Transposable elements in yeasts

With the development of new sequencing technologies in the past decade, yeast genomes have been extensively sequenced and their structures investigated. Transposable elements (TEs) are ubiquitous in eukaryotes and constitute a limited part of yeast genomes. However, due to their ability to move in genomes and generate dispersed repeated sequences, they contribute to modeling yeast genomes and thereby induce plasticity. This review assesses the TE contents of yeast genomes investigated so far. Their diversity and abundance at the inter- and intraspecific levels are presented, and their effects on gene expression and genome stability is considered. Recent results concerning TE-host interactions are also analyzed.     

Transposable elements.

Transposable elements comprise a major fraction of eukaryotic genomes. They are studied both because of their intrinsic biological interest and because they can be exploited as valuable research tools. Many interesting papers dealing with various aspects of the biology of these elements have been published during the past year and a number of new elements have been reported. Four areas in which particularly valuable contributions have been made are the mechanisms of transposition, the regulation of transposition, the use of transposable elements as research tools, and the biological function of transposable elements.     

Transposable elements in medaka fish

DNA-based transposable elements appear to have been nearly or completely inactivated in vertebrates. Therefore the elements of the medaka fish Oryzias latipes that still have transposition activity provide precious materials for studying transposition mechanisms, as well as the evolution, of transposable elements in vertebrates. Fortunately, the medaka fish has a strong background for genetic and evolutionary studies. The advantages of this host species and their elements, together with results so far obtained, are here described.     

Transposable elements in disease-associated cryptic exons

Transposable elements (TEs) make up a half of the human genome, but the extent of their contribution to cryptic exon activation that results in genetic disease is unknown. Here, a comprehensive survey of 78 mutation-induced cryptic exons previously identified in 51 disease genes revealed the presence of TEs in 40 cases (51%). Most TE-containing exons were derived from short interspersed nuclear elements (SINEs), with Alus and mammalian interspersed repeats (MIRs) covering >18 and >16% of the exonized sequences, respectively. The majority of SINE-derived cryptic exons had splice sites at the same positions of the Alu/MIR consensus as existing SINE exons and their inclusion in the mRNA was facilitated by phylogenetically conserved changes that improved both traditional and auxiliary splicing signals, thus marking intronic TEs amenable for pathogenic exonization. The overrepresentation of MIRs among TE exons is likely to result from their high average exon inclusion levels, which reflect their strong splice sites, a lack of splicing silencers and a high density of enhancers, particularly (G)AA(G) motifs. These elements were markedly depleted in antisense Alu exons, had the most prominent position on the exon–intron gradient scale and are proposed to promote exon definition through enhanced tertiary RNA interactions involving unpaired (di)adenosines. The identification of common mechanisms by which the most dynamic parts of the genome contribute both to new exon creation and genetic disease will facilitate detection of intronic mutations and the development of computational tools that predict TE hot-spots of cryptic exon activation.     

Transposable elements in the Animal Kingdom

Transposable elements (TEs) are commonly thought to be of universal occurrence in eukaryotes. Analysis of complete higher eukaryotic genomes confirms TE status as substantial genome components and provides insights into their role in shaping the genome structure of extant eukaryotes. This review addresses several recently investigated problems in transposon biology, including potential roles of promoter organization in transposon function and evolution, the ubiquity of TEs in numerous phyla of the animal kingdom, and possible connections between transposon content and the mode of reproduction.     

Transposable elements and fitness in Drosophila melanogaster

Transposable elements constitute a significant fraction of the Drosophila melanogaster genome. The five families of moderately repeated transposable elements identified to date occupy dispersed and variable genomic locations, but have relatively constant copy numbers per individual. What effect to these elements have on the fitness of the individuals harboring them? Experimental evidence relating to this question is reviewed. The relevant data fall into two broad categories. The first involves the determination of the distribution of transposable elements in natural populations, by restriction mapping or in situ hybridization, and the comparison of the observed distribution with different theoretical expectations. The second approach is to study directly the effects of new transposable element-induced mutations on fitness. The P family of transposable elements is a particularly efficient mutagen, and the results of experiments in which initially P-free chromosomes are contaminated with P elements are discussed with regard to P-induced fitness mutations.     

Transposable elements controlling genetic instabilities in mammals

It is proposed that the instabilities in gene action of some alleles at certain loci in the mouse (e.g., a, c, H-2 Mi, p, pe, T, Va, W), which do not seem to conform to traditional hypotheses of gene action, are better interpretable in the light of modern studies of transposable DNA elements (insertion sequences and transposons of prokaryotic organisms; controlling elements of maize; transposable controlling elements of Drosophila). Some phenotypic evidence in the mouse in support of this hypothesis is presented for the a, Mi, p, and W loci, which affect pigmentation.     

Transposable elements and fitness of bacteria

A stochastic model was designed to describe the evolution of bacterial cultures during 10,000 generations. It is based on a decreasing law for the generation of beneficial mutations as they become fixed in the genomes. Seven beneficial mutations on average were necessary to improve the relative fitness from 1.0 to 1.43 and the model was consistent with the population biology and the genetic data of 12 experimental lines. In one bacterial line, comparison between the model and the data suggests that pivotal mutations mediated by insertion sequences account for a large part of bacterial adaptation. In a more detailed analysis of one simulation, it was shown that only 0.01% of the mutations generated by a population over 10,000 generations can go to fixation as a consequence of their improved fitness. However in the model, the probability of being better fit than its parent should be set initially at ca. 10% to promote an evolution similar to the observed data.     

Transposable elements and host genome evolution

Several recent reports have challenged the idea that transposable elements (TEs) are mainly 'selfish' or 'junk' DNA with little importance for host evolution. It has been proposed that TEs have the potential to provide host genomes with the ability to enhance their own evolution. They might also be a major source of genetic diversity, allowing response to environmental changes. Because the relationships between TEs and host genomes are highly variable, and because the selfish, junk and beneficial DNA hypotheses are by no means mutually exclusive, a single label for these relationships appears to be inappropriate and potentially misleading.     

转座因子和宿主基因组的进化

转座因子主要是一些“自在”或“无功能”的DNA,其对宿主进化无关紧要的观点受到了质疑。新近的报道指出,它们有增强宿主基因组自身进化,对环境变化作出反应的潜在能力,很可能是遗传多样性的主要源泉。     

Transposable elements and the dynamic somatic genome

Although alterations in the genomes of somatic cells cannot be passed on to future generations, they can have beneficial or detrimental effects on the host organism, depending on the context in which they occur. This review outlines the ways in which transposable elements have important consequences for somatic cell genomes.