A selfish origin for recombination

Recent findings of molecular biology show that recombination is initiated by interactions between homologous chromosomes and that an allele can induce the initiation of recombination on the homolog. Since gene conversion at the site of initiation is strong enough to promote the transmission of that allele, recombination may be a way for a self-promoting element to spread, even if it gives no advantage to the individual or to the population. I develop a simple model and discuss available molecular evidence in support of this hypothesis. A consequent argument is that with asexual reproduction the evolution of recombination leads to an intragenomic conflict, and a possible outcome of this conflict may be the origin of sexual reproduction.     

Isolation of human germ-line DNA suitable for recombinant DNA studies

Dna from human sperm cells can be isolated with size and purity sufficient for use in recombinant DNA research. The DNA averages 100 000 base pairs (bp) in size (about 70.10(6) daltons) and is free of somatic cell, bacterial, and viral DNA. It can therefore be cloned under P2 + EK2 conditions as stipulated in the 1978 NIH Guidelines for recombinant DNA research.     

Interspersed DNA element restricted to a specific group of telomeres in the dipteran Chironomus pallidivittatus.

Telomeres in the dipteran Chironomus pallidivittatus terminate with 340bp tandem DNA repeats belonging to different subfamilies with characteristic intertelomeric distribution. We have now found, interspersed between such repeats, a composite element of approx. 1400bp present in two similar size variants, with several components of nontelomeric origin. There were about 50 copies of the element, predominantly or exclusively present in a previously defined group of telomeres, characterized by a unique set of telomeric tandem repeat subfamilies. Elements were integrated at irregular distances from each other, and intervening telomeric tandem repeat DNA was variable in composition. Nevertheless, the flanks immediately surrounding the elements were identical for different elements; in other words, there was a site-specific insertion. We suggest that this selective invasion of a small part of the genome by an interspersed, probably rapidly evolving element is best explained by repeated gene conversions.     

Identification of a fully-functional hobo transposable element and its use for germ-line transformation of Drosophila.

The transposable element hobo can be mobilized to induce a variety of genetic abnormalities within the germ-line of Drosophila melanogaster. Strains containing hobos have 3.0 kb elements and numerous smaller derivatives of the element. By analogy with other transposable element systems, it is likely that only the 3.0 kb elements are capable of inducing hobo mobilization. Here, we report that a cloned 3.0 kb hobo, called HFL1, is able to mediate germ-line transformation and therefore is an autonomous (fully-functional) transposable element. Germ-line transformation was observed when HFL1 and a marked hobo element were co-injected into recipient embryos devoid of endogenous hobos. Integration did not occur in the absence of the 3.0 kb element. A single copy of the marked hobo transposon inserted at each site, and the target sites were widely distributed throughout the genome. Integration occurred at (or very near) the termini of hobo, without internal rearrangement of the hobo or marker gene sequences. The hobo transformation system will allow us to determine the structural and regulatory features of hobo responsible for its mobilization and will provide novel approaches for the molecular and genetic manipulation of the Drosophila genome.     

Homing endonuclease genes: the rise and fall and rise again of a selfish element

Homing endonuclease genes (HEGs) are selfish genetic elements that spread by first cleaving chromosomes that do not contain them and then getting copied across to the broken chromosome as a byproduct of the repair process. The success of this strategy will depend on the opportunities for homing--in other words, the frequency with which HEG(+) and HEG(-) chromosomes come into contact--which varies widely among host taxa. HEGs are also unusual in that the selection pressure for endonuclease function disappears if they become fixed in a population, which makes them susceptible to degeneration and imposes a need for regular horizontal transmission between species. HEGs will be selected to reduce the harm done to the host organism, and this is expected to influence the evolution of their sequence specificity and maturase functions. HEGs may also be domesticated by their hosts, and are currently being put to human uses.     

DNA and telomeres: beginnings and endings

How a cell deals with its DNA ends is a question that returns us to the very beginnings of modern telomere biology. It is also a question we are still asking today because it is absolutely essential that a cell correctly distinguishes between natural chromosomal DNA ends and broken DNA ends, then processes each appropriately - preserving the one, rejoining the other. Effective end-capping of mammalian telomeres has a seemingly paradoxical requirement for proteins more commonly associated with DNA double strand break (DSB) repair. Ku70, Ku80, DNA-PKcs (the catalytic subunit of DNA-dependent protein kinase), Xrcc4 and Artemis all participate in DSB repair through nonhomologous end-joining (NHEJ). Somewhat surprisingly, mutations in any of these genes cause spontaneous chromosomal end-to-end fusions that maintain large blocks of telomeric sequence at the points of fusion, suggesting loss or failure of a critical terminal structure, rather than telomere shortening, is at fault. Nascent telomeres produced via leading-strand DNA synthesis are especially susceptible to these end-to-end fusions, suggesting a crucial difference in the postreplicative processing of telomeres that is linked to their mode of replication. Here we will examine the dual roles played by DNA repair proteins. Our review of this rapidly advancing field primarily will focus on mammalian cells, and cannot include even all of this. Despite these limitations, we hope the review will serve as a useful gateway to the literature, and will help to frame the major issues in this exciting and rapidly progressing field. Our apologies to those whose work we are unable to include.     

Introduction of a functional P element into the germ-line of Drosophila hawaiiensis

When a plasmid carrying a P-transposable element (derived from Drosophila melanogaster) is injected into young embryos of D. hawaiiensis, the P-element sequence from the plasmid transposes into the germ-line chromosomes. The introduction of this P element into D. hawaiiensis provides an opportunity to study the behavior of the transposable element in a novel context. Germ-line transposition and numerical increase of the P elements are readily detected in D. hawaiiensis. Thus these aspects of P-element function do not require chromosomal or cytoplasmic properties that are unique to D. melanogaster. Since D. hawaiiensis is among those Drosophila that are most distantly related to D. melanogaster, these results suggest that P-element-mediated transformation may function in many species.     

The yeast 2 micron plasmid: strategies for the survival of a selfish DNA

Summary The designation of the yeast 2 circle as a selfish DNA molecule has been confirmed by demonstrating that the plasmid is lost with exponential kinetics from haploid yeast populations grown in continuous culture. We show that plasmid-free yeast cells have a growth rate advantage of some 1.5%–3% over their plasmid-containing counterparts. This finding makes the ubiquity of this selfish DNA in yeast strains puzzling. Two other factors probably account for its survival. First, the rate of plasmid loss was reduced by allowing haploid populations to enter stationary phase periodically. Second, it was not possible to isolate a plasmid-free segregant from a diploid yeast strain. Competition experiments demonstrated that stability in a diploid is conferred at the level of segregation and that plasmid-free diploid cells are at a selective advantage compared with their plasmid-containing counterparts. Yeast cells in nature are usually homothallic and must frequently pass through both diploid and stationary phases. The 2 plasmid appears to have evolved a survival strategy which exploits these two features of its host's life cycle.     

Structure of the Drosophila HeT-A transposon: a retrotransposon-like element forming telomeres

Telomeres of Drosophila appear to be very different from those of other organisms. A transposable element, HeT-A, plays a major role in forming telomeres and may be the sole structural element, since telomerase-generated repeats are not found. HeT-A transposes only to chromosome ends. It appears to be a retrotransposon but has novel structural features, which may be related to its telomere functions. A consensus sequence from cloned HeT-A elements defines an element of 6 kb. The coding region has retrotransposon-like overlapping open reading frames (ORFs) with a –1 frameshift in a sequence resembling the frameshift region of the mammalian HIV-1 retrovirus. Both the HeT-A ORFs contain motifs suggesting RNA binding. HeT-A-specific features include a long non-coding region, 3 of the ORFs, which makes up about half of the element. This region has a regular array of imperfect sequence repeats and ends with oligo(A), marking the end of the element and suggesting a polyadenylated RNA transposition intermediate. This 3 repeat region may have a structural role in heterochromatin. The most distal part of each complete HeT-A on the chromosome, the region 5 of the ORFs, has unusual conserved features, which might produce a terminal structure for the chromosome.     

Short telomeres induce a DNA damage response in Saccharomyces cerevisiae

Telomerase-deficient Saccharomyces cerevisiae cells show a progressive decrease in telomere length. When grown for several days in log phase, the tlc1Delta cells initially display wild-type growth kinetics with subsequent loss of growth potential after which survivors are generated via RAD52-dependent homologous recombination. We found that chromosome loss in these telomerase-deficient cells only increased after a significant decline in growth potential of the culture. At earlier stages of growth, as the telomerase-deficient cells began to show loss of growth potential, the cells arrested in G2/M and showed RNR3 induction and Rad53p phosphorylation. These responses were dependent on RAD24 and MEC1, suggesting that short telomeres are recognized as DNA damage and signal G2/M arrest.     

Organization of DNA sequences and replication origins at yeast telomeres

We have shown that the DNA sequences adjacent to the telomeres of Saccharomyces cerevisiae chromosomes are highly conserved and contain a high density of replication origins. The salient features of these telomeres can be summarized as follows. There are three moderately repetitive elements present at the telomeres: the 131 sequence (1 to 1.5 kb), the highly conserved Y sequence (5.2 kb), and the less conserved X sequence (0.3 to 3.75 kb). There is a high density of replication origins spaced about 6.7 kb apart at the telomeres. These replication origins are part of the X or the Y sequences. Some of the 131-Y repetitive units are tandemly arranged. The terminal sequence T (about 0.33 to 0.6 kb) is different from the 131, X, or Y sequences and is heterogeneous in length. The order of these sequences from the telomeric end towards the centromere is T-(Y-131)n-X-, where n ranges from 1 to no more than 4. Although these telomeric sequences are conserved among S. cerevisiae strains, they show striking divergence in certain closely related yeast species.     

Caenorhabditis elegans dna-2 is involved in DNA repair and is essential for germ-line development

Caenorhabditis elegans germ cell proliferation and development were severely damaged in second generation dna-2 homozygotes. Even in the first generation, a much higher incidence of aberrant chromosomes in oocytes and resultantly higher embryonic lethality were found vs. wild type, when DNA breaks were induced by gamma-rays or camptothecin. The deficiency of dna-2 in combination with RNA interference on mre-11 gene expression synergistically aggravated germ-line development, especially oocyte formation. These results suggest that C. elegans Dna-2 is involved in a DNA repair pathway paralleling homologous recombination or non-homologous end joining with mre-11 participation.     

A finite element model for analyzing shear wave propagation observed in magnetic resonance elastography

Magnetic resonance elastography (MRE) is a novel non-invasive approach to determine material stiffness by using a conventional magnetic resonance imaging (MRI) system incorporated with an oscillating motion-sensitizing gradient to detect nodal displacements produced by a shear excitation wave. The effects of material properties, excitation frequency, boundary conditions, and applied tension on shear wavelength measurement must be examined before MRE can become a useful diagnostic tool. We propose finite element (FE) modeling as a robust method to systematically study the effects of these parameters. An axisymmetric FE model was generated with ABAQUS to simulate agarose gel phantoms. The effects of material stiffness, density, and excitation frequency on propagating shear wavelength were examined individually. The effect of the boundary conditions on shear wavelength was also demonstrated. Results of shear wavelength from MRE measurement were compared with the results of FE model, which showed good agreement between the methods.