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PubMed2004

Computational analysis of transposable element sequences.

This chapter provides a simple guide for the computational analysis of transposable element (TE) sequences. Web links are provided for a number of sequence analysis applications, and their potential use in the analysis of TE sequences is briefly described. The level of detail provided is intended to be sufficient for a naive user to begin to analyze TE sequences in silico. The emphasis is placed on the identification, retrieval and manipulation of TE sequences. Information is also provided on the evolutionary study of TE sequences including the use phylogenetics programs.

Animals↗
PubMedDate not supplied

Chromatin structure in a region of a yeast transposable element regulating adjacent gene expression.

The chromatin structure of a portion of yeast transposable elements known to be responsible for regulation of the expression of the adjacent HIS4 gene has been investigated, using the nuclease probe micrococcal nuclease. Yeast strains containing Ty917 or derivatives of this element that possess either a His-, weak His+, or strong His+ phenotype were examined. The chromatin at the Ty/HIS4 junction region was accessible to micrococcal nuclease. A partial nucleosome ladder was observed upon digestion with micrococcal nuclease indicating the presence of three phased nucleosomes located in Ty sequences upstream of the HIS4 gene. Phased nucleosomes could not be detected upstream of the HIS4 gene in wild-type cells. These data suggest that nucleosomal structure is not a major contributor to Ty917-regulated adjacent gene expression at HIS4.

Chromatin↗
PubMed2003

Initiation of silencing of maize MuDR/Mu transposable elements.

Homology-dependent gene silencing contributes to genomic stability through suppression of transposable elements. Co-ordinate epigenetic silencing is the main regulatory mechanism controlling dispersed, multicopy MuDR/Mu elements responsible for Mutator activity in maize. Silencing eliminates transposition and proceeds through transcriptional inactivation of MuDR genes and DNA methylation of the terminal inverted repeats (TIRs) in both the regulatory MuDR and non-autonomous Mu elements. In plants with active MuDR/Mu elements, initiation of silencing coincides with nuclear retention of non-polyadenylated RNA derived from MuDR and recently described MuDR homologs (hMuDR elements). Nuclear accumulation of MuDR/hMuDR RNA is developmentally progressive, paralleling loss of Mutator activity and is predictive of loss of Mu somatic excision in the progeny. A high ratio of nuclear to cytoplasmic RNA is the earliest molecular marker for MuDR silencing suggesting that the nuclear RNA may trigger transcriptional silencing. We also demonstrate the constitutive presence of small transposon-specific RNAs of 21-26 nucleotides in all maize lines tested, independent of the Mutator activity. The role of the small RNAs in transposon silencing and translational regulation of transposon-encoded proteins is discussed.

Cell Nucleus↗
PubMed2004

Maintenance of a large pericentric inversion generated by the hobo transposable element in a transgenic line of Drosophila melanogaster.

The impact of the hobo transposable element in the global reorganization of the Drosophila melanogaster genome has been investigated in transgenic lines generated by the injection of hobo elements into the Hikone strain, which lacked them previously. Extensive surveys of transgenic lines followed for 250 generations have identified 13 inversions with hobo inserts at most breakpoints. One of these inversions is pericentric on chromosome 2. It has been maintained in the line where it was discovered and in several sublines at frequencies from 0.19 to 0.45, generating stable chromosomal polymorphisms, similar to cosmopolitan paracentric inversions in natural populations. Individuals homozygous for this inversion were viable and fertile, allowing the creation of a new homozygous strain.

Animals↗
PubMed1989

Evidence that mutation patterns vary among Drosophila transposable elements.

In Drosophila melanogaster, codon usage in the open reading frames (ORFs) of transposable elements (TEs) differs greatly from that in other ORFs. In addition, while the ORFs from a single element are similar, there is considerable variation among elements. In the TE ORFs there are no indications of selection for the codons prevalent in the other D. melanogaster genes, but rather codon usage can be succinctly summarized in terms of the base composition at silent sites. We suggest that the particular silent site base composition of each TE is determined by an individual pattern of mutation. In many of the TEs there is an ORF encoding a protein with homology to reverse transcriptase; the amino acid sequences of these are quite divergent, and so it is possible that each of these incorporates certain mismatched bases at different frequencies during replication.

Animals↗
PubMed2003

Modification of heat-shock gene expression in Drosophila melanogaster populations via transposable elements.

We report multiple cases in which disruption of hsp70 regulatory regions by transposable element (TE) insertions underlies natural variation in expression of the stress-inducible molecular chaperone Hsp70 in Drosophila melanogaster. Three D. melanogaster populations from different continents are polymorphic for jockey or P element insertions in the promoter of the hsp70Ba gene. All three TE insertions are within the same 87-bp region of hsp70Ba promoter, and we suggest that the distinctive promoter architecture of hsp genes may make them vulnerable to TE insertions. Each of the TE insertions reduces Hsp70 levels, and RNase protection assays demonstrate that such insertions can reduce transcription of the hsp70Ba gene. In addition, the TEs alter two measures of organismal fitness, inducible thermotolerance and female reproductive success. Thus, transposition can create quantitative genetic variation in gene expression within populations, on which natural selection can act.

Analysis of Variance↗
PubMed1996

Selection against transposable elements in D. simulans and D. melanogaster.

The insertion site numbers of the transposable elements (TEs) copia, mdg1, 412 and gypsy were determined in various natural populations of Drosophila melanogaster and D. simulans by in situ hybridization. We showed that, while all elements except gypsy had many insertion sites scattered over the chromosomes in D. melanogaster, only the 412 element in D. simulans presented a high number of insertions, and this number was lower than in D. melanogaster. This low 412 site number per genome in D. simulans was associated with a lower proportion of insertions on the X chromosome in comparison with D. melanogaster, as determined in diploid genomes (0.090 for D. simulans against 0.137 for D. melanogaster) and in haploid genomes (0.102 against 0.146), each value being, moreover, lower than the value of 0.20 expected on the hypothesis of no selection against insertional mutations. These results suggest that selection is a major mechanism explaining 412 copy number regulation in Drosophila, and is stronger in D. simulans than in D. melanogaster.

Animals↗
PubMed1998

Microsatellites, transposable elements and the X chromosome.

Variability at microsatellite (MS) loci is generally perceived as resulting from an interaction between mutation and genetic drift and, to a lesser extent, selection and recombination. Less investigated has been the reason for MS accumulation in genomes. We present here a simple model that could account for the variation in density of MS loci, assuming that they are created either through replication slippage or in association with transposable elements. Microsatellites then evolve under the forces cited above. We use this framework to revisit two results obtained from high-density genomic maps of the human and mouse genomes built with thousands of CA repeats: MS loci are (1) less variable and (2) less dense on the X chromosome than on autosomes. The first result is most likely explained by differential mutation on the X chromosome and the autosomes. The second result may be explained by differential mutation, provided the distributions of MS loci are still not at equilibrium. Selection, acting either directly on large allele size or indirectly on the transposable elements associated with MS, may explain the same result. The framework developed here is a first step toward more rigorous models, calling for additional data.

Animals↗
PubMed2006

Do transposable elements really contribute to proteomes?

Recent studies indicate that the initial classification of transposable elements (TEs) as 'useless', 'selfish' or 'junk' pieces of DNA is not an accurate one. TEs seem to have complex regulatory functions and contribute to the coding regions of many genes. Because this contribution had been documented only at transcript level, we searched for evidence that would also support the translation of TE cassettes. Our findings suggest that the proportion of proteins with TE-encoded fragments (approximately 0.1%), although probably underestimated, is much less than what the data at transcript level suggest (approximately 4%). In all cases, the TE cassettes are derived from old TEs, consistent with the idea that incorporation (exaptation) of TE fragments into functional proteins requires long evolutionary periods. We therefore argue that functional proteins are unlikely to contain TE cassettes derived from young TEs, the role of which is probably limited to regulatory functions.

Animals↗
PubMed1990

Interstrain crosses enhance excision of Tc1 transposable elements in Caenorhabditis elegans.

We report here an unusual activation of the Tc1 transposable element system in Caenorhabditis elegans. Germline Tc1 activity, as measured by reversion of unc-22::Tc1 alleles, is elevated 50- to 100-fold by certain crosses. For example, unc-22::Tc1 reversion is 1 x 10(-3) in a mut-6 IV strain and less than 1 x 10(-6) in a non-mutator strain, but in the unc-22::Tc1 progeny of a cross between mut-6 hermaphrodites and non-mutator males, reversion is 10(-1). The reciprocal cross does not induce this enhancement of reversion. Results similar to those for mut-6 were obtained using a mut-5 II strain. The mutator hermaphrodite by nonmutator male cross per se is not required for the enhancement of reversion, as mut-5 hermaphrodites x mut-6/+ males also induce unc-22 revertants at an elevated frequency. This reversion enhancement appears to depend on a maternal component inherited from a mutator strain, suggesting that the regulation of Tc1 activity may be complex.

Alleles↗
PubMed1998

A race-specific insertion of transposable element IS801 in Pseudomonas syringae pv. phaseolicola.

The isolation and cloning of a random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) band specific for Pseudomonas syringae pv. phaseolicola race 1 allowed us to design a pair of primers that amplify 1.2-kb race 1-specific and 2.7-kb race 2-specific fragments, providing a rapid method for the identification of races by standard PCR methods. Restriction analysis revealed identical endonuclease sites in both fragments but the race 2 fragment contains a 1.5-kb insertion, identified as transposable element IS801 by sequence comparison. One complete and one partial open reading frame (ORF), each with a high probability of encoding a protein, have been identified in the 1.2-kb fragment common to both race 1 and race 2 sequences. As IS801 disrupts the partial ORF in the race 2 fragment, the complete sequence of this ORF has been obtained as well as its promoter region. The possibility that it may encode an avirulence gene is discussed as well as the role of transposable elements in pathogen evolution.

Base Sequence↗
PubMed1987

An interchromosomal gene conversion of the Drosophila dunce locus identified with restriction site polymorphisms: a potential involvement of transposable elements in gene conversion.

Females heterozygous for the two alleles dnc2 and dncM14 of the X-linked gene dunce (dnc), and carrying a copy of dnc+ on the second chromosome, have produced a cluster of six dnc+ progeny X-chromosomes from recombination experiments. Restriction site polymorphisms have been used as genetic markers to follow the parentage of dnc locus segments in these chromosomes. All six chromosomes are identical with respect to the spectrum of restriction site markers they carry in the dnc+ chromosomal region. In the progeny chromosomes, this region is comprised of sequences like the dncM14 X-chromosome and the translocation copy of dnc+. Sequences flanking the dnc gene in the progeny chromosomes are like the dncM14 chromosome. Internal to the gene but near the 5' end, is a segment from the dnc+ translocation which has apparently originated from an interchromosomal and premeiotic gene conversion event. In addition, two transposable elements have inserted into the progeny chromosomes, one towards the 5' end of dnc and the other near the 3' end. The insertion of these elements occurred premeiotically since all six chromosomes are structurally identical. The data are interpreted with respect to a potential role of transposable element transposition in the process of gene conversion.

3',5'-Cyclic-AMP Phosphodiesterases↗
PubMed1994

Tn5401, a new class II transposable element from Bacillus thuringiensis.

A new class II (Tn3-like) transposable element, designated Tn5401, was recovered from a sporulation-deficient variant of Bacillus thuringiensis subsp. morrisoni EG2158 following its insertion into a recombinant plasmid. Sequence analysis of the insert revealed a 4,837-bp transposon with two large open reading frames, in the same orientation, encoding proteins of 36 kDa (306 residues) and 116 kDa (1,005 residues) and 53-bp terminal inverted repeats. The deduced amino acid sequence for the 36-kDa protein shows 24% sequence identity with the TnpI recombinase of the B. thuringiensis transposon Tn4430, a member of the phage integrase family of site-specific recombinases. The deduced amino acid sequence for the 116-kDa protein shows 42% sequence identity with the transposase of Tn3 but only 28% identity with the TnpA transposase of Tn4430. Two small open reading frames of unknown function, designated orf1 (85 residues) and orf2 (74 residues), were also identified. Southern blot analysis indicated that Tn5401, in contrast to Tn4430, is not commonly found among different subspecies of B. thuringiensis and is not typically associated with known insecticidal crystal protein genes. Transposition was studied with B. thuringiensis by using plasmid pEG922, a temperature-sensitive shuttle vector containing Tn5401. Tn5401 transposed to both chromosomal and plasmid target sites but displayed an apparent preference for plasmid sites. Transposition was replicative and resulted in the generation of a 5-bp duplication at the target site. Transcriptional start sites within Tn5401 were mapped by primer extension analysis. Two promoters, designated PL and PR, direct the transcription of orf1-orf2 and tnpI-tnpA, respectively, and are negatively regulated by TnpI. Sequence comparison of the promoter regions of Tn5401 and Tn4430 suggests that the conserved sequence element ATGTCCRCTAAY mediates TnpI binding and cointegrate resolution. The same element is contained within the 53-bp terminal inverted repeats, thus accounting for their unusual lengths and suggesting an additional role for TnpI in regulating Tn5401 transposition.

Amino Acid Sequence↗
PubMed1991

Molecular analysis of the Bg-rbg transposable element system of Zea mays L.

The two components of the Bg-rbg transposable element system of maize have been cloned. The Bg element, isolated from the mutable allele wx-m32:: Bg is inserted in the intron of the Waxy (Wx) gene between exons 12 and 13. The length of the element is of 4869 bp. Bg has 5 bp terminal inverted repeats, and generates upon insertion an 8 bp direct duplication of the target sequence. Both ends of the Bg element contain a 76 bp direct repeat adjacent to the terminal inverted repeats. The hexamer motif TATCGGC is here repeated several times in direct or inverse orientation. The rbg element was isolated from the mutable allele o2m(r) where it is located in the promoter region of the Opaque-2 (O2) gene. rbg is approximately 4.5 kb in length, has terminal inverted repeats identical to those of the Bg element, and is also flanked by an 8 bp direct duplication at the target site. Like Bg, rbg carries the 76 bp direct repeats. Restriction enzyme analysis reveals that, compared to Bg, the receptor element is distinguishable by small deletion and insertion events. Sequence data indicate that not more than 75% homology exists at the DNA level between the rbg element and the autonomous Bg element.

Alleles↗
PubMed1980

DNA rearrangements associated with a transposable element in yeast.

The his4-912 mutation results from insertion of a 6200 bp transposable element into the his4 gene of yeast. In order to clone the his4-912 mutation, the plasmid pBR322 was integrated into the his4 gene by means of yeast transformation, and then the vector sequences and the his4-912 insertion element were excised as a single restriction fragment. This his 4-912 insertion element is homologous to Ty1, a family of repetitive yeast DNA sequences. His+ revertants derived from the his4-912 mutant carry a number of chromosomal aberrations including deletions, translocations, a transposition and an inversion. The majority of His+ revertants result from deletions which have both endpoints within the element and which leave behind only 300 bp of the insertion element. Other derivatives of the his4-912 mutant carry deletions which have one endpoint in the insertion element and one endpoint in the his4 coding sequence. In two His+ revertants carrying reciprocal translocations, the chromosome III translocation breakpoints occur within the his4-912 insertion element. A His+ revertant carrying an inversion of most of the left arm of chromosome III may be an intermediate in transposition of the his4-912 insertion element to a new site on chromosome III.

Base Sequence↗
PubMed2004

Annotation of a 95-kb Populus deltoides genomic sequence reveals a disease resistance gene cluster and novel class I and class II transposable elements.

Poplar has become a model system for functional genomics in woody plants. Here, we report the sequencing and annotation of the first large contiguous stretch of genomic sequence (95 kb) of poplar, corresponding to a bacterial artificial chromosome clone mapped 0.6 centiMorgan from the Melampsora larici-populina resistance locus. The annotation revealed 15 putative genetic objects, of which five were classified as hypothetical genes that were similar only with expressed sequence tags from poplar. Ten putative objects showed similarity with known genes, of which one was similar to a kinase. Three other objects corresponded to the toll/interleukin-1 receptor/nucleotide-binding site/leucine-rich repeat class of plant disease resistance genes, of which two were predicted to encode an amino terminal nuclear localization signal. Four objects were homologous to the Ty1/ copia family of class I transposable elements, one of which was designated Retropop and interrupted one of the disease resistance genes. Two other objects constituted a novel Spm-like class II transposable element, which we designated Magali.

Amino Acid Sequence↗
PubMedDate not supplied

Similarity of the Cin1 repetitive family of Zea mays to eukaryotic transposable elements.

It has been suggested that the middle repetitive class of sequences that make up a large proportion of the eukaryotic genome have been amplified and dispersed by DNA transposition. Transposition is a phenomenon first postulated by Barbara McClintock on the basis of her genetic analysis of mutants in Zea mays. Since then, DNA transposition has been studied genetically in various plant systems and is well documented on the molecular level in both prokaryotes and eukaryotes. This has included the isolation of DNA inserts at various loci in several plants; however, the prevalence of transposition in plants is not established. We report here DNA nucleotide sequence data which show that some members of the Cin1 middle repetitive family of maize have features characteristic of known transposable elements. One cloned Cin1 repeat has a 6-base pair (bp) perfect inverted repeat sequence at its ends. The terminal five base pairs (5' TGTTG . . . CAACA 3') are identical to the termini of Drosophila copia transposable elements. Two other Cin1 alleles are flanked by 5-bp direct repeats. A comparison is made with the long terminal repeat (LTR) of the copia-Ty1-retrovirus families of moveable genetic elements.

Base Sequence↗
PubMed2002

Remarkable compartmentalization of transposable elements and pseudogenes in the heterochromatin of the Tetraodon nigroviridis genome.

Tetraodon nigroviridis is among the smallest known vertebrate genomes and as such represents an interesting model for studying genome architecture and evolution. Previous studies have shown that Tetraodon contains several types of tandem and dispersed repeats, but that their overall contribution is >10% of the genome. Using genomic library hybridization, fluorescent in situ hybridization, and whole genome shotgun and directed sequencing, we have investigated the global and local organization of repeat sequences in Tetraodon. We show that both tandem and dispersed repeat elements are compartmentalized in specific regions that correspond to the short arms of small subtelocentric chromosomes. The concentration of repeats in these heterochromatic regions is in sharp contrast to their paucity in euchromatin. In addition, we have identified a number of pseudogenes that have arisen through either duplication of genes or the retro-transcription of mRNAs. These pseudogenes are amplified to high numbers, some with more than 200 copies, and remain almost exclusively located in the same heterochromatic regions as transposable elements. The sequencing of one such heterochromatic region reveals a complex pattern of duplications and inversions, reminiscent of active and frequent rearrangements that can result in the truncation and hence inactivation of transposable elements. This tight compartmentalization of repeats and pseudogenes is absent in large vertebrate genomes such as mammals and is reminiscent of genomes that remain compact during evolution such as Drosophila and Arabidopsis.

Animals↗