils Stein, Klaus F X Mayer, Heidrun Gundlach
Background: While transposable elements (TEs) comprise the bulk of plant genomic DNA, how they contribute to genome structure and organization is still poorly understood. Especially in large genomes where TEs make the majority of genomic DNA, it is still unclear whether TEs target specific chromosomal regions or whether they simply accumulate where they are best tolerated. Results: Here, we present an analysis of the repetitive fraction of the 5100 Mb barley genome, the largest angiosperm genome to have a near-complete sequence assembly...
2017: Mobile DNA
Alexander Suh, Sandra Bachg, Stephen Donnellan, Leo Joseph, Jürgen Brosius, Jan Ole Kriegs, Jürgen Schmitz
Background: Passeriformes ("perching birds" or passerines) make up more than half of all extant bird species. The genome of the zebra finch, a passerine model organism for vocal learning, was noted previously to contain thousands of short interspersed elements (SINEs), a group of retroposons that is abundant in mammalian genomes but considered largely inactive in avian genomes. Results: Here we resolve the deep phylogenetic relationships of passerines using presence/absence patterns of SINEs...
2017: Mobile DNA
Ken-Ichi Shimosuga, Kei Fukuda, Hiroyuki Sasaki, Kenji Ichiyanagi
Background: Intracisternal A particle (IAP) is one of the most transpositionally active retrotransposons in the mouse genome, but its expression varies between cell types. This variation is believed to arise from differences in the epigenetic state (e.g., DNA methylation) of the 5' long terminal repeat (LTR), where transcription starts. However, owing to the high copy number and high sequence similarity between copies, it is difficult to analyze the epigenetic states of individual IAP LTRs in a comprehensive manner...
2017: Mobile DNA
Irina R Arkhipova
In recent years, much attention has been paid to comparative genomic studies of transposable elements (TEs) and the ensuing problems of their identification, classification, and annotation. Different approaches and diverse automated pipelines are being used to catalogue and categorize mobile genetic elements in the ever-increasing number of prokaryotic and eukaryotic genomes, with little or no connectivity between different domains of life. Here, an overview of the current picture of TE classification and evolutionary relationships is presented, updating the diversity of TE types uncovered in sequenced genomes...
2017: Mobile DNA
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