A unique repetitive DNA sequence in the Myxococcus xanthus genome.

We found a novel type of repetitive DNA sequence in the Myxococcus xanthus genome. The first repetitive sequence is located in the spacer region between the ops and tps genes. We cloned five other repetitive sequences using the first repetitive sequence as a probe and determined their nucleotide sequences. Comparison of these sequences revealed that the repetitive sequences consist of a 87-bp core sequence and that some clones share additional homology on their flanking regions.     

A peculiar repetitive sequence in the rat genome

We report here a new type of peculiar repetitive sequence, A15T(TC)9T12, which was detected at 750 base pairs (bp) upstream of a rat calmodulin processed pseudogene by DNA sequencing of cloned DNA fragments. This sequence element could possibly form a cruciform structure with a 12-AT-pair stem, exposing (CT)9 sequences as a loop. S1 nuclease protection experiments failed to identify this element as a cruciform structure but instead detected an alternating purine pyrimidine tract at 50 bp downstream of this element. Total genomic Southern blotting showed that the rat genome contains only a few of these elements.     

The macrosatellites of the Toulouse goose: the major tandemly repetitive DNA in the toulouse goose genome

This paper examines the principal classes of repetitive DNA of the Toulouse goose (Anser anser) genome. There are four major classes and they are tandem repeats of less than 200 base pairs (bp). The longest repeat (class A) is 190 bp long and starts with a HinfI site. Class B is 43 bp long, commencing with a FokI site. Classes A and B show no extensive homology to DNA sequences held on a current data base (Genbank) but were confirmed to exist as major repeats in another strain of goose, the Emden goose (Anser anser) genome. Classes C and D are 5-bp repeats of 5' GAGAG 3' and 5' GGGAA 3', respectively. The macrosatellites C and D were compared with a current data base (Genbank) and were found to exist in a variety of other organisms as satellites.     

A conserved tandemly repeated DNA sequence inCruciferae

Several HindIII monomer units of a tandemly repeated nuclear DNA sequence ofBrassica campestris andBrassica juncea (Cruciferae) have been cloned and sequenced. The monomer units, of 177 bp length, are AT-rich and share 88% homology between themselves and more than 65% homology with similar repeats of otherCruciferae likeBrassica oleracea, Sinapis alba andRaphanus sativus. Thus unlike the rapid divergence of tandemly repeated satellite DNA in other organisms, this DNA element is highly conserved thus indicating its importance.     

A tandemly repetitive centromeric DNA sequence of the fish Hoplias malabaricus (Characiformes: Erythrinidae) is derived from 5S rDNA

A substantial fraction of the eukaryotic genome consists of repetitive DNA sequences that include satellites, minisatellites, microsatellites, and transposable elements. Although extensively studied for the past three decades, the molecular forces that generate, propagate and maintain repetitive DNAs in the genomes are still discussed. To further understand the dynamics and the mechanisms of evolution of repetitive DNAs in vertebrate genome, we searched for repetitive sequences in the genome of the fish species Hoplias malabaricus. A satellite sequence, named 5SHindIII-DNA, which has a conspicuous similarity with 5S rRNA genes and spacers was identified. FISH experiments showed that the 5S rRNA bona fide gene repeats were clustered in the interstitial position of two chromosome pairs of H. malabaricus, while the satellite 5SHindIII-DNA sequences were clustered in the centromeric position in nine chromosome pairs of the species. The presence of the 5SHindIII-DNA sequences in the centromeres of several chromosomes indicates that this satellite family probably escaped from the selective pressure that maintains the structure and organization of the 5S rDNA repeats and become disperse into the genome. Although it is not feasible to explain how this sequence has been maintained in the centromeric regions, it is possible to hypothesize that it may be involved in some structural or functional role of the centromere organization.     

Why repetitive DNA is essential to genome function

There are clear theoretical reasons and many well-documented examples which show that repetitive, DNA is essential for genome function. Generic repeated signals in the DNA are necessary to format expression of unique coding sequence files and to organise additional functions essential for genome replication and accurate transmission to progeny cells. Repetitive DNA sequence elements are also fundamental to the cooperative molecular interactions forming nucleoprotein complexes. Here, we review the surprising abundance of repetitive DNA in many genomes, describe its structural diversity, and discuss dozens of cases where the functional importance of repetitive elements has been studied in molecular detail. In particular, the fact that repeat elements serve either as initiators or boundaries for heterochromatin domains and provide a significant fraction of scaffolding/matrix attachment regions (S/MARs) suggests that the repetitive component of the genome plays a major architectonic role in higher order physical structuring. Employing an information science model, the 'functionalist' perspective on repetitive DNA leads to new ways of thinking about the systemic organisation of cellular genomes and provides several novel possibilities involving repeat elements in evolutionarily significant genome reorganisation. These ideas may facilitate the interpretation of comparisons between sequenced genomes, where the repetitive DNA component is often greater than the coding sequence component.     

Small cytoplasmic poly(A)+RNA, homologous to the B2 repetitive sequence of the mouse genome, is present in ribonucleoproteins

Small cytoplasmic poly(A) + RNA homologous to a highly repeated sequence B2 of the mouse genome (scB2 RNA) was not found as free RNA within a cell. This RNA is bound to small (12-18S) ribonucleoprotein particles as well as to heavy RNP particles, apparently informosomes. After deproteinization of the heavy RNP the major part of scB2 RNA molecules cosedimented with heavy RNAs. It seems that scB2 RNA is associated with mRNA in informosomes via short complementary regions. About half of the scB2 RNA molecules was revealed in the cytoskeleton fraction. The possibility that scB2 RNAs are involved in mRNA transport or in the regulation of mRNA translation is discussed.     

A new middle repetitive sequence of Nicotiana plumbaginifolia genome

A middle repetitive sequence NPR18 was isolated from Nicotiana plumbaginifolia nuclear genome [8]. Sequences homologous to the repeat are dispersed through genomes of several Nicotiana species. compute-assisted data analysis of NPR18 primary sequence reveals several features attributed to mobile genetic elements: an AT content higher than average for nuclear DNA of genus Nicotiana plants; a number of direct and inverted repeats. Some of the repeats displayed homology to the terminal and subterminal repeats of Ac/Ds-like plant elements.     

A new repetitive sequence uniquely present in the decay-accelerating factor genes

 The decay-accelerating factor (DAF, CD55) protects cells from autologous complement attack on self cell membranes. We have previously reported that the seventh exon encoding the serine/threonine-rich(S/T)-abc region of the guinea pig DAF gene is composed of five homologous repeats of about 51 base pairs, and that differential usage of these repeats produces the various lengths observed in the S/T region of guinea pig DAF. In this study, we found that the seventh intron of the guinea pig DAF gene was wholly composed of 18 tandem repeats homologous to the repeating unit of the S/T-abc exon. This type of repetitive structure, although the number of repeats was variable, was also found in the corresponding exons and introns of all DAF genes of other species so far tested including human and seven other primates and mouse, in which alternative splicing in this region has not been found. This suggested that generation of the repetitive sequences spanning the exon and intron regions had occurred before the diversification of these species. In addition, all the intron sequences of the tested DAF genes had no stop codon when they were presumably translated in the same reading frame as the seventh and eighth exons, except for that of one of two duplicated mouse DAF genes. These findings and significant interspecies identities of the intron sequence suggest that the intron sequence conceivably could be translated in some tissues and/or in some stages of development although to date we have not yet succeeded in detecting mRNA for this region. Received: 7 July 1997 / Revised: 11 August 1997     

Population biology of the parasitic phase of Ostertagia circumcincta

Four current models for the parasitic phase of the Ostertagia circumcincta life-cycle were evaluated with respect to their ability to represent the outcome of experimental infection studies and the population biology of the parasite in the field. Neither of the two discrete-time models was able to mimic the rise and fall in parasite numbers that characterize trickle infection experiments. When the infection rate is constant, both models predict that parasite numbers will eventually reach an asymptotic equilibrium value. This happens because both models are formulated such that parasite mortality is constant when the infection rate is constant. The two continuous-time models are able to mimic trickle infection experiments because both of them represent parasite mortality as an increasing function of the infection rate and the duration of infection. However, the continuous-time models do not adequately represent the demography of the parasitic phase in the field because neither of them takes any account of the effect of variations in infection rate from host to host on the overall mean parasite death rate.     

A novel repetitive DNA sequence in the genus Oryza

Summary Repetitive DNA sequences in the genus Oryza (rice) represent a large fraction of the nuclear DNA. The isolation and characterization of major repetitive DNA sequences will lead to a better understanding of rice genome organization and evolution. Here we report the characterization of a novel repetitive sequence, CC-1, from the CC genome. This repetitive sequence is present as long tandem arrays with a repeat unit 194 bp in length in the CC-diploid genome but 172 bp in length in the BBCC and CCDD tetraploid genomes. This repetitive sequence is also present, though at lower copy numbers, in the AA and BB genomes, but is absent in the EE and FF genomes. Hybridization experiments revealed considerable differences both in copy numbers and in restriction fragment patterns of CC-1 both between and within rice species. The results support the hypothesis that the CC genome is more closely related to the AA genome than to the BB genome, and most distantly related to the EE and FF genomes.     

Genome composition and tandemly repetitive sequence at some centromeres in the lizard Podarcis s. sicula Raf.

A detailed study on the genome of the lizard P. sicula has been carried out using restriction enzyme analysis followed by identification and cloning of a repetitive DNA fraction. The results show that P. sicula generally possesses a quite homogeneous genome composition, with a single tandemly repetitive sequence family that is easily visualized after digestion of genomic DNA with Taq I. The cloned repeating unit of this satellite (260 bp) has been designed pLCSl. In-situ hybridisation shows that this satellite is localized in the centromeric region. Dot blot experiments show that sequences similar to pLCSl are present in other species of the same family of lizards.     

A new human alphoid-like repetitive DNA sequence

A new tandemly repetitive sequence family, having the 170 bp basic repeat characteristic of alphoid sequences, has been identified in the human genome. Its organization in the whole genome and on chromosome 21 is different from that of any of the previously described alphoid families. Members of this new family are unusually heterogeneous in sequence, and there are a number of variant sequence classes. Some of the variant classes exist in separate genomic domains, and even on a single chromosome the members of such a class are not significantly intermixed with members of another class.