Статті в журналах: "Insertion elements"

1

Olmeda-López, Héctor, Andrés Corral-Lugo, and Michael J. McConnell. "Effect of Subinhibitory Concentrations of Antibiotics and Disinfectants on ISAba-Mediated Inactivation of Lipooligosaccharide Biosynthesis Genes in Acinetobacter baumannii." Antibiotics 10, no. 10 (October 16, 2021): 1259. http://dx.doi.org/10.3390/antibiotics10101259.

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Inactivation of the lipooligosaccharide (LOS) biosynthesis genes lpxA, lpxC and lpxD by ISAba insertion elements results in high-level resistance to colistin in A. baumannii. In the present study, we quantify the rate of spontaneous insertional inactivation of LOS biosynthesis genes by ISAba elements in the ATCC 19606-type strain and two multidrug clinical isolates. Using insertional inactivation of lpxC by ISAba11 in the ATCC 19606 strain as a model, we determine the effect of several subinhibitory concentrations of the antibiotics, namely tetracycline, ciprofloxacin, meropenem, kanamycin and rifampicin, as well as the disinfectants ethanol and chlorhexidine on ISAba11 insertion frequencies. Notably, subinhibitory concentrations of tetracycline significantly increased ISAba11 insertion, and rifampicin completely inhibited the emergence of colistin resistance due to ISAba11 inactivation of lpxC. Sequencing of ISAba11 insertion sites within the lpxC gene demonstrated that insertions clustered between nucleotides 382 and 618 (58.3% of unique insertions detected), indicating that this may be a hotspot for ISAba11 insertion. The alignment of insertion sites revealed a semi-conserved AT-rich consensus sequence upstream of the ISAba11 insertion site, suggesting that ISAba11 insertion sites may be sequence-dependent. This study explores previously uncharacterized aspects regarding the acquisition of colistin resistance through insertional activation in LOS biosynthesis genes in A. baumannii.

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2

Vieira, C., and C. Biémont. "Selection against transposable elements in D. simulans and D. melanogaster." Genetical Research 68, no. 1 (August 1996): 9–15. http://dx.doi.org/10.1017/s0016672300033838.

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SummaryThe insertion site numbers of the transposable elements (TEs) copia, mdgl, 412 and gypsy were determined in various natural populations of Drosophila melanogaster and D. simulans by in situ hybridization. We showed that, while all elements except gypsy had many insertion sites scattered over the chromosomes in D. melanogaster, only the 412 element in D. simulans presented a high number of insertions, and this number was lower than in D. melanogaster. This low 412 site number per genome in D. simulans was associated with a lower proportion of insertions on the X chromosome in comparison with D. melanogaster, as determined in diploid genomes (0·090 for D. simulans against 0·137 for D. melanogaster) and in haploid genomes (0·102 against 0·146), each value being, moreover, lower than the value of 0·20 expected on the hypothesis of no selection against insertional mutations. These results suggest that selection is a major mechanism explaining 412 copy number regulation in Drosophila, and is stronger in D. simulans than in D. melanogaster.

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3

Hoogland, Christine, and Christian Biémont. "Chromosomal Distribution of Transposable Elements in Drosophila melanogaster Test of the Ectopic Recombination Model for Maintenance of Insertion Site Number." Genetics 144, no. 1 (September 1, 1996): 197–204. http://dx.doi.org/10.1093/genetics/144.1.197.

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Abstract Data of insertion site localization and site occupancy frequency of P, hobo, I, copia, mdg1, mdg3, 412, 297, and roo transposable elements (TEs) on the polytene chromosomes of Drosophila melanogaster were extracted from the literature. We show that TE insertion site number per chromosomal division was significantly correlated with the amount of DNA. The insertion site number weighted by DNA content was not correlated with recombination rate for all TEs except hobo, for which a positive correlation was detected. No global tendency emerged in the relationship between TE site occupancy frequency, weighted by DNA content, and recombination rate; a strong negative correlation was, however, found for the 3L arm. A possible dominant deleterious effect of chromosomal rearrangements due to recombination between TE insertions is thus not the main factor explaining the dynamics of TEs, since this hypothesis implies a negative relationship between recombination rate and both TE insertion site number and site occupancy frequency. The alternative hypothesis of selection against deleterious effects of insertional mutations is discussed.

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4

Carlson, Corey M., Adam J. Dupuy, Sabine Fritz, Kevin J. Roberg-Perez, Colin F. Fletcher, and David A. Largaespada. "Transposon Mutagenesis of the Mouse Germline." Genetics 165, no. 1 (September 1, 2003): 243–56. http://dx.doi.org/10.1093/genetics/165.1.243.

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Abstract Sleeping Beauty is a synthetic “cut-and-paste” transposon of the Tc1/mariner class. The Sleeping Beauty transposase (SB) was constructed on the basis of a consensus sequence obtained from an alignment of 12 remnant elements cloned from the genomes of eight different fish species. Transposition of Sleeping Beauty elements has been observed in cultured cells, hepatocytes of adult mice, one-cell mouse embryos, and the germline of mice. SB has potential as a random germline insertional mutagen useful for in vivo gene trapping in mice. Previous work in our lab has demonstrated transposition in the male germline of mice and transmission of novel inserted transposons in offspring. To determine sequence preferences and mutagenicity of SB-mediated transposition, we cloned and analyzed 44 gene-trap transposon insertion sites from a panel of 30 mice. The distribution and sequence content flanking these cloned insertion sites was compared to 44 mock insertion sites randomly selected from the genome. We find that germline SB transposon insertion sites are AT-rich and the sequence ANNTANNT is favored compared to other TA dinucleotides. Local transposition occurs with insertions closely linked to the donor site roughly one-third of the time. We find that ∼27% of the transposon insertions are in transcription units. Finally, we characterize an embryonic lethal mutation caused by endogenous splicing disruption in mice carrying a particular intron-inserted gene-trap transposon.

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5

Hesselbarth, Judith, Christiane Werckenthin, Babett Liebisch, and S. Schwarz. "Insertion elements in Staphylococcus intermedius." Letters in Applied Microbiology 20, no. 3 (March 1995): 180–83. http://dx.doi.org/10.1111/j.1472-765x.1995.tb00421.x.

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6

LADEVEZE, VERONIQUE, IBO GALINDO, NICOLE CHAMINADE, LUIS PASCUAL, GEORGES PERIQUET, and FRANCOISE LEMEUNIER. "Transmission pattern of hobo transposable element in transgenic lines of Drosophila melanogaster." Genetical Research 71, no. 2 (April 1998): 97–107. http://dx.doi.org/10.1017/s0016672398003127.

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This study is an attempt to trace the fate of hobo elements in the genomes of E strains of Drosophila melanogaster that have been transfected with pHFL1, a plasmid containing an autonomous hobo. Such long-term population studies (over 105 generations) could be very useful for better understanding the population and genomic dynamics of transposable elements and their pattern of insertions. Molecular analyses of hobo elements in the transfected lines were performed using Southern blots of XhoI-digested genomic DNAs. The complete element was observed in all six injected lines. In two lines we observed, at generation 100, two deleted elements, which did not correspond to Th1 and Th2. The results obtained by the in situ method show that the number of hybridization sites increases in each line and prove that the hobo element may be amplified in an RM genome. The hobo activity does not seem to be systematically correlated with the number of hobo elements. After generation 85, the evolution of the hobo element's insertion site number depends on the injected line. In all lines, the total number of insertions remains quite small, between 0 and 11. Hobo elements are located on each of the chromosomal arms. We describe ‘hotspots’ – insertion sites present in all lines and in all generations. On the 3R arm, a short inversion appeared once at generation 85.

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7

Appelt, Jens U., Frank A. Giordano, Marcel Zimmermann, Stephan Weinhard, Nadja Grund, Agnes Hotz-Wagenblatt, W. Jens Zeller, Heike Allgayer, Stefan Fruehauf, and Stephanie Laufs. "Genes Involved in Acute Leukemias Are Favored Targets of HIV Vector Integration." Blood 110, no. 11 (November 16, 2007): 3738. http://dx.doi.org/10.1182/blood.v110.11.3738.3738.

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Abstract Insertional mutagenesis and development of leukemia following retroviral gene therapy has created intense interest in assessing the safety of viral vectors for further gene therapy trials. Using the gtsg.org database we analyzed more than 14,900 different viral integration sites of ASLV, FIV, FV, HIV, MLV and SIV based vectors in terms of insertions into fragile sites, cancer genes, transcription factor binding sites, CpG islands, and repetitive elements (SINE, LINE, LTR elements). When we compared these data with our newly generated random set, containing 1,000,000 random integrations, we discovered that the gene density on fragile sites strongly correlates to the HIV vector insertion frequency. Furthermore, we report a up to a five fold increased frequency of HIV, MLV and SIV insertions in cancer genes. The majority of cancer genes preferentially hit by HIV viruses were found associated to acute leukemias, while MLV and SIV vector insertion sites are seen more evenly spread over the cancer gene repertoire. When analyzing different cell entities, it turned out that CD34+ hematopoetic stem cells had highest rates of intragenic insertions and hosted significantly more HIV and FV insertions in cancer genes than other cell types, such as HeLa, T cells, 293T cells, macrophages, fibroblasts, or SupT1 cells.

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8

Vincent, A., and T. D. Petes. "Mitotic and meiotic gene conversion of Ty elements and other insertions in Saccharomyces cerevisiae." Genetics 122, no. 4 (August 1, 1989): 759–72. http://dx.doi.org/10.1093/genetics/122.4.759.

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Abstract We examined meiotic and mitotic gene conversion events involved in deletion of Ty elements and other insertions from the genome of the yeast Saccharomyces cerevisiae. We found that Ty elements and one other insertion were deleted by mitotic gene conversion less frequently than point mutations at the same loci. One non-Ty insertion similar in size to Ty, however, did not show this bias. Mitotic conversion events deleting insertions were more frequently associated with crossing over than those deleting point mutations. In meiosis, conversion events duplicating the element were more common than those that deleted the element for one of the loci (HIS4) examined.

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9

Haandrikman, A. J., C. van Leeuwen, J. Kok, P. Vos, W. M. de Vos, and G. Venema. "Insertion elements on lactococcal proteinase plasmids." Applied and Environmental Microbiology 56, no. 6 (1990): 1890–96. http://dx.doi.org/10.1128/aem.56.6.1890-1896.1990.

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10

Aigner, Martin, and Douglas B. West. "Sorting by insertion of leading elements." Journal of Combinatorial Theory, Series A 45, no. 2 (July 1987): 306–9. http://dx.doi.org/10.1016/0097-3165(87)90022-7.

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11

Eraclio, Giovanni, Giovanni Ricci, and Maria Grazia Fortina. "Insertion sequence elements in Lactococcus garvieae." Gene 555, no. 2 (January 2015): 291–96. http://dx.doi.org/10.1016/j.gene.2014.11.019.

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12

Hargrove, Phillip W., Steven Kepes, Hideki Hanawa, Cheng Cheng, Geoff Neale, Arthur W. Nienhuis, and Derek A. Persons. "Assessment of Changes in Gene Expression Caused by Insertions of a Globin Lentiviral Vector Containing Globin Regulatory Elements or a Lentiviral Vector Containing Retroviral LTR Elements." Blood 104, no. 11 (November 16, 2004): 497. http://dx.doi.org/10.1182/blood.v104.11.497.497.

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Abstract The development of lymphoid leukemia in two children with X-SCID who underwent gene therapy was partially due to activation of the LMO-2 proto-oncogene by the retroviral LTR of the vector which inserted nearby (Hacein-Bey-Abina et al., Science 2003), highlighting the importance of vector design on the potential to activate genes near vector integration sites. As gene therapy vectors for other blood disorders are evaluated, it seems prudent to assess the safety issues regarding insertion for each particular vector in appropriate pre-clinical models. We have focused on developing γ-globin lentiviral vectors for gene therapy of the hemoglobin disorders and have documented correction of a murine model of β-thalassemia in the absence of observable adverse events (Persons et al., Blood 2003; Hanawa et al., Blood 2004). To more thoroughly evaluate the potential for vector-induced genotoxicity, we have examined whether self-inactivating (SIN) γ-globin lentiviral vectors containing erythroid-specific, β-globin locus enhancer elements can alter the expression of genes nearby the vector insertion site, as the retroviral LTR did in the X-SCID trial. To ascertain whether an integrated globin vector could influence endogenous transcriptional activity in erythroid precursors, 15 clonal spleen colony erythroblast populations (≥ 95% erythroid) containing lentiviral globin vector insertions and 15 untransduced control clones were derived from bone marrow cells of β-thalassemic mice. The transcriptional profile of each clone was determined using the Affymetrix Mouse 430A microarray (representing ~15,000 genes). Expression of 4500–6000 genes was observed in all samples. Ligation-mediated PCR was used to obtain the vector-genomic DNA junction sequences, allowing identification of vector insertion locations in 13 of the clones using the NCBI database. Of these, 6 globin vector clones had 16 genes, including N-ras, which were located within 100kb of the vector insertion site and were represented on the array. Only one gene, D3Jfr1, encoding a “cold shock” DNA binding protein and which was disrupted by an intronic vector insertion, had a change in signal value relative to the mean signal value of the controls. Real time RT-PCR confirmed a 4-fold reduction in expression of this gene. Both microarray and real time RT-PCR demonstrated that expression of N-ras was unchanged. For comparison, 15 clones with insertions of a lentiviral vector containing the MSCV retroviral LTR, were also derived, along with 10 additional mock control clones. We are currently analyzing the expression of some 116 genes that lie within 300kb of the vector insertions, relative to the mean expression level in the 25 mock transduced clones. Additionally, we have expanded analysis of the globin vector clones to evaluate changes in expression of 107 genes located within 300kb of the vector insertions. These data should prove useful to assess whether integrated SIN globin lentiviral vectors containing erythroid-specific regulatory elements have a propensity to alter transcriptional activity in the progeny of genetically modified hematopoietic stem cells, relative to vectors containing viral LTR elements.

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13

Eanes, Walter F., Cedric Wesley, Jody Hey, David Houle, and James W. Ajioka. "The fitness consequences of P element insertion in Drosophila melanogaster." Genetical Research 52, no. 1 (August 1988): 17–26. http://dx.doi.org/10.1017/s0016672300027269.

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SummaryIn this study we estimate the frequency at which P-element insertion events, as identified by in situ hybridization, generate lethal and mild viability mutations. The frequency of lethal mutations generated per insertion event was 0·004. Viability dropped an average of 1% per insertion event. Our results indicate that it is deletions and rearrangements resulting from the mobilization of P elements already in place and not the insertions per se that cause the drastic effects on viability and fitness observed in most studies of P–M dysgenesis-derived mutations. Elements of five other families (I, copia, 412, B104, and gypsy) were not mobilized in these crosses. Finally, we contrast the density of P elements on the X chromosome with the density on the four autosomal arms in a collection of thirty genomes from an African population. The relative number of P elements on the X chromosome is too high to be explained by either a hemizygous selection or a neutrality model. The possible reasons for the failure to detect selection are discussed.

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14

Roseman, R. R., E. A. Johnson, C. K. Rodesch, M. Bjerke, R. N. Nagoshi, and P. K. Geyer. "A P element containing suppressor of hairy-wing binding regions has novel properties for mutagenesis in Drosophila melanogaster." Genetics 141, no. 3 (November 1, 1995): 1061–74. http://dx.doi.org/10.1093/genetics/141.3.1061.

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Abstract P elements are widely used as insertional mutagens to tag genes, facilitating molecular cloning and analyses. We modified a P element so that it carried two copies of the suppressor of Hairy-wing [su(Hw)] binding regions isolated from the gypsy transposable element. This transposon was mobilized, and the genetic consequences of its insertion were analyzed. Gene expression can be altered by the su(Hw) protein as a result of blocking the interaction between enhancer/silencer elements and their promoter. These effects can occur over long distances and are general. Therefore, a composite transposon (SUPor-P for suppressor-P element) combines the mutagenic efficacy of the gypsy element with the controllable transposition of P elements. We show that, compared to standard P elements, this composite transposon causes an expanded repertoire of mutations and produces alleles that are suppressed by su(Hw) mutations. The large number of heterochromatic insertions obtained is unusual compared to other insertional mutagenesis procedures, indicating that the SUPor-P transposon may be useful for studying the structural and functional properties of heterochromatin.

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15

Zidi, Marwa, Khouloud Klai, Johann Confais, Benoît Chénais, Aurore Caruso, Françoise Denis, Maha Khemakhem, and Nathalie Casse. "Genome-Wide Screening of Transposable Elements in the Whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae), Revealed Insertions with Potential Insecticide Resistance Implications." Insects 13, no. 5 (April 19, 2022): 396. http://dx.doi.org/10.3390/insects13050396.

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Transposable elements (TEs) are genetically mobile units that move from one site to another within a genome. These units can mediate regulatory changes that can result in massive changes in genes expression. In fact, a precise identification of TEs can allow the detection of the mechanisms involving these elements in gene regulation and genome evolution. In the present study, a genome-wide analysis of the Hemipteran pest Bemisia tabaci was conducted using bioinformatics tools to identify, annotate and estimate the age of TEs, in addition to their insertion sites, within or near of the defensome genes involved in insecticide resistance. Overall, 1,292,393 TE copies were identified in the B. tabaci genome grouped into 4872 lineages. A total of 699 lineages were found to belong to Class I of TEs, 1348 belong to Class II, and 2825 were uncategorized and form the largest part of TEs (28.81%). The TE age estimation revealed that the oldest TEs invasion happened 14 million years ago (MYA) and the most recent occurred 0.2 MYA with the insertion of Class II TE elements. The analysis of TE insertion sites in defensome genes revealed 94 insertions. Six of these TE insertions were found within or near previously identified differentially expressed insecticide resistance genes. These insertions may have a potential role in the observed insecticide resistance in these pests.

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16

Chen, Jiann-Hwa, Wen-Ben Hsu, and Jiing-Luen Hwang. "Two Amino Acid Residues of Transposase Contributing to Differential Transposability of IS1 Elements inEscherichia coli." Journal of Bacteriology 180, no. 19 (October 1, 1998): 5279–83. http://dx.doi.org/10.1128/jb.180.19.5279-5283.1998.

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ABSTRACT Escherichia coli W3110 contains four types of IS1 elements in the chromosome. Using an insertion element entrapping system, we collected 116 IS1 plasmid insertion mutants, which resulted from a minimum of 26 independent IS1 insertion events. All of them had insertions of IS1 of the IS1A (IS1E and IS1G) type. Inspection of the transposase sequences of the four IS1 types and the IS1 of the resistance plasmid R100 showed that two amino acid residues, His-193 and Leu-217 of transposase, might contribute to differential transposability of IS1 elements in W3110. The two amino acid residues of the transposase in IS1A (IS1E and IS1G) were altered separately by site-directed mutagenesis, and each mutant was found to mediate transposition at a frequency about 30-fold lower than that of IS1A (IS1E and IS1G). Thus, the assumption that His-193 and Leu-217 of transposase contribute to differential transposability of IS1 elements in W3110 was confirmed.

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17

Mahillon, Jacques, and Michael Chandler. "Insertion Sequences." Microbiology and Molecular Biology Reviews 62, no. 3 (September 1, 1998): 725–74. http://dx.doi.org/10.1128/mmbr.62.3.725-774.1998.

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SUMMARY Insertion sequences (ISs) constitute an important component of most bacterial genomes. Over 500 individual ISs have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. The last 10 years have also seen some striking advances in our understanding of the transposition process itself. Not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic elements and, for several of these, a detailed understanding of the transposition process at the chemical level. This review presents a general overview of the organization and function of insertion sequences of eubacterial, archaebacterial, and eukaryotic origins with particular emphasis on bacterial elements and on different aspects of the transposition mechanism. It also attempts to provide a framework for classification of these elements by assigning them to various families or groups. A total of 443 members of the collection have been grouped in 17 families based on combinations of the following criteria: (i) similarities in genetic organization (arrangement of open reading frames); (ii) marked identities or similarities in the enzymes which mediate the transposition reactions, the recombinases/transposases (Tpases); (iii) similar features of their ends (terminal IRs); and (iv) fate of the nucleotide sequence of their target sites (generation of a direct target duplication of determined length). A brief description of the mechanism(s) involved in the mobility of individual ISs in each family and of the structure-function relationships of the individual Tpases is included where available.

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18

Natsoulis, G., W. Thomas, M. C. Roghmann, F. Winston, and J. D. Boeke. "Ty1 transposition in Saccharomyces cerevisiae is nonrandom." Genetics 123, no. 2 (October 1, 1989): 269–79. http://dx.doi.org/10.1093/genetics/123.2.269.

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Abstract A large collection of Ty1 insertions in the URA3 and LYS2 loci was generated using a GAL1-Ty1 fusion to augment the transposition frequency. The sites of insertion of most of these Ty elements were sequenced. There appears to be a gradient of frequency of insertion from the 5' end (highest frequency) to the 3' end (lowest frequency) of both loci. In addition we observed hotspots for transposition. Twelve of the 82 Ty1 insertions in the URA3 locus were inserted in exactly the same site. Hotspots were also observed in the LYS2 locus. All hotspots were in the transcribed part of the genes. Alignment of the sites of insertion and of the neighboring sequences only reveals very weak sequence similarities.

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19

Dalby, B., A. J. Pereira, and L. S. Goldstein. "An inverse PCR screen for the detection of P element insertions in cloned genomic intervals in Drosophila melanogaster." Genetics 139, no. 2 (February 1, 1995): 757–66. http://dx.doi.org/10.1093/genetics/139.2.757.

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Abstract We developed a screening approach that utilizes an inverse polymerase chain reaction (PCR) to detect P element insertions in or near previously cloned genes in Drosophila melanogaster. We used this approach in a large scale genetic screen in which P elements were mobilized from sites on the X chromosome to new autosomal locations. Mutagenized flies were combined in pools, and our screening approach was used to generate probes corresponding to the sequences flanking each site of insertion. These probes then were used for hybridization to cloned genomic intervals, allowing individuals carrying insertions in them to be detected. We used the same approach to perform repeated rounds of sib-selection to generate stable insertion lines. We screened 16,100 insert bearing individuals and recovered 11 insertions in five intervals containing genes encoding members of the kinesin superfamily in Drosophila melanogaster. In addition, we recovered an insertion in the region including the Larval Serum Protein-2 gene. Examination by Southern hybridization confirms that the lines we recovered represent genuine insertions in the corresponding genomic intervals. Our data indicates that this approach will be very efficient both for P element mutagenesis of new genomic regions and for detection and recovery of "local" P element transposition events. In addition, our data constitutes a survey of preferred P element insertion sites in the Drosophila genome and suggests that insertion sites that are mutable at a rate of approximately 10(-4) are distributed every 40-50 kb.

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20

Baek, Jin-Eon, Woo-Young Chin, Ji-Woong Choi, Tae-Hyun Eom, Young-Cheol Jeon, and Yang Lee. "INSERTION-OF-FACTORS-PROPERTY ON NILPOTENT ELEMENTS." Bulletin of the Korean Mathematical Society 49, no. 2 (March 31, 2012): 381–94. http://dx.doi.org/10.4134/bkms.2012.49.2.381.

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21

Naas, T. "S2 Insertion sequences, transposons and repeated elements." International Journal of Antimicrobial Agents 29 (March 2007): S1. http://dx.doi.org/10.1016/s0924-8579(07)70008-0.

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22

Aprianto, Dedi, and I. Nyoman Subudiartha. "INSERTING THE SASAKNESE LOCAL WISDOMS IN ENGLISH CURRICULUM DEVELOPMENT FOR VOCATIONAL HIGH SCHOOLS." EXPOSURE : JURNAL PENDIDIKAN BAHASA INGGRIS 9, no. 2 (November 15, 2020): 352–69. http://dx.doi.org/10.26618/exposure.v9i2.4194.

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This study is the process of English curriculum development aims at analyzing the targets needs, learning needs, and the patterns of local wisdom insertion. This study was conducted through Focused Group Discussion (FGD), semi-structured interview, and content analsysis were used for 12 vocational school teachers and 2 officals of the state and private government institutions (The Department of Education and Culture, NTB Province the Institute of ROWOT Nusantara Lombok). Necessity, the results of the target need analysis on local knowledge and language competence for developing skills and abilities, needs based, and contextual learning. Lacks, the gaps as the fundamental problems elicited from the current curriculum. Wants, the students’ desire to knowledge and vocational background-based curriculum contents. English learning design is associated with tourism competencies embedded with local wisdoms. The local wisdoms’ elements which can be developed into the English curriculum, that is, values of knowledge, social norms, and cultural acculturations, the marriage systems, patterns of family, and the other social cultural activities, and the elements of aesthetics. The patterns of insertion can be done through designing with paradigm of pedagogical orientation, insertion models, insertions in content of materials designed by developing the language skills, the use of teaching-learning methods with local insertions, developing student exercises-based insertions.

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23

DÍAZ-GONZÁLEZ, JULIA, J. FERNANDO VÁZQUEZ, JESÚS ALBORNOZ, and ANA DOMÍNGUEZ. "Long-term evolution of the roo transposable element copy number in mutation accumulation lines of Drosophila melanogaster." Genetics Research 93, no. 3 (May 6, 2011): 181–87. http://dx.doi.org/10.1017/s0016672311000103.

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SummaryThe rate of insertion of transposable elements (TEs) is a fundamental parameter to understand both their dynamics and role in the evolution of the eukaryotic genome. Nonetheless, direct estimates of insertion rates are scarce because transposition is in general a rare phenomenon. A great deal of our previous work on transposition was based on a set of long-term mutation accumulation (MA) lines of Drosophila melanogaster started in 1987 (Oviedo lines), where roo was found highly active, with a rate of insertion of 7×10−4 insertions per element and generation, as compared with other 15 TE families that presented transposition rates around 10−5. Here, we study the evolution of the roo transposition rate, by in situ hybridization, after 60–75 additional generations of MA in two subsets of the Oviedo lines, O and O′, which had achieved average numbers of roo insertions of 77 and 84, respectively. In the O lines, insertions accumulated at a rate that remained constant (7×10−4 insertions per element and generation); however, the subset of lines O′ showed a lower accumulation rate of 4×10−4 insertions per element per generation, suggesting a regulation of transposition that depends on the number of elements. However, one of the O′ lines reached a number of 103 insertions, departing from the group mean by 4·6 sd, and showing that it escapes regulation. Hence, ‘de novo’ mutations affecting the regulation of transposition are relatively common. These results are discussed in relation to the possible mechanisms of containment of TEs.

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24

Lauermann, Vit, Monika Hermankova, and Jef D. Boeke. "Increased Length of Long Terminal Repeats Inhibits Ty1 Transposition and Leads to the Formation of Tandem Multimers." Genetics 145, no. 4 (April 1, 1997): 911–22. http://dx.doi.org/10.1093/genetics/145.4.911.

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The Ty1 retrotransposon of Saccharomyces cerevisiae is bounded by long-terminal repeats (LTRs). We have constructed a variety of Ty1 elements in which the LTR length has been increased from the normal length of 334 bp to >2 kb. Although small insertions in the LTR have minimal effects on transposition frequency, larger insertions dramatically reduce it. Nevertheless, elements with long LTRs are incorporated into the genome at a low frequency. Most of these rare insertion events represent Ty1 tandem (head to tail) multimers.

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25

Ajioka, James W., and Walter F. Eanes. "The accumulation of P-elements on the tip of the X chromosome in populations of Drosophila melanogaster." Genetical Research 53, no. 1 (February 1989): 1–6. http://dx.doi.org/10.1017/s0016672300027798.

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SummaryLittle information exists about the mechanisms that determine the fate of mobile elements in natural populations. In this study we catalogue the distribution of 638 P-elements across 114 X chromosomes in samples drawn from three natural populations of Drosophila melanogaster. There is an extremely high occurrence of elements at the tip relative to the rest of the euchromatic chromosome. We demonstrate that the distribution of de novo insertions of the P-element on a specific laboratory chromosome is markedly different; no P-elements were recovered at the tip in the 243 insertion events recorded. In contrast, insertion data for the π2 chromosome suggests an elevated rate associated with the tip site although it does not appear sufficient to explain the large differential accumulation on wild chromosomes. This raises the issue of inter chromosome (or tip) variation in relative rates, as well as the possibility that rates of elimination are lower at the tip.

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26

Chalker, D. L., and S. B. Sandmeyer. "Transfer RNA genes are genomic targets for de Novo transposition of the yeast retrotransposon Ty3." Genetics 126, no. 4 (December 1, 1990): 837–50. http://dx.doi.org/10.1093/genetics/126.4.837.

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Abstract Insertions of the yeast element Ty3 resulting from induced retrotransposition were characterized in order to identify the genomic targets of transposition. The DNA sequences of the junctions between Ty3 and flanking DNA were determined for two insertions of an unmarked element. Each insertion was at position -17 from the 5' end of a tRNA-coding sequence. Ninety-one independent insertions of a marked Ty3 element were studied by Southern blot analysis. Pairs of independent insertions into seven genomic loci accounted for 14 of these insertions. The DNA sequence flanking the insertion site was determined for at least one member of each pair of integrated elements. In each case, insertion was at position -16 or -17 relative to the 5' end of one of seven different tRNA genes. This proportion of genomic loci used twice for Ty3 integration is consistent with that predicted by a Poisson distribution for a number of genomic targets roughly equivalent to the estimated number of yeast tRNA genes. In addition, insertions upstream of the same tRNA gene in one case were at different positions, but in all cases were in the same orientation. Thus, genomic insertions of Ty3 in a particular orientation are apparently specified by the target, while the actual position of the insertion relative to the tRNA-coding sequence can vary slightly.

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27

Staddon, Jack H., Edward M. Bryan, Dawn A. Manias, and Gary M. Dunny. "Conserved Target for Group II Intron Insertion in Relaxase Genes of Conjugative Elements of Gram-Positive Bacteria." Journal of Bacteriology 186, no. 8 (April 15, 2004): 2393–401. http://dx.doi.org/10.1128/jb.186.8.2393-2401.2004.

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ABSTRACT The lactococcal group II intron Ll.ltrB interrupts the ltrB relaxase gene within a region that encodes a conserved functional domain. Nucleotides essential for the homing of Ll.ltrB into an intronless version of ltrB are found exclusively at positions required to encode amino acids broadly conserved in a family of relaxase proteins of gram-positive bacteria. Two of these relaxase genes, pcfG from the enterococcal plasmid pCF10 and the ORF4 gene in the streptococcal conjugative transposon Tn5252, were shown to support Ll.ltrB insertion into the conserved motif at precisely the site predicted by sequence homology with ltrB. Insertion occurred through a mechanism indistinguishable from retrohoming. Splicing and retention of conjugative function was demonstrated for pCF10 derivatives containing intron insertions. Ll.ltrB targeting of a conserved motif of a conjugative element suggests a mechanism for group II intron dispersal among bacteria. Additional support for this mechanism comes from sequence analysis of the insertion sites of the E.c.I4 family of bacterial group II introns.

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28

Wuitschick, Jeffrey D., Paul R. Lindstrom, Alison E. Meyer, and Kathleen M. Karrer. "Homing Endonucleases Encoded by Germ Line-Limited Genes in Tetrahymena thermophila Have APETELA2 DNA Binding Domains." Eukaryotic Cell 3, no. 3 (June 2004): 685–94. http://dx.doi.org/10.1128/ec.3.3.685-694.2004.

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ABSTRACT Three insertion elements were previously found in a family of germ line-limited mobile elements, the Tlr elements, in the ciliate Tetrahymena. Each of the insertions contains an open reading frame (ORF). Sequence analysis of the deduced proteins encoded by the elements suggests that they are homing endonucleases. The genes are designated TIE1-1, TIE2-1, and TIE3-1 for Tetrahymena insertion-homing endonuclease. The endonuclease motif occupies the amino terminal half of each TIE protein. The C-terminal regions of the proteins are similar to the APETELA2 DNA binding domain of plant transcription factors. The TIE1 and TIE3 elements belong to families of repeated sequences in the germ line micronuclear genome. Comparison of the genes and the deduced proteins they encode suggests that there are at least two distinct families of homing endonuclease genes, each of which appears to be preferentially associated with a specific region of the Tlr elements. The TIE1 and TIE3 elements and their cognates undergo programmed elimination from the developing somatic macronucleus of Tetrahymena. The possible role of homing endonuclease-like genes in the DNA breakage step in developmentally programmed DNA elimination in Tetrahymena is discussed.

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29

Woodford, Neil, Antoinette-Mary A. Adebiyi, Marie-France I. Palepou, and Barry D. Cookson. "Diversity of VanA Glycopeptide Resistance Elements in Enterococci from Humans and Nonhuman Sources." Antimicrobial Agents and Chemotherapy 42, no. 3 (March 1, 1998): 502–8. http://dx.doi.org/10.1128/aac.42.3.502.

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ABSTRACT Elements mediating VanA glycopeptide resistance in 106 diverse enterococci from humans and nonhuman sources were compared with the prototype VanA transposon, Tn1546, in Enterococcus faecium BM4147. The isolates included 64 from individual patients at 15 hospitals in the United Kingdom (isolated between 1987 and 1996) and 42 from nonhuman sources in the United Kingdom (27 from raw meat, 7 from animal feces, and 8 from sewage). VanA elements were assigned to 24 groups (designated groups A to X) with primers that amplified 10 overlapping fragments of Tn1546. Ten groups of elements were found only in human enterococci, eight groups of elements were unique to nonhuman strains, and six groups of elements were common in enterococci from all sources. Elements indistinguishable from Tn1546 (group A) were observed more frequently in enterococci from nonhuman sources (34 versus 9%) but were identified in enterococci that caused outbreaks in hospital patients between 1987 and 1995. The most common group found in human enterococci (group H; 33%) was rarely observed in enterococci from other sources (5%). Group H elements differed from Tn1546 in three regions and included a novel insertion sequence, designated IS1542, between orf2 and vanR. The VanA elements of 14 other groups had a similar insertion at this position and/or distinct insertions at other positions. We conclude that VanA elements in enterococci are heterogeneous, although all show regions of homology with Tn1546. Furthermore, the elements most common among the human and nonhuman enterococci studied were different. This approach may be useful for monitoring the evolution of VanA resistance and may also be applicable in local “snapshot” epidemiological studies. However, as transposition events involving insertion sequences accounted for the differences observed between several groups, the stability of the elements must be assessed before their true epidemiological significance can be determined.

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30

Storer, Jessica M., Jerilyn A. Walker, Catherine E. Rockwell, Grayce Mores, Thomas O. Beckstrom, Joseph D. Orkin, Amanda D. Melin, Kimberley A. Phillips, Christian Roos, and Mark A. Batzer. "Recently Integrated Alu Elements in Capuchin Monkeys: A Resource for Cebus/Sapajus Genomics." Genes 13, no. 4 (March 24, 2022): 572. http://dx.doi.org/10.3390/genes13040572.

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Capuchins are platyrrhines (monkeys found in the Americas) within the Cebidae family. For most of their taxonomic history, the two main morphological types of capuchins, gracile (untufted) and robust (tufted), were assigned to a single genus, Cebus. Further, all tufted capuchins were assigned to a single species, Cebus apella, despite broad geographic ranges spanning Central and northern South America. In 2012, tufted capuchins were assigned to their genus, Sapajus, with eight currently recognized species and five Cebus species, although these numbers are still under debate. Alu retrotransposons are a class of mobile element insertion (MEI) widely used to study primate phylogenetics. However, Alu elements have rarely been used to study capuchins. Recent genome-level assemblies for capuchins (Cebus imitator; [Cebus_imitator_1.0] and Sapajus apella [GSC_monkey_1.0]) facilitated large scale ascertainment of young lineage-specific Alu insertions. Reported here are 1607 capuchin specific and 678 Sapajus specific Alu insertions along with candidate oligonucleotides for locus-specific PCR assays for many elements. PCR analyses identified 104 genus level and 51 species level Alu insertion polymorphisms. The Alu datasets reported in this study provide a valuable resource that will assist in the classification of archival samples lacking phenotypic data and for the study of capuchin phylogenetic relationships.

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31

Voelker, R. A., J. Graves, W. Gibson, and M. Eisenberg. "Mobile element insertions causing mutations in the Drosophila suppressor of sable locus occur in DNase I hypersensitive subregions of 5'-transcribed nontranslated sequences." Genetics 126, no. 4 (December 1, 1990): 1071–82. http://dx.doi.org/10.1093/genetics/126.4.1071.

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Abstract The locations of 16 mobile element insertions causing mutations at the Drosophila suppressor of sable [su(s)] locus were determined by restriction mapping and DNA sequencing of the junction sites. The transposons causing the mutations are: P element (5 alleles), gypsy (3 alleles), 17.6, HMS Beagle, springer, Delta 88, prygun, Stalker, and a new mobile element which was named roamer (2 alleles). Four P element insertions occur in 5' nontranslated leader sequences, while the fifth P element and all 11 non-P elements inserted into the 2053 nucleotide, 5'-most intron that is spliced from the 5' nontranslated leader approximately 100 nucleotides upstream of the translation start. Fifteen of the 16 mobile elements inserted within a approximately 1900 nucleotide region that contains seven 100-200-nucleotide long DNase I-hypersensitive subregions that alternate with DNase I-resistant intervals of similar lengths. The locations of these 15 insertion sites correlate well with the roughly estimated locations of five of the DNase I-hypersensitive subregions. These findings suggest that the features of chromatin structure that accompany gene activation may also make the DNA susceptible to insertion of mobile elements.

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32

Zhang, Zhongge, Ming Ren Yen, and Milton H. Saier. "Precise Excision of IS5 from the Intergenic Region between the fucPIK and the fucAO Operons and Mutational Control of fucPIK Operon Expression in Escherichia coli." Journal of Bacteriology 192, no. 7 (January 22, 2010): 2013–19. http://dx.doi.org/10.1128/jb.01085-09.

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ABSTRACT Excision of transposable genetic elements from host DNA occurs at low frequencies and is usually imprecise. A common insertion sequence element in Escherichia coli, IS5, has been shown to provide various benefits to its host by inserting into specific sites. Precise excision of this element had not previously been demonstrated. Using a unique system, the fucose (fuc) regulon, in which IS5 insertion and excision result in two distinct selectable phenotypes, we have demonstrated that IS5 can precisely excise from its insertion site, restoring the wild-type phenotype. In addition to precise excision, several “suppressor” insertion, deletion, and point mutations restore the wild-type Fuc+ phenotype to various degrees without IS5 excision. The possible bases for these observations are discussed.

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33

Backus, Ad. "Het Intergenerationele Codewisseling-Continuum Binnen De Turkse Gemeenschap in Nederland." Spreken in moedertaal en vreemde taal 54 (January 1, 1996): 25–37. http://dx.doi.org/10.1075/ttwia.54.03bac.

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New data on Turkish-Dutch codeswitching (CS) have uncovered patterns not previously attested in this language pair. It turns out that three different generations within the immigrant community switch in three different ways. For the first generation, CS mostly concerns the occasional insertion of Dutch nouns in Turkish sentences. The intermediate generation switches much more frequently and in a much more varied way. The second generation also practices a lot of CS, but the type of switching is virtually always of an alternational, not insertional, nature. Insertional CS further seems to lend support to a model of speech production in which some elements are uttered with greater awareness than others. High awareness stimulates CS. Various aspects of linguistic elements, as well as of the act of speaking, are involved in determining an element's level of awareness.

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34

Payer, Lindsay M., Jared P. Steranka, Wan Rou Yang, Maria Kryatova, Sibyl Medabalimi, Daniel Ardeljan, Chunhong Liu, Jef D. Boeke, Dimitri Avramopoulos, and Kathleen H. Burns. "Structural variants caused by Alu insertions are associated with risks for many human diseases." Proceedings of the National Academy of Sciences 114, no. 20 (May 2, 2017): E3984—E3992. http://dx.doi.org/10.1073/pnas.1704117114.

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Interspersed repeat sequences comprise much of our DNA, although their functional effects are poorly understood. The most commonly occurring repeat is the Alu short interspersed element. New Alu insertions occur in human populations, and have been responsible for several instances of genetic disease. In this study, we sought to determine if there are instances of polymorphic Alu insertion variants that function in a common variant, common disease paradigm. We cataloged 809 polymorphic Alu elements mapping to 1,159 loci implicated in disease risk by genome-wide association study (GWAS) (P < 10−8). We found that Alu insertion variants occur disproportionately at GWAS loci (P = 0.013). Moreover, we identified 44 of these Alu elements in linkage disequilibrium (r2 > 0.7) with the trait-associated SNP. This figure represents a >20-fold increase in the number of polymorphic Alu elements associated with human phenotypes. This work provides a broader perspective on how structural variants in repetitive DNAs may contribute to human disease.

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35

Sadler, Michael, Melanie R. Mormile, and Ronald L. Frank. "Characterization of the IS200/IS605 Insertion Sequence Family in Halanaerobium Hydrogeniformans." Genes 11, no. 5 (April 29, 2020): 484. http://dx.doi.org/10.3390/genes11050484.

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Mobile DNA elements play a significant evolutionary role by promoting genome plasticity. Insertion sequences are the smallest prokaryotic transposable elements. They are highly diverse elements, and the ability to accurately identify, annotate, and infer the full genomic impact of insertion sequences is lacking. Halanaerobium hydrogeniformans is a haloalkaliphilic bacterium with an abnormally high number of insertion sequences. One family, IS200/IS605, showed several interesting features distinct from other elements in this genome. Twenty-three loci harbor elements of this family in varying stages of decay, from nearly intact to an ends-only sequence. The loci were characterized with respect to two divergent open reading frames (ORF), tnpA and tnpB, and left and right ends of the elements. The tnpB ORF contains two nearly identical insert sequences that suggest recombination between tnpB ORF is occurring. From these results, insertion sequence activity can be inferred, including transposition capability and element interaction.

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36

Guiamatsia, I., Brian G. Falzon, and G. A. O. Davies. "Automatic Insertion of Cohesive Elements for Delamination Modelling." Key Engineering Materials 383 (June 2008): 53–66. http://dx.doi.org/10.4028/www.scientific.net/kem.383.53.

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Composite damage modelling with cohesive elements has initially been limited to the analysis of interface damage or delamination. However, their use is also being extended to the analysis of inplane tensile failure arising from matrix or fibre fracture. These interface elements are typically placed at locations where failure is likely to occur, which infers a certain a priori knowledge of the crack propagation path(s). In the case of a crack jump for example, the location of the jump is usually not obvious, and the simulation would require the placement of cohesive elements at all element faces. A better option, presented here, is to determine the potential location of cohesive elements and insert them during the analysis. The aim of this work is to enable the determination of the crack path, as part of the solution process. A subroutine has been developed and implemented in the commercial finite element package ABAQUS/Standard[1] in order to automatically insert cohesive elements within a pristine model, on the basis of the analysis of the current stress field. Results for the prediction of delamination are presented in this paper.

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37

Bedzyk, L. A., N. B. Shoemaker, K. E. Young, and A. A. Salyers. "Insertion and excision of Bacteroides conjugative chromosomal elements." Journal of Bacteriology 174, no. 1 (1992): 166–72. http://dx.doi.org/10.1128/jb.174.1.166-172.1992.

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38

Pfeifer, Felicitas. "Insertion elements and genome organization of Halobacterium halobium." Systematic and Applied Microbiology 7, no. 1 (March 1986): 36–40. http://dx.doi.org/10.1016/s0723-2020(86)80121-7.

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39

Ryan, Margret, Jerry D. Johnson, and Lee A. Bulla Jr. "Insertion sequence elements in Bacillus thuringiensis subsp. darmstadiensis." Canadian Journal of Microbiology 39, no. 7 (July 1, 1993): 649–58. http://dx.doi.org/10.1139/m93-094.

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Two variants of insertion sequence IS231, named IS231G and H, were isolated from Bacillus thuringiensis subsp. darmstadiensis 73-E-10-2 (BTD2), an isolate toxic to dipteran insects, and characterized by DNA sequence analysis. They are encoded consecutively as direct repeats on an EcoRI fragment of 5.6 kilo base pairs. Direct tandem repeats of IS231 elements have not been previously reported. Both elements are closely related to other members of the IS231 family that have been isolated from B. thuringiensis strains toxic to lepidopteran as well as to dipteran insects. A close correlation exists between the evolutionary relationships of the IS231 sequences determined to date and the toxicity spectrum of the host cell. Probing of BTD2 DNA with a radiolabeled IS231G fragment demonstrated that IS231 elements are located on 55- and 34-MDa plasmids as well as on chromosomal DNA. Chromosomal DNA, but not plasmids, from BTD2 also hybridizes to another, unrelated insertion sequence, IS240, from B. thuringiensis subsp. israelensis, an isolate toxic to dipteran insects. BTD2, therefore, contains IS elements once thought to reside exclusively in either dipteran- or lepidopteran-specific subspecies of B. thuringiensis.Key words: IS231, IS240, mobile elements.

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40

Brown, A. R., A. C. Townsley, and S. G. B. Amyes. "Diversity of Tn1546 Elements in Clinical Isolates of Glycopeptide-Resistant Enterococci from Scottish Hospitals." Antimicrobial Agents and Chemotherapy 45, no. 4 (April 1, 2001): 1309–11. http://dx.doi.org/10.1128/aac.45.4.1309-1311.2001.

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ABSTRACT The Tn1546-related elements of 48 Van glycopetide-resistant enterococci were compared. Ten distinct Tn1546 types were identified with variation primarily due to IS1542 and IS1216V-like insertions. Clonal isolates frequently differed in their Tn1546 type, indicating instability of Tn1546-related elements. A putative hybrid promoter was identified, generated upstream ofvanR by the insertion of IS1542. The presence of this hybrid promoter was associated with constitutive expression of the van genes and elevated teicoplanin resistance.

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41

Tang, Zuojian, Jared P. Steranka, Sisi Ma, Mark Grivainis, Nemanja Rodić, Cheng Ran Lisa Huang, Ie-Ming Shih, et al. "Human transposon insertion profiling: Analysis, visualization and identification of somatic LINE-1 insertions in ovarian cancer." Proceedings of the National Academy of Sciences 114, no. 5 (January 17, 2017): E733—E740. http://dx.doi.org/10.1073/pnas.1619797114.

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Mammalian genomes are replete with interspersed repeats reflecting the activity of transposable elements. These mobile DNAs are self-propagating, and their continued transposition is a source of both heritable structural variation as well as somatic mutation in human genomes. Tailored approaches to map these sequences are useful to identify insertion alleles. Here, we describe in detail a strategy to amplify and sequence long interspersed element-1 (LINE-1, L1) retrotransposon insertions selectively in the human genome, transposon insertion profiling by next-generation sequencing (TIPseq). We also report the development of a machine-learning–based computational pipeline, TIPseqHunter, to identify insertion sites with high precision and reliability. We demonstrate the utility of this approach to detect somatic retrotransposition events in high-grade ovarian serous carcinoma.

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42

Morozova, Maria S. "Albanian Elements in the Slavic speech of Golo Bordo Bilinguals: Code-Mixing or Borrowing?" Slovene 9, no. 2 (2020): 372–94. http://dx.doi.org/10.31168/2305-6754.2020.9.2.16.

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The article considers contact-related phenomena found in the Slavic speech of bilinguals in the multiethnic region of Golo Bordo, Northeastern Albania. Most inhabitants of the Slavic part of the region master the local Western Macedonian dialect and the literary Albanian language. The material for the study includes dialect texts previously published in [Steinke, Ylli 2008; Соболев et al. 2013], examples from [Asenova 2016] and field materials collected by the author. Particular attention is paid to the insertion of Albanian nouns and verbs in the Macedonian speech of bilinguals. The article analyzes the ways to integrate the Albanian nouns, the examples of non-integrated verb insertions, and the models of adaptation of verbs. An attempt is made to provide a theoretical understanding of the described phenomena as either borrowing or code-mixing. The notion of “congruent lexicalization” [Muysken 2000] is used for the interpretation of phenomena such as the insertion of morphologically integrated Albanian nouns and non-integrated verbs used in their Albanian grammatical forms.

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43

Wright, Stephen I., Quang Hien Le, Daniel J. Schoen, and Thomas E. Bureau. "Population Dynamics of anAc-like Transposable Element in Self- and Cross-Pollinating Arabidopsis." Genetics 158, no. 3 (July 1, 2001): 1279–88. http://dx.doi.org/10.1093/genetics/158.3.1279.

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AbstractTheoretical models predict that the mating system should be an important factor driving the dynamics of transposable elements in natural populations due to differences in selective pressure on both element and host. We used a PCR-based approach to examine the abundance and levels of insertion polymorphism of Ac-III, a recently identified Ac-like transposon family, in natural populations of the selfing plant Arabidopsis thaliana and its close outcrossing relative, Arabidopsis lyrata. Although several insertions appeared to be ancient and shared between species, there is strong evidence for recent activity of this element family in both species. Sequences of the regions flanking insertions indicate that all Ac-III transposons segregating in natural populations are in noncoding regions and provide no evidence for local transposition events. Transposon display analysis suggests the presence of slightly higher numbers of insertion sites per individual but fewer total polymorphic insertions in the self-pollinating A. thaliana than A. lyrata. Element insertions appear to be segregating at significantly lower frequencies in A. lyrata than A. thaliana, which is consistent with a reduction in transposition rate, reduction in effective population size, or reduced efficacy of natural selection against element insertions in selfing populations.

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44

Storer, Jessica M., Jerilyn A. Walker, Lydia C. Rewerts, Morgan A. Brown, Thomas O. Beckstrom, Scott W. Herke, Christian Roos, and Mark A. Batzer. "Owl Monkey Alu Insertion Polymorphisms and Aotus Phylogenetics." Genes 13, no. 11 (November 8, 2022): 2069. http://dx.doi.org/10.3390/genes13112069.

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Owl monkeys (genus Aotus), or “night monkeys” are platyrrhine primates in the Aotidae family. Early taxonomy only recognized one species, Aotus trivirgatus, until 1983, when Hershkovitz proposed nine unique species designations, classified into red-necked and gray-necked species groups based predominately on pelage coloration. Recent studies questioned this conventional separation of the genus and proposed designations based on the geographical location of wild populations. Alu retrotransposons are a class of mobile element insertion (MEI) widely used to study primate phylogenetics. A scaffold-level genome assembly for one Aotus species, Aotus nancymaae [Anan_2.0], facilitated large-scale ascertainment of nearly 2000 young lineage-specific Alu insertions. This study provides candidate oligonucleotides for locus-specific PCR assays for over 1350 of these elements. For 314 Alu elements across four taxa with multiple specimens, PCR analyses identified 159 insertion polymorphisms, including 21 grouping A. nancymaae and Aotus azarae (red-necked species) as sister taxa, with Aotus vociferans and A. trivirgatus (gray-necked) being more basal. DNA sequencing identified five novel Alu elements from three different taxa. The Alu datasets reported in this study will assist in species identification and provide a valuable resource for Aotus phylogenetics, population genetics and conservation strategies when applied to wild populations.

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45

Kwong, Shiyang, Anthony E. Woods, Peter J. Mirtschin, Ruowen Ge, and R. Kini. "The recruitment of blood coagulation factor X into snake venom gland as a toxin." Thrombosis and Haemostasis 102, no. 09 (2009): 469–78. http://dx.doi.org/10.1160/th09-03-0162.

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SummaryTrocarin D is a prothrombin activator from the Tropidechis carinatus venom. It is a functional and structural homologue to mammalian blood coagulation factor Xa.Trocarin D is hypothesised to have evolved from its factor X counterpart (TrFX) through gene duplication and recruitment.The genes of trocarin D and TrFX have significant sequence identities, except for insertions/deletions in their intron 1 and promoter regions. In trocarin D intron 1 region, there are three insertions and two deletions. In trocarin D promoter region, there is a novel 264 bp insertion which has potential cis-elements.This insertion is termed as Venom Recruitment/Switch Element (VERSE) and is hypothesised to account for switching the low-level constitutive expression of factor X in the liver to the high-level inducible expression of trocarin D in the venom gland. To understand the role of VERSE in the trocarin D expression,its cis-elements were characterised by luciferase assays in mammalian cell lines as well as snake venom gland cells. The ability of VERSE to drive luciferase expression is comparable to that of the trocarin D promoter. The predicted cis-elements are important in promoting expression as their mutagenesis resulted in lower luciferase expression.VERSE minimal core promoter and three novel cis-elements (two up-regulatory and one suppressor elements) were identified using deletion/site-directed mutagenesis studies. VERSE is primarily responsible for the increase of trocarin D expression. The insertions/deletions within trocarin D intron 1 need to be characterised for their role in tissue-specific and inducible expression of trocarin D.

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46

Grech, Leanne, Daniel C. Jeffares, Christoph Y. Sadée, María Rodríguez-López, Danny A. Bitton, Mimoza Hoti, Carolina Biagosch, et al. "Fitness Landscape of the Fission Yeast Genome." Molecular Biology and Evolution 36, no. 8 (May 11, 2019): 1612–23. http://dx.doi.org/10.1093/molbev/msz113.

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Abstract The relationship between DNA sequence, biochemical function, and molecular evolution is relatively well-described for protein-coding regions of genomes, but far less clear in noncoding regions, particularly, in eukaryote genomes. In part, this is because we lack a complete description of the essential noncoding elements in a eukaryote genome. To contribute to this challenge, we used saturating transposon mutagenesis to interrogate the Schizosaccharomyces pombe genome. We generated 31 million transposon insertions, a theoretical coverage of 2.4 insertions per genomic site. We applied a five-state hidden Markov model (HMM) to distinguish insertion-depleted regions from insertion biases. Both raw insertion-density and HMM-defined fitness estimates showed significant quantitative relationships to gene knockout fitness, genetic diversity, divergence, and expected functional regions based on transcription and gene annotations. Through several analyses, we conclude that transposon insertions produced fitness effects in 66–90% of the genome, including substantial portions of the noncoding regions. Based on the HMM, we estimate that 10% of the insertion depleted sites in the genome showed no signal of conservation between species and were weakly transcribed, demonstrating limitations of comparative genomics and transcriptomics to detect functional units. In this species, 3′- and 5′-untranslated regions were the most prominent insertion-depleted regions that were not represented in measures of constraint from comparative genomics. We conclude that the combination of transposon mutagenesis, evolutionary, and biochemical data can provide new insights into the relationship between genome function and molecular evolution.

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47

Woods, Wayne G., Katrina Ngui, and Michael L. Dyall-Smith. "An Improved Transposon for the Halophilic ArchaeonHaloarcula hispanica." Journal of Bacteriology 181, no. 22 (November 15, 1999): 7140–42. http://dx.doi.org/10.1128/jb.181.22.7140-7142.1999.

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ABSTRACT An improved transposon (ThD73) for Haloarcula hispanica is described. Based on the halobacterial insertion sequence ISH28, it showed little target sequence specificity but was biased toward a lower G+C content. Twenty randomly selected ThD73 mutants were analyzed, and the DNA flanking their insertions revealed several recognizable sequences, including two (unrelated) ISH elements.

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48

Huff, Chad D., Jinchuan Xing, Alan R. Rogers, David Witherspoon, and Lynn B. Jorde. "Mobile elements reveal small population size in the ancient ancestors of Homo sapiens." Proceedings of the National Academy of Sciences 107, no. 5 (January 19, 2010): 2147–52. http://dx.doi.org/10.1073/pnas.0909000107.

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The genealogies of different genetic loci vary in depth. The deeper the genealogy, the greater the chance that it will include a rare event, such as the insertion of a mobile element. Therefore, the genealogy of a region that contains a mobile element is on average older than that of the rest of the genome. In a simple demographic model, the expected time to most recent common ancestor (TMRCA) is doubled if a rare insertion is present. We test this expectation by examining single nucleotide polymorphisms around polymorphic Alu insertions from two completely sequenced human genomes. The estimated TMRCA for regions containing a polymorphic insertion is two times larger than the genomic average (P < <10−30), as predicted. Because genealogies that contain polymorphic mobile elements are old, they are shaped largely by the forces of ancient population history and are insensitive to recent demographic events, such as bottlenecks and expansions. Remarkably, the information in just two human DNA sequences provides substantial information about ancient human population size. By comparing the likelihood of various demographic models, we estimate that the effective population size of human ancestors living before 1.2 million years ago was 18,500, and we can reject all models where the ancient effective population size was larger than 26,000. This result implies an unusually small population for a species spread across the entire Old World, particularly in light of the effective population sizes of chimpanzees (21,000) and gorillas (25,000), which each inhabit only one part of a single continent.

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Cancian, Mariana, Tiago Minuzzi Freire da Fontoura Gomes, and Elgion Lucio Silva Loreto. "Somatic Mobilization: High Somatic Insertion Rate of mariner Transposable Element in Drosophila simulans." Insects 13, no. 5 (May 12, 2022): 454. http://dx.doi.org/10.3390/insects13050454.

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Although transposable elements (TEs) are usually silent in somatic tissues, they are sometimes mobilized in the soma and can potentially have biological consequences. The mariner element is one of the TEs involved in somatic mobilization (SM) in Drosophila and has a high rate of somatic excision. It is also known that temperature is an important factor in the increase of the mariner element SM in the fly. However, it is important to emphasize that excision is only one step of TE transposition, and the final step in this process is insertion. In the present study, we used an assay based on sequencing of the mariner flanking region and developed a pipeline to identify novel mariner insertions in Drosophila simulans at 20 and 28 °C. We found that flies carrying two mariner copies (one autonomous and one non-autonomous) had an average of 236.4 (±99.3) to 279 (±107.7) new somatic insertions at 20 °C and an average of 172.7 (±95.3) to 252.6 (±67.3) at 28 °C. In addition, we detected fragments containing mariner and others without mariner in the same regions with low-coverage long-read sequencing, indicating the process of excision and insertion. In conclusion, a low number of autonomous copies of the mariner transposon can promote a high rate of new somatic insertions during the developmental stages of Drosophila. Additionally, the developed method seems to be sensitive and adequate for the verification and estimation of somatic insertion.

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Wright, David A., and Daniel F. Voytas. "Potential Retroviruses in Plants: Tat1 Is Related to a Group of Arabidopsis thaliana Ty3/gypsy Retrotransposons That Encode Envelope-Like Proteins." Genetics 149, no. 2 (June 1, 1998): 703–15. http://dx.doi.org/10.1093/genetics/149.2.703.

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Abstract Tat1 was originally identified as an insertion near the Arabidopsis thaliana SAM1 gene. We provide evidence that Tat1 is a retrotransposon and that previously described insertions are solo long terminal repeats (LTRs) left behind after the deletion of coding regions of full-length elements. Three Tat1 insertions were characterized that have retrotransposon features, including a primer binding site complementary to an A. thaliana asparagine tRNA and an open reading frame (ORF) with ~44% amino acid sequence similarity to the gag protein of the Zea mays retrotransposon Zeon-1. Tat1 elements have large, polymorphic 3′ noncoding regions that may contain transduced DNA sequences; a 477-base insertion in the 3′ noncoding region of the Tat1-3 element contains part of a related retrotransposon and sequences similar to the nontranslated leader sequence of AT-P5C1, a gene for pyrroline-5-carboxylate reductase. Analysis of DNA sequences generated by the A. thaliana genome project identified 10 families of Ty3/gypsy retrotransposons, which share up to 51 and 62% amino-acid similarity to the ORFs of Tat1 and the A. thaliana Athila element, respectively. Phylogenetic analyses resolved the plant Ty3/gypsy elements into two lineages, one of which includes homologs of Tat1 and Athila. Four families of A. thaliana elements within the Tat/Athila lineage encode a conserved ORF after integrase at a position occupied by the envelope gene in retroviruses and in some insect Ty3/gypsy retrotransposons. Like retroviral envelope genes, this ORF encodes a transmembrane domain and, in some insertions, a putative secretory signal sequence. This suggests that Tat/Athila retrotransposons may produce enveloped virions and may be infectious.

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