Academic literature on the topic 'Selfish DNA element'
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Journal articles on the topic "Selfish DNA element"
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Milner, David S., Jeremy G. Wideman, Courtney W. Stairs, Cory D. Dunn, and Thomas A. Richards. "A functional bacteria-derived restriction modification system in the mitochondrion of a heterotrophic protist." PLOS Biology 19, no. 4 (April 23, 2021): e3001126. http://dx.doi.org/10.1371/journal.pbio.3001126.
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The overarching trend in mitochondrial genome evolution is functional streamlining coupled with gene loss. Therefore, gene acquisition by mitochondria is considered to be exceedingly rare. Selfish elements in the form of self-splicing introns occur in many organellar genomes, but the wider diversity of selfish elements, and how they persist in the DNA of organelles, has not been explored. In the mitochondrial genome of a marine heterotrophic katablepharid protist, we identify a functional type II restriction modification (RM) system originating from a horizontal gene transfer (HGT) event involving bacteria related to flavobacteria. This RM system consists of an HpaII-like endonuclease and a cognate cytosine methyltransferase (CM). We demonstrate that these proteins are functional by heterologous expression in both bacterial and eukaryotic cells. These results suggest that a mitochondrion-encoded RM system can function as a toxin–antitoxin selfish element, and that such elements could be co-opted by eukaryotic genomes to drive biased organellar inheritance.
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Fullmer, Matthew S., Matthew Ouellette, Artemis S. Louyakis, R. Thane Papke, and Johann Peter Gogarten. "The Patchy Distribution of Restriction–Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria." Genes 10, no. 3 (March 19, 2019): 233. http://dx.doi.org/10.3390/genes10030233.
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Restriction–modification (RM) systems in bacteria are implicated in multiple biological roles ranging from defense against parasitic genetic elements, to selfish addiction cassettes, and barriers to gene transfer and lineage homogenization. In bacteria, DNA-methylation without cognate restriction also plays important roles in DNA replication, mismatch repair, protein expression, and in biasing DNA uptake. Little is known about archaeal RM systems and DNA methylation. To elucidate further understanding for the role of RM systems and DNA methylation in Archaea, we undertook a survey of the presence of RM system genes and related genes, including orphan DNA methylases, in the halophilic archaeal class Halobacteria. Our results reveal that some orphan DNA methyltransferase genes were highly conserved among lineages indicating an important functional constraint, whereas RM systems demonstrated patchy patterns of presence and absence. This irregular distribution is due to frequent horizontal gene transfer and gene loss, a finding suggesting that the evolution and life cycle of RM systems may be best described as that of a selfish genetic element. A putative target motif (CTAG) of one of the orphan methylases was underrepresented in all of the analyzed genomes, whereas another motif (GATC) was overrepresented in most of the haloarchaeal genomes, particularly in those that encoded the cognate orphan methylase.
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Ma, Chien-Hui, Deepanshu Kumar, Makkuni Jayaram, Santanu K. Ghosh, and Vishwanath R. Iyer. "The selfish yeast plasmid exploits a SWI/SNF-type chromatin remodeling complex for hitchhiking on chromosomes and ensuring high-fidelity propagation." PLOS Genetics 19, no. 10 (October 9, 2023): e1010986. http://dx.doi.org/10.1371/journal.pgen.1010986.
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Extra-chromosomal selfish DNA elements can evade the risk of being lost at every generation by behaving as chromosome appendages, thereby ensuring high fidelity segregation and stable persistence in host cell populations. The yeast 2-micron plasmid and episomes of the mammalian gammaherpes and papilloma viruses that tether to chromosomes and segregate by hitchhiking on them exemplify this strategy. We document for the first time the utilization of a SWI/SNF-type chromatin remodeling complex as a conduit for chromosome association by a selfish element. One principal mechanism for chromosome tethering by the 2-micron plasmid is the bridging interaction of the plasmid partitioning proteins (Rep1 and Rep2) with the yeast RSC2 complex and the plasmid partitioning locus STB. We substantiate this model by multiple lines of evidence derived from genomics, cell biology and interaction analyses. We describe a Rep-STB bypass system in which a plasmid engineered to non-covalently associate with the RSC complex mimics segregation by chromosome hitchhiking. Given the ubiquitous prevalence of SWI/SNF family chromatin remodeling complexes among eukaryotes, it is likely that the 2-micron plasmid paradigm or analogous ones will be encountered among other eukaryotic selfish elements.
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Futcher, B., E. Reid, and D. A. Hickey. "Maintenance of the 2 micron circle plasmid of Saccharomyces cerevisiae by sexual transmission: an example of a selfish DNA." Genetics 118, no. 3 (March 1, 1988): 411–15. http://dx.doi.org/10.1093/genetics/118.3.411.
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Abstract Many eukaryotic mobile elements have been identified, but few have any obvious function. This has led to the proposal that many such elements may be parasitic DNA. We have used the 2 micron circle plasmid of Saccharomyces cerevisiae as a model system to investigate the maintenance of a cryptic genetic element. We find that under certain conditions this plasmid can spread through experimental populations despite demonstrable selection against it. This spread is dependent upon outbreeding, suggesting that cell to cell transmission of the plasmid during the yeast sexual cycle can counterbalance selection, and maintain the plasmid in populations. This result provides experimental support for the idea that some mobile elements may be parasitic DNA.
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Sau, Soumitra, Michael N. Conrad, Chih-Ying Lee, David B. Kaback, Michael E. Dresser, and Makkuni Jayaram. "A selfish DNA element engages a meiosis-specific motor and telomeres for germ-line propagation." Journal of Cell Biology 205, no. 5 (June 9, 2014): 643–61. http://dx.doi.org/10.1083/jcb.201312002.
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The chromosome-like mitotic stability of the yeast 2 micron plasmid is conferred by the plasmid proteins Rep1-Rep2 and the cis-acting locus STB, likely by promoting plasmid-chromosome association and segregation by hitchhiking. Our analysis reveals that stable plasmid segregation during meiosis requires the bouquet proteins Ndj1 and Csm4. Plasmid relocalization from the nuclear interior in mitotic cells to the periphery at or proximal to telomeres rises from early meiosis to pachytene. Analogous to chromosomes, the plasmid undergoes Csm4- and Ndj1-dependent rapid prophase movements with speeds comparable to those of telomeres. Lack of Ndj1 partially disrupts plasmid–telomere association without affecting plasmid colocalization with the telomere-binding protein Rap1. The plasmid appears to engage a meiosis-specific motor that orchestrates telomere-led chromosome movements for its telomere-associated segregation during meiosis I. This hitherto uncharacterized mode of germ-line transmission by a selfish genetic element signifies a mechanistic variation within the shared theme of chromosome-coupled plasmid segregation during mitosis and meiosis.
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Sullins, Jennifer A., Anna L. Coleman-Hulbert, Alexandra Gallegos, Dana K. Howe, Dee R. Denver, and Suzanne Estes. "Complex Transmission Patterns and Age-Related Dynamics of a Selfish mtDNA Deletion." Integrative and Comparative Biology 59, no. 4 (July 18, 2019): 983–93. http://dx.doi.org/10.1093/icb/icz128.
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Abstract Despite wide-ranging implications of selfish mitochondrial DNA (mtDNA) elements for human disease and topics in evolutionary biology (e.g., speciation), the forces controlling their formation, age-related accumulation, and offspring transmission remain largely unknown. Selfish mtDNA poses a significant challenge to genome integrity, mitochondrial function, and organismal fitness. For instance, numerous human diseases are associated with mtDNA mutations; however, few genetic systems can simultaneously represent pathogenic mitochondrial genome evolution and inheritance. The nematode Caenorhabditis briggsae is one such system. Natural C. briggsae isolates harbor varying levels of a large-scale deletion affecting the mitochondrial nduo-5 gene, termed nad5Δ. A subset of these isolates contains putative compensatory mutations that may reduce the risk of deletion formation. We studied the dynamics of nad5Δ heteroplasmy levels during animal development and transmission from mothers to offspring in genetically diverse C. briggsae natural isolates. Results support previous work demonstrating that nad5Δ is a selfish element and that heteroplasmy levels of this deletion can be quite plastic, exhibiting high degrees of inter-family variability and divergence between generations. The latter is consistent with a mitochondrial bottleneck effect, and contrasts with previous findings from a laboratory-derived model uaDf5 mtDNA deletion in C. elegans. However, we also found evidence for among-isolate differences in the ability to limit nad5Δ accumulation, the pattern of which suggested that forces other than the compensatory mutations are important in protecting individuals and populations from rampant mtDNA deletion expansion over short time scales.
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Torres-Padilla, Maria-Elena. "On transposons and totipotency." Philosophical Transactions of the Royal Society B: Biological Sciences 375, no. 1795 (February 10, 2020): 20190339. http://dx.doi.org/10.1098/rstb.2019.0339.
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Our perception of the role of the previously considered ‘selfish’ or ‘junk’ DNA has been dramatically altered in the past 20 years or so. A large proportion of this non-coding part of mammalian genomes is repetitive in nature, classified as either satellites or transposons. While repetitive elements can be termed selfish in terms of their amplification, such events have surely been co-opted by the host, suggesting by itself a likely altruistic function for the organism at the subject of such natural selection. Indeed numerous examples of transposons regulating the functional output of the host genome have been documented. Transposons provide a powerful framework for large-scale relatively rapid concerted regulatory activities with the ability to drive evolution. Mammalian totipotency has emerged as one key stage of development in which transposon-mediated regulation of gene expression has taken centre stage in the past few years. During this period, large-scale (epigenetic) reprogramming must be accomplished in order to activate the host genome. In mice and men, one particular element murine endogenous retrovirus with leucine tRNA primer (MERVL) (and its counterpart human ERVL (HERVL)) appears to have acquired roles as a key driving force in this process. Here, I will discuss and interpret the current knowledge and its implications regarding the role of transposons, particularly of long interspersed nuclear elements (LINE-1s) and endogenous retroviruses (ERVs), in the regulation of totipotency. This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.
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Oberhofer, Georg, Tobin Ivy, and Bruce A. Hay. "Gene drive and resilience through renewal with next generation Cleave and Rescue selfish genetic elements." Proceedings of the National Academy of Sciences 117, no. 16 (April 3, 2020): 9013–21. http://dx.doi.org/10.1073/pnas.1921698117.
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Gene drive-based strategies for modifying populations face the problem that genes encoding cargo and the drive mechanism are subject to separation, mutational inactivation, and loss of efficacy. Resilience, an ability to respond to these eventualities in ways that restore population modification with functional genes, is needed for long-term success. Here, we show that resilience can be achieved through cycles of population modification with “Cleave and Rescue” (ClvR) selfish genetic elements. ClvR comprises a DNA sequence-modifying enzyme such as Cas9/gRNAs that disrupts endogenous versions of an essential gene and a recoded version of the essential gene resistant to cleavage. ClvR spreads by creating conditions in which those lacking ClvR die because they lack functional versions of the essential gene. Cycles of modification can, in principle, be carried out if two ClvR elements targeting different essential genes are located at the same genomic position, and one of them, ClvRn+1, carries a Rescue transgene from an earlier element, ClvRn. ClvRn+1 should spread within a population of ClvRn, while also bringing about a decrease in its frequency. To test this hypothesis, we first show that multiple ClvRs, each targeting a different essential gene, function when located at a common chromosomal position in Drosophila. We then show that when several of these also carry the Rescue from a different ClvR, they spread to transgene fixation in populations fixed for the latter and at its expense. Therefore, genetic modifications of populations can be overwritten with new content, providing an ongoing point of control.
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Ma, Chien-Hui, Bo-Yu Su, Anna Maciaszek, Hsiu-Fang Fan, Piotr Guga, and Makkuni Jayaram. "A Flp-SUMO hybrid recombinase reveals multi-layered copy number control of a selfish DNA element through post-translational modification." PLOS Genetics 15, no. 6 (June 26, 2019): e1008193. http://dx.doi.org/10.1371/journal.pgen.1008193.
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Petraccioli, Agnese, Nicola Maio, Rosa Carotenuto, Gaetano Odierna, and Fabio Maria Guarino. "The Satellite DNA PcH-Sat, Isolated and Characterized in the Limpet Patella caerulea (Mollusca, Gastropoda), Suggests the Origin from a Nin-SINE Transposable Element." Genes 15, no. 5 (April 25, 2024): 541. http://dx.doi.org/10.3390/genes15050541.
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Satellite DNA (sat-DNA) was previously described as junk and selfish DNA in the cellular economy, without a clear functional role. However, during the last two decades, evidence has been accumulated about the roles of sat-DNA in different cellular functions and its probable involvement in tumorigenesis and adaptation to environmental changes. In molluscs, studies on sat-DNAs have been performed mainly on bivalve species, especially those of economic interest. Conversely, in Gastropoda (which includes about 80% of the currently described molluscs species), studies on sat-DNA have been largely neglected. In this study, we isolated and characterized a sat-DNA, here named PcH-sat, in the limpet Patella caerulea using the restriction enzyme method, particularly HaeIII. Monomeric units of PcH-sat are 179 bp long, AT-rich (58.7%), and with an identity among monomers ranging from 91.6 to 99.8%. Southern blot showed that PcH-sat is conserved in P. depressa and P. ulyssiponensis, while a smeared signal of hybridization was present in the other three investigated limpets (P. ferruginea, P. rustica and P. vulgata). Dot blot showed that PcH-sat represents about 10% of the genome of P. caerulea, 5% of that of P. depressa, and 0.3% of that of P. ulyssiponensis. FISH showed that PcH-sat was mainly localized on pericentromeric regions of chromosome pairs 2 and 4–7 of P. caerulea (2n = 18). A database search showed that PcH-sat contains a large segment (of 118 bp) showing high identity with a homologous trait of the Nin-SINE transposable element (TE) of the patellogastropod Lottia gigantea, supporting the hypothesis that TEs are involved in the rising and tandemization processes of sat-DNAs.
Dissertations / Theses on the topic "Selfish DNA element"
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Girard, Fabien. "Tethering of molecular parasites on inactive chromatin in eukaryote nucleus." Electronic Thesis or Diss., Sorbonne université, 2023. http://www.theses.fr/2023SORUS661.
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Les plasmides naturels sont courants chez les procaryotes, mais peu ont été documentés chez les eucaryotes. Le plasmide naturel 2µ présent dans la levure bourgeonnante Saccharomyces cerevisiae est l'un des mieux caractérisés. Cet élément génétique très stable coexiste avec son hôte depuis des millions d'années, ségrégeant efficacement à chaque division cellulaire par un mécanisme qui reste mal compris. En utilisant la ligature de proximité (Hi-C, Micro-C) pour cartographier les contacts entre le plasmide 2µ et les chromosomes de levure dans des dizaines de conditions biologiques différentes, nous avons constaté que le plasmide 2µ se fixe préférentiellement sur des régions à faible activité transcriptionnelle, correspondant souvent à de longs gènes inactifs. Les acteurs communs de la structure des chromosomes, tels que les membres des complexes de maintenance structurale des chromosomes (SMC), ne sont pas impliqués dans ces contacts qui dépendent plutôt d'un signal nucléosomique associé à une déplétion de l'ARN Pol II. Ces contacts sont stables tout au long du cycle cellulaire et peuvent être établis en quelques minutes. Cette stratégie peut aussi être trouvée dans d'autres types de molécules d'ADN et d'autres espèces que S. cerevisiae, comme le suggère le schéma de liaison du plasmide naturel le long des régions silencieuses des chromosomes de Dictyostelium discoideumNatural plasmids are common in prokaryotes but few have been documented in eukaryotes. The natural 2µ plasmid present in budding yeast Saccharomyces cerevisiae is one of the most well characterized. This highly stable genetic element coexists with its host for millions of years, efficiently segregating at each cell division through a mechanism that remains poorly understood. Using proximity ligation (Hi-C, MicroC) to map the contacts between the 2µ and yeast chromosomes under dozens of different biological conditions, we found that the plasmid tether preferentially on regions with low transcriptional activity, often corresponding to long inactive genes, throughout the cell cycle. Common players in chromosome structure such as members of the structural maintenance of chromosome complexes (SMC) are not involved in these contacts, and depend instead on a nucleosomal signal associated with a depletion of RNA Pol II. These contacts are highly stable, and can be established within minutes. Our data show that the plasmid segregates by binding to transcriptionally silent regions of the host chromosomes. This strategy may concern other types of DNA molecules and species beyond S. cerevisiae, as suggested by the binding pattern of the natural Ddp5 plasmid along Dictyostelium discoideum chromosomes’ silent regions
Book chapters on the topic "Selfish DNA element"
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Brookfield, J. F. Y. "| Transposable elements as selfish DNA." In Mobile Genetic Elements, 130–53. Oxford University PressOxford, 1995. http://dx.doi.org/10.1093/oso/9780199634057.003.0006.
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Abstract Biologists seek functional explanations for the attributes of organisms. Such explanations show the advantage that the attribute gives to the organism. Any attribute, including components of the genome, can potentially be explained in this way. The belief that such functional explanations are appropriate rests on the tenet of the Neo-Darwinian evolutionary theory that states that the only systematic mechanism by which genes or other DNA sequences can spread through populations is through differences in the fitnesses of their carriers. Transposable elements, however, increase in number either directly or indirectly during transposition, and thus could potentially spread without increasing the fitness of their hosts. This non-Darwinian behaviour illegitimizes functional explanations and requires us to seek causal explanations for the presence of transposable elements in genomes, incorporating both their own molecular properties and their effects on their hosts. One class of explanations are those in which the effects of transposable elements on their hosts are negative. In other words, they are ‘selfish DNAs’ (1, 2). In this chapter, I will discuss some of the ideas and experiments indicating the selfishness or otherwise of transposable genetic elements. For details of the structures of various classes of transposable elements and the mechanisms of their transposition, the reader should consult other chapters in this volume. I will concentrate mainly on the elements in sexually reproducing diploid eukaryotes, for which the data sets of the distributions and frequencies of elements are often more complete, and for which the Neo-Darwinian population genetics synthesis provides a framework for considerations of transposable element evolution. I will strive, however, to highlight the ways in which the evolutionary process affecting prokaryotic transposable elements shows important similarities to and differences from the diploid paradigm.
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King, David G., Edward N. Trifonov, and Yechezkel Kashi. "Tuning Knobs in the Genome: Evolution of Simple Sequence Repeats by Indirect Selection." In The Implicit Genome, 77–90. Oxford University PressNew York, NY, 2006. http://dx.doi.org/10.1093/oso/9780195172706.003.0005.
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Abstract Simple sequence repeats (SSRs) are highly mutable sites that are distributed throughout eukaryotic genomes. They often occur as functional elements within genes and gene-regulatory regions where mutational changes in repeat number provide extensive variation with minimal genetic load. Implicit in this mutability is the potential for rapid and reversible adjustment of quantitative traits. Although these repetitive elements have been regarded as “junk” or “selfish” DNA, their unique properties are consistent with indirect selection for a “tuning knob” function that facilitates efficient evolutionary adaptation.
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Silvertown, Jonathan. "Naked selfishness." In Selfish Genes to Social Beings, 176–85. Oxford University PressOxford, 2024. http://dx.doi.org/10.1093/oso/9780198876397.003.0015.
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Abstract Gene selfishness is not in itself a barrier to cooperation; in fact, it is the reverse. We have seen repeatedly how self-interested cooperation evolves because of the benefits it brings to team players. But cooperation does not just produce benefits; it also creates opportunities for cheats. Cheating reaches its most extreme in the genomic parasites that exploit the replication machinery of the cell. Viruses are a familiar example, and they are arguably nature’s oldest professional cheats. Another class of genomic parasites is the transposable elements (TEs), which comprise over half our DNA. The variety of TEs is enormous and their nefarious strategies various—some are even parasitic within other TEs. Eukaryote genomes are not alone in containing TEs; bacterial chromosomes also have them, but in bacteria they are usually deleted and not allowed by natural selection to accumulate. The exceptions are TEs that team up with genes that are of positive advantage to their bacterial host, for example in conferring antibiotic resistance. In contrast to bacteria, it is clear from the sheer numbers of TEs that accumulate in eukaryotes that deletion is not so ready an option. The reason boils down to the difference in generation time between bacteria (c. 20 minutes) and most eukaryotes (25 years in humans). Short generation time and huge population size in bacteria sharpen the blade of natural selection, but the reverse blunts its ability to remove TEs from eukaryote genomes.
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Sætre, Glenn-Peter, and Mark Ravinet. "Genomes and the origin of genetic variation." In Evolutionary Genetics, 25–48. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198830917.003.0002.
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Error and chance events, random mutations, are necessary prerequisites for evolution to happen. In a perfect world with no mutations there would be no evolution because no genetic variation would be generated that natural selection or genetic drift could work upon. This chapter first reviews how DNA is organized into genomes and genes in bacteria, archaea, and, in greater detail, eukaryotes. A surprising finding is that only a small fraction of the eukaryote genome consists of coding sequence. Evolutionary processes that can explain the presence of large amounts of noncoding DNA and the repetitive structure of the genome are reviewed, with emphasis on the roles that selfish genetic elements and unequal crossing over play. The chapter further explores the mechanisms that cause mutation and how new genes and protein functions originate.
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Elliott, David, and Michael Ladomery. "RNA editing." In Molecular Biology of RNA. Oxford University Press, 2015. http://dx.doi.org/10.1093/hesc/9780199671397.003.0013.
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This chapter discusses how open reading frames (ORFs) of some RNAs can be altered after transcription by RNA editing. The chapter highlights the important role RNA editing plays in keeping selfish DNA elements in the genome in check. It also mentions the significant role RNA editing plays in enabling tRNAs to translate mRNAs efficiently, which is a process that is conserved between bacteria and eukaryotes. The chapter explains how RNA editing changes the sequence of RNAs once they have already been transcribed. It analyses RNA editing through base modification that changes the chemical identity of nucleotides already present within the transcript.
Conference papers on the topic "Selfish DNA element"
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Palencsárné Kasza, Marianna. "Digitális átállás – Minőség – lehetőségek az EQAVET terén." In Networkshop. HUNGARNET Egyesület, 2022. http://dx.doi.org/10.31915/nws.2022.11.
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A 21. század új kihívása, hogy az ipar 4.0 követelményeihez igazított szakképzési rendszert kell kialakítani. A magyar kormány által elfogadott Szakképzés 4.0 stratégia a gazdaság változó kihívásaira reagál, pontos képet ad a helyzetről és felvázolja a tervezett beavatkozásokat. A szakképzés minőségének javítása érdekében valamennyi szakképző intézményben minőségirányítási rendszert vezetnek be, amelynek elemei kompatibilisek lesznek az EQAVET rendszerrel, és azonos indikatív jellemzőket használnak, így az intézmények tevékenysége és eredményei európai szinten összehasonlíthatóvá válnak. Az EQAVET magyarországi bevezetése során a digitalizációs követelmények minden önértékelési ciklusba bekerültek. Az intézmények és a tanárok értékelését és fejlődését támogatja a Digitális Névjegyrendszer (DNR), az innovatív oktatási technológiák használatának elősegítésével megvalósuló hatékony tanulás önértékelési eszköze (SELFIE) és a DigCompEdu önértékelési rendszer.