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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.
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Metzger, Michael J., Ashley N. Paynter, Mark E. Siddall, and Stephen P. Goff. "Horizontal transfer of retrotransposons between bivalves and other aquatic species of multiple phyla." Proceedings of the National Academy of Sciences 115, no. 18 (April 18, 2018): E4227—E4235. http://dx.doi.org/10.1073/pnas.1717227115.
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The LTR retrotransposon Steamer is a selfish endogenous element in the soft-shell clam genome that was first detected because of its dramatic amplification in bivalve transmissible neoplasia afflicting the species. We amplified and sequenced related retrotransposons from the genomic DNA of many other bivalve species, finding evidence of horizontal transfer of retrotransposons from the genome of one species to another. First, the phylogenetic tree of the Steamer-like elements from 19 bivalve species is markedly discordant with host phylogeny, suggesting frequent cross-species transfer throughout bivalve evolution. Second, sequences nearly identical to Steamer were identified in the genomes of Atlantic razor clams and Baltic clams, indicating recent transfer. Finally, a search of the National Center for Biotechnology Information sequence database revealed that Steamer-like elements are present in the genomes of completely unrelated organisms, including zebrafish, sea urchin, acorn worms, and coral. Phylogenetic incongruity, a patchy distribution, and a higher similarity than would be expected by vertical inheritance all provide evidence for multiple long-distance cross-phyla horizontal transfer events. These data suggest that over both short- and long-term evolutionary timescales, Steamer-like retrotransposons, much like retroviruses, can move between organisms and integrate new copies into new host genomes.
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Mehta, Shwetal, Xian-Mei Yang, Makkuni Jayaram, and Soundarapandian Velmurugan. "A Novel Role for the Mitotic Spindle during DNA Segregation in Yeast: Promoting 2μm Plasmid-Cohesin Association." Molecular and Cellular Biology 25, no. 10 (May 15, 2005): 4283–98. http://dx.doi.org/10.1128/mcb.25.10.4283-4298.2005.
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ABSTRACT The 2μm circle plasmid in Saccharomyces cerevisiae is a model for a stable, high-copy-number, extrachromosomal “selfish” DNA element. By combining a partitioning system and an amplification system, the plasmid ensures its stable propagation and copy number maintenance, even though it does not provide any selective advantage to its host. Recent evidence suggests that the partitioning system couples plasmid segregation to chromosome segregation. We now demonstrate an unexpected and unconventional role for the mitotic spindle in the plasmid-partitioning pathway. The spindle specifies the nuclear address of the 2μm circle and promotes recruitment of the cohesin complex to the plasmid-partitioning locus STB. Only the nuclear microtubules, and not the cytoplasmic ones, are required for loading cohesin at STB. In cells recovering from nocodazole-induced spindle depolymerization and G2/M arrest, cohesin-STB association can be established coincident with spindle restoration. This postreplication recruitment of cohesin is not functional in equipartitioning. However, normally acquired cohesin can be inactivated after replication without causing plasmid missegregation. In the mtw1-1 mutant yeast strain, the plasmid cosegregates with the spindle and the spindle-associated chromosomes; by contrast, a substantial number of the chromosomes are not associated with the spindle. These results are consistent with a model in which the spindle promotes plasmid segregation in a chromosome-linked fashion.
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Jayaram, Makkuni, Keng-Ming Chang, Chien-Hui Ma, Chu-Chun Huang, Yen-Ting Liu, and Soumitra Sau. "Topological similarity between the 2μm plasmid partitioning locus and the budding yeast centromere: evidence for a common evolutionary origin?" Biochemical Society Transactions 41, no. 2 (March 21, 2013): 501–7. http://dx.doi.org/10.1042/bst20120224.
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The partitioning locus STB of the selfish plasmid, the 2μm circle, of Saccharomyces cerevisiae is essential for the propagation of this multi-copy extra-chromosomal DNA element with nearly chromosome-like stability. The functional competence of STB requires the plasmid-coded partitioning proteins Rep1 and Rep2 as well as host-coded proteins. Host factors that associate with STB in a Rep1- and Rep2-dependent manner also interact with centromeres, and play important roles in chromosome segregation. They include the cohesin complex and the centromere-specific histone H3 variant Cse4. The genetically defined point centromere of S. cerevisiae differs starkly from the much more widespread epigenetically specified regional centromeres of eukaryotes. The particularly small size of the S. cerevisiae centromere and the association of chromosome segregation factors with STB raise the possibility of an evolutionary link between these two partitioning loci. The unusual positive supercoiling harboured by the S. cerevisiae centromere and STB in vivo in their functional states, unveiled by recent experiments, bolsters the notion of their potential descent from an ancestral plasmid partitioning locus.
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Miller, Danny E., Ana P. Dorador, Kelley Van Vaerenberghe, Angela Li, Emily K. Grantham, Stefan Cerbin, Celeste Cummings, et al. "Off-target piRNA gene silencing in Drosophila melanogaster rescued by a transposable element insertion." PLOS Genetics 19, no. 2 (February 21, 2023): e1010598. http://dx.doi.org/10.1371/journal.pgen.1010598.
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Transposable elements (TE) are selfish genetic elements that can cause harmful mutations. In Drosophila, it has been estimated that half of all spontaneous visible marker phenotypes are mutations caused by TE insertions. Several factors likely limit the accumulation of exponentially amplifying TEs within genomes. First, synergistic interactions between TEs that amplify their harm with increasing copy number are proposed to limit TE copy number. However, the nature of this synergy is poorly understood. Second, because of the harm posed by TEs, eukaryotes have evolved systems of small RNA-based genome defense to limit transposition. However, as in all immune systems, there is a cost of autoimmunity and small RNA-based systems that silence TEs can inadvertently silence genes flanking TE insertions. In a screen for essential meiotic genes in Drosophila melanogaster, a truncated Doc retrotransposon within a neighboring gene was found to trigger the germline silencing of ald, the Drosophila Mps1 homolog, a gene essential for proper chromosome segregation in meiosis. A subsequent screen for suppressors of this silencing identified a new insertion of a Hobo DNA transposon in the same neighboring gene. Here we describe how the original Doc insertion triggers flanking piRNA biogenesis and local gene silencing. We show that this local gene silencing occurs in cis and is dependent on deadlock, a component of the Rhino-Deadlock-Cutoff (RDC) complex, to trigger dual-strand piRNA biogenesis at TE insertions. We further show how the additional Hobo insertion leads to de-silencing by reducing flanking piRNA biogenesis triggered by the original Doc insertion. These results support a model of TE-mediated gene silencing by piRNA biogenesis in cis that depends on local determinants of transcription. This may explain complex patterns of off-target gene silencing triggered by TEs within populations and in the laboratory. It also provides a mechanism of sign epistasis among TE insertions, illuminates the complex nature of their interactions and supports a model in which off-target gene silencing shapes the evolution of the RDC complex.
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Yang, Xian-Mei, Shwetal Mehta, Dina Uzri, Makkuni Jayaram, and Soundarapandian Velmurugan. "Mutations in a Partitioning Protein and Altered Chromatin Structure at the Partitioning Locus Prevent Cohesin Recruitment by the Saccharomyces cerevisiae Plasmid and Cause Plasmid Missegregation." Molecular and Cellular Biology 24, no. 12 (June 15, 2004): 5290–303. http://dx.doi.org/10.1128/mcb.24.12.5290-5303.2004.
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ABSTRACT The 2μm circle is a highly persistent “selfish” DNA element resident in the Saccharomyces cerevisiae nucleus whose stability approaches that of the chromosomes. The plasmid partitioning system, consisting of two plasmid-encoded proteins, Rep1p and Rep2p, and a cis-acting locus, STB, apparently feeds into the chromosome segregation pathway. The Rep proteins assist the recruitment of the yeast cohesin complex to STB during the S phase, presumably to apportion the replicated plasmid molecules equally to daughter cells. The DNA-protein and protein-protein interactions of the partitioning system, as well as the chromatin organization at STB, are important for cohesin recruitment. Rep1p variants that are incompetent in binding to Rep2p, STB, or both fail to assist the assembly of the cohesin complex at STB and are nonfunctional in plasmid maintenance. Preventing the cohesin-STB association without impeding Rep1p-Rep2p-STB interactions also causes plasmid missegregation. During the yeast cell cycle, the Rep1p and Rep2p proteins are expelled from STB during a short interval between the late G1 and early S phases. This dissociation and reassociation event ensures that cohesin loading at STB is replication dependent and is coordinated with chromosomal cohesin recruitment. In an rsc2Δ yeast strain lacking a specific chromatin remodeling complex and exhibiting a high degree of plasmid loss, neither Rep1p nor the cohesin complex can be recruited to STB. The phenotypes of the Rep1p mutations and of the rsc2Δ mutant are consistent with the role of cohesin in plasmid partitioning being analogous to that in chromosome partitioning.
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van Wyk, Stephanie, Christopher H. Harrison, Brenda D. Wingfield, Lieschen De Vos, Nicolaas A. van der Merwe, and Emma T. Steenkamp. "The RIPper, a web-based tool for genome-wide quantification of Repeat-Induced Point (RIP) mutations." PeerJ 7 (August 26, 2019): e7447. http://dx.doi.org/10.7717/peerj.7447.
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Background The RIPper (http://theripper.hawk.rocks) is a set of web-based tools designed for analyses of Repeat-Induced Point (RIP) mutations in the genome sequences of Ascomycota. The RIP pathway is a fungal genome defense mechanism that is aimed at identifying repeated and duplicated motifs, into which it then introduces cytosine to thymine transition mutations. RIP thus serves to deactivate and counteract the deleterious consequences of selfish or mobile DNA elements in fungal genomes. The occurrence, genetic context and frequency of RIP mutations are widely used to assess the activity of this pathway in genomic regions of interest. Here, we present a bioinformatics tool that is specifically fashioned to automate the investigation of changes in RIP product and substrate nucleotide frequencies in fungal genomes. Results We demonstrated the ability of The RIPper to detect the occurrence and extent of RIP mutations in known RIP affected sequences. Specifically, a sliding window approach was used to perform genome-wide RIP analysis on the genome assembly of Neurospora crassa. Additionally, fine-scale analysis with The RIPper showed that gene regions and transposable element sequences, previously determined to be affected by RIP, were indeed characterized by high frequencies of RIP mutations. Data generated using this software further showed that large proportions of the N. crassa genome constitutes RIP mutations with extensively affected regions displaying reduced GC content. The RIPper was further useful for investigating and visualizing changes in RIP mutations across the length of sequences of interest, allowing for fine-scale analyses. Conclusion This software identified RIP targeted genomic regions and provided RIP statistics for an entire genome assembly, including the genomic proportion affected by RIP. Here, we present The RIPper as an efficient tool for genome-wide RIP analyses.
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Dandy, Alvin Try, Agus Suharjono Ekomadyo, and Hadi Jaya Putra. "PRODUKSI DAN KONSUMSI RUANG PARIWISATA MELALUI SWAFOTO INSTAGRAM. STUDI KASUS KOTA TUA JAKARTA." LANGKAU BETANG: JURNAL ARSITEKTUR 9, no. 2 (October 28, 2022): 173. http://dx.doi.org/10.26418/lantang.v9i2.53974.
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Kegiatan pariwisata menciptakan realitas paralel dalam ruang urban berupa ruang pariwisata. Dalam ruang pariwisata, elemen urban mengalami transformasi melalui tourist gaze. Kawasan Kota Tua Jakarta bertransformasi dari pusat administrasi VOC (Perusahaan Hindia Timur Belanda) menjadi kawasan wisata di Provinsi DKI Jakarta. Bangunan-bangunan VOC berhenti menjadi objek arsitektur fungsional dan bertransformasi menjadi latar foto bagi wisatawan dalam suatu narasi pariwisata. Penelitian ini membahas produksi dan konsumsi ruang pariwisata di Kota Tua Jakarta melalui teknologi dan tourist gaze kontemporer, yaitu melalui selfie (swafoto) dan situs media sosial Instagram. Penelitian ini merupakan penelitian deskriptif kualitatif yang meninjau deskripsi historis Kota Tua Jakarta dan swafoto turis Kota Tua Jakarta yang diunggah ke Instagram. Produksi ruang di Kota Tua Jakarta dibaca berdasarkan teori Lefebvre mengenai produksi ruang sosial dan konsep yang diajukan Farías dalam membingkai ruang urban menjadi ruang pariwisata. Kemudian, swafoto wisatawan dianalisis menggunakan qualitative content analysis untuk menemukan pola konsumsi ruang pariwisata Kota Tua Jakarta. Penelitian menemukan bahwa wisatawan hampir selalu tampil lebih dominan dibandingkan bangunan yang turut ditampilkan dalam swafoto. Penelitian menyimpulkan bahwa swafoto wisatawan membingkai dan mereduksi elemen urban Kota Tua Jakarta menjadi komoditas visual dalam sebuah ruang pariwisata. Penelitian ini diharapkan berkontribusi dalam diskusi mengenai kegiatan pariwisata kontemporer terkait tempat-tempat bersejarah. PRODUCTION AND CONSUMPTION OF TOURISM SPACE THROUGH INSTAGRAM SELFIES. A CASE STUDY OF KOTA TUA JAKARTATourist activities create destination space as a parallel reality in an urban space. In destination space, urban elements are transformed through the tourist gaze. Kota Tua Jakarta began as the administration center of VOC (Netherlands East Indies Company) and turned into a tourist destination in Jakarta Special Capital Region. VOC administrative buildings stopped serving their original functions and transformed into mere backgrounds for tourists’ selfies. This study aims to explore the production and consumption of the destination space in Kota Tua Jakarta in regard to technology and the contemporary tourist gaze (selfie and Instagram). This article is a descriptive qualitative study in which historical narratives of Kota Tua Jakarta and tourist selfies in Kota Tua Jakarta are analyzed. The production of space in Kota Tua Jakarta in this article follows Henri Lefebvre’s production of social space and the concept presented by Ignacio Farías in framing urban space into destination space. Tourist selfies in Kota Tua Jakarta are analyzed with qualitative content analysis to find the consumption pattern of the destination space. This study finds that tourists almost always dominate the selfie scene relative to the buildings in the photograph. The study concludes that tourist selfies frame and reduce the urban elements of Kota Tua Jakarta into mere visual commodities inside a destination space. This study will offer a perspective on the discourse of contemporary tourist practice regarding historical sites
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Bird, Adrian. "Does DNA methylation control transposition of selfish elements in the germline?" Trends in Genetics 13, no. 12 (December 1997): 469–70. http://dx.doi.org/10.1016/s0168-9525(97)01310-3.
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Sau, Soumitra, Santanu Kumar Ghosh, Yen-Ting Liu, Chien-Hui Ma, and Makkuni Jayaram. "Hitchhiking on chromosomes: A persistence strategy shared by diverse selfish DNA elements." Plasmid 102 (March 2019): 19–28. http://dx.doi.org/10.1016/j.plasmid.2019.01.004.
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Geng, Peng, Sean P. Leonard, Dennis M. Mishler, and Jeffrey E. Barrick. "Synthetic Genome Defenses against Selfish DNA Elements Stabilize Engineered Bacteria against Evolutionary Failure." ACS Synthetic Biology 8, no. 3 (January 31, 2019): 521–31. http://dx.doi.org/10.1021/acssynbio.8b00426.
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Dimitri, Patrizio, and Nikolaj Junakovic. "Revising the selfish DNA hypothesis: new evidence on accumulation of transposable elements in heterochromatin." Trends in Genetics 15, no. 4 (April 1999): 123–24. http://dx.doi.org/10.1016/s0168-9525(99)01711-4.
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Ariyanto, Ahmad Fajar, Satriana Didiek Isnanta, and Ernasthan Budi Prasetyo. "PERANCANGAN KARYA SENI INSTALASI SEBAGAI ELEMEN ARTISTIK SPOT SWAFOTO DI RUANG PUBLIK BERNUANSA LOKAL." Acintya Jurnal Penelitian Seni Budaya 14, no. 2 (December 27, 2022): 144–51. http://dx.doi.org/10.33153/acy.v14i2.4550.
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ABSTRAKSwafoto berkaitan erat dengan citra yang dipersepsikan seseorang atas dirinya sendiri (self image). Swafoto telah menjadi gaya hidup tidak hanya masyarakat perkotaan tetapi juga sudah sampai ke pinggiran. swafoto pada area wisata/ publik, hal ini juga tidak terlepas dari perubahan gaya hidup generasi muda yang kini gemar melakukan travelling.Fenomena swafoto ini akhirnya mempengaruhi pengelola ruang komersial seperti kafe untuk mendekorasi ulang interiornya dengan menyediakan spot swafoto sebagai salah satu dayatarik usahanya. Gaya hidup swafoto dan perkembangan teknologi informasi terutama media sosial seperti facebook dan Instagram telah memberi keuntungan bagi pengelola ruang komersiil dan pemerintah daerah. Dengan menyediakan spot swafoto, usahanya maupun destinasi wisatanya telah dipromosikan karena diseberluaskan melalui akun Facebook atau IG wisatawannya.Sayangnya spot swafoto sekarang yang telah ada di kafe-kafe maupun di destinasi wisata yang dikelola oleh pemerintah daerah masih terkesan seragam atau minimal jauh dari kultur setempat. Oleh karena itu perlu sebuah penelitian yang bertujuan untuk membuat Rancangan Prototipe Seni Instalasi Sebagai Elemen Artistik Spot Swafoto di Ruang Publik bernuansa budaya lokal.Penelitian ini didesain sebagai penelitian eksperimentatif dengan menggunakan metode Kreasi Artistik yang memiliki tahapan riset dengan pendekatan etik dan riset dengan pendekatan emik sebagai dasar penciptaan karya, dan kedua, tahapan penciptaan karya berisi: eksperimentasi, perenungan dan pembentukan. Penelitian ini didesain sebagai penelitin terapan dengan durasi selama enam bulan. Luaran penelitian ini adalah: draft rtikel ilmiah, produk inovasi dan KI. Kata kunci; seni instalasi; spot swafoto, budaya lokal, ruang publik ABSTRACTSelfie is closely related to the image that a person perceives of himself (self image). Selfie has become a lifestyle not only for urban people but has also reached the outskirts. selfies in tourist/public areas, this is also inseparable from the changing lifestyles of the younger generation who are now fond of traveling.This selfie phenomenon has finally influenced the managers of commercial spaces such as cafes to redecorate their interiors by providing selfie spots as one of the attractions of their business. The selfie lifestyle and the development of information technology, especially social media such as Facebook and Instagram, have provided benefits for commercial space managers and local governments. By providing selfie spots, their businesses and tourist destinations have been promoted because they are disseminated through their Facebook accounts or tourists' IG accounts.Unfortunately, the selfie spots that already exist in cafes and tourist destinations managed by local governments still seem uniform or at least far from local culture. Therefore, a research is needed that aims to create a Prototype Design of Installation Art as an Artistic Element of a Selfie Spot in a Public Space with the nuances of local culture.This research is designed as an experimental research using the Artistic Creation method which has research stages with an ethical approach and research with an emic approach as the basis for creating works, and second, the stages of creating works consist of: experimentation, reflection and formation. This study was designed as an applied research with a duration of six months. The outputs of this research are: drafts of scientific articles, innovation products and IP. Keywords; installation art; selfie spot, local culture, public space
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Drost, Hajk-Georg, and Diego H. Sanchez. "Becoming a Selfish Clan: Recombination Associated to Reverse-Transcription in LTR Retrotransposons." Genome Biology and Evolution 11, no. 12 (November 25, 2019): 3382–92. http://dx.doi.org/10.1093/gbe/evz255.
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Abstract Transposable elements (TEs) are parasitic DNA bits capable of mobilization and mutagenesis, typically suppressed by host’s epigenetic silencing. Since the selfish DNA concept, it is appreciated that genomes are also molded by arms-races against natural TE inhabitants. However, our understanding of evolutionary processes shaping TEs adaptive populations is scarce. Here, we review the events of recombination associated to reverse-transcription in LTR retrotransposons, a process shuffling their genetic variants during replicative mobilization. Current evidence may suggest that recombinogenic retrotransposons could beneficially exploit host suppression, where clan behavior facilitates their speciation and diversification. Novel refinements to retrotransposons life-cycle and evolution models thus emerge.
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Susek, R. E., and S. L. Lindquist. "hsp26 of Saccharomyces cerevisiae is related to the superfamily of small heat shock proteins but is without a demonstrable function." Molecular and Cellular Biology 9, no. 11 (November 1989): 5265–71. http://dx.doi.org/10.1128/mcb.9.11.5265-5271.1989.
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Analysis of the cloned gene confirms that hsp26 of Saccharomyces cerevisiae is a member of the small heat shock protein superfamily. Previous mutational analysis failed to demonstrate any function for the protein. Further experiments presented here demonstrate that hsp26 has no obvious regulatory role and no major effect on thermotolerance. It is possible that the small heat shock protein genes originated as primitive viral or selfish DNA elements.
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Susek, R. E., and S. L. Lindquist. "hsp26 of Saccharomyces cerevisiae is related to the superfamily of small heat shock proteins but is without a demonstrable function." Molecular and Cellular Biology 9, no. 11 (November 1989): 5265–71. http://dx.doi.org/10.1128/mcb.9.11.5265.
Full textAbstract:
Analysis of the cloned gene confirms that hsp26 of Saccharomyces cerevisiae is a member of the small heat shock protein superfamily. Previous mutational analysis failed to demonstrate any function for the protein. Further experiments presented here demonstrate that hsp26 has no obvious regulatory role and no major effect on thermotolerance. It is possible that the small heat shock protein genes originated as primitive viral or selfish DNA elements.
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Robillard, Émilie, Arnaud Le Rouzic, Zheng Zhang, Pierre Capy, and Aurélie Hua-Van. "Experimental evolution reveals hyperparasitic interactions among transposable elements." Proceedings of the National Academy of Sciences 113, no. 51 (December 5, 2016): 14763–68. http://dx.doi.org/10.1073/pnas.1524143113.
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Transposable elements (TEs) are repeated DNA sequences that can constitute a substantial part of genomes. Studying TEs’ activity, interactions, and accumulation dynamics is thus of major interest to understand genome evolution. Here, we describe the transposition dynamics of cut-and-pastemarinerelements during experimental (short- and longer-term) evolution inDrosophila melanogaster. Flies with autonomous and nonautonomousmarinercopies were introduced in populations containing no activemariner, and TE accumulation was tracked by quantitative PCR for up to 100 generations. Our results demonstrate that (i) activemarinerelements are highly invasive and characterized by an elevated transposition rate, confirming their capacity to spread in populations, as predicted by the “selfish-DNA” mechanism; (ii) nonautonomous copies act as parasites of autonomousmarinerelements by hijacking the transposition machinery produced by activemariner, which can be considered as a case of hyperparasitism; (iii) this behavior resulted in a failure of active copies to amplify which systematically drove the whole family to extinction in less than 100 generations. This study nicely illustrates how the presence of transposition-competitive variants can deeply impair TE dynamics and gives clues to the extraordinary diversity of TE evolutionary histories observed in genomes.
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Brand, Cara L., and Mia T. Levine. "Functional Diversification of Chromatin on Rapid Evolutionary Timescales." Annual Review of Genetics 55, no. 1 (November 23, 2021): 401–25. http://dx.doi.org/10.1146/annurev-genet-071719-020301.
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Repeat-enriched genomic regions evolve rapidly and yet support strictly conserved functions like faithful chromosome transmission and the preservation of genome integrity. The leading resolution to this paradox is that DNA repeat–packaging proteins evolve adaptively to mitigate deleterious changes in DNA repeat copy number, sequence, and organization. Exciting new research has tested this model of coevolution by engineering evolutionary mismatches between adaptively evolving chromatin proteins of one species and the DNA repeats of a close relative. Here, we review these innovative evolution-guided functional analyses. The studies demonstrate that vital, chromatin-mediated cellular processes, including transposon suppression, faithful chromosome transmission, and chromosome retention depend on species-specific versions of chromatin proteins that package species-specific DNA repeats. In many cases, the ever-evolving repeats are selfish genetic elements, raising the possibility that chromatin is a battleground of intragenomic conflict.
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Mishra, Vibhor, Jasleen Singh, Feng Wang, Yixiang Zhang, Akihito Fukudome, Jonathan C. Trinidad, Yuichiro Takagi, and Craig S. Pikaard. "Assembly of a dsRNA synthesizing complex: RNA-DEPENDENT RNA POLYMERASE 2 contacts the largest subunit of NUCLEAR RNA POLYMERASE IV." Proceedings of the National Academy of Sciences 118, no. 13 (March 22, 2021): e2019276118. http://dx.doi.org/10.1073/pnas.2019276118.
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In plants, transcription of selfish genetic elements such as transposons and DNA viruses is suppressed by RNA-directed DNA methylation. This process is guided by 24-nt short-interfering RNAs (siRNAs) whose double-stranded precursors are synthesized by DNA-dependent NUCLEAR RNA POLYMERASE IV (Pol IV) and RNA-DEPENDENT RNA POLYMERASE 2 (RDR2). Pol IV and RDR2 coimmunoprecipitate, and their activities are tightly coupled, yet the basis for their association is unknown. Here, we show that an interval near the RDR2 active site contacts the Pol IV catalytic subunit, NRPD1, the largest of Pol IV’s 12 subunits. Contacts between the catalytic regions of the two enzymes suggests that RDR2 is positioned to rapidly engage the free 3′ ends of Pol IV transcripts and convert these single-stranded transcripts into double-stranded RNAs (dsRNAs).
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Lower, Sarah E., Anne-Marie Dion-Côté, Andrew G. Clark, and Daniel A. Barbash. "Special Issue: Repetitive DNA Sequences." Genes 10, no. 11 (November 6, 2019): 896. http://dx.doi.org/10.3390/genes10110896.
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Repetitive DNAs are ubiquitous in eukaryotic genomes and, in many species, comprise the bulk of the genome. Repeats include transposable elements that can self-mobilize and disperse around the genome and tandemly-repeated satellite DNAs that increase in copy number due to replication slippage and unequal crossing over. Despite their abundance, repetitive DNAs are often ignored in genomic studies due to technical challenges in identifying, assembling, and quantifying them. New technologies and methods are now allowing unprecedented power to analyze repetitive DNAs across diverse taxa. Repetitive DNAs are of particular interest because they can represent distinct modes of genome evolution. Some repetitive DNAs form essential genome structures, such as telomeres and centromeres, that are required for proper chromosome maintenance and segregation, while others form piRNA clusters that regulate transposable elements; thus, these elements are expected to evolve under purifying selection. In contrast, other repeats evolve selfishly and cause genetic conflicts with their host species that drive adaptive evolution of host defense systems. However, the majority of repeats likely accumulate in eukaryotes in the absence of selection due to mechanisms of transposition and unequal crossing over. However, even these “neutral” repeats may indirectly influence genome evolution as they reach high abundance. In this Special Issue, the contributing authors explore these questions from a range of perspectives.
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Arkhipova, Irina R., and Irina A. Yushenova. "To Be Mobile or Not: The Variety of Reverse Transcriptases and Their Recruitment by Host Genomes." Biochemistry (Moscow) 88, no. 11 (November 2023): 1754–62. http://dx.doi.org/10.1134/s000629792311007x.
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Abstract Reverse transcriptases (RT), or RNA-dependent DNA polymerases, are unorthodox enzymes that originally added a new angle to the conventional view of the unidirectional flow of genetic information in the cell from DNA to RNA to protein. First discovered in vertebrate retroviruses, RTs were since re-discovered in most eukaryotes, bacteria, and archaea, spanning essentially all domains of life. For retroviruses, RTs provide the ability to copy the RNA genome into DNA for subsequent incorporation into the host genome, which is essential for their replication and survival. In cellular organisms, most RT sequences originate from retrotransposons, the type of self-replicating genetic elements that rely on reverse transcription to copy and paste their sequences into new genomic locations. Some retroelements, however, can undergo domestication, eventually becoming a valuable addition to the overall repertoire of cellular enzymes. They can be beneficial yet accessory, like the diversity-generating elements, or even essential, like the telomerase reverse transcriptases. Nowadays, ever-increasing numbers of domesticated RT-carrying genetic elements are being discovered. It may be argued that domesticated RTs and reverse transcription in general is more widespread in cellular organisms than previously thought, and that many important cellular functions, such as chromosome end maintenance, may evolve from an originally selfish process of converting RNA into DNA.
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Arkhipova, I. R., and I. A. Yushenova. "To be mobile or not: the variety of reverse transcriptases and their recruitment by host genomes." Биохимия 88, no. 11 (December 15, 2023): 2127–37. http://dx.doi.org/10.31857/s0320972523110088.
Full textAbstract:
Reverse transcriptases (RT), or RNA-dependent DNA polymerases, are unorthodox enzymes that originally added a new angle to the conventional view of the unidirectional flow of genetic information in the cell from DNA to RNA to protein. First discovered in vertebrate retroviruses, RTs were since re-discovered in most eukaryotes, bacteria, and archaea, spanning essentially all domains of life. For retroviruses, RTs provide the ability to copy the RNA genome into DNA for subsequent incorporation into the host genome, which is essential for their replication and survival. In cellular organisms, most RT sequences originate from retrotransposons, the type of self-replicating genetic elements that rely on reverse transcription to copy and paste their sequences into new genomic locations. Some retroelements, however, can undergo domestication, eventually becoming a valuable addition to the overall repertoire of cellular enzymes. They can be beneficial yet accessory, like the diversity-generating elements, or even essential, like the telomerase reverse transcriptases. Nowadays, ever-increasing numbers of domesticated RT-carrying genetic elements are being discovered. It may be argued that domesticated RTs and reverse transcription in general is more widespread in cellular organisms than previously thought, and that many important cellular functions, such as chromosome end maintenance, may evolve from an originally selfish process of converting RNA into DNA.
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Wagner, Josiah T., Dana K. Howe, Suzanne Estes, and Dee R. Denver. "Mitochondrial DNA Variation and Selfish Propagation Following Experimental Bottlenecking in Two Distantly Related Caenorhabditis briggsae Isolates." Genes 11, no. 1 (January 10, 2020): 77. http://dx.doi.org/10.3390/genes11010077.
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Understanding mitochondrial DNA (mtDNA) evolution and inheritance has broad implications for animal speciation and human disease models. However, few natural models exist that can simultaneously represent mtDNA transmission bias, mutation, and copy number variation. Certain isolates of the nematode Caenorhabditis briggsae harbor large, naturally-occurring mtDNA deletions of several hundred basepairs affecting the NADH dehydrogenase subunit 5 (nduo-5) gene that can be functionally detrimental. These deletion variants can behave as selfish DNA elements under genetic drift conditions, but whether all of these large deletion variants are transmitted in the same preferential manner remains unclear. In addition, the degree to which transgenerational mtDNA evolution profiles are shared between isolates that differ in their propensity to accumulate the nduo-5 deletion is also unclear. We address these knowledge gaps by experimentally bottlenecking two isolates of C. briggsae with different nduo-5 deletion frequencies for up to 50 generations and performing total DNA sequencing to identify mtDNA variation. We observed multiple mutation profile differences and similarities between C. briggsae isolates, a potentially species-specific pattern of copy number dysregulation, and some evidence for genetic hitchhiking in the deletion-bearing isolate. Our results further support C. briggsae as a practical model for characterizing naturally-occurring mtgenome variation and contribute to the understanding of how mtgenome variation persists in animal populations and how it presents in mitochondrial disease states.
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Oberhofer, Georg, Tobin Ivy, and Bruce A. Hay. "Split versions of Cleave and Rescue selfish genetic elements for measured self limiting gene drive." PLOS Genetics 17, no. 2 (February 18, 2021): e1009385. http://dx.doi.org/10.1371/journal.pgen.1009385.
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Gene drive elements promote the spread of linked traits, providing methods for changing the composition or fate of wild populations. Drive mechanisms that are self-limiting are attractive because they allow control over the duration and extent of trait spread in time and space, and are reversible through natural selection as drive wanes. Self-sustainingCleave and Rescue(ClvR) elements include a DNA sequence-modifying enzyme such as Cas9/gRNAs that disrupts endogenous versions of an essential gene, a tightly linked recoded version of the essential gene resistant to cleavage (theRescue), and a Cargo.ClvRspreads by creating loss-of-function (LOF) conditions in which those withoutClvRdie because they lack functional copies of the essential gene. We use modeling to show that when theRescue-Cargo and one or both components required for LOF allele creation (Cas9 and gRNA) reside at different locations (splitClvR), drive ofRescue-Cargo is self-limiting due to a progressive decrease in Cas9 frequency, and thus opportunities for creation of LOF alleles, as spread occurs. Importantly, drive strength and duration can be extended in a measured manner—which is still self-limiting—by moving the two components close enough to each other that they experience some degree of linkage. With linkage, Cas9 transiently experiences drive by hitchhiking withRescue-Cargo until linkage disequilibrium between the two disappears, a function of recombination frequency and number of generations, creating a novel point of control. We implement splitClvRinDrosophila, with key elements on different chromosomes. Cargo/Rescue/gRNAs spreads to high frequency in a Cas9-dependent manner, while the frequency of Cas9 decreases. These observations show that measured, transient drive, coupled with a loss of future drive potential, can be achieved using the simple toolkit that make upClvRelements—Cas9 and gRNAs and aRescue/Cargo.
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Massey, Steven E., and Bud Mishra. "Origin of biomolecular games: deception and molecular evolution." Journal of The Royal Society Interface 15, no. 146 (September 2018): 20180429. http://dx.doi.org/10.1098/rsif.2018.0429.
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Biological macromolecules encode information: some of it to endow the molecule with structural flexibility, some of it to enable molecular actions as a catalyst or a substrate, but a residual part can be used to communicate with other macromolecules. Thus, macromolecules do not need to possess information only to survive in an environment, but also to strategically interact with others by sending signals to a receiving macromolecule that can properly interpret the signal and act suitably. These sender–receiver signalling games are sustained by the information asymmetry that exists among the macromolecules. In both biochemistry and molecular evolution, the important role of information asymmetry remains largely unaddressed. Here, we provide a new unifying perspective on the impact of information symmetry between macromolecules on molecular evolutionary processes, while focusing on molecular deception. Biomolecular games arise from the ability of biological macromolecules to exert precise recognition, and their role as units of selection, meaning that they are subject to competition and cooperation with other macromolecules. Thus, signalling game theory can be used to better understand fundamental features of living systems such as molecular recognition, molecular mimicry, selfish elements and ‘junk’ DNA. We show how deceptive behaviour at the molecular level indicates a conflict of interest, and so provides evidence of genetic conflict. This model proposes that molecular deception is diagnostic of selfish behaviour, helping to explain the evasive behaviour of transposable elements in ‘junk’ DNA, for example. Additionally, in this broad review, a range of major evolutionary transitions are shown to be associated with the establishment of signalling conventions, many of which are susceptible to molecular deception. These perspectives allow us to assign rudimentary behaviour to macromolecules, and show how participation in signalling games differentiates biochemistry from abiotic chemistry.
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Ma’rifatul Faiqoh, Naning, and R. Umi Baroroh. "Teori Belajar Humanistik Dan Implikasinya Pada Maharah Istima'." Urwatul Wutsqo: Jurnal Studi Kependidikan dan Keislaman 9, no. 2 (September 17, 2020): 213–28. http://dx.doi.org/10.54437/urwatulwutsqo.v9i2.183.
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Recently, many educational theories grow up based on the assumptions in some problems. This article explores humanistic learning theory and its implications for learning Arabic at maharah istima ', using library research, since the data and information were collected in the form of a continuous library with discussion, then the researcher analyzed the data using content analysis method. The results shows that the application of maharah istima ' learning Arabic includes learning objectives, learning models, using media, culture and students’ background. Carl Rogers' humanistic theory emphasizes deep humanity, does not contain selfish, individualistic elements or authoritarian, they do not have to follow our opinion, so this theory focuses on the student center, that focused on the cognitive, affective and psychomotor aspects by giving students their rights, being humanized, recognized and accepted, from which students will be optimistic in voicing contents of their mind.
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Stitzer, Michelle C., Sarah N. Anderson, Nathan M. Springer, and Jeffrey Ross-Ibarra. "The genomic ecosystem of transposable elements in maize." PLOS Genetics 17, no. 10 (October 14, 2021): e1009768. http://dx.doi.org/10.1371/journal.pgen.1009768.
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Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. Genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between attributes of the genomic environment and the survival of TE copies and families. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences reveal a diversity of survival strategies of TE families. Together these generate a rich ecology of the genome, with each TE family representing the evolution of a distinct ecological niche. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.
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Fischer, Sylvia E. J. "Activity and Silencing of Transposable Elements in C. elegans." DNA 4, no. 2 (April 2, 2024): 129–40. http://dx.doi.org/10.3390/dna4020007.
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Since the discovery of transposable elements (TEs) in maize in the 1940s by Barbara McClintock transposable elements have been described as junk, as selfish elements with no benefit to the host, and more recently as major determinants of genome structure and genome evolution. TEs are DNA sequences that are capable of moving to new sites in the genome and making additional copies of themselves while doing so. To limit the propagation of TEs, host silencing mechanisms are directed at transposon-encoded genes that are required for mobilization. The mutagenic properties of TEs, the potential of TEs to form new genes and affect gene expression, together with the host silencing mechanisms, shape eukaryotic genomes and drive genome evolution. While TEs constitute more than half of the genome in many higher eukaryotes, transposable elements in the nematode C. elegans form a relatively small proportion of the genome (approximately 15%). Genetic studies of transposon silencing, and the discovery of RNA interference (RNAi) in C. elegans, propelled Caenorhabditis elegans (C. elegans) to the forefront of studies of RNA-based mechanisms that silence TEs. Here, I will review the transposable elements that are present and active in the C. elegans genome, and the host defense mechanisms that silence these elements.
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Marasca, Federica, Erica Gasparotto, Benedetto Polimeni, Rebecca Vadalà, Valeria Ranzani, and Beatrice Bodega. "The Sophisticated Transcriptional Response Governed by Transposable Elements in Human Health and Disease." International Journal of Molecular Sciences 21, no. 9 (April 30, 2020): 3201. http://dx.doi.org/10.3390/ijms21093201.
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Transposable elements (TEs), which cover ~45% of the human genome, although firstly considered as “selfish” DNA, are nowadays recognized as driving forces in eukaryotic genome evolution. This capability resides in generating a plethora of sophisticated RNA regulatory networks that influence the cell type specific transcriptome in health and disease. Indeed, TEs are transcribed and their RNAs mediate multi-layered transcriptional regulatory functions in cellular identity establishment, but also in the regulation of cellular plasticity and adaptability to environmental cues, as occurs in the immune response. Moreover, TEs transcriptional deregulation also evolved to promote pathogenesis, as in autoimmune and inflammatory diseases and cancers. Importantly, many of these findings have been achieved through the employment of Next Generation Sequencing (NGS) technologies and bioinformatic tools that are in continuous improvement to overcome the limitations of analyzing TEs sequences. However, they are highly homologous, and their annotation is still ambiguous. Here, we will review some of the most recent findings, questions and improvements to study at high resolution this intriguing portion of the human genome in health and diseases, opening the scenario to novel therapeutic opportunities.
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Durdevic, Zeljko, Ramesh S. Pillai, and Anne Ephrussi. "Transposon silencing in the Drosophila female germline is essential for genome stability in progeny embryos." Life Science Alliance 1, no. 5 (September 17, 2018): e201800179. http://dx.doi.org/10.26508/lsa.201800179.
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The Piwi-interacting RNA pathway functions in transposon control in the germline of metazoans. The conserved RNA helicase Vasa is an essential Piwi-interacting RNA pathway component, but has additional important developmental functions. Here, we address the importance of Vasa-dependent transposon control in the Drosophila female germline and early embryos. We find that transient loss of vasa expression during early oogenesis leads to transposon up-regulation in supporting nurse cells of the fly egg-chamber. We show that elevated transposon levels have dramatic consequences, as de-repressed transposons accumulate in the oocyte where they cause DNA damage. We find that suppression of Chk2-mediated DNA damage signaling in vasa mutant females restores oogenesis and egg production. Damaged DNA and up-regulated transposons are transmitted from the mother to the embryos, which sustain severe nuclear defects and arrest development. Our findings reveal that the Vasa-dependent protection against selfish genetic elements in the nuage of nurse cell is essential to prevent DNA damage–induced arrest of embryonic development.
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Mendoza, Hector, Michael H. Perlin, and Jan Schirawski. "Mitochondrial Inheritance in Phytopathogenic Fungi—Everything Is Known, or Is It?" International Journal of Molecular Sciences 21, no. 11 (May 29, 2020): 3883. http://dx.doi.org/10.3390/ijms21113883.
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Mitochondria are important organelles in eukaryotes that provide energy for cellular processes. Their function is highly conserved and depends on the expression of nuclear encoded genes and genes encoded in the organellar genome. Mitochondrial DNA replication is independent of the replication control of nuclear DNA and as such, mitochondria may behave as selfish elements, so they need to be controlled, maintained and reliably inherited to progeny. Phytopathogenic fungi meet with special environmental challenges within the plant host that might depend on and influence mitochondrial functions and services. We find that this topic is basically unexplored in the literature, so this review largely depends on work published in other systems. In trying to answer elemental questions on mitochondrial functioning, we aim to introduce the aspect of mitochondrial functions and services to the study of plant-microbe-interactions and stimulate phytopathologists to consider research on this important organelle in their future projects.
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Balzano, Elisa, and Simona Giunta. "Centromeres under Pressure: Evolutionary Innovation in Conflict with Conserved Function." Genes 11, no. 8 (August 10, 2020): 912. http://dx.doi.org/10.3390/genes11080912.
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Centromeres are essential genetic elements that enable spindle microtubule attachment for chromosome segregation during mitosis and meiosis. While this function is preserved across species, centromeres display an array of dynamic features, including: (1) rapidly evolving DNA; (2) wide evolutionary diversity in size, shape and organization; (3) evidence of mutational processes to generate homogenized repetitive arrays that characterize centromeres in several species; (4) tolerance to changes in position, as in the case of neocentromeres; and (5) intrinsic fragility derived by sequence composition and secondary DNA structures. Centromere drive underlies rapid centromere DNA evolution due to the “selfish” pursuit to bias meiotic transmission and promote the propagation of stronger centromeres. Yet, the origins of other dynamic features of centromeres remain unclear. Here, we review our current understanding of centromere evolution and plasticity. We also detail the mutagenic processes proposed to shape the divergent genetic nature of centromeres. Changes to centromeres are not simply evolutionary relics, but ongoing shifts that on one side promote centromere flexibility, but on the other can undermine centromere integrity and function with potential pathological implications such as genome instability.
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L. Sholehuddin. "Ekologi dan Kerusakan Lingkungan dalam Persepektif Al-Qur’an." Jurnal Al-Fanar 4, no. 2 (August 31, 2021): 113–34. http://dx.doi.org/10.33511/alfanar.v4n2.113-134.
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Ecosystem is an overall unified arrangement of elements of the environment that influence each other in creating balance, order and sustainability. The discourse on environmental conservation has become an actual issue in the midst of the threat of a global crisis as a consequence of disasters, climate change, global warming, erratic seasonal changes, decreased quality of life and the threat of destruction of the earth. This condition triggers the anxiety and worry of mankind about the extinction of the earth. This study will answer how the Koran talks about the environment and its impact on human life. The design of this research is a qualitative type of literature. The data collection technique is the documentation of collecting environmental damage verses. The analysis uses a comparative interpretive, namely examining verses on environmental damage, comparing them, then concluding them through inductive thinking. The results of the study prove that environmental damage is caused by polytheists, hypocrites, greedy and selfish people. Solutions for strengthening monotheism, awareness of environmental law, and moral natural resource management.
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Walworth, Nathan, Ulrike Pfreundt, William C. Nelson, Tracy Mincer, John F. Heidelberg, Feixue Fu, John B. Waterbury, et al. "Trichodesmiumgenome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle." Proceedings of the National Academy of Sciences 112, no. 14 (March 23, 2015): 4251–56. http://dx.doi.org/10.1073/pnas.1422332112.
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Understanding the evolution of the free-living, cyanobacterial, diazotrophTrichodesmiumis of great importance because of its critical role in oceanic biogeochemistry and primary production. Unlike the other >150 available genomes of free-living cyanobacteria, only 63.8% of theTrichodesmium erythraeum(strain IMS101) genome is predicted to encode protein, which is 20–25% less than the average for other cyanobacteria and nonpathogenic, free-living bacteria. We use distinctive isolates and metagenomic data to show that low coding density observed in IMS101 is a common feature of theTrichodesmiumgenus, both in culture and in situ. Transcriptome analysis indicates that 86% of the noncoding space is expressed, although the function of these transcripts is unclear. The density of noncoding, possible regulatory elements predicted inTrichodesmium, when normalized per intergenic kilobase, was comparable and twofold higher than that found in the gene-dense genomes of the sympatric cyanobacterial generaSynechococcusandProchlorococcus, respectively. ConservedTrichodesmiumnoncoding RNA secondary structures were predicted between most culture and metagenomic sequences, lending support to the structural conservation. Conservation of these intergenic regions in spatiotemporally separatedTrichodesmiumpopulations suggests possible genus-wide selection for their maintenance. These large intergenic spacers may have developed during intervals of strong genetic drift caused by periodic blooms of a subset of genotypes, which may have reduced effective population size. Our data suggest that transposition of selfish DNA, low effective population size, and high-fidelity replication allowed the unusual “inflation” of noncoding sequence observed inTrichodesmiumdespite its oligotrophic lifestyle.
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Lee, Gloria, Nicholas A. Sherer, Neil H. Kim, Ema Rajic, Davneet Kaur, Niko Urriola, K. Michael Martini, Chi Xue, Nigel Goldenfeld, and Thomas E. Kuhlman. "Testing the retroelement invasion hypothesis for the emergence of the ancestral eukaryotic cell." Proceedings of the National Academy of Sciences 115, no. 49 (November 19, 2018): 12465–70. http://dx.doi.org/10.1073/pnas.1807709115.
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Phylogenetic evidence suggests that the invasion and proliferation of retroelements, selfish mobile genetic elements that copy and paste themselves within a host genome, was one of the early evolutionary events in the emergence of eukaryotes. Here we test the effects of this event by determining the pressures retroelements exert on simple genomes. We transferred two retroelements, human LINE-1 and the bacterial group II intron Ll.LtrB, into bacteria, and find that both are functional and detrimental to growth. We find, surprisingly, that retroelement lethality and proliferation are enhanced by the ability to perform eukaryotic-like nonhomologous end-joining (NHEJ) DNA repair. We show that the only stable evolutionary consequence in simple cells is maintenance of retroelements in low numbers, suggesting how retrotransposition rates and costs in early eukaryotes could have been constrained to allow proliferation. Our results suggest that the interplay between NHEJ and retroelements may have played a fundamental and previously unappreciated role in facilitating the proliferation of retroelements, elements of which became the ancestors of the spliceosome components in eukaryotes.
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Hutin, Stephanie, Wai Li Ling, Nicolas Tarbouriech, Guy Schoehn, Clemens Grimm, Utz Fischer, and Wim P. Burmeister. "The Vaccinia Virus DNA Helicase Structure from Combined Single-Particle Cryo-Electron Microscopy and AlphaFold2 Prediction." Viruses 14, no. 10 (October 7, 2022): 2206. http://dx.doi.org/10.3390/v14102206.
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Poxviruses are large DNA viruses with a linear double-stranded DNA genome circularized at the extremities. The helicase-primase D5, composed of six identical 90 kDa subunits, is required for DNA replication. D5 consists of a primase fragment flexibly attached to the hexameric C-terminal polypeptide (res. 323–785) with confirmed nucleotide hydrolase and DNA-binding activity but an elusive helicase activity. We determined its structure by single-particle cryo-electron microscopy. It displays an AAA+ helicase core flanked by N- and C-terminal domains. Model building was greatly helped by the predicted structure of D5 using AlphaFold2. The 3.9 Å structure of the N-terminal domain forms a well-defined tight ring while the resolution decreases towards the C-terminus, still allowing the fit of the predicted structure. The N-terminal domain is partially present in papillomavirus E1 and polyomavirus LTA helicases, as well as in a bacteriophage NrS-1 helicase domain, which is also closely related to the AAA+ helicase domain of D5. Using the Pfam domain database, a D5_N domain followed by DUF5906 and Pox_D5 domains could be assigned to the cryo-EM structure, providing the first 3D structures for D5_N and Pox_D5 domains. The same domain organization has been identified in a family of putative helicases from large DNA viruses, bacteriophages, and selfish DNA elements.
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Bozanic, Josko. "Ethics of the Sea – Experience of the Vis Archipelago Fishermen." Colloquia Humanistica, no. 4 (December 31, 2015): 137–46. http://dx.doi.org/10.11649/ch.2015.008.
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Ethics of the Sea – Experience of the Vis Archipelago FishermenThis paper is based on the author's years-long research of the experience of fishermen of the island of Vis, their ethics and mutual relationships in the extreme conditions of fishing at distant open sea islands of the Adriatic where they were continously exposed to pirate attacks, open sea elements, with boats powered by wind or man, in small living quarters of a boat and fiercely competing with each other for survival. In such extreme conditions the only answer to the challenge of survival was mutual solidarity, willingness to help another, the principle of egalitarianism and mutual respect. The author also speaks about the transethnic culture of people living at sea, the phenomenon of the sea as the liquid element which does not divide but rather connects different shores, cultures and languages. He speaks about the insular world whose most important social principle is - work, manufacture as the basis of survival, sacrificing for another and high value of an individual who deserves to be held in esteem through his work and sacrifice as the corrective of selfish interests. Etyka morza – doświadczenie rybaków z wyspy VisArtykuł opiera się na wieloletnich badaniach autora nad doświadczeniem rybaków z wyspy Vis (Chorwacja), ich etyką i wzajemnymi relacjami w trudnych warunkach na odległych wyspach adriatyckich, gdzie nieustannie byli narażeni na ataki piratów, kaprysy otwartego morza; posługiwali się łodziami żaglowymi i wiosłowymi, żyjąc na małej przestrzeni i rywalizując między sobą o przetrwanie. W tak skrajnych warunkach jedynym wyjściem, by przetrwać, była wzajemna solidarność, troska o innego, zasada równości i wzajemny szacunek. Autor mówi też o transetnicznej kulturze ludów żyjących na morzu, zjawisku morza jako płynnego elementu, który nie dzieli, lecz raczej łączy różne brzegi, kultury i języki. Opisuje wyspiarski świat, gdzie najważniejszą zasadą społeczną jest praca, poświęcenie dla innego oraz wysoka wartość jednostki, która zasługuje na szacunek dzięki pracy i ofiarności, łagodzącym indywidualne interesy.
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Igolkina, Anna A., Arsenii Zinkevich, Kristina O. Karandasheva, Aleksey A. Popov, Maria V. Selifanova, Daria Nikolaeva, Victor Tkachev, Dmitry Penzar, Daniil M. Nikitin, and Anton Buzdin. "H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks." Cells 8, no. 9 (September 5, 2019): 1034. http://dx.doi.org/10.3390/cells8091034.
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Background: Transposons are selfish genetic elements that self-reproduce in host DNA. They were active during evolutionary history and now occupy almost half of mammalian genomes. Close insertions of transposons reshaped structure and regulation of many genes considerably. Co-evolution of transposons and host DNA frequently results in the formation of new regulatory regions. Previously we published a concept that the proportion of functional features held by transposons positively correlates with the rate of regulatory evolution of the respective genes. Methods: We ranked human genes and molecular pathways according to their regulatory evolution rates based on high throughput genome-wide data on five histone modifications (H3K4me3, H3K9ac, H3K27ac, H3K27me3, H3K9me3) linked with transposons for five human cell lines. Results: Based on the total of approximately 1.5 million histone tags, we ranked regulatory evolution rates for 25075 human genes and 3121 molecular pathways and identified groups of molecular processes that showed signs of either fast or slow regulatory evolution. However, histone tags showed different regulatory patterns and formed two distinct clusters: promoter/active chromatin tags (H3K4me3, H3K9ac, H3K27ac) vs. heterochromatin tags (H3K27me3, H3K9me3). Conclusion: In humans, transposon-linked histone marks evolved in a coordinated way depending on their functional roles.
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Mukherjee, Ayan. "Sensing Non-sense in Animal Sex From Perspective of Transposable Elements." Animal Reproduction Update 1, no. 2 (2021): 1–9. http://dx.doi.org/10.48165/aru.2021.1201.
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Evolution of vertebrate species took shape through millions of years, where sex played an important role in maintenance of a lineage, genetic diversifications and reproductive isolation. On due course of sexual evolution, sex determination strategies have been proposed to flow from temperature dependent sex determination to genetic sex determination, which has been demonstrated as XY system in mammals and ZW system in birds. In contrary to this established conception, different lineages showed to have overlapping sex determining strategies. While searching possible reasons for these phenomenons, researchers observed that gene content of sex chromosomes is highly variable as far as their location and prevalence is concerned, which otherwise suggested autosomal origin of sex chromosomes. Although the exact mechanisms of gene transfer and thereby origin of sex chromosomes are yet to be unveiled, but chromosomal rearrangement and introgression has been hypothesized to be the possible effector. Transposable elements (TEs) are long been considered to be ‘Selfish’ or ‘Junk’ DNA material as most of the non-coding genomic regions are comprised by TEs, which did not make any sense to be a part of species genome. But recently, TEs are being considered to be a nature’s tool for biological innovation by creating new regulatory elements, new coding sequences, genetic disruption and chromosomal remodelling. So, this has been postulated that TEs could facilitate rearrangement and introgression, which ultimately lead to evolution of sex chromosomes and sex determining genes through positive selection. Prevalence of highly repetitive sequences in sex chromosomes, particularly in Y, makes it a hot bed for TEs mediated rearrangement and introgression. In this review, I tried to discuss whether it makes any sense to focus on the role of TEs in sexual evolution of animals.
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Vihinen, Mauno. "Individual Genetic Heterogeneity." Genes 13, no. 9 (September 10, 2022): 1626. http://dx.doi.org/10.3390/genes13091626.
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Genetic variation has been widely covered in literature, however, not from the perspective of an individual in any species. Here, a synthesis of genetic concepts and variations relevant for individual genetic constitution is provided. All the different levels of genetic information and variation are covered, ranging from whether an organism is unmixed or hybrid, has variations in genome, chromosomes, and more locally in DNA regions, to epigenetic variants or alterations in selfish genetic elements. Genetic constitution and heterogeneity of microbiota are highly relevant for health and wellbeing of an individual. Mutation rates vary widely for variation types, e.g., due to the sequence context. Genetic information guides numerous aspects in organisms. Types of inheritance, whether Mendelian or non-Mendelian, zygosity, sexual reproduction, and sex determination are covered. Functions of DNA and functional effects of variations are introduced, along with mechanism that reduce and modulate functional effects, including TARAR countermeasures and intraindividual genetic conflict. TARAR countermeasures for tolerance, avoidance, repair, attenuation, and resistance are essential for life, integrity of genetic information, and gene expression. The genetic composition, effects of variations, and their expression are considered also in diseases and personalized medicine. The text synthesizes knowledge and insight on individual genetic heterogeneity and organizes and systematizes the central concepts.
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Bastiaans, E., D. K. Aanen, A. J. M. Debets, R. F. Hoekstra, B. Lestrade, and M. F. P. M. Maas. "Regular bottlenecks and restrictions to somatic fusion prevent the accumulation of mitochondrial defects in Neurospora." Philosophical Transactions of the Royal Society B: Biological Sciences 369, no. 1646 (July 5, 2014): 20130448. http://dx.doi.org/10.1098/rstb.2013.0448.
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The replication and segregation of multi-copy mitochondrial DNA (mtDNA) are not under strict control of the nuclear DNA. Within-cell selection may thus favour variants with an intracellular selective advantage but a detrimental effect on cell fitness. High relatedness among the mtDNA variants of an individual is predicted to disfavour such deleterious selfish genetic elements, but experimental evidence for this hypothesis is scarce. We studied the effect of mtDNA relatedness on the opportunities for suppressive mtDNA variants in the fungus Neurospora carrying the mitochondrial mutator plasmid pKALILO. During growth, this plasmid integrates into the mitochondrial genome, generating suppressive mtDNA variants. These mtDNA variants gradually replace the wild-type mtDNA, ultimately culminating in growth arrest and death. We show that regular sequestration of mtDNA variation is required for effective selection against suppressive mtDNA variants. First, bottlenecks in the number of mtDNA copies from which a ‘ Kalilo ’ culture started significantly increased the maximum lifespan and variation in lifespan among cultures. Second, restrictions to somatic fusion among fungal individuals, either by using anastomosis-deficient mutants or by generating allotype diversity, prevented the accumulation of suppressive mtDNA variants. We discuss the implications of these results for the somatic accumulation of mitochondrial defects during ageing.