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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 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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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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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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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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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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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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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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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 family is not conserved within phage clusters and has a disparate distribution across divergent phage groups. We determined that two of the three insertion elements have a patchy distribution within the methylase protein family. Additionally, we found that the third insertion element is likely a second homing endonuclease, and that all three elements (the intein, the homing endonuclease, and what we refer to as the ShiLan domain) have different insertion sites that are conserved in the methylase gene family. Furthermore, we find strong evidence that both the intein and ShiLan domain are partaking in long-distance horizontal gene transfer events between divergent methylases in disparate phage hosts within the already dispersed methylase distribution. The reticulate evolutionary history of methylases and their insertion elements reveals high rates of gene transfer and within-gene recombination in actinophages.
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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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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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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 phage oriented left to right relative to the direction of bgl transcription. One hot spot within the CAP binding domain had the opposite (right-to-left) orientation of phage insertion. The DNA segment lying between these two Mu hot-spot clusters is extremely A/T rich (80%) and is an efficient target for insertion sequences during stationary phase. IS1 insertions that activate the bgl operon resulted in a decrease in Mu insertions near the CAP binding site. Mu transposition in vitro differed significantly from the in vivo transposition pattern, having a new hot-spot cluster at the border of the A/T-rich segment. Transposon hot-spot behavior and orientation bias may relate to an asymmetry of transposon DNA-protein complexes and to interactions with proteins that produce transcriptionally silenced chromatin.
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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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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 direction from the P22 packaging site, pac. Phage particles in an induced lysate of a Mud-P22 lysogen contain DNA molecules corresponding to several minutes of chromosomal DNA adjacent to the site of prophage insertion and transduce nearby genetic markers with high efficiencies. Mud-P22 prophages have been introduced into an F' episome by transposition; resident Mud insertions on the Salmonella chromosome may be converted to Mud-P22 insertions by homologous recombination in P22-mediated transductional crosses.
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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 isolates. The chromosomal region surrounding attB varied among the isolates studied and appears to be a common insertion point for acquired foreign DNA. Insertions of up to 15.1 kb were found containing open reading frames with homology to enterotoxin genes, restriction-modification systems, transposases, and several sequences that have not been previously described in staphylococci. Two groups, containing eight and four isolates, had sequences found in known SCCmec elements, suggesting SCCmec elements may have evolved through repeated DNA insertions at this locus. In addition, the attB sequences of the majority of MSSA isolates in this collection differ from the attB sequences of strains for which integrase-mediated SCCmec insertion or excision has been demonstrated, suggesting that some S. aureus isolates may lack the ability to site-specifically integrate SCCmec into their chromosomes.
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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 sequence are occupied by these transposable elements at many different chromosomal locations (K. O'Hare and G. M. Rubin, Cell 34:25-36, 1983). An additional level of specificity of P-element insertions is described in this paper. Of 14 mutations induced in the complex locus Notch by hybrid dysgenesis, 13 involved P-element insertions at or near the transcription start site of the gene. This clustering was not seen in other transposable element-induced mutations of Notch. DNA sequences homologous to the previously described consensus target for P-element insertion are not preferentially located in this region of the locus. The choice of a chromosomal site for integration appears to be based on more subtle variations in chromosome structure that are probably associated with activation or expression of the target gene.
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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 sequence are occupied by these transposable elements at many different chromosomal locations (K. O'Hare and G. M. Rubin, Cell 34:25-36, 1983). An additional level of specificity of P-element insertions is described in this paper. Of 14 mutations induced in the complex locus Notch by hybrid dysgenesis, 13 involved P-element insertions at or near the transcription start site of the gene. This clustering was not seen in other transposable element-induced mutations of Notch. DNA sequences homologous to the previously described consensus target for P-element insertion are not preferentially located in this region of the locus. The choice of a chromosomal site for integration appears to be based on more subtle variations in chromosome structure that are probably associated with activation or expression of the target gene.
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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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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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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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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 were stably transmitted to the descendant species, some exhibiting copy number variation, whereas their sequence divergence followed the species phylogeny. Many euchromatic ARs have sequence characteristics of (peri)centromeric alpha repeats suggesting heterochromatin as a source of dispersed euchromatic ARs. The majority of euchromatic ARs are inserted in the vicinity of other repetitive elements such as L1, Alu, and ERV or are embedded within them. Irrespective of the insertion context, each AR insertion seems to be unique and once inserted, ARs do not seem to be subsequently spread to new genomic locations. In spite of association with (retro)transposable elements, there is no indication that such elements play a role in ARs proliferation. The presence of short duplications at most of ARs insertion sites suggests site-directed recombination between homologous motifs in ARs and in the target genomic sequence, probably mediated by extrachromosomal circular DNA, as a mechanism of spreading within euchromatin.
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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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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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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 region. In contrast, c-vac mutants analyzed to date incurred neither insertion elements nor deletions. Deletion events within pHH1 occur at high frequencies during the development of a H. halobium culture. The investigation of the fusion regions resulting from deletion events indicates that insertion elements are involved. The analysis of pHH1 deletion variants led to a 4 kilobase pair DNA region containing the origin of replication of the pHH1 plasmid.Key words: gas vacuole protein gene, plasmid dynamics, deletions, insertion elements.
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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 review, the special tumourigenesis mechanism of Alu elements in human cancers is discussed, and the application of Alu elements in various tumour liquid biopsy is summarised.
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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 variable-sized inverted repeats that contain only an outer domain. The middle and insertion segments of both classes carry sequences that also are found unassociated from the inverted repeats at many other genomic locations. We conclude that the TU elements are modular structures composed of inverted repeats plus other sequence domains that are themselves members of different families of dispersed repetitive sequences. Such modular elements may have a role in the dispersion and rearrangement of genomic DNA segments.
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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.
Full textAbstract:
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 variable-sized inverted repeats that contain only an outer domain. The middle and insertion segments of both classes carry sequences that also are found unassociated from the inverted repeats at many other genomic locations. We conclude that the TU elements are modular structures composed of inverted repeats plus other sequence domains that are themselves members of different families of dispersed repetitive sequences. Such modular elements may have a role in the dispersion and rearrangement of genomic DNA segments.
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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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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 distachyon as a model and produced DNA methylation and transcriptome profiles for 11 natural accessions. In contrast to what is observed in Arabidopsis thaliana, we found that TEs have a limited impact on methylation spreading and that only few TE families are associated with a low expression of their adjacent genes. Interestingly, we found that a subset of TE insertion polymorphisms is associated with differential gene expression across accessions. Thus, although not having a global impact on gene expression, distinct TE insertions may contribute to specific gene expression patterns in B. distachyon.
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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 molecules. Two of these insertions and all four deletions were obtained through the sequencing of 395 cDNA clones (∼110,000 nucleotides) from CD38+IgD− germinal center, and CD38−IgD− memory B cell populations from a single human tonsil. No germline genes that could have encoded these six cDNA clones were found after an extensive characterization of the genomic VH4 repertoire of the tonsil donor. These six insertions or deletions and three additional insertion events isolated from other sources occurred as triplets or multiples thereof, leaving the transcripts in frame. Additionally, 8 of 9 of these events occurred in the CDR1 or CDR2, following a pattern consistent with selection, and making it unlikely that these events were artifacts of the experimental system. The lack of similar instances in unmutated IgD+CD38− follicular mantle cDNA clones statistically associates these events to the somatic hypermutation process (P = 0.014). Close scrutiny of the 9 insertion/deletion events reported here, and of 25 additional insertions or deletions collected from the literature, suggest that secondary structural elements in the DNA sequences capable of producing loop intermediates may be a prerequisite in most instances. Furthermore, these events most frequently involve sequence motifs resembling known intrinsic hotspots of somatic hypermutation. These insertion/deletion events are consistent with models of somatic hypermutation involving an unstable polymerase enzyme complex lacking proofreading capabilities, and suggest a downregulation or alteration of DNA repair at the V locus during the hypermutation process.
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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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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 of Mycobacterium tuberculosis. Its structure, insertion site, and putative transposase all conform with the conventions of the IS900family, suggesting that it is a new member of this family. IS1547 was detected only in isolates of the M. tuberculosis complex, where it had highly polymorphic restriction fragment length polymorphism patterns, suggesting that it may be a useful genetic marker for identifying isolates of the M. tuberculosis complex and for distinguishing different strains ofM. tuberculosis. ipl is a preferential locus for IS6110 insertion where there are eight known different insertion sites for IS6110. Surprisingly, the DNA sequence of ipl is now known to be a part of IS1547, meaning that IS1547 is a preferential site for IS6110 insertion.
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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 at least 100-fold lower than the baseline level of uninterrupted mariner elements. Although composite vectors with inverted duplications were unable to be mobilized at detectable frequencies, vectors with large direct duplications of mariner could be mobilized. A vector consisting of two virtually complete elements flanking exogenous DNA yielded a frequency of somatic eye-color mosaicism of ~10% and a frequency of germline excision of 0.04%. These values are far smaller than those observed for uninterrupted elements. The results imply that efficient mobilization of mariner in vivo requires the presence and proper spacing of sequences internal to the element as well as the inverted repeats.
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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 the genomic distribution of L1. The contrasted distribution of L1 and Alu elements suggests that postinsertional processes play a major role in shaping L1 distribution. The most likely mechanism is the loss of recently integrated L1 elements that are deleterious (negative selection) either because of disruption of gene function or their ability to mediate ectopic recombination. By comparison, the retention of L1 elements because of some positive effect is limited to a small fraction of the genome. Understanding the respective importance of insertion bias and selection will require a better knowledge of insertion mechanisms and the dynamics of L1 inserts in populations.
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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 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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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 through deletion of individual domains. We found that the exact spacing between most of the conserved domains is noncritical, as insertions in the spacer regions were tolerated with no influence on complementation ability. All conserved domains, however, are essential for sustained mitotic growth of S. cerevisiae and for enzymatic activity in vitro. A series of topoisomerase II carboxy-terminal truncations were investigated with respect to the ability to support viability, cellular localization, and enzymatic properties. The analysis showed that the divergent carboxy-terminal region of human topoisomerase IIalpha is dispensable for catalytic activity but contains elements that specifically locate the protein to the nucleus.
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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 the region in the North Carolina population. The frequency of large insertions, which usually correspond to transposable genetic elements, is significantly lower than has been observed in autosomal regions of the genome. This is predicted for X-linked loci by certain models of transposable element evolution, where copy number is restricted by virtue of the recessive deleterious effects of the insertions. Our results appear to support such models. The deficiency of insertions may in this case be enhanced by hitch-hiking effects arising from the high level of disequilibrium.
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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 TEs impact genome structure, we performed comparative spatial analyses between different TE classes and genomic features, including genic regions and CpG islands. Our results showed a depletion of all TEs in the coding sequence and revealed patterns of species- and element-specific attraction in the transcript. Trends of attraction in the distance tests also suggested significant TE activity in regions adjacent to genes. In particular, the enrichment of small, non-autonomous TE insertions in introns and near coding regions supports the hypothesis that the genomic distribution of TEs is the product of a balance of the TE insertion preference in open chromatin regions and the purifying selection against TEs within genes.
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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 the next year, genome sequencing, assembly, and annotation for P. gingivalis W83 will be completed. Because repetitive elements complicate the assembly of randomly sequenced DNA fragments, we isolated and sequenced the flanking regions of IS1126 copies in strain W83. We also isolated and sequenced the flanking regions of IS1126copies in strain ATCC 33277 in order to compare insertion sites in phylogenetically divergent strains. We identified 37 new sequences flanking IS1126 from strain ATCC 33277 and 30 from strain W83. The insertion element was found between genes except where it transposed into another insertion element. Examination of identifiable flanking genes or open reading frames indicated that the insertion sites were different in the two strains, except that both strains possess an insertion adjacent to the Lys-gingipain gene (J. P. Lewis and F. L. Macrina, Infect. Immun. 66:3035–3042, 1998). Most of the genes or sequences flanking IS1126 in ATCC 33277 were present in W83 but were contiguous and not insertion element associated. Thus, where genes were identified in both strains, their order was maintained, indicating that the two genomes are organized similarly, but the loci of IS1126 are different. In both strains, insertion element-associated duplicated target sites were lost from several copies of IS1126, providing evidence of homologous recombination between elements. Larger organizational differences between the genomes, such as deletions and inversions, may result from insertion element-mediated recombination events.
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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, interrupted by several introns. The product of this gene contains a putative tyrosine recombinase near its middle, and a region similar in sequence to the DNA-binding domains of several fungal transcription factors near its C-terminus. The element contains no long repeat sequences, but is bordered by short direct repeats which may have been produced by its insertion into the host genome by recombination. Many of the structural features of crypton Cn1 are conserved in the other known cryptons, suggesting that these elements represent the functional forms. The presence of cryptons in ascomycetes and basidiomycetes suggests that this is an ancient group of elements (>400 million years old). Sequence comparisons suggest that cryptons may be related to the DIRS1 and Ngaro1 groups of tyrosine-recombinase-encoding retrotransposons.
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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 collection of 39 strains isolated in various parts of the world over the last 40 years. Extensive differences between strains were detected, and similar insertion/deletion events appear to be present in the genomes of strains with very different origins. In two instances, insertion of foreign DNA appears to have displaced original S. mutans genes. Together with previous results on the occurrence of deletions in genes associated with sugar metabolism, the results indicate that S. mutans has a core genome and a dispensable genome, and that dispensable genes have become widely distributed through horizontal transfer.
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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 trimmed down by Flp-mediated recombination to just the lacZ reporter, so that the (beta)-galactosidase pattern is not influenced by sequences inside the P element. Twenty insertions into the bithorax complex express (beta)-galactosidase in segmentally limited patterns, reflecting the segmental domains of the bithorax complex where the elements reside. The mapping of segmental domains has now been revised, with enlargement of the abx/bx, bxd/pbx, and the iab-3 domains. The FRT sites in the P elements permit recombination between pairs of elements on opposite chromosomes, to generate duplications or deletions of the DNA between the two insertion sites. Using this technique, the length of the Ultrabithorax transcription unit was varied from 37 to 138 kb, but there was surprisingly little effect on Ultrabithorax function.
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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 were two variants of the 220-bp insertion, differing at two nucleotide positions at one of the termini. Other DNA molecules had complete or partial deletions of these structures and surrounding sequences in the viral enhancer. However, the end of the insertion at nucleotide 142 was frequently preserved. The viral early and late promoter activity of the variant regulatory regions was tested in a luciferase reporter assay by using transfected NIH 3T3 cells. In relation to the standard-type DNA, all variants, including a G272T mutant, had much stronger late promoters. In contrast, the early promoter activity was influenced in a positive or negative direction by individual mutations. Also, the activity of the viral origin of DNA replication was affected by the sequence variation of the regulatory region, although the effects were smaller than for the late promoter. Analysis by Southern blotting and quantification using dot blots showed that approximately 103 copies of material related to the 220-bp insert in murine pneumotropic virus DNA was present in mouse and human DNA but not in Escherichia coli DNA. Moreover, analysis by PCR indicated that there were multiple copies in the mouse genome of sequences that were identical or closely related to the 220-bp viral DNA segment. These data together with the nucleotide sequence analysis suggest that the 220-bp insertion is related to a transposable element of a novel type.
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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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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 DNA. Additionally, a short polypeptide containing the N-terminal putative DNA-binding motifs was footprinted on the DNA target site. These combined findings revealed that one protein subunit binds the R2 RNA template and the DNA 10 to 40 bp upstream of the insertion site. This subunit cleaves the first DNA strand and uses that cleavage to prime reverse transcription of the R2 RNA transcript. Another protein subunit(s) uses the N-terminal DNA binding motifs to bind to the 18 bp of target DNA downstream of the insertion site and is responsible for cleavage of the second DNA strand. A complete model for the R2 integration reaction is presented, which with minor modifications is adaptable to other non-LTR retrotransposons.
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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 the 180-bp knob-associated repeated DNA sequence used as a probe. Cloned knob DNA segments revealed a complex organization in which blocks of tandemly arranged 180-bp repeating units are interrupted by insertions of other repeated DNA sequences, mostly represented by individual full size copies of retrotransposable elements. There is an obvious preference for the integration of retrotransposable elements into certain sites (hot spots) of the 180-bp repeat. Sequence microheterogeneity including point mutations and duplications was found in copies of 180-bp repeats. The 180-bp repeats within an array all had the same polarity. Restriction maps constructed for 23 cloned knob DNA fragments revealed the positions of polymorphic sites and sites of integration of insertion elements. Discovery of the interspersion of retrotransposable elements among blocks of tandem repeats in maize and some other organisms suggests that this pattern may be basic to heterochromatin organization for eukaryotes.
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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.
Full textAbstract:
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 polymorphism among IS appears to be far less frequent than in eukaryotic transposons, indicating that nonfunctional elements comprise a smaller fraction of bacterial transposon populations than found in eukaryotes. IS present in other species of enteric bacteria are substantially divergent from E. coli elements, indicating that IS are mobilized among bacterial species at a reduced rate. However, homologs of IS1 and IS3 from diverse species provide evidence that recombination events and horizontal transfer of IS among species have both played major roles in the evolution of these elements. IS3 elements from E. coli and Shigella show multiple, nested, intragenic recombinations with a distantly related transposon, and IS1 homologs from diverse taxa reveal a mosaic structure indicative of multiple recombination and horizontal transfer events.
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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.
Full textAbstract:
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 colors of six different P[en] insertions in the escargot gene suggest an interaction between P[en]-encoded and genome-encoded PS sites. I hypothesize that white gene expression from P[en] is repressed by the formation of a protein complex which is initiated at the engrailed PS sites and also requires interactions with flanking genomic DNA. Genes were sought which influence the function of PS sites. Mutations in some Polycomb and trithorax group genes were found to affect the eye color from some P[en] insertion sites. However, different mutations affected expression from different P[en] insertion sites and no one mutation was found to affect expression from all P[en] insertion sites examined. These results suggest that white expression from P[en] is not directly regulated by members of the Polycomb and trithorax group genes, but in some cases can be influenced by them. I propose that engrailed PS sites normally act to promote interactions between distantly located engrailed regulatory sites and the engrailed promoter.