Retrotransposon reverse-transcriptase-mediated repair of chromosomal breaks

Transposons in filamentous fungi--facts and perspectives

Transposons are ubiquitous genetic elements discovered so far in all investigated prokaryotes and eukaryotes. In remarkable contrast to all other genes, transposable elements are able to move to new locations within their host genomes. Transposition of transposons into coding sequences and their initiation of chromosome rearrangements have tremendous impact on gene expression and genome evolution. While transposons have long been known in bacteria, plants, and animals, only in recent years has there been a significant increase in the number of transposable elements discovered in filamentous fungi. Like those of other eukaryotes, each fungal transposable element is either of class or of class II. While class I elements transpose by a RNA intermediate and employ reverse transcriptases, class II elements transpose directly at the DNA level. We present structural and functional features for such transposons that have been identified so far in filamentous fungi. Emphasis is given to specific advantages or unique features when fungal systems are used to study transposable elements, e.g., the evolutionary impact of transposons in coenocytic organisms and possible experimental approaches toward horizontal gene transfer. Finally, we focus on the potential of transposons for tagging and identifying fungal genes.

Repeats in genomic DNA: mining and meaning

For hundreds of millions of years, perhaps from the very beginning of their evolutionary history, eukaryotic cells have been habitats and junkyards for countless generations of transposable elements, preserved in repetitive DNA sequences. Analysis of these sequences, combined with experimental research, reveals a history of complex 'intracellular ecosystems' of transposable elements that are inseparably associated with genomic evolution.

Galectin-3 and L1 retrotransposons in human breast carcinomas

Galectin-3 is a galactoside binding protein found at elevated levels in a wide variety of neoplastic cells and thought to be involved in cognitive cellular interactions during transformation and metastasis. Previously, we have shown that introduction of human galectin-3 (Mr 31,000) cDNA into the human breast cancer cells BT-549 which are galectin-3 null and non-tumorigenic in nude mice resulted in the establishment of four galectin-3 expressing clones. Three of them acquired tumorigenicity when inoculated in the mammary fat pad of nude mice. Here, we questioned what is the molecular difference between the nude mouse tumorigenic and non-tumorigenic galectin-3 expressing BT-549 cell clones. Differential display analysis and Northern blotting revealed that, unlike the tumorigenic clones, neither the parental cells nor the non-tumorigenic clone expressed a 6.5 Kb transcript. A 607 bp PCR (polymerase chain reaction) product from the differentially displayed mRNA revealed a 93% sequence homology with the human L1 retrotransposon previously suggested to play a role in the pathobiology of some breast cancers. In addition, we show that the two gene products, i.e., galectin-3 and L1, are co-expressed in breast carcinoma specimens and in other nude mouse tumorigenic cell lines.

Dispersed repetitive DNA has spread to new genomes since polyploid formation in cotton

Polyploid formation has played a major role in the evolution of many plant and animal genomes; however, surprisingly little is known regarding the subsequent evolution of DNA sequences that become newly united in a common nucleus. Of particular interest is the repetitive DNA fraction, which accounts for most nuclear DNA in higher plants and animals and which can be remarkably different, even in closely related taxa. In one recently formed polyploid, cotton (Gossypium barbadense L.; AD genome), 83 non-cross-hybridizing DNA clones contain dispersed repeats that are estimated to comprise about 24% of the nuclear DNA. Among these, 64 (77%) are largely restricted to diploid taxa containing the larger A genome and collectively account for about half of the difference in DNA content between Old World (A) and New World (D) diploid ancestors of cultivated AD tetraploid cotton. In tetraploid cotton, FISH analysis showed that some A-genome dispersed repeats appear to have spread to D-genome chromosomes. Such spread may also account for the finding that one, and only one, D-genome diploid cotton, Gossypium gossypioides, contains moderate levels of (otherwise) A-genome-specific repeats in addition to normal levels of D-genome repeats. The discovery of A-genome repeats in G. gossypioides adds genome-wide support to a suggestion previously based on evidence from only a single genetic locus that this species may be either the closest living descendant of the New World cotton ancestor, or an adulterated relic of polyploid formation. Spread of dispersed repeats in the early stages of polyploid formation may provide a tag to identify diploid progenitors of a polyploid. Although most repetitive clones do not correspond to known DNA sequences, 4 correspond to known transposons, most contain internal subrepeats, and at least 12 (including 2 of the possible transposons) hybridize to mRNAs expressed at readily discernible levels in cotton seedlings, implicating transposition as one possible mechanism of spread. Integration of molecular, phylogenetic, and cytogenetic analysis of dispersed repetitive DNA may shed new light on evolution of other polyploid genomes, as well as providing valuable landmarks for many aspects of genome analysis.

Drosophila telomere elongation

Drosophila melanogaster has an unusual telomere elongation mechanism. Instead of short repeats that are synthesized by telomerase, long retrotransposons, HeT-A and TART, transpose to the ends of chromosomes. This mechanism generates tandem arrays of these elements at the chromosome ends, in which all elements are oriented with their oligo(A) tails towards the centromere. Structural features of HeT-A and TART elements may provide clues as to their transposition mechanism. Drosophila telomere length polymorphism is mainly due to terminal retrotransposon arrays that differ between chromosome tips and that change with time. In addition, stable terminal chromosome deletions can be generated that do not contain terminal HeT-A and TART arrays, suggesting that, unlike the equivalent terminal repeats in yeast and humans, the presence and length of terminal arrays in Drosophila may not be critical for cell cycle progression.

Double-strand break repair mediated by DNA end-joining

DNA double-strand breaks formed by ionizing irradiation or other stresses are repaired by homologous recombination or DNA end-joining. This review focuses on the mechanism of double-strand break repair mediated by DNA end-joining, in which many factors have recently been identified. After DNA double-strand breakage, DNA end-joining takes place between the DNA ends that have nonhomologous sequences or very short regions ofhomology. The broken DNA is repaired if the DNA end-joining occurs in the same molecule, while it causes chromosome aberrations such as deletions, insertions, translocations and inversions if it occurs between different molecules. Rad50 and its relatives, Ku-proteins, DNA ligase VI and silencing factors, are involved in DNA end-joining in yeast and mammalian cells. These findings led us to propose a model in which the formation of a heterochromatin-like complex at broken ends is an important element in DNA end-joining.

Replication errors during in vivo Ty1 transposition are linked to heterogeneous RNase H cleavage sites

We previously identified a mutational hotspot upstream of the Ty1 U5-primer binding site (PBS) border and proposed a novel mechanism to account for this phenomenon during Ty1 replication. In this report, we verify key points of our model and show that in vivo RNase H cleavage of Ty1 RNA during minus-strand strong-stop synthesis creates heterogeneous 5' RNA ends. The preferred cleavage sites closest to the PBS are 6 and 3 bases upstream of the U5-PBS border. Minus-strand cDNA synthesis terminates at multiple sites determined by RNase H cleavage, and DNA intermediates frequently contain 3'-terminal sequence changes at or near their template ends. These data indicate that nontemplated terminal base addition during reverse transcription is a real in vivo phenomenon and suggest that this mechanism is a major source of sequence variability among retrotransposed genetic elements.

tRNA genes and retroelements in the yeast genome

A survey of tRNA genes and retroelements (Ty) in the genome of the yeast Saccharomyces cerevisiae is presented. Aspects of genomic organization and evolution of these genetic entities and their interplay are discussed. Attention is also given to the relationship between tRNA gene multiplicity and codon selection in yeast and the role of Ty elements.

Transposable element-host interactions: regulation of insertion and excision

Transposable elements propagate by inserting into new locations in the genomes of the hosts they inhabit. Their transposition might thus negatively affect the fitness of the host, suggesting the requirement for a tight control in the regulation of transposable element mobilization. The nature of this control depends on the structure of the transposable element. DNA elements encode a transposase that is necessary, and in most cases sufficient, for mobilization. In general, regulation of these elements depends on intrinsic factors with little direct input from the host. Retrotransposons require an RNA intermediate for transposition, and their frequency of mobilization is controlled at multiple steps by the host genome by regulating both their expression levels and their insertional specificity. As a result, a symbiotic relationship has developed between transposable elements and their host. Examples are now emerging showing that transposons can contribute significantly to the well being of the organisms they populate.

Mobile elements inserted in the distant past have taken on important functions

Current evidence on the long-term evolutionary effect of insertion of sequence elements is reviewed. There are three criteria for inclusion of an example: (i) the element was inserted far in the past and thus the event is not a transient mutation; (ii) the element is a member of a large group of similar sequences; (iii) the element now serves a useful function. There are 21 examples from Drosophila, sea urchin, human and mouse genomes that meet these criteria. Taken together, these examples show that the insertion of sequence elements in the genome has been a significant source of regulatory variation in evolution.

Non-homologous DNA end joining in plant cells is associated with deletions and filler DNA insertions

Double strand DNA breaks in plants are primarily repaired via non-homologous end joining. However, little is known about the molecular events underlying this process. We have studied non-homologous end joining of linearized plasmid DNA with different termini configurations following transformation into tobacco cells. A variety of sequences were found at novel end junctions. Joining with no sequence alterations was rare. In most cases, deletions were found at both ends, and rejoining usually occurred at short repeats. A distinct feature of plant junctions was the presence of relatively large, up to 1.2 kb long, insertions (filler DNA), in approximately 30% of the analyzed clones. The filler DNA originated either from internal regions of the plasmid or from tobacco genomic DNA. Some insertions had a complex structure consisting of several reshuffled plasmid-related regions. These data suggest that double strand break repair in plants involves extensive end degradation, DNA synthesis following invasion of ectopic templates and multiple template switches. Such a mechanism is reminiscent of the synthesis-dependent recombination in bacteriophage T4. It can also explain the frequent 'DNA scrambling' associated with illegitimate recombination in plants.

Functional differences between the human LINE retrotransposon and retroviral reverse transcriptases for in vivo mRNA reverse transcription

We have analysed the reverse transcriptase (RT) activity of the human LINE retrotransposon and that of two retroviruses, using an in vivo assay within mammalian (murine and human) cells. The assay relies on transfection of the cells with expression vectors for the RT of the corresponding elements and PCR analysis of the DNA extracted 2-4 days post-transfection using primers bracketing the intronic domains of co-transfected reporter genes or of cellular genes. This assay revealed high levels of reverse-transcribed cDNA molecules, with the intron spliced out, with expression vectors for the LINE. Generation of cDNA molecules requires LINE ORF2, whereas ORF1 is dispensable. Deletion derivatives within the 3.8 kb LINE ORF2 allowed further delineation of the RT domain: > 0.7 kb at the 5'-end of the LINE ORF2 is dispensable for reverse transcription, consistent with this domain being an endonuclease-like domain, as well as 1 kb at the 3'-end, a putative RNase H domain. Conversely, the RT of the two retroviruses tested, Moloney murine leukemia virus and human immunodeficiency virus, failed to produce similar reverse transcripts. These experiments demonstrate a specific and high efficiency reverse transcription activity for the LINE RT, which applies to RNA with no sequence specificity, including those from cellular genes, and which might therefore be responsible for the endogenous activity that we previously detected within mammalian cells through the formation of pseudogene-like structures.

A phosphoglycerate mutase brain isoform (PGAM 1) pseudogene is localized within the human Menkes disease gene (ATP7 A)

We have identified a phosphoglycerate mutase brain isoform (PGAM 1, PGAM B) cDNA that is localized between exons 1 and 2 of the Menkes disease gene (ATP7 A, MNK) at Xq13.3. The cDNA shows 98% identity to the previously identified PGAM 1 cDNA (Sakoda et al., J. Biol. Chem. 263 (1988) 16899-16905) and probably represents a recent retroposition of this parent PGAM 1 mRNA. Although the typical features of a processed pseudogene are present, the open reading frame (ORF) of this PGAM cDNA is potentially expressed. There are 11 bp changes in the 765 bp ORF, none of which are nonsense mutations or deletions. The region upstream from the ORF shows some features of a possible promoter region, although it lacks a CpG island often associated with functional promoters. We analyzed the expression of this PGAM 1 cDNA using RT-PCR followed by restriction enzyme digestion based on a 1 bp missmatch in this cDNA to distinguish it from normal PGAM 1 gene expression. With this sensitive method, we could not find expression in any of the tissues examined. Taken together, we conclude that the PGAM 1 cDNA upstream from exon 2 of the Menkes gene is likely to be a processed pseudogene originating from a very recent retroposition of a PGAM 1 transcript. To our knowledge this is the first report of a pseudogene located within a gene.

Homing endonucleases: keeping the house in order

Homing endonucleases are rare-cutting enzymes encoded by introns and inteins. They have striking structural and functional properties that distinguish them from restriction enzymes. Nomenclature conventions analogous to those for restriction enzymes have been developed for the homing endonucleases. Recent progress in understanding the structure and function of the four families of homing enzymes is reviewed. Of particular interest are the first reported structures of homing endonucleases of the LAGLIDADG family. The exploitation of the homing enzymes in genome analysis and recombination research is also summarized. Finally, the evolution of homing endonucleases is considered, both at the structure-function level and in terms of their persistence in widely divergent biological systems.

The zebrafish BMP4 gene: sequence analysis and expression pattern during embryonic development

We have isolated zebrafish BMP4 gene from a zebrafish genomic DNA library. The size of the isolated BMP4 gene was approximately 14.9 kb. The isolated gene contained two exons which formed the complete coding region together with part of the 3'-noncoding region. The deduced BMP4 protein sequence contained 400 amino acids. Sequence comparison showed that it shared 73% amino acid sequence identity with that of human and mouse BMP4. An intron with a size of 8,963 bp was present between two coding exons. Danio retroposon A (DANA)-like retroposon was located in the intron. It contained four conserved boxes and was flanked by a pair of direct repeats of 9 nucleotide sequence (GTTTTAATA). During embryonic development of the zebrafish, a 3.8-kb BMP4 mRNA was detected from gastrula stage up to a month-old hatching larvae via Northern blot analysis. In addition, the use of reverse transcription polymerase chain reaction further demonstrated the presence of BMP4 mRNA in both the early developmental stages (i.e., cleavage and blastula) and in adult fish. Developmental expression of BMP4 protein was also analyzed. Trace amounts of an 18-kD protein were detected at pharyngula stage, while the production increased from hatching larvae to adult fish. In adult fish, the expression of BMP4 mRNA was observed in brain, heart, digestive tracts, testes, and jaw. The results suggest that the zebrafish BMP4 gene may play important roles during zebrafish development.

Transposable elements as sources of variation in animals and plants

A tremendous wealth of data is accumulating on the variety and distribution of transposable elements (TEs) in natural populations. There is little doubt that TEs provide new genetic variation on a scale, and with a degree of sophistication, previously unimagined. There are many examples of mutations and other types of genetic variation associated with the activity of mobile elements. Mutant phenotypes range from subtle changes in tissue specificity to dramatic alterations in the development and organization of tissues and organs. Such changes can occur because of insertions in coding regions, but the more sophisticated TE-mediated changes are more often the result of insertions into 5' flanking regions and introns. Here, TE-induced variation is viewed from three evolutionary perspectives that are not mutually exclusive. First, variation resulting from the intrinsic parasitic nature of TE activity is examined. Second, we describe possible coadaptations between elements and their hosts that appear to have evolved because of selection to reduce the deleterious effects of new insertions on host fitness. Finally, some possible cases are explored in which the capacity of TEs to generate variation has been exploited by their hosts. The number of well documented cases in which element sequences appear to confer useful traits on the host, although small, is growing rapidly.

Reln(rl-Alb2), an allele of reeler isolated from a chlorambucil screen, is due to an IAP insertion with exon skipping

The reeler Albany2 mutation (Reln(rl-Alb2) in the mouse is an allele of reeler isolated during a chlorambucil mutagenesis screen. Homozygous animals had drastically reduced concentrations of reelin mRNA, in which an 85-nt exon was absent. At the genomic level, the mutation was shown to be due to an intracisternal A-particle insertion leading to exon skipping. This appears to be the first observation of retrotransposon insertion during chlorambucil mutagenesis.

Molecular origin of the mosaic sequence arrangements of higher primate alpha-globin duplication units

The human adult alpha-globin locus consists of three pairs of homology blocks (X, Y, and Z) interspersed with three nonhomology blocks (I, II, and III), and three Alu family repeats, Alu1, Alu2, and Alu3. It has been suggested that an ancient primate alpha-globin-containing unit was ancestral to the X, Y, and Z and the Alu1/Alu2 repeats. However, the evolutionary origin of the three nonhomologous blocks has remained obscure. We have now analyzed the sequence organization of the entire adult alpha-globin locus of gibbon (Hylobates lar). DNA segments homologous to human block I occur in both duplication units of the gibbon alpha-globin locus. Detailed interspecies sequence comparisons suggest that nonhomologous blocks I and II, as well as another sequence, IV, were all part of the ancestral alpha-globin-containing unit prior to its tandem duplication. However, sometime thereafter, block I was deleted from the human alpha1-globin-containing unit, and block II was also deleted from the alpha2-globin-containing unit in both human and gibbon. These were probably independent events both mediated by independent illegitimate recombination processes. Interestingly, the end points of these deletions coincide with potential insertion sites of Alu family repeats. These results suggest that the shaping of DNA segments in eukaryotic genomes involved the retroposition of repetitive DNA elements in conjunction with simple DNA recombination processes.

Many human L1 elements are capable of retrotransposition

Using a selective screening strategy to enrich for active L1 elements, we isolated 13 full-length elements from a human genomic library. We tested these and two previously-isolated L1s (L1.3 and L1.4) for reverse transcriptase (RT) activity and the ability to retrotranspose in HeLa cells. Of the 13 newly-isolated L1s, eight had RT activity and three were able to retrotranspose. L1.3 and L1.4 possessed RT activity and retrotransposed at remarkably high frequencies. These studies bring the number of characterized active human L1 elements to seven. Based on these and other data, we estimate that 30-60 active L1 elements reside in the average diploid genome.

Transposable elements: how non-LTR retrotransposons do it

The source of the enzyme activity responsible for the transposition of retrotransposons of the type that lack terminal repeats has at last been identified: in L1Hs elements, it is encoded by the second open reading frame and is a nuclease related to the apurinic repair endonucleases.

Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons

It is commonly accepted that the reverse-transcribed cellular RNA molecules, called retroposons, integrate at staggered breaks in mammalian chromosomes. However, unlike what was previously thought, most of the staggered breaks are not generated by random nicking. One of the two nicks involved is primarily associated with the 5'-TTAAAA hexanucleotide and its variants derived by a single base substitution, particularly A --> G and T --> C. It is probably generated in the antisense strand between the consensus bases 3'-AA and TTTT complementary to 5'-TTAAAA. The sense strand is nicked at variable distances from the TTAAAA consensus site toward the 3' end, preferably within 15-16 base pairs. The base composition near the second nicking site is also nonrandom at positions preceding the nick. On the basis of the observed sequence patterns it is proposed that integration of mammalian retroposons is mediated by an enzyme with endonucleolytic activity. The best candidate for such enzyme may be the reverse transcriptase encoded by the L1 non-long-terminal-repeat retrotransposon, which contains a freshly reported domain homologous to the apurinic/apyrimidinic (AP) endonuclease family [Martin, F., Olivares, M., Lopez, M. C. & Alonso, C. (1996) Trends Biochem. Sci. 21, 283-285; Feng, Q., Moran, J. V., Kazazian, H. H. & Boeke, J. D. (1996) Cell 87, 905-916] and shows nicking in vitro with preference for targets similar to 5'-TTAAAA/3'-AATTTT consensus sequence [Feng, Q., Moran, J. V., Kazazian, H. H. & Boeke, J. D. (1996) Cell 87, 905-916]. A model for integration of mammalian retroposons based on the presented data is discussed.

Evolutionary links between telomeres and transposable elements

Transposable elements are abundant in the genomes of higher organisms but are usually thought to affect cells only incidentally, by transposing in or near a gene and influencing its expression. Telomeres of Drosophila chromosomes are maintained by two non-LTR retrotransposons, HeT-A and TART. These are the first transposable elements with identified roles in chromosome structure. We suggest that these elements may be evolutionarily related to telomerase; in both cases an enzyme extends the end of a chromosome by adding DNA copied from an RNA template. The evolution of transposable elements from chromosomal replication mechanisms may have occurred multiple times, although in other organisms the new products have not replaced the endogenous telomerase, as they have in Drosophila. This is somewhat reminiscent of the oncogenes that have arisen from cellular genes. Perhaps the viruses that carry oncogenes have also arisen from cellular genetic systems.

Capture of retrotransposon DNA at the sites of chromosomal double-strand breaks

Non-homologous repair of broken chromosomes in Saccharomyces cerevisiae can be studied at a defined location by expressing the site-specific HO endonuclease that cuts the mating-type (MAT) locus. When homologous recombination is prevented, most double-strand breaks are repaired by non-homologous end-joinings similar to those observed in mammalian cells. About 1% of non-homologous repair events were exceptional, having 'captured' approximately 100 base pairs of DNA within the HO cleavage site. In each case, the insertion came from yeast's retrotransposon Tyl element. Four of the five contained the R-U5 region, which is the first part of Tyl messenger RNA to be converted to complementary DNA. The capture of cDNA fragments at the sites of double-strand breaks may account for the way that pseudogenes and long and short interspersed sequences (LINES and SINES) have been inserted at many locations in the mammalian genome.