Mermaid: a family of short interspersed repetitive elements widespread in vertebrates

Oxidative stress and genetic markers of suboptimal antioxidant defense in the aging brain: a theoretical review

Normal aging involves a gradual breakdown of physiological processes that leads to a decline in cognitive functions and brain integrity, yet the onset and progression of decline are variable among older individuals. While many biological changes may contribute to this degree of variability, oxidative stress is a key mechanism of the aging process that can cause direct damage to cellular architecture within the brain. Oligodendrocytes are at a high risk for oxidative damage due to their role in myelin maintenance and production and limited repair mechanisms, suggesting that white matter may be particularly vulnerable to oxidative activity. Antioxidant defense enzymes within the brain, such as superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), and glutathione-S-transferase (GST), are crucial for breaking down the harmful end products of oxidative phosphorylation. Previous studies have revealed that allele variations of polymorphisms that encode these antioxidants are associated with abnormalities in SOD, CAT, GPx, and GST activity in the central nervous system. This review will focus on the role of oxidative stress in the aging brain and the impact of decreased antioxidant defense on brain integrity and cognitive function. Directions for future research investigations of antioxidant defense genes will also be discussed.

Decrease in cytosine methylation at CpG island shores and increase in DNA fragmentation during zebrafish aging

Age-related changes in DNA methylation have been demonstrated in mammals, but it remains unclear as to the generality of this phenomenon in vertebrates, which is a criterion for the fundamental cause of senescence. Here we showed that the zebrafish genome gradually and clearly lost methylcytosine in somatic cells, but not in male germ cells during aging, and that age-dependent hypomethylation preferentially occurred at a particular domain called the CpG island shore, which is associated with vertebrates' genes and has been shown to be hypomethylated in humans with age. We also found that two CpG island shores hypomethylated in zebrafish oocytes were de novo methylated in fertilized eggs, which suggests that the zebrafish epigenome is reset upon fertilization, enabling new generations to restart with a heavily methylated genome. Furthermore, we observed an increase in cleavage of the zebrafish genome to an oligonucleosome length in somatic cells from the age of 12 months, which is suggestive of an elevated rate of apoptosis in the senescent stage.

Inverse PCR-based method for isolating novel SINEs from genome

Short interspersed elements (SINEs) are moderately repetitive DNA sequences in eukaryotic genomes. Although eukaryotic genomes contain numerous SINEs copy, it is very difficult and laborious to isolate and identify them by the reported methods. In this study, the inverse PCR was successfully applied to isolate SINEs from Opsariichthys bidens genome in Eastern Asian Cyprinid. A group of SINEs derived from tRNA(Ala) molecular had been identified, which were named Opsar according to Opsariichthys. SINEs characteristics were exhibited in Opsar, which contained a tRNA(Ala)-derived region at the 5' end, a tRNA-unrelated region, and AT-rich region at the 3' end. The tRNA-derived region of Opsar shared 76 % sequence similarity with tRNA(Ala) gene. This result indicated that Opsar could derive from the inactive or pseudogene of tRNA(Ala). The reliability of method was tested by obtaining C-SINE, Ct-SINE, and M-SINEs from Ctenopharyngodon idellus, Megalobrama amblycephala, and Cyprinus carpio genomes. This method is simpler than the previously reported, which successfully omitted many steps, such as preparation of probes, construction of genomic libraries, and hybridization.

Fish transposons and their potential use in aquaculture

A large part of repetitive DNA of vertebrate genomes have been identified as transposon elements (TEs) or mobile sequences. Although TEs detected to date in most vertebrates are inactivated, active TEs have been found in fish and a salmonid TE has been successfully reactivated by molecular genetic manipulation from inactive genomic copies (Sleeping Beauty, SB). Progress in the understanding of the dynamics, control and evolution of fish TEs will allow the insertion of selected sequences into the fish genomes of germ cells to obtain transgenics or to identify genes important for growth and/or of somatic cells to improve DNA vaccination. Expectations are high for new possible applications to fish of this well developed technology for mammals. Here, we review the present state of knowledge of inactive and active fish TEs and briefly discuss how their possible future applications might be used to improve fish production in aquaculture.

Identification of a gene required for de novo DNA methylation of the zebrafish no tail gene

The zebrafish no tail gene (ntl) is indispensable for tail and notochord development. We have shown previously that ntl is de novo methylated during early embryogenesis. To find the gene that de novo methylates ntl and understand the meaning of this methylation, we cloned seven genes that encode the conserved catalytic domain of methyltransferases. We found that injection of antisense morpholino oligonucleotides against one of them, termed dnmt7, into eggs significantly reduced the level of ntl methylation, although no apparent phenotype was induced by the injection. Inhibition of Dnmt7 activity did not change the level of genome-wide methylation nor did it affect de novo methylation of injected plasmid DNA, indicating that Dnmt7 specifically methylates ntl in the genome.

Gamera, a family of LINE-like repetitive sequences widely distributed in medaka and related fishes

A family of repetitive sequences, designated Gamera, has been identified in the genome of the Hainan medaka fish Oryzias curvinotus, a closely related species to the common medaka fish O. latipes. Sequencing and Southern blot analyses of this family revealed: (1) amino acid sequence similarity to reverse transcriptase domains of long interspersed nuclear elements (LINEs); (2) 5' truncation of dispersed copies; and (3) the disruption of another genetic element, indicating a past transposition event. These results suggest that Gamera belongs to the LINE superfamily. Gamera is widely distributed in the genus Oryzias, and the phylogenetic relationship might indicate its presence in the common ancestor of the genus.

Selachian cytogenetics: a review

The karyotype of Chondrichthyes is still the least investigated among vertebrates. Over the last 40 years, the karyotypes of 63 out of the 1100 known species (5.73%) have been described in literature, namely seven squalomorph, one squatinomorph, 20 galeomorph, 33 batoid and two holocephalian species. Generally, the diploid number ranges from a minimum of 28 to a maximum of 106 elements, with more frequent values observed between 50 and 100 chromosomes. None of the four superorders is characterized by a peculiar chromosome set or morphology; the number of uniarmed and biarmed elements is variable in all the karyotypes, and microchromosomes are often present. The general trend in all groups seems to be a progressive reduction of the telocentric chromosome number in the most specialized species, followed by the loss of the microchromosomes. Polyploidy, followed by diploidization events and Robertsonian rearrangements, might have played a key role in the karyological evolution of elasmobranch fish. Chondrichthyes have the largest genome sizes among vertebrates, with the exception of dipnoans and urodeles. In the whole class, the species examined vary greatly in size, from 3 to 34pg/N: the lowest values have been observed in holocephalians, while galeoids and batoids have a DNA amount ranging from 5 to 15 pg/N. Squaloids show heterogeneous DNA amounts, ranging from 8 to 34 pg/N. In more recent years, karyological studies have provided new data on the characterization of selachian karyotypes by C-banding, NOR staining, restriction enzymes in situ digestion and FISH with specific DNA probes, such as telomeric and SINE sequences.

The skeletal muscle alpha-actin gene of channel catfish (Ictalurus punctatus) and its association with piscine specific SINE elements

The alpha-actin gene of channel catfish (Ictalurus punctatus) was cloned and sequenced. The gene has a similar organization and exhibited a high level of sequence similarity to those from other vertebrate animals. The upstream region of the alpha-actin gene included a TATA box, a CAAT box, three E-boxes, and a CArG box. Nested deletion segments containing these transcriptional motifs were fused to the reporter gene chloramphenicol acetyl transferase (CAT). Transfection of the clones into C2C12 cells indicated that all these motifs are required for transcriptional activities. The channel catfish alpha-actin gene is associated with two distinct short interspersed repetitive elements (SINEs). The first SINE element showed high levels of sequence similarity to the zebrafish Mermaid element, while the second SINE element is not similar to the Mermaid element except for an 8bp sequence CCCCGTGC suggesting their evolutionary linkage. However, the second SINE element appeared to co-exist with the Mermaid element in most cases and therefore was designated as the Merman element. Approximately 9000 copies and 1200 copies of the Mermaid and Merman elements exist per haploid channel catfish genome, respectively. BLAST searches indicated that both the Mermaid and the Merman elements were frequently associated with gene sequences, mostly those of aquatic animals, suggesting their evolutionary origin in association with aquatic organisms and their function in shaping the evolution of genomes in aquatic animals.

A detailed linkage map of medaka, Oryzias latipes: comparative genomics and genome evolution

We mapped 633 markers (488 AFLPs, 28 RAPDs, 34 IRSs, 75 ESTs, 4 STSs, and 4 phenotypic markers) for the Medaka Oryzias latipes, a teleost fish of the order Beloniformes. Linkage was determined using a reference typing DNA panel from 39 cell lines derived from backcross progeny. This panel provided unlimited DNA for the accumulation of mapping data. The total map length of Medaka was 1354.5 cM and 24 linkage groups were detected, corresponding to the haploid chromosome number of the organism. Thirteen to 49 markers for each linkage group were obtained. Conserved synteny between Medaka and zebrafish was observed for 2 independent linkage groups. Unlike zebrafish, however, the Medaka linkage map showed obvious restriction of recombination on the linkage group containing the male-determining region (Y) locus compared to the autosomal chromosomes.

Zebrafish genetic map with 2000 microsatellite markers

The zebrafish is the first vertebrate organism used for large-scale genetic screens seeking genes critical to development. These screens have been quite successful, with more than 1800 recessive mutations discovered that speak to morphogenesis of the vertebrate embryo. The cloning of the mutant genes depends on a dense genetic map. The 2000 markers we present here, using microsatellite (CA) repeats, provides 1.2-cM average resolution. One centimorgan in zebrafish is about 0. 74 megabase, so, for many mutations, these markers are close enough to begin positional cloning by YAC walks.

A role for DNA methylation in gastrulation and somite patterning

DNA methylation constitutes an important epigenetic factor in the control of genetic information. In this study, we analyzed expression of the DNA methyltransferase gene and examined DNA methylation patterns during early development of the zebrafish. Maternal transcripts of the zebrafish DNA methyltransferase gene (MTase) are ubiquitously present at high levels in early embryos with overall levels decreasing after the blastula stage. At 24 h, methyltransferase mRNA is predominantly found in the brain, neural tube, eyes, and differentiating somites. Expression of MTase in the somites is highest in the anterior cells of the somites. Despite the high levels of MTase mRNA in blastula-stage embryos, we observe DNA hypomethylation at the blastula and gastrula stages compared to sperm or older embryos. Zebrafish embryos treated with 5-azacytidine (5-azaC) and 5-aza-2-deoxycytidine (5-azadC), nucleotide analogs known to induce cellular differentiation and DNA hypomethylation in mammalian cells, exhibit DNA hypomethylation and developmental perturbations. These defects are specifically observed in embryos treated at the beginning of the blastula period, just prior to midblastula transition. The most common phenotype is the loss of tail and abnormal patterning of somites. Head development is also affected in some embryos. Histological and in situ hybridization analyses reveal whole or partial loss of a differentiated notochord and midline muscle in treated embryos. When examined during gastrulation, 5-azaC-treated embryos have a shortened and thickened axial mesoderm. We propose that DNA methylation is required for normal gastrulation and subsequent patterning of the dorsal mesoderm.

The tyrosinase gene from medakafish: transgenic expression rescues albino mutation

We have determined the 9.8 kb genomic nucleotide sequence of the tyrosinase gene and its 5 upstream region from a teleost, medakafish (Oryzias latipes), and shown that the coding region is composed of five exons and four introns, spanning 4.7 kb. While the number and sizes of the exons were found to be similar to those of mammalian tyrosinase genes, however, the total size of the coding region (4.7 kb) was demonstrated to be less than one tenth those of mouse (ca. 70 kb) and human (> 70 kb) genes. Primer extension analysis revealed that the transcription initiation site starts with a long untranslated leader sequence (340 nucleotide long) from the AUG start codon. A characteristic CATGTG sequence known as a putative regulatory motif in melanocyte-specific genes was present in the 131st base upstream from the initiation site, while other typical regulatory elements such as the TATA-box or M-box common to terrestrial vertebrates were lacking. Transgenic experiments were carried out by microinjecting two kinds of plasmid clones into fertilized eggs of the albino i(l) mutant: one consisting of the genomic tyrosinase gene with the 10 kb 5 upstream region and the other the tyrosinase cDNA with the 3 kb 5 upstream region. The results showed that 53 and 45 of 114 and 118 transgenic eggs, respectively, developed normally beyond hatching and 15 and 10 exhibited a mosaic pattern of pigmentation. Despite the absence of typical regulatory elements like a TATA-box in both cases correct melanin pigmentation was obtained without ectopic expression. Thus, transgenic expression rescued from the albino-i(l) mutation, and the i locus of the medaka genome can be concluded to encode the tyrosinase gene.

Repetitive elements and their genetic applications in zebrafish

Repetitive elements provide important clues about chromosome dynamics, evolutionary forces, and mechanisms for exchange of genetic information between organisms. Repetitive sequences, especially the mobile elements, have many potential applications in genetic research. DNA transposons and retroposons are routinely used for insertional mutagenesis, gene mapping, gene tagging, and gene transfer in several model systems. Once they are developed for the zebrafish, they will greatly facilitate the identification, mapping, and isolation of genes involved in development as well as the investigation of the evolutionary processes that have been shaping eukaryotic genomes. In this review repetitive elements are characterized in terms of their lengths and other physical properties, copy numbers, modes of amplification, and mobilities within a single genome and between genomes. Examples of how they can be used to screen genomes for species and individual strain differences are presented. This review does not cover repetitive gene families that encode well-studied products such as rRNAs, tRNAs, and the like.