Characteristics of the distribution of DNA repetitive sequences in the sex chromosomes of 4 species of rodent

Four rodent species with very large heterochromatic regions on the sex chromosomes have been studied using in situ DNA/DNA hybridization techniques. Repetitious DNA fractions were obtained at C0t 0-0.01. Heterochromatic regions of X and X chromosomes of Cricetulus barabensis and Phodopus sungorus, and the heterochromatic long arm of the Y chromosome of Mesocricetus auratus do not contain disproportionately high amounts of repeated DNA sequences. Heterochromatic regions on sex chromosomes of Microtus subarvalis contain high amounts of repeated DNA sequences. Additional heterochromatic autosomal arms, a heterochromatic arm of the X chromosome, and a short arm of the Y chromosome of Mesocricetus auratus contain high amounts of repeated DNA sequences too.     

Conserved repeated DNA sequences in vertebrate sex chromosomes

Summary Satellite DNA isolated from female Elapid snakes contains nucleotide sequences which are quantitatively derived from the W sex-determining chromosome. Certain of these sequences are highly conserved in vertebrates, including mammals, where they are arranged in a sex-specific pattern in Southern blots. Sex reversed mice (Sxr) show a DNA arrangement of these sequences in conformity with their phenotypic sex, suggesting that this DNA is closely connected with the determination of sex. In situ hybridization of the snake sequences with mouse chromosomes reveals a concentration of related DNA at the proximal tip of the mouse Y chromosome. The possible nature and significance of these observations is discussed.     

Localization of specific repetitive DNA sequences in individual rice chromosomes

This paper describes the characterization and chromosomal distribution of three different rice (Oryza sativa) repetitive DNA sequences. The three sequences were characterized by sequence analysis, which gave 355, 498 and 756 bp for the length of the repeat unit in Os48, OsG3-498 and OsG5-756, respectively. Copy number determination by quantitative DNA slot-blot hybridization analysis showed 4000, 1080 and 920 copies, respectively, per haploid rice genome for the three sequences. In situ DNA hybridization analysis revealed that 95% of the silver grains detected with the Os48 probe were localized to euchromatic ends of seven long arms and one short arm out of the 12 rice chromosomes. For the OsG3-498 repetitive sequence, the majority of silver grains (58%) were also clustered at the same chromosomal ends as that of Os48. The minority (28%) of silver grains were located at heterochromatic short arms and centromeric regions. For the OsG5-756 repetitive sequence, 81% of the silver grains labeled the heterochromatic short arms and regions flanking all of the 12 centromeres. Thus, each of these three repetitive sequences was distributed at specific defined chromosomal locations rather than randomly at many chromosomal locations. The approximate copy number of a given repetitive DNA sequence at any specific chromosomal location was calculated by combining the information from in situ DNA hybridization analysis and the total copy number as determined by DNA slot-blot hybridization.by J. Huberman     

Distribution of repetitive DNA sequences in Vicia faba chromosomes

In situ hybridization of labelled complementary RNA transcribed from whole DNA to metaphase chromosomes indicates the presence of repetitive DNA in both euchromatin and heterochromatin of the Vicia faba genome.     

Simple repetitive sequences are associated with differentiation of the sex chromosomes in the guppy fish

Summary Hybridization of restriction enzymedigested genomic guppy (Poecilia reticulata, Poeciliidae) DNA with the oligonucleotide probe (GACA)₄ revealed a male-specific simple tandem repeat locus, which defines the Y chromosome in outbred populations. The related (GATA)₄ probe identifies certain males with the red color phenotype. In contrast only in two out of eight laboratory guppy strains was the typical (GACA)₄ band observed. By specific staining of the constitutive heterochromatin one pair of chromosomes could also be identified as the sex chromosomes, confirming the XX/XY mechanism of sex determination. All males exhibit Y chromosomes with a large region of telomeric heterochromatin. Hybridization in situ with nonradioactively labeled oligonucleotide probes localized the (GACA)_n repeats to this heterochromatic portion. Together these results may be regarded as a recent paradigm for the differentiation of heteromorphic sex chromosomes from a pair of autosomes during the course of evolution. According to the fish model system, this may have happened in several independent consecutive steps.     

Absence of repetitive DNA sequences associated with sex chromosomes in natural populations of the Trinidad guppy (Poecilia reticulata)

The genus Poecilia has been widely studied as a model for the evolution of sex chromosomes. In the course of molecular studies on population genetic structure and sexual selection in the Trinidad guppy, we examined our preparations for male-linked, repetitive DNA polymorphisms. We have not obtained any evidence of male-specific polymorphisms, in contrast to an earlier study. Our results have significant implications for theories on the evolution of sex chromosomes.Correspondence to: F. Breden     

Chromosomal distribution of repetitive DNA sequences highlights the independent differentiation of multiple sex chromosomes in two closely related fish species

The arrangement of 6 repetitive DNA sequences in the mitotic and meiotic sex chromosomes of 2 Erythrinidae fish, namely Hoplias malabaricus and Erythrinus erythrinus, both with a multiple X(1)X(1)X(2)X(2)/X(1)X(2)Y sex chromosome system, was analyzed using fluorescence in situ hybridization. The distribution patterns of the repetitive sequences were distinct for each species. While some DNA repeats were species-specific, others were present in the sex chromosomes of both species at different locations. These data, together with the different morphological types of sex chromosomes and the distinct chromosomal rearrangements associated with the formation of the neo-Y chromosomes, support the plasticity of sex chromosome differentiation in the Erythrinidae family. Our present data highlight that the sex chromosomes in fish species may follow diverse differentiation patterns, even in the same type of sex chromosome system present in cofamiliar species.     

The use of repetitive DNA in cytogenetic studies of plant sex chromosomes

The structure of sex chromosomes in plants was analyzed by fluorescent in situ hybridization (FISH) with repetitive DNAs. FISH probes were successfully obtained from DNA libraries that were amplified from microdissected sex chromosomes. Some probes hybridized to the subtelomeric regions, where many kinds of repetitive DNAs are located with intrachromosomal similarity of their repeat units rather than interchromosomal similarity. For example, FISH with the subtelomeric repetitive sequence can easily show the location of the pseudoautosomal region (PAR) on the X chromosome of Silene latifolia. The other probes were localized on the interstitial region of the sex chromosomes. The interstitial region contains chloroplast DNAs or neighboring sequences of the internal telomeres, suggesting insertion or translocation occurred during differentiation of the sex chromosome. These data are very informative for understanding the structure of the plant sex chromosomes and their evolutionary process.     

Mapping of repetitive bovine DNA sequences on cattle Y chromosomes.

Three male-specific PCR products of the sequences BC1.2, lambda ES6.0, and BRY.1 were used as probes for Southern blot analyses. Each of these probes generated a complex male-specific band pattern, which showed some quantitative variations among bulls. Hybridization patterns obtained with the BC1.2 and lambda ES6.0 PCR products were interrelated. Chromosomal locations of these repeats were determined by hybridizing the tritiated PCR products in situ to male metaphase spreads. The BC1.2 and lambda ES6.0 PCR products hybridized to Yp13-->p12, whereas the BRY.1 PCR product hybridized over the entire Y chromosome. In addition, the BC1.2 and lambda ES6.0 PCR products hybridized to the distal half of the acrocentric Y chromosome of Bos indicus, indicating that the short arm of the B. taurus Y chromosome is homologous with the telomeric end of the B. indicus Y and supporting the notion that the Y chromosomes of these two species differ by a pericentric inversion.     

Analysis of repetitive DNA in chromosomes by flow cytometry

We developed a flow cytometry method, chromosome flow fluorescence in situ hybridization (FISH), called CFF, to analyze repetitive DNA in chromosomes using FISH with directly labeled peptide nucleic acid (PNA) probes. We used CFF to measure the abundance of interstitial telomeric sequences in Chinese hamster chromosomes and major satellite sequences in mouse chromosomes. Using CFF we also identified parental homologs of human chromosome 18 with different amounts of repetitive DNA.     

Analysis of rat repetitive DNA sequences.

Parameters of repetitive sequence organization have been measured in the rat genome. Experiments using melting, hydroxylapatite binding, and single strand specific nuclease digestion have been used to measure the number, length, and arrangement of repeated DNA sequences. Renaturation and melting or S1 nuclease digestion of 1.0 kbp DNA fragment show about 20% of rat DNA sequences are 3000-fold repeated. Renatured duplexes from 4.0 kbp DNA fragments display two repetitive size fractions after nuclease digestion. About 60% of the repeated sequences are 0.2-0.4 kbp long while the remainder are longer than 1.5 kbp. The arrangement of the repeated sequences has been measured by hydroxylapatite fractionation of DNA fragments of varying lengths bearing a repeated sequence. Repeated DNA sequences are interspersed among 2.5 kbp long nonrepeated sequences throughout more than 70% of the rat genome. There are approximately 350 different 3000-fold short repeated sequences in the rat interspersed among 600,000 nonrepeated DNA sequences.     

Periodically interspersed repetitive sequences may govern higher-order DNA coiling in chromatin and chromosomes

The interspersed periodic arrangement of repetitive and unique sequences in eukaryotic DNAs is proposed as the underlying molecular basis for higher-order DNA coiling in chromatin and mitotic chromosomes. It is assumed that (i) two types of interspersed repetitive sequences are distributed strictly periodically throughout the genome, splitting the single copy DNA into short and long periods respectively in such a pattern that each long period is composed of a definite number of short periods and repeats (ii) the short and long periods make the turn lengths of the solenoid and supersolenoid structures respectively determing their diameters; (iii) specific proteins interact with each type of repeats making cross ties between nearby repeats of each class helping to form, constrain, and stabilize the solenoid and the supersolenoid structures; (iv) the long period may be equated with the basic chromomere unit. The model predicts: (i) splitting of contiguous genes by inserted repetitive sequences; and (ii) two types of genomes differing in the hierarchy of DNA coiling.     

The sequences of the human sex chromosomes

The sequences of both of the human sex chromosomes and of a substantial part of the chimpanzee Y chromosome have now been determined, and most of the protein-coding genes have been identified. The X chromosome codes for more than 800 proteins but the Y chromosome for only approximately 60, illustrating their very different evolutionary histories since their origin from an autosomal pair approximately 300 million years ago and explaining their differential importance in disease. These sequences have provided the basis for understanding normal patterns of variation, such as the distribution of SNPs, and patterns of linkage disequilibrium. In addition, they have been useful for identifying variants associated with simple Mendelian disorders such as microphthalmia or mental retardation, and more complex disorders such as osteoporosis.     

尼罗罗非鱼线粒体基因组全序列测定与系统进化分析

参照已报道的鱼类线粒体基因序列,通过PCR扩增与测序,获得了全长为16627bp的尼罗罗非鱼线粒体基因组全序列,共编码13种蛋白质基因、2种rRNA基因、22种tRNA基因和1段控制区序列.H-链碱基组成具有明显的AT偏向性.由H-链编码的蛋白质基因在第3位密码子上相对于前2个密码子具有一定的G排斥性.L-链编码蛋白质基因在碱基组成上与H-链编码基因存在差异.编码基因除COI以GTG作为起始密码子外,其它均以ATG起始.终止密码子有2种,分别为不完全T-或TA-和TAA.L-链复制起始区位于WANCY区域(tRNATrp-tRNAAla-tRNAAsn-tRNACys-tRNATyr)的tRNAAsn和tRNACys基因间,长度为33bp.系统发育分析显示,源于非洲的口孵鱼属、蓝首鱼属和球丽鱼属聚为单系群,其中口孵鱼属莫桑比克罗非鱼先与同属罗非鱼KM-2006聚类后再与尼罗罗非鱼聚类.     

Some remarks on the use of TaqI to detect highly repetitive DNA sequences in human chromosomes

In the attempt to conclude investigation of the action of restriction endonucleases on eukaryote chromosomes, we carried out a series of experiments digesting in situ human metaphase chromosomes with AluI/TaqI followed by Giemsa staining. We focused on the centromeric regions of chromosomes1, 2 and 16 and noted that those areas appeared as intensely stained blocks after AluI digestion, but were dramatically reduced in size or completely destroyed after subsequent TaqI treatment. These results permitted us to draw some conclusions on the highly repetitive DNA composition of these regions, in terms of alphoid and classical satellite DNAs.     

Microsatellite DNA markers for genetic mapping in Oreochromis niloticus

The isolation of seven tri-, and 133 di-nucleotide microsatellite markers from a tilapia, Oreochromis niloticus , is described. An efficient methodology for isolating large numbers of such markers and their potential applications in applied aquaculture and evolutionary genetics are discussed.     

The 5S rDNA related repetitive sequences in the sex chromosomes of the spiny eel (Mastacembelus aculeatus)

The karyotype of the spiny eel (Mastacembelus aculeatus) has highly evolved heteromorphic sex chromosomes. X and Y chromosomes differ from each other in the distribution of heterochromatin blocks. To characterize the repetitive sequences in these heterochromatic regions, we microdissected the X chromosome, constructed an X chromosome library, amplified the genomic DNA using PCR and isolated a repetitive sequence DNA family by screening the library. All family members were clusters of two simple repetitive monomers, MaSRS1 and MaSRS2. We detected a conserved 5S rDNA gene sequence within monomer MaSRS2; thus, tandem-arranged MaSRS1s and MaSRS2s may co-compose 5S rDNA multigenes and NTSs in M. aculeatus. FISH analysis revealed that MaSRS1 and MaSRS2were the main components of the heterochromatic regions of the X and Y chromosomes. This finding contributes additional data about differentiation of heteromorphic sex chromosomes in lower vertebrates.