The most unkindest cut of all

Roles of epigenome in mammalian spermatogenesis

Mammalian spermatogenesis is a successive process consisting of spermatogonial proliferation, spermatocytic meiosis, and spermiogenesis, representing the maturation of haploid spermatids. During the process, 25-75 % of the expected sperm yield is thought to be lost through apoptosis. In addition, spermatogenesis is considered to be a process undergoing successive heterochromatinization, finally reaching a complete condensed form in the sperm head. Thus, cell proliferation, differentiation and death may be strictly regulated by epigenetic factors in this process. This review describes the current understanding of the role of epigenome in spermatogenesis, especially focusing on the following aspects; DNA methylation, modification of histones, and small RNA function. These epigenetic factors affect each other and play a central role in events essential for spermatogenesis, fertilization and embryogenesis, through the regulation of gene expression, transposon activities, meiotic sex chromosome inactivation, histone remodeling and genome imprinting. Finally, a brief discussion of future avenues of study is highlighted.

Medfly transposable elements: diversity, evolution, genomic impact and possible applications

The medfly genome has been shown to contain a rich assortment of transposable elements from the mariner, Tc1, hAT and gypsy/Ty3 families. These elements display different levels of diversity, abundance and distribution in the genome. The presence of actively transposing elements in the medfly genome is revealed by hybrid dysgenesis phenomena, insertion site polymorphisms and other genetic instabilities. The medfly has been a target of transformation studies involving the exogenous elements Minos, Hermes and piggyBac from three families. The presence of active endogenous homologous elements can have important implications for the stability of such transgenic lines. The potential applications of endogenous elements for medfly population analysis and control are discussed.

Cytogenetic and molecular analysis of the pufferfish Tetraodon fluviatilis (Osteichthyes)

In view of their compact genome, pufferfish (Tetraodontiformes) have been proposed as model animal for the study of the vertebrate genome. Despite such interest, cytogenetic information about puffers is still scanty. To fill this gap, a cytogenetic analysis of T. fluviatilis has been performed using both classical and molecular techniques. C-banding, followed by DAPI staining, evidenced that in T. fluviatilis, like all other puffer species so far examined, heterochromatin is essentially AT-rich and it is located at centromeres, whereas staining with CMA3, silver staining and FISH with a 28S ribosomal RNA gene DNA probe showed 2-4 nucleolar organizing regions (NORs) located in heterochromatic regions in the considered puffer species. FISH with the 5S probe put in evidence both in T. fluviatilis and in T. nigroviridis only a 5S cluster per haploid genome that is physically unlinked with the major ribosomal RNA genes including the 28S rRNA genes. Hybridization with the (TTAGGG)n probe showed in all the puffers brightly fluorescent signals uniform both in size and intensity at the end of all the chromosomes. Finally, mariner-like elements (MLEs) have been identified in T. fluviatilis and they have located into the NOR-associated heterochromatin.

Self-inflicted wounds, template-directed gap repair and a recombination hotspot. Effects of the mariner transposase

Aberrant repair products of mariner transposition occur at a frequency of approximately 1/500 per target element per generation. Among 100 such mutations in the nonautonomous element peach, most had aberrations in the 5' end of peach (40 alleles), in the 3' end of peach (11 alleles), or a deletion of peach with or without deletion of flanking genomic DNA (29 alleles). Most mariner mutations can be explained by exonuclease "nibble" and host-mediated repair of the double-stranded gap created by the transposase, in contrast to analogous mutations in the P element. In mariner, mutations in the 5' inverted repeat are smaller and more frequent than those in the 3' inverted repeat, but secondary mutations in target elements with a 5' lesion usually had 3' lesions resembling those normally found at the 5' end. We suggest that the mariner transposase distinguishes between the 5' and 3' ends of the element, and that the 5' end is relatively more protected after strand scission. We also find: (1) that homolog-dependent gap repair is a frequent accompaniment to mariner excision, estimated as 30% of all excision events; and (2) that mariner is a hotspot of recombination in Drosophila females, but only in the presence of functional transposase.

Large deletions at the t(9;22) breakpoint are common and may identify a poor-prognosis subgroup of patients with chronic myeloid leukemia

The hallmark of chronic myeloid leukemia (CML) is theBCR-ABL fusion gene, which is usually formed as a result of the t(9;22) translocation. Patients with CML show considerable heterogeneity both in their presenting clinical features and in the time taken for evolution to blast crisis. In this study, metaphase fluorescence in situ hybridization showed that a substantial minority of patients with CML had large deletions adjacent to the translocation breakpoint on the derivative 9 chromosome, on the additional partner chromosome in variant translocations, or on both. The deletions spanned up to several megabases, had variable breakpoints, and could be detected by microsatellite polymerase chain reaction in unfractionated bone marrow and purified peripheral blood granulocytes. The deletions were likely to occur early and possibly at the time of the Philadelphia (Ph) chromosome translocation: deletions were detected at diagnosis in 11 patients, were found in all Ph-positive metaphases, and were more prevalent in patients with variant Ph chromosomes. Kaplan-Meier analysis showed a median survival time of 36 months in patients with a deletion; patients without a detectable deletion survived > 90 months. The survival-time difference was significant on log-rank analysis (P = .006). Multivariate analysis demonstrated that the prognostic importance of deletion status was independent of age, sex, percentage of peripheral blood blasts, and platelet count. Our data therefore suggest that an apparently simple, balanced translocation may result not only in the generation of a dominantly acting fusion oncogene but also in the loss of one or more genes that influence disease progression.

DNA METHYLATION IN PLANTS

Methylation of cytosine residues in DNA provides a mechanism of gene control. There are two classes of methyltransferase in Arabidopsis; one has a carboxy-terminal methyltransferase domain fused to an amino-terminal regulatory domain and is similar to mammalian methyltransferases. The second class apparently lacks an amino-terminal domain and is less well conserved. Methylcytosine can occur at any cytosine residue, but it is likely that clonal transmission of methylation patterns only occurs for cytosines in strand-symmetrical sequences CpG and CpNpG. In plants, as in mammals, DNA methylation has dual roles in defense against invading DNA and transposable elements and in gene regulation. Although originally reported as having no phenotypic consequence, reduced DNA methylation disrupts normal plant development.

Modern thoughts on an ancyent marinere: function, evolution, regulation

The mariner/Tc1 superfamily of transposable elements is one of the most diverse and widespread Class II transposable elements. Within the larger assemblage, the mariner-like elements (MLEs) and the Tc1-like elements (TLEs) are distinct families differing characteristically in the composition of the "D,D(35)E" cation-binding domain. Based on levels of sequence similarity, the elements in each family can be subdivided further into several smaller subfamilies. MLEs and TLEs both have an extraordinarily wide host range. They are abundant in insect genomes and other invertebrates and are found even in some vertebrate species including, in the case of mariner, humans, in which one element on chromosome 17p has been implicated as a hotspot of recombination. In spite of the extraordinary evolutionary success of the elements, virtually nothing is known about their mode of regulation within genomes. There is abundant evidence that the elements are disseminated to naive host genomes by horizontal transmission, and there is a substantial base of evidence for inference about the subsequent population dynamics. Studies of engineered mariner elements and induced mutations in the transposase have identified two mechanisms that may be operative in mariner regulation. One mechanism is overproduction inhibition, in which excessive wild-type transposase reduces the rate of excision of a target element. A second mechanism is dominant-negative complementation, in which certain mutant transposase proteins antagonize the activity of the wild-type transposase. The latter process may help explain why the vast majority of MLEs in nature undergo "vertical inactivation" by multiple mutations and, eventually, stochastic loss. There is also evidence that mariner/Tc1 elements can be mobilized in hybrid dysgenesis; in particular, certain dysgenic crosses in Drosophila virilis result in mobilization of a TLE designated Paris as well as the mobilization of other unrelated transposable elements.

Molecular evolution of an ancient mariner transposon, Hsmar1, in the human genome

A confident consensus sequence for Hsmar1, the first mariner transposon recognized in the human genome, was generated using three genomic and 15 cDNA sequences. It is thought to represent the ancestrally active copy that invaded an early primate genome. The consensus is 1287 base pairs (bp) long, has 30 bp perfect inverted terminal repeats (ITRs), and encodes a 343 amino acid (aa) mariner transposase. Each copy has diverged from the consensus largely independently of the others and mostly neutrally, and most are now defective. They differ from the consensus by an average of 7.8% in DNA sequence and 7.5 indels per kilobase, both of which values indicate that the copies were formed about 50 Myr ago. On average, only 20% of the 73 surmised CpG hypermutable sites in the consensus remain. A remarkable exception to this loss of functionality is revealed by a set of ten cDNA clones derived from a particular genomic copy that has diverged only 2.4% from the consensus, retained 54% of its hypermutable CpG pairs, and which has a full-length transposase open reading frame. The complete sequence of one of these cDNAs (NIB1543) indicates that the transposase gene of this copy may have been conserved because it is spliced to a human cellular gene encoding a SET domain protein. A specific PCR assay was used to reveal the presence of Hsmar1 copies in all primates examined representing all major lineages, but not in close relatives of primates. PCR fragments cloned and sequenced from a representative sample of primates confirmed that Hsmar1 copies are present in all major lineages, and also revealed another cecropia subfamily mariner in prosimians only, and a third highly divergent mariner present in the greater slow loris Nycticebus coucang. There are about 200 copies of Hsmar1 in the human genome, as well as +/-2400 copies of a derived 80 bp paired ITR structure and +/-4600 copies of solo ITRs. Thus, this transposon had a considerable insertional mutagenic effect on past primate genomes.

Cytosine methylation and the ecology of intragenomic parasites

Most of the 5-methylcytosine in mammalian DNA resides in transposons, which are specialized intragenomic parasites that represent at least 35% of the genome. Transposon promoters are inactive when methylated and, over time, C-->T transition mutations at methylated sites destroy many transposons. Apart from that subset of genes subject to X inactivation and genomic imprinting, no cellular gene in a non-expressing tissue has been proven to be methylated in a pattern that prevents transcription. It has become increasingly difficult to hold that reversible promoter methylation is commonly involved in developmental gene control; instead, suppression of parasitic sequence elements appears to be the primary function of cytosine methylation, with crucial secondary roles in allele-specific gene expression as seen in X inactivation and genomic imprinting.

EST! EST!! EST!!!

A recently published study has identified a set of candidate genes for human diseases based on findings from Drosophila. Each human expressed sequence tag (EST) in a large database was compared with all known Drosophila genes. After eliminating matches between genes of already known function, the remaining sequences were mapped in the human genome. In each region, the phenotypes of all known human diseases were compared with the phenotypes of known Drosophila mutations in order to identify candidate genes for the human diseases. Are the correspondences real or coincidental?