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PubMed1983

A family of repeated DNA sequences, one of which resides in the second intervening sequence of the mouse dihydrofolate reductase gene.

One member of a repeated sequence family has been found in the second intron of the mouse dihydrofolate reductase gene. The family consists of approximately 20 members/haploid genome, two of which have been sequenced and found to contain a 480-base pair region of homology with a significant amount of sequence divergence. Rat, Chinese hamster, Syrian hamster, and human DNAs contain homologous repetitious elements, and the four rodent species have a member of this family associated with the dihydrofolate reductase gene.

Animals↗
PubMed1982

The Red function of phage lambda mediates the alteration of an interspersed repeated DNA sequence from the kangaroo rat Dipodomys ordii.

The kangaroo rat D. ordii is shown to contain an interspersed repeated sequence 3.25 kb in length. This sequence undergoes alteration (deletions) when cloned into a Red+ lambda vector but is stable in a Red- vector. Using the Red- clone it is shown that deletions are the result of the activity of the lambda Red, or E. coli RecE, recombination systems. Mixed infection experiments demonstrate that this activity is acting in trans. The deletions appear to yield fragments of specific size, suggesting that the recombination system is recognizing a specific sequence. The demonstration of small homologous fragments in the animal genomic DNA suggests that a similar system of recombination may exist in D. ordii.

Animals↗
PubMed1979

Arrangement of a highly repeated DNA sequence in the genome and chromatin of the African green monkey.

The DNA of the African green monkey contains three components that are distinguishable by the kinetics of reassociation. The rapidly reassociating component represents about 20% of the total DNA and is composed almost entirely of a sequence (AGMr(HindIII)-1) which is repeated 6.8 x 10(6) times. The majority of the AGMr(HindIII)-1 sequences are organized in long tandem repeats of a segment of 172 base pairs in length. However, a fraction of the AGMr (HindIII)-1 sequences is interspersed with another 37% of the genome. The structure of the chromatin containing the AGMr-(HindIII)-1 sequence is indistinguishable from that containing total DNA. Furthermore, there is nothing inherent in the nucleotide sequence of AGMr(HindIII)-1 which specifies a unique location for nucleosomes.

Animals↗
PubMed2000

A novel repeated sequence DNA originated from a Tc1-like transposon in water green frog Rana esculenta.

We have identified and characterized a highly repetitive family, called R.e./Tc1 in the genome of the green water frog Rana esculenta. This family consists of tandemly repeated sequences, localized at the centromeric regions of chromosomes as shown by Southern blot and 'in situ' hybridization. The repeat unit contains a residue of a Tc1-like transposon by Haematobia irritans fly, bordered by two short direct repeats of 9 bp. Tc1 remnant lays near a sequence identical to Homo sapiens Werner syndrome gene stretch. These sequence data suggest that R.e./Tc1 element was probably originated from a transposition event and a duplication via DNA mechanism of the R.e./Tc1 unit that could give rise to the observed tandem array.

Animals↗
PubMedDate not supplied

Cloning of a major repeat DNA sequence from Pyura stolonifera.

We have cloned a 147-bp Hind III fragment from a marine ascidian Pyura stolonifera. This sequence is arranged in tandem in arrays up to 20 kb in size and represents more than 5% of the total genomic DNA. The basic 147-bp unit was isolated from Hind III-digested genomic DNA and cloned into M13. Sequence analysis of seven clones revealed that the sequence is AT rich (75%) and can be separated from main band DNA by equilibrium density gradient centrifugation in the presence of the ligand dye Hoechst 33258. The sequence is highly conserved and is changed only by single base substitution mutations in the different clones. Use of this sequence as a probe demonstrated varying degrees of hybridization with DNA isolated from a wide range of other ascidians. Northern blot analysis revealed the presence of RNA hybridizing to the repeat in unfertilized eggs but transcription of this sequence was not evident in the adult organism.

Animals↗
PubMed1994

Dirofilaria repens: cloning and characterization of a repeated DNA sequence for the diagnosis of dirofilariasis in dogs, Canis familiaris.

A highly repetitive DNA element from the genome of the filarial nematode Dirofilaria repens has been cloned and sequenced. The 176-base pair repeating units are arranged in direct tandem and are clustered in the parasite genome. All repeats appear to belong to a single family although some elements have diverged significantly. The repeats are present in about 15,000 copies and constitute approximately 3.0% of the parasite genome. The cloned repetitive sequence hybridized only to D. repens DNA and was sensitive enough to detect 250 to 500 pg of D. repens DNA, a single microfilariae in infected blood samples, and a single third stage larvae in mosquitoes. The high specificity and sensitivity of the cloned fragment makes it ideal as a diagnostic probe for detecting D. repens in both the host and the vector.

Animals↗
PubMed1993

Localization of tandemly repeated DNA sequences in beetle chromosomes by fluorescent in situ hybridization.

In situ hybridization to chromosomes and nuclei of Tenebrio molitor shows the massive presence of a species-specific satellite DNA in all chromosomes and six sites of rDNA in mitotic chromosomes. These sites are located in two autosomal pairs and in the X and Y chromosomes. In a related species, Misolampus goudoti, in which two different families of highly repetitive DNA have been previously characterized, one family is located in centromeric regions of all chromosomes with the exception of chromosome Y, while the other repeated DNA family is present both in centromeric and distal regions of all chromosomes. rRNA genes in this species are present in a medium-sized autosomal pair only. These results show that molecular cytogenetics can be applied to coleopteran chromosomes and open the way for a physical mapping of DNA sequences in these organisms. The results also provide insights into the type of meiotic association of the X and Y chromosomes in Coleoptera and the distribution of repeated DNAs within the genome of these insects.

Animals↗
PubMed1980

Analysis of highly repeated DNA sequences of rat with EcoR1 endonuclease.

Cleavage of rat liver nuclear DNA with EcolR1 restriction endonuclease yields 14 discrete fragments ranging from 2300 to 93 base pairs in length, representing approx. 10.5% of the rat genome. Fragments of 1500, 180, and 93 base pairs are reiterated over 100 000 times; fragments of 2300, 880, 290, and 200 base pairs are reiterated over 20 000 times; the remaining fragments are present in over 1000 copies per genome. When compared to whole rate DNA, 11 were 1-5% richer in A . T base pairs and five were 1.5-2.5 times more methylated. From the criteria of the banding patterns in complete and incomplete digests, base composition and extent of methylation, none of these fragments appeared to be generated as oligomers of a basic shorter repeat. The reassociation of EcoR1 fragments was monitored on hydroxyapatite and by S1 nuclease treatment in order to assess band reiteration frequency and the possibility of interpersion or short internal repeats. The renaturation of the four smallest EcoR1 fragments gave no indication of short internal repeats from hyperpolymer formation nor interpersion with lower frequency sequences by size reduction after S1 nuclease treatment. Anomalous renaturation of several large fragments was observed, possibly due to internal repeats.

Animals↗
PubMed1990

Potential genetic functions of tandem repeated DNA sequence blocks in the human genome are based on a highly conserved "chromatin folding code".

This review is based on a thorough description of the structure and sequence organization of tandemly organized repetitive DNA sequence families in the human genome; it is aimed at revealing the locus-specific sequence organization of tandemly repetitive sequence structures as a highly conserved DNA sequence code. These repetitive so-called "super-structures" or "higher-order" structures are able to attract specific nuclear proteins. I shall define this code therefore as a "chromatin folding code". Since locus-specific superstructures of tandemly repetitive sequence units are present not only in the chromosome centromere or telomere region but also on the arms of the chromosomes, I assume that their chromatin folding code may contribute to, or even organize, the folding pathway of the chromatin chain in the nucleus. The "chromatin folding code" is based on its specific "chromatin code", which describes the sequence dependence of the helical pathway of the DNA primary sequence (i.e., secondary structure) entrapping the histone octamers in preferential positions. There is no periodicity in the distribution of the nucleosomes along the DNA chain. The folding pathway of the nucleosomal chromatin chain is however still flexible and determined by e.g., the length of the DNA chain between the nucleosomes. The fixation and stabilization of the chromatin chain in the space of the nucleus (i.e., its "functional state") may be mediated by additionally unique DNA protein interactions that are dictated by the "chromatin folding code". The unique DNA-protein interactions around the centromeres of human chromosomes are revealed for example by their "C-banding". I wish to stress that it is not my aim to relate each block of repetitive DNA sequences to a specific "chromatin folding code", but I shall demonstrate that there is an inherent potential for tandem repeated sequence units to develop a locus-specific repetitive higher order structure; this potential may create a specific chromatin folding code whenever a selection force exists at the position of this repetitive DNA structure in the genome.

Chromatin↗
PubMed2002

The 2.1-kb inverted repeat DNA sequences flank the mat2,3 silent region in two species of Schizosaccharomyces and are involved in epigenetic silencing in Schizosaccharomyces pombe.

The mat2,3 region of the fission yeast Schizosaccharomyces pombe exhibits a phenomenon of transcriptional silencing. This region is flanked by two identical DNA sequence elements, 2.1 kb in length, present in inverted orientation: IRL on the left and IRR on the right of the silent region. The repeats do not encode any ORF. The inverted repeat DNA region is also present in a newly identified related species, which we named S. kambucha. Interestingly, the left and right repeats share perfect identity within a species, but show approximately 2% bases interspecies variation. Deletion of IRL results in variegated expression of markers inserted in the silent region, while deletion of the IRR causes their derepression. When deletions of these repeats were genetically combined with mutations in different trans-acting genes previously shown to cause a partial defect in silencing, only mutations in clr1 and clr3 showed additive defects in silencing with the deletion of IRL. The rate of mat1 switching is also affected by deletion of repeats. The IRL or IRR deletion did not cause significant derepression of the mat2 or mat3 loci. These results implicate repeats for maintaining full repression of the mat2,3 region, for efficient mat1 switching, and further support the notion that multiple pathways cooperate to silence the mat2,3 domain.

Gene Silencing↗
PubMed1993

Germ line-restricted, highly repeated DNA sequences and their chromosomal localization in a Japanese hagfish (Eptatretus okinoseanus).

The various species of Japanese hagfish, namely, Eptatretus okinoseanus (types A and B), Eptatretus burgeri and Myxine garmani, are known to eliminate a fraction of their chromosomes during early embryogenesis. High molecular weight DNA from germ line cells and somatic cells of these hagfish species was isolated and digested with different restriction enzymes. The DNA fragments were separated by agarose gel electrophoresis. Digestion with BamHI and DraI generated two weak bands and one weak band, respectively, that were estimated to be about 90, and 180 bp and about 90 bp long and were limited to the germ line DNA in both types of E. okinoseanus. DNA filter hybridization experiments showed that the two BamHI fragments and the one DraI fragment were present almost exclusively in the germ line DNA of E. okinoseanus. Thus, these DNA fragments appear to be eliminated during embryogenesis. Moreover, evidence was obtained that these fragments are highly and tandemly repeated. Molecular cloning and sequence analysis revealed that the BamHI fragments are mainly composed of a family of closely related sequences that are 95 bp long (EEEo1, for Eliminated Element of E. okinoseanus 1), and the DraI fragment is composed of another family of closely related sequences that are 85 bp long (EEEo2). The two DNA families account for about 19% of the total eliminated DNA in E. okinoseanus type A. Fluorescence in situ hybridization experiments demonstrated that the two families of DNA are located on several C-band-positive, small chromosomes that are limited to germ cells in both types of E. okinoseanus.

Animals↗
PubMed1979

Conservation of repeated DNA sequences in aneuploid human tumor cells.

A series of human neuroectodermal tumors, all containing more than the normal diploid DNA, and each with its own distinct chromosome mode, were studied using restriction enzyme cleavage and specific DNA sequence hybridization. Methods described were quite sensitive and quantitative and as few as 40 molecules with a given restriction site were reproducibly detected in total nuclear DNA. Analysis of several fluorescent gel bands associated with different chromosomal domains revealed no changes between any of the tumor and normal cells. Specific probe hybridization, using purified complex repeating sequences, indicated fidelity of base sequence, as well as preservation of the relative amounts of each of a number of minor related multimers in both the tumor and normal cells. Centromeric regions containing arrays of such sequences may be maintained in these tumor cells and furthermore it is possible that some of these cells are polyploid with respect to DNA sequences, rather than aneuploid as their chromosome profiles suggest.

Aneuploidy↗
PubMed2005

Preferential elimination of repeated DNA sequences from the paternal, Nicotiana tomentosiformis genome donor of a synthetic, allotetraploid tobacco.

Nicotiana tabacum (tobacco, 2n = 4x = 48) is a natural allotetraploid combining two ancestral genomes closely related to modern Nicotiana sylvestris and Nicotiana tomentosiformis. Here we examine the immediate consequences of allopolyploidy on genome evolution using 20 S4-generation plants derived from a single synthetic, S0 plant made by Burk in 1973 (Th37). Using molecular and cytogenetic methods we analysed 14 middle and highly repetitive sequences that together total approximately 4% of the genome. Two repeats related to endogenous geminiviruses (GRD5) and pararetroviruses (NtoEPRV), and two classes of satellite repeats (NTRS, A1/A2) were partially or completely eliminated at variable frequency (25-60%). These sequences are all from the N. tomentosiformis parent. Genomic in situ hybridization revealed additivity in chromosome numbers in two plants (2n = 48), while a third was aneuploid for an N. tomentosiformis-origin chromosome (2n = 49). Two plants had homozygous translocations between chromosomes of the S- and T-genomes. * The data demonstrate that genetic changes in synthetic tobacco were fast, targeted to the paternal N. tomentosiformis-donated genome, and some of the changes showed concordance with changes that presumably occurred during evolution of natural tobacco.

Biological Evolution↗
PubMed2003

Description of a tandem repeated DNA sequence of Echinostoma caproni and methods for its detection in snail and plankton samples.

Echinostome larval stages in the snail have a great potential as effective competitors for the control of schistosomes and adult worms can cause painful intestinal diseases in humans. Ecology and transmission of the larval stages of trematodes are poorly understood, especially because their identification in field-collected samples by microscopy is difficult. We cloned, sequenced and analysed a 192 bp tandem repreated DNA sequence of Echinostoma caproni (EcSau3A), an often discussed antagonist of Schistosoma mansoni in Biomphalaria snails. PCR primers against this sequence can detect less than 10 fg of E. caproni DNA, 2 miracidia in snails 1 day p.i., 1 metacercaria in 50 mg snail tissue and 1 cercaria in 50 mg plankton with high specificity. Methods described in this study can support the discovery of fundamental ecological principles on distribution, host specificity and epidemiology of E. caproni larvae under field conditions.

Animals↗
PubMed1993

Variability and evolution of highly repeated DNA sequences in the genus Beta.

Satellite DNA from wild beet species was separated from restriction endonuclease digested genomic DNA by polyacrylamide gel electrophoresis. Two nonhomologous HaeIII satellite DNA repeats were cloned from the wild beet Beta trigyna. The type I repeat is 140-149 bp long and AT rich, while the type II is 162 bp in size and GC rich. A third repetitive HaeIII element cloned from the related wild beet B. corolliflora was shown to be organized as a HinfI satellite DNA family in the cultivated beet B. vulgaris ssp. vulgaris and the wild beet B. vulgaris ssp. maritima. This type III satellite monomer is 149 bp long and contains a high number of short direct subrepeats. The monomer was found in different genomic organizations and copy numbers in all sections of the genus Beta indicating an amplification early in the phylogeny. The HaeIII repeats from B. trigyna are characterized by a lower variability and form long tandem arrays in the genomes of Corollinae species. The investigation of the distribution of all three sequence families provided data that may contribute to the solution of taxonomic problems of the genus Beta and be useful in the characterization of hybrids and derived lines with alien wild beet chromosomes.

Base Sequence↗
PubMed1986

The presence of repeated DNA sequences and a partial restriction map of the pSym of Rhizobium fredii USDA193.

The large, 350-kb Sym (symbiotic) plasmid pRjaUSDA193 of Rhizobium fredii was examined to determine the frequency of repeated sequences present and to produce a physical and genetic map of a large region of the plasmid. A novel hybridization method, the Southern Cross, revealed that the plasmid pRjaUSDA193 contained many repeated sequences and assisted in restriction enzyme mapping of a 100-kb region containing nod genes. A cosmid clone bank was prepared with the broad-host-range cosmid pVK102. The restriction enzymes HindIII, HpaI, and KpnI were used to construct a physical map of overlapping clones. Labeled nod gene sequences were used to determine their location in the mapped region.

Chromosome Mapping↗
PubMed1983

Repeated DNA sequences upstream from HIS1 also occur at several other co-regulated genes in Saccharomyces cerevisiae.

The HIS1 gene of Saccharomyces cerevisiae encodes ATP phosphoribosyltransferase, the first enzyme in the pathway of histidine biosynthesis. We have cloned this gene by complementation of a his1 auxotroph. The HIS1 coding region was localized within the cloned segment by assay of subcloned fragments for their ability to complement a his1 auxotroph. We determined the DNA sequence of the HIS1 region defined by this complementation test. S1 nuclease and exonuclease VII mapping of the 5' and 3' termini of HIS1 mRNA reveal considerable heterogeneity at both ends of the transcript, especially the 5' end which displays 13 different termini that span a 110-base pair region. Northern analysis shows that derepression of HIS1 enzyme activity under conditions of amino acid deprivation can be accounted for by an increase in the steady state level of HIS1 mRNA. There are no large differences between the relative levels of HIS1 mRNA molecules with different 5' termini in repressed and derepressed cells. In the DNA sequence upstream from the 5' termini of HIS1 mRNA we have found four closely related copies of a 9-base pair sequence. This sequence is also repeated in the 5' noncoding regions of HIS4, HIS3, and TRP5. Closely related sequences are not found flanking a number of other yeast genes, suggesting that the repeated sequence plays a role in the regulation of amino acid biosynthetic genes subject to the general amino acid control.

ATP Phosphoribosyltransferase↗
PubMed2005

Novel repeated DNA sequences in safflower (Carthamus tinctorius L.) (Asteraceae): cloning, sequencing, and physical mapping by fluorescence in situ hybridization.

Two novel repetitive DNA sequences, pCtKpnI-1 and pCtKpnI-2, were isolated from Carthamus tinctorius (2n = 2x = 24) and cloned. Both represent tandemly repeated sequences. The pCtKpnI-1 and pCtKpnI-2 clones constitute repeat units of 343-345 bp and 367 bp, respectively, with 63% sequence heterogeneity between the two. Fluorescence in situ hybridization (FISH) was employed on metaphase chromosomes of C. tinctorius using, simultaneously, pCtKpnI-1 and pCtKpnI-2 repeated sequences. The pCtKpnI-1 sequence was found to be exclusively localized at subtelomeric regions on most of the chromosomes. On the other hand, sequence of the pCtKpnI-2 clone was distributed on two nucleolar and one nonnucleolar chromosome pairs. The satellite, and the intervening chromosome segment between the primary and secondary constrictions, in the two nucleolar chromosome pairs were wholly constituted by pCtKpnI-2 repeated sequence. The pCtKpnI-2 repeated sequence, showing partial homology to intergenic spacer (IGS) of 18S-25S ribosomal RNA genes of an Asteraceae taxon (Centaurea stoebe), and the 18S-25S rRNA gene clusters were located at independent, but juxtaposed sites in the nucleolar chromosomes. Variability in the number, size, and location of the two repeated sequences provided identification of most of the chromosomes in the otherwise not too distinctive homologues within the complement. This article reports the start of a molecular cytogenetics program targeting the genome of safflower, a major world oil crop about whose genetics very little is known.

Base Sequence↗