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Artículos de revistas sobre el tema "Insertion elements, DNA"

Autor: Grafiati

Publicado: 4 de junio de 2021

Última modificación: 1 de febrero de 2023

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1

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 f

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2

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 trans

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3

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

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4

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 si

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5

Yin, Bin, and David A. Largaespada. "PCR-based procedures to isolate insertion sites of DNA elements." BioTechniques 43, no. 1 (July 2007): 79–84. http://dx.doi.org/10.2144/000112474.

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6

Paskewitz, Susan M., and Frank H. Collins. "Site-specific ribosomal DNA insertion elements inAnopheles gambiaeandA.arbiensis: nucleotide sequence of gene-element boundaries." Nucleic Acids Research 17, no. 20 (1989): 8125–33. http://dx.doi.org/10.1093/nar/17.20.8125.

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7

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

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8

Gosselin, Sophia P., Danielle R. Arsenault, Catherine A. Jennings, and Johann Peter Gogarten. "The Evolutionary History of a DNA Methylase Reveals Frequent Horizontal Transfer and Within-Gene Recombination." Genes 14, no. 2 (January 21, 2023): 288. http://dx.doi.org/10.3390/genes14020288.

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Inteins, often referred to as protein introns, are highly mobile genetic elements that invade conserved genes throughout the tree of life. Inteins have been found to invade a wide variety of key genes within actinophages. While in the process of conducting a survey of these inteins in actinophages, we discovered that one protein family of methylases contained a putative intein, and two other unique insertion elements. These methylases are known to occur commonly in phages as orphan methylases (possibly as a form of resistance to restriction–modification systems). We found that the methylase fa

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9

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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10

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-glob

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11

Manna, Dipankar, Xiuhua Wang, and N. Patrick Higgins. "Mu and IS1 Transpositions Exhibit Strong Orientation Bias at the Escherichia coli bgl Locus." Journal of Bacteriology 183, no. 11 (June 1, 2001): 3328–35. http://dx.doi.org/10.1128/jb.183.11.3328-3335.2001.

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ABSTRACT The region upstream of the Escherichia coli bgloperon is an insertion hot spot for several transposons. Elements as distantly related as Tn1, Tn5, and phage Mu home in on this location. To see what characteristics result in a high-affinity site for transposition, we compared in vivo and in vitro Mu transposition patterns near the bgl promoter. In vivo, Mu insertions were focused in two narrow zones of DNA nearbgl, and both zones exhibited a striking orientation bias. Five hot spots upstream of the bgl cyclic AMP binding protein (CAP) binding site had Mu insertions exclusively with the

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12

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 prec

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13

Youderian, P., P. Sugiono, K. L. Brewer, N. P. Higgins, and T. Elliott. "Packaging specific segments of the Salmonella chromosome with locked-in Mud-P22 prophages." Genetics 118, no. 4 (April 1, 1988): 581–92. http://dx.doi.org/10.1093/genetics/118.4.581.

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Abstract Hybrid genetic elements, Mud-P and Mud-Q (collectively, Mud-P22s), have been constructed that carry two-thirds of the temperate Salmonella phage P22 genome sandwiched between the ends of transposon Mu. Insertions of these elements in the Salmonella chromosome generate locked-in P22 prophages that cannot excise. Upon induction (as a consequence of the inactivation of P22 c2 repressor), a locked-in prophage replicates its DNA in situ, resulting in the amplification of neighboring regions of the chromosome and the processive packaging of three contiguous headsful of adjacent DNA in one d

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14

Noto, Michael J., Barry N. Kreiswirth, Alastair B. Monk, and Gordon L. Archer. "Gene Acquisition at the Insertion Site for SCCmec, the Genomic Island Conferring Methicillin Resistance in Staphylococcus aureus." Journal of Bacteriology 190, no. 4 (December 14, 2007): 1276–83. http://dx.doi.org/10.1128/jb.01128-07.

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ABSTRACT Staphylococcus aureus becomes resistant to methicillin by acquiring a genomic island, known as staphylococcal chromosome cassette mec (SCCmec), which contains the methicillin resistance determinant, mecA. SCCmec is site-specifically integrated into the staphylococcal chromosome at a locus known as the SCCmec attachment site (attB). In an effort to gain a better understanding of the potential that methicillin-sensitive S. aureus (MSSA) isolates have for acquiring SCCmec, the nucleotide sequences of attB and surrounding DNA regions were examined in a diverse collection of 42 MSSA isolat

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15

Kelley, M. R., S. Kidd, R. L. Berg, and M. W. Young. "Restriction of P-element insertions at the Notch locus of Drosophila melanogaster." Molecular and Cellular Biology 7, no. 4 (April 1987): 1545–48. http://dx.doi.org/10.1128/mcb.7.4.1545-1548.1987.

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P elements move about the Drosophila melanogaster genome in a nonrandom fashion, preferring some chromosomal targets for insertion over others (J. C. J. Eeken, F. H. Sobels, V. Hyland, and A. P. Schalet, Mutat. Res. 150:261-275, 1985; W. R. Engels, Annu. Rev. Genet. 17:315-344, 1983; M. D. Golubovsky, Y. N. Ivanov, and M. M. Green, Proc. Natl. Acad. Sci. USA 74:2973-2975, 1977; M. J. Simmons and J. K. Lim, Proc. Natl. Acad. Sci. USA 77:6042-6046, 1980). Some of this specificity may be due to recognition of a particular DNA sequence in the target DNA; derivatives of an 8-base-pair consensus seq

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16

Kelley, M. R., S. Kidd, R. L. Berg, and M. W. Young. "Restriction of P-element insertions at the Notch locus of Drosophila melanogaster." Molecular and Cellular Biology 7, no. 4 (April 1987): 1545–48. http://dx.doi.org/10.1128/mcb.7.4.1545.

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P elements move about the Drosophila melanogaster genome in a nonrandom fashion, preferring some chromosomal targets for insertion over others (J. C. J. Eeken, F. H. Sobels, V. Hyland, and A. P. Schalet, Mutat. Res. 150:261-275, 1985; W. R. Engels, Annu. Rev. Genet. 17:315-344, 1983; M. D. Golubovsky, Y. N. Ivanov, and M. M. Green, Proc. Natl. Acad. Sci. USA 74:2973-2975, 1977; M. J. Simmons and J. K. Lim, Proc. Natl. Acad. Sci. USA 77:6042-6046, 1980). Some of this specificity may be due to recognition of a particular DNA sequence in the target DNA; derivatives of an 8-base-pair consensus seq

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17

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 st

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18

Schalkwyk, Leonard C., Robert L. Charlebois, and W. Ford Doolittle. "Insertion sequences on plasmid pHV1 of Haloferax volcanii." Canadian Journal of Microbiology 39, no. 2 (February 1, 1993): 201–6. http://dx.doi.org/10.1139/m93-028.

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We have searched the cloned 86 kilo base pair plasmid pHV1 from Haloferax volcanii for repeated sequence elements, of which we expected it to be a rich source. It contains five copies of the previously characterized element ISH51 and a total of five copies of three uncharacterized elements. pHV1 is part of an AT-rich fraction of the DNA that is likely to be a preferred site for IS insertion.Key words: Haloferax volcanii, pHV1 repeated sequence elements, ISH51.

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19

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 <

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20

Feliciello, Isidoro, Željka Pezer, Dušan Kordiš, Branka Bruvo Mađarić, and Đurđica Ugarković. "Evolutionary History of Alpha Satellite DNA Repeats Dispersed within Human Genome Euchromatin." Genome Biology and Evolution 12, no. 11 (October 20, 2020): 2125–38. http://dx.doi.org/10.1093/gbe/evaa224.

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Abstract Major human alpha satellite DNA repeats are preferentially assembled within (peri)centromeric regions but are also dispersed within euchromatin in the form of clustered or short single repeat arrays. To study the evolutionary history of single euchromatic human alpha satellite repeats (ARs), we analyzed their orthologous loci across the primate genomes. The continuous insertion of euchromatic ARs throughout the evolutionary history of primates starting with the ancestors of Simiformes (45–60 Ma) and continuing up to the ancestors of Homo is revealed. Once inserted, the euchromatic ARs

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21

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 eleme

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22

Usdin, K., and A. V. Furano. "Insertion of L1 elements into sites that can form non-B DNA." Journal of Biological Chemistry 264, no. 34 (December 1989): 20736–43. http://dx.doi.org/10.1016/s0021-9258(19)47125-1.

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23

Pfeifer, Felicitas, Ulrike Blaseio, and Mary Horne. "Genome structure of Halobacterium halobium: plasmid dynamics in gas vacuole deficient mutants." Canadian Journal of Microbiology 35, no. 1 (January 1, 1989): 96–100. http://dx.doi.org/10.1139/m89-015.

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Halobacterium halobium contains two gas vacuole protein genes that are located in plasmid pHH1 (p-vac) and in the chromosomal DNA (c-vac). The mutation frequency for these genes is different: the constitutively expressed p-vac gene is mutated with a frequency of 10−2, while the chromosomal gene expressed in the stationary phase of growth is mutated with a frequency of 10−5. The difference in the mutation susceptibility is due to the dynamics of plasmid pHH1. p-vac gene mutations are caused (i) by the integration of an insertion element or (ii) by a deletion event encompassing the p-vac gene re

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24

Jiang, Yun, Wei Zong, Shaoqing Ju, Rongrong Jing, and Ming Cui. "Promising member of the short interspersed nuclear elements (Alu elements): mechanisms and clinical applications in human cancers." Journal of Medical Genetics 56, no. 10 (March 9, 2019): 639–45. http://dx.doi.org/10.1136/jmedgenet-2018-105761.

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Alu elements are one of most ubiquitous repetitive sequences in human genome, which were considered as the junk DNA in the past. Alu elements have been found to be associated with human diseases including cancers via events such as amplification, insertion, recombination or RNA editing, which provide a new perspective of oncogenesis at both DNA and RNA levels. Due to the prevalent distribution, Alu elements are widely used as target molecule of liquid biopsy. Alu-based cell-free DNA shows feasible application value in tumour diagnosis, postoperative monitoring and adjuvant therapy. In this rev

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25

Hoffman-Liebermann, B., D. Liebermann, L. H. Kedes, and S. N. Cohen. "TU elements: a heterogeneous family of modularly structured eucaryotic transposons." Molecular and Cellular Biology 5, no. 5 (May 1985): 991–1001. http://dx.doi.org/10.1128/mcb.5.5.991-1001.1985.

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We describe here a family of foldback transposons found in the genome of the higher eucaryote, the sea urchin Strongylocentrotus purpuratus. Two major classes of TU elements have been identified by analysis of genomic DNA and TU element clones. One class consists of largely similar elements with long terminal inverted repeats (IVRs) containing outer and inner domains and sharing a common middle segment that can undergo deletions. Some of these elements contain insertions. The second class is highly heterogeneous, with many different middle segments nonhomologous to those of the first-class and

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26

Hoffman-Liebermann, B., D. Liebermann, L. H. Kedes, and S. N. Cohen. "TU elements: a heterogeneous family of modularly structured eucaryotic transposons." Molecular and Cellular Biology 5, no. 5 (May 1985): 991–1001. http://dx.doi.org/10.1128/mcb.5.5.991.

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We describe here a family of foldback transposons found in the genome of the higher eucaryote, the sea urchin Strongylocentrotus purpuratus. Two major classes of TU elements have been identified by analysis of genomic DNA and TU element clones. One class consists of largely similar elements with long terminal inverted repeats (IVRs) containing outer and inner domains and sharing a common middle segment that can undergo deletions. Some of these elements contain insertions. The second class is highly heterogeneous, with many different middle segments nonhomologous to those of the first-class and

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27

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

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28

Wyler, Michele, Christoph Stritt, Jean-Claude Walser, Célia Baroux, and Anne C. Roulin. "Impact of Transposable Elements on Methylation and Gene Expression across Natural Accessions of Brachypodium distachyon." Genome Biology and Evolution 12, no. 11 (August 27, 2020): 1994–2001. http://dx.doi.org/10.1093/gbe/evaa180.

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Abstract Transposable elements (TEs) constitute a large fraction of plant genomes and are mostly present in a transcriptionally silent state through repressive epigenetic modifications, such as DNA methylation. TE silencing is believed to influence the regulation of adjacent genes, possibly as DNA methylation spreads away from the TE. Whether this is a general principle or a context-dependent phenomenon is still under debate, pressing for studying the relationship between TEs, DNA methylation, and nearby gene expression in additional plant species. Here, we used the grass Brachypodium distachy

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29

De Gregorio, Eliana, Chiara Abrescia, M. Stella Carlomagno, and Pier Paolo Di Nocera. "Asymmetrical Distribution of Neisseria Miniature Insertion Sequence DNA Repeats among Pathogenic and Nonpathogenic Neisseria Strains." Infection and Immunity 71, no. 7 (July 2003): 4217–21. http://dx.doi.org/10.1128/iai.71.7.4217-4221.2003.

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ABSTRACT Neisseria miniature insertion sequences (nemis) are miniature DNA insertion sequences found in Neisseria species. Out of 57 elements closely flanking cellular genes analyzed by PCR, most were conserved in Neisseria meningitidis but not in N. lactamica strains. Since mRNAs spanning nemis are processed by RNase III at hairpins formed by element termini, gene sets could selectively be regulated in meningococci at the posttranscriptional level.

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Wilson, Patrick C., Odette de Bouteiller, Yong-Jun Liu, Kathleen Potter, Jacques Banchereau, J. Donald Capra, and Virginia Pascual. "Somatic Hypermutation Introduces Insertions and Deletions into Immunoglobulin V Genes." Journal of Experimental Medicine 187, no. 1 (January 5, 1998): 59–70. http://dx.doi.org/10.1084/jem.187.1.59.

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During a germinal center reaction, random mutations are introduced into immunoglobulin V genes to increase the affinity of antibody molecules and to further diversify the B cell repertoire. Antigen-directed selection of B cell clones that generate high affinity surface Ig results in the affinity maturation of the antibody response. The mutations of Ig genes are typically basepair substitutions, although DNA insertions and deletions have been reported to occur at a low frequency. In this study, we describe five insertion and four deletion events in otherwise somatically mutated VH gene cDNA mol

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31

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

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32

Fang, Z., C. Doig, N. Morrison, B. Watt, and K. J. Forbes. "Characterization of IS1547, a New Member of the IS900 Family in the Mycobacterium tuberculosis Complex, and Its Association with IS6110." Journal of Bacteriology 181, no. 3 (February 1, 1999): 1021–24. http://dx.doi.org/10.1128/jb.181.3.1021-1024.1999.

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ABSTRACT Unlike classically defined insertion sequence (IS) elements, which are delimited by their inverted terminal repeats, some IS elements do not have inverted terminal repeats. Among this group of atypical IS elements, IS116, IS900, IS901, and IS1110 have been proposed as members of the IS900 family of elements, not only because they do not have inverted terminal repeats but also because they share other features such as homologous transposases and particular insertion sites. In this study, we report a newly identified IS sequence, IS1547, which was first identified in a clinical isolate

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33

Lozovsky, Elena R., Dmitry Nurminsky, Ernst A. Wimmer, and Daniel L. Hartl. "Unexpected Stability of mariner Transgenes in Drosophila." Genetics 160, no. 2 (February 1, 2002): 527–35. http://dx.doi.org/10.1093/genetics/160.2.527.

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Abstract A number of mariner transformation vectors based on the mauritiana subfamily of transposable elements were introduced into the genome of Drosophila melanogaster and examined for their ability to be mobilized by the mariner transposase. Simple insertion vectors were constructed from single mariner elements into which exogenous DNA ranging in size from 1.3 to 4.5 kb had been inserted; composite vectors were constructed with partial or complete duplications of mariner flanking the exogenous DNA. All of the simple insertion vectors showed levels of somatic and germline excision that were

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Graham, Todd, and Stephane Boissinot. "The Genomic Distribution of L1 Elements: The Role of Insertion Bias and Natural Selection." Journal of Biomedicine and Biotechnology 2006 (2006): 1–5. http://dx.doi.org/10.1155/jbb/2006/75327.

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LINE-1 (L1) retrotransposons constitute the most successful family of retroelements in mammals and account for as much as 20% of mammalian DNA. L1 elements can be found in all genomic regions but they are far more abundant in AT-rich, gene-poor, and low-recombining regions of the genome. In addition, the sex chromosomes and some genes seem disproportionately enriched in L1 elements. Insertion bias and selective processes can both account for this biased distribution of L1 elements. L1 elements do not appear to insert randomly in the genome and this insertion bias can at least partially explain

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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 estimat

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36

Jensen, S., A. H. Andersen, E. Kjeldsen, H. Biersack, E. H. Olsen, T. B. Andersen, O. Westergaard, and B. K. Jakobsen. "Analysis of functional domain organization in DNA topoisomerase II from humans and Saccharomyces cerevisiae." Molecular and Cellular Biology 16, no. 7 (July 1996): 3866–77. http://dx.doi.org/10.1128/mcb.16.7.3866.

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The functional domain structure of human DNA topoisomerase IIalpha and Saccharomyces cerevisiae DNA topoisomerase II was studied by investigating the abilities of insertion and deletion mutant enzymes to support mitotic growth and catalyze transitions in DNA topology in vitro. Alignment of the human topoisomerase IIalpha and S. cerevisiae topoisomerase II sequences defined 13 conserved regions separated by less conserved or differently spaced sequences. The spatial tolerance of the spacer regions was addressed by insertion of linkers. The importance of the conserved regions was assessed throug

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Beech, Robin N., and Andrew J. Leigh Brown. "Insertion-deletion variation at the yellow-achaete-scute region in two natural populations of Drosophila melanogaster." Genetical Research 53, no. 1 (February 1989): 7–15. http://dx.doi.org/10.1017/s0016672300027804.

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SummaryWe have surveyed the region of the X chromosome of Drosophila melanogaster which encodes the yellow, achaete and scute genes for restriction map variation. Two natural populations, one from North Carolina, U.S.A. and the other from southern Spain were screened for variation at about 70 restriction sites and for variation due to DNA insertion or deletion events in 120 kilobases of DNA. Mean heterozygosity per nucleotide was estimated to be 0·0024 and 15 large insertions were found in the 49 chromosomes screened. Extensive disequilibrium between polymorphic sites was found across much of

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Paulat, Nicole S., Erin McGuire, Krishnamurthy Subramanian, Austin B. Osmanski, Diana D. Moreno-Santillán, David A. Ray, and Jinchuan Xing. "Transposable Elements in Bats Show Differential Accumulation Patterns Determined by Class and Functionality." Life 12, no. 8 (August 4, 2022): 1190. http://dx.doi.org/10.3390/life12081190.

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Bat genomes are characterized by a diverse transposable element (TE) repertoire. In particular, the genomes of members of the family Vespertilionidae contain both active retrotransposons and active DNA transposons. Each TE type is characterized by a distinct pattern of accumulation over the past ~40 million years. Each also exhibits its own target site preferences (sometimes shared with other TEs) that impact where they are likely to insert when mobilizing. Therefore, bats provide a great resource for understanding the diversity of TE insertion patterns. To gain insight into how these diverse

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39

Dong, Hong, Tsute Chen, Floyd E. Dewhirst, Robert D. Fleischmann, Claire M. Fraser, and Margaret J. Duncan. "Genomic Loci of the Porphyromonas gingivalis Insertion Element IS1126." Infection and Immunity 67, no. 7 (July 1, 1999): 3416–23. http://dx.doi.org/10.1128/iai.67.7.3416-3423.1999.

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ABSTRACT The Porphyromonas gingivalis genome contains multiple copies of insertion element IS1126. When chromosomal DNA digests of different strains were probed with IS1126, between 25 and 35 hybridizing fragments per genome were detected, depending on the strain. Unrelated strains had very different restriction fragment length polymorphism (RFLP) patterns. When different laboratory copies of a specific strain were examined, the IS1126 RFLP patterns were very similar but small differences were observed, indicating that element-associated changes had occurred during laboratory passage. Within t

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Goodwin, Timothy J. D., Margaret I. Butler, and Russell T. M. Poulter. "Cryptons: a group of tyrosine-recombinase-encoding DNA transposons from pathogenic fungi." Microbiology 149, no. 11 (November 1, 2003): 3099–109. http://dx.doi.org/10.1099/mic.0.26529-0.

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A new group of transposable elements, which the authors have named cryptons, was detected in several pathogenic fungi, including the basidiomycete Cryptococcus neoformans, and the ascomycetes Coccidioides posadasii and Histoplasma capsulatum. These elements are unlike any previously described transposons. An archetypal member of the group, crypton Cn1, is 4 kb in length and is present at a low but variable copy number in a variety of C. neoformans strains. It displays interstrain variations in its insertion sites, suggesting recent mobility. The internal region contains a long gene, interrupte

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Waterhouse, Janet C., and Roy R. B. Russell. "Dispensable genes and foreign DNA in Streptococcus mutans." Microbiology 152, no. 6 (June 1, 2006): 1777–88. http://dx.doi.org/10.1099/mic.0.28647-0.

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A range of properties, including the ability to utilize various sugars, bind macromolecules and produce mutacins, are known to vary in their occurrence in different strains of Streptococcus mutans. In addition, insertion-sequence elements show a limited distribution and sequencing of the genome of S. mutans UA159 has revealed the presence of putative genomic islands of atypical base composition indicative of foreign DNA. PCR primers flanking regions suspected of having inserted DNA were designed on the basis of the genome sequence of S. mutans UA159 and used to explore variation in a collectio

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Bender, W., and A. Hudson. "P element homing to the Drosophila bithorax complex." Development 127, no. 18 (September 15, 2000): 3981–92. http://dx.doi.org/10.1242/dev.127.18.3981.

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P elements containing a 7 kb DNA fragment from the middle of the Drosophila bithorax complex insert preferentially into the bithorax complex or into the adjacent chromosome regions. This ‘homing’ property is similar to that reported for the engrailed promoter (Hama, C., Ali, Z. and Kornberg, T. B. (1990) Genes Dev. 4, 1079–1093). The 7 kb fragment does not contain any known promoter, but it acts as a boundary element separating adjacent segmental domains. An enhancer-trap P element was constructed with the homing fragment and the selectable marker flanked by FRT sites. P insertions can be trim

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Zhang, Shouting, and Göran Magnusson. "Cellular Mobile Genetic Elements in the Regulatory Region of the Pneumotropic Mouse Polyomavirus Genome: Structure and Function in Viral Gene Expression and DNA Replication." Journal of Virology 77, no. 6 (March 15, 2003): 3477–86. http://dx.doi.org/10.1128/jvi.77.6.3477-3486.2003.

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ABSTRACT DNA from the murine pneumotropic virus was extracted from virus in lung tissue of infected mice, and the regulatory region of the genome was amplified by PCR. The regulatory region of individual plasmid cloned DNA molecules appeared to have heterogeneous enhancer segments, whereas the protein-coding part of the genome had a uniform length. Nucleotide sequence analysis revealed that the majority of the DNA molecules had a structure differing from the standard type. A 220-bp insertion at nucleotide position 142 with a concomitant deletion of nucleotides 143 to 148 was prominent. There w

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UMEDA, Masaaki, Hisako OHTSUBO, and Eiichi OHTSUBO. "Diversification of the rice Waxy gene by insertion of mobile DNA elements into introns." Japanese Journal of Genetics 66, no. 5 (1991): 569–86. http://dx.doi.org/10.1266/jjg.66.569.

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45

McGurk, Michael P., and Daniel A. Barbash. "Double insertion of transposable elements provides a substrate for the evolution of satellite DNA." Genome Research 28, no. 5 (March 27, 2018): 714–25. http://dx.doi.org/10.1101/gr.231472.117.

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Meirsman, Catherine De, Jos Desair, Jos Vanderleyden, August P. van Gool, and Geroge C. Jen. "Similarities between nucleotide sequences of insertion elements ofAgrobacterium tumefaciensandPseudomonas savastanoiin relation toAgrobacterium tumefaciensTC-DNA." Nucleic Acids Research 15, no. 24 (1987): 10591. http://dx.doi.org/10.1093/nar/15.24.10591.

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Christensen, Shawn M., and Thomas H. Eickbush. "R2 Target-Primed Reverse Transcription: Ordered Cleavage and Polymerization Steps by Protein Subunits Asymmetrically Bound to the Target DNA." Molecular and Cellular Biology 25, no. 15 (August 1, 2005): 6617–28. http://dx.doi.org/10.1128/mcb.25.15.6617-6628.2005.

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ABSTRACT R2 elements are non-long terminal repeat retrotransposons that specifically insert into 28S rRNA genes of many animal groups. These elements encode a single protein with reverse transcriptase and endonuclease activities as well as specific DNA and RNA binding properties. In this report, gel shift experiments were conducted to investigate the stoichiometry of the DNA, RNA, and protein components of the integration reaction. The enzymatic functions associated with each of the protein complexes were also determined, and DNase I digests were used to footprint the protein onto the target D

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48

Ananiev, E. V., R. L. Phillips, and H. W. Rines. "Complex Structure of Knob DNA on Maize Chromosome 9: Retrotransposon Invasion into Heterochromatin." Genetics 149, no. 4 (August 1, 1998): 2025–37. http://dx.doi.org/10.1093/genetics/149.4.2025.

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Abstract The recovery of maize (Zea mays L.) chromosome addition lines of oat (Avena sativa L.) from oat × maize crosses enables us to analyze the structure and composition of specific regions, such as knobs, of individual maize chromosomes. A DNA hybridization blot panel of eight individual maize chromosome addition lines revealed that 180-bp repeats found in knobs are present in each of these maize chromosomes, but the copy number varies from ~100 to 25,000. Cosmid clones with knob DNA segments were isolated from a genomic library of an oat-maize chromosome 9 addition line with the help of t

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Lawrence, J. G., H. Ochman, and D. L. Hartl. "The evolution of insertion sequences within enteric bacteria." Genetics 131, no. 1 (May 1, 1992): 9–20. http://dx.doi.org/10.1093/genetics/131.1.9.

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Abstract To identify mechanisms that influence the evolution of bacterial transposons, DNA sequence variation was evaluated among homologs of insertion sequences IS1, IS3 and IS30 from natural strains of Escherichia coli and related enteric bacteria. The nucleotide sequences within each class of IS were highly conserved among E. coli strains, over 99.7% similar to a consensus sequence. When compared to the range of nucleotide divergence among chromosomal genes, these data indicate high turnover and rapid movement of the transposons among clonal lineages of E. coli. In addition, length polymorp

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Kassis, J. A. "Unusual properties of regulatory DNA from the Drosophila engrailed gene: three "pairing-sensitive" sites within a 1.6-kb region." Genetics 136, no. 3 (March 1, 1994): 1025–38. http://dx.doi.org/10.1093/genetics/136.3.1025.

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Abstract We have previously shown that a 2-kb fragment of engrailed DNA can suppress expression of a linked marker gene, white, in the P element vector CaSpeR. This suppression is dependent on the presence of two copies of engrailed DNA-containing P elements (P[en]) in proximity in the Drosophila genome (either in cis or in trans). In this study, the 2-kb fragment was dissected and found to contain three fragments of DNA which could mediate white suppression [called "pairing-sensitive sites" (PS)]. A PS site was also identified in regulatory DNA from the Drosophila escargot gene. The eye color

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