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PubMed1982

Structural organization of rat ribosomal genes restriction endonuclease analysis of genomic and cloned ribosomal DNAs.

Structural organization of the rat ribosomal repeating unit was studied using hybridization of blotted restriction fragments of total rat DNA with alpha-32P-labeled cDNA probe synthesized on the 18S and 28S rRNAs. A detailed restriction endonuclease map was constructed, the 18S and 28S rRNA genes mapped and the sizes of the rat ribosomal repeating units determined. Considerable site heterogeneity of rat rDNA was revealed in both nontranscribed and external transcribed spacers. Recombinant phages containing the whole set of transcribed regions and a considerable part of a nontranscribed spacer of the rDNA were selected from the rat gene library. The restriction maps of the cloned rDNA fragments are in good agreement with the map constructed by Southern's technique, add to this map and support the existence of site heterogeneity in ribosomal repeating units. Proximal to the 3'-end of the 28S rRNA gene an internally repetitive region was found, each repeating unit being equal to approx. 150 bp. The site for transcription initiation was mapped 4.0-4.5 kb upstream from the 5'-end of the 18S rRNA gene. Frequently reiterated interspersed sequences were found in the nontranscribed spacer at approx. 2-3 kb distance from both ends of the transcribed region.

Animals↗
PubMed1979

Interspersion of highly repetitive DNA with single copy DNA in the genome of the red crab, Geryon quinquedens.

Kinetic analysis of the reassociation of 420 nucleotide (NT) long fragments has shown that essentially all of the repetitive sequences of the DNA of the red crab Geryon quinquedens are highly repetitive. There are negligible amounts of low and intermediate repetitive DNAs. Though atypical of most eukaryotes, this pattern has been observed in all other brachyurans (true crabs) studied (1,2). The major repetitive component is subdivided into short runs of 300 NT and longer runs of greater than 1200 NT while the minor component has an average sequence length of 400 NT. Both components reassociate at rates commonly observed for satellite DNAs. Unique among eukaryotes the organization of the genome includes single copy DNA contiguous to short runs (approximately 300 NT) of both repetitive components. Although patent satellites are not present, subsets of the repetitive DNA have been isolated by either restriction endonuclease digestion or by centrifugation in Ag+ or Hg2+/Cs2SO4 density gradients.

Animals↗
PubMed1994

Molecular evolution: codes, clocks, genes and genomes.

The discoveries, advancements and continuing controversies in the field of molecular evolution are reviewed. Topics summarized are (1) the evolution of the genetic code, (2) gene evolution including the demonstration of homology, estimation of sequence divergence, phylogenetic trees, the molecular clock and the origin of genes and gene families by various genetic mechanisms, and (3) eukaryotic genome evolution, including the highly repeated satellite sequences, the interspersed and potentially mobile repeated sequences and the unique sequence fraction of the genome.

Biological Evolution↗
PubMed1978

Fractionation of renatured repetitive human DNA according to thermal stability, sequence length, and renaturation rate.

Renatured repetitive human DNA sequences have been fractionated according to three criteria: length, thermal stability, and rate of renaturation. Satellite sequences are found in the long repetitive sequence fractions and renatured satellite sequences are well base paired by the criterion of thermal stability. No satellites are observed in short repeated sequences. Short repeated sequences are interspersed with single copy sequences and are poorly base paired. This implies satellite components are relatively homogeneous in base sequence whereas short interspersed repeated sequences are inexact copies of each other. A method for isolating satellite DNAs based on their high thermal stabilities is discussed.

Base Sequence↗
PubMed1990

Unusual molecular characteristics of a repeat sequence island within a Giemsa-positive band on the mouse X chromosome.

The mouse genome contains 50 copies of a long complex repeat unit localized as a repeat sequence island to the A3 Giemsa-positive (dark) band on the mouse X chromosome. The repeat units are not tandemly arranged but are juxtaposed and inserted by unrelated sequences of high repetition. The repeat sequence island possesses two notable features that have been suggested as diagnostic features of mammalian Giemsa-positive bands. First, the repeat sequence island encompasses a 1-megabase region devoid of CpG islands; second, it features a high concentration of L1 long interspersed repeat sequences.

Animals↗
PubMedDate not supplied

[Formation of the genome of the alligator gar Lepisosteus osseus (Ganoidomorpha) genome].

Genome structure of the alligator gar was studied by means of a comparison of reassociation kinetics of short and long DNA fragments, an estimation of hyperchromicity of reassociated repetitive DNA as a function of fragments length, and length estimation of S1-resistant duplexes by gel filtration. It was shown that most of the repeated sequences in the alligator gar DNA are no less than 2000 b.p. long and weakly divergent. Little or no interspersion of unique and short repeated sequences were observed in this genome. No highly divergent repeats were found in the alligator gar genome.

Animals↗
PubMed1996

Mermaid, a family of short interspersed repetitive elements, is useful for zebrafish genome mapping.

A family of short interspersed repetitive elements (SINEs), designated mermaid, is present in the genomes of fish, amphibian and primates, but absent in the mouse genome. We have demonstrated that the sequences of the mermaid family are highly polymorphic in the zebrafish genome as in the human genome. We have also shown that the mermaid sequence can be used to recover zebrafish specific DNA from zebrafish-mouse cell hybrids by using mermaid-specific oligonucleotides as PCR primers. Thus, the mermaid family serves as a valuable genetic tool for the zebrafish genome mapping.

Animals↗
PubMed2000

Genome complexity and organization in the red imported fire ant Solenopsis invicta Buren.

The red imported fire ant Solenopsis invicta is the most destructive invading arthropod in the southern United States, yet little is known about its genome complexity and organization. Here we report the size, organization and GC content of S. invicta genome. DNA reassociation kinetics using S1 nuclease assay and a modified second-order kinetics model indicated that the S. invicta genome is approximately 0.62 picograms or 5.91 x 10(8) base pairs, composed of 36% unique, 41% moderately repetitive and 23% highly repetitive/foldback sequences. Comparison of the reassociation kinetics of short and long DNA fragments revealed that the sequence arrangement follows a pattern of short period interspersion, as in most organisms with relatively large genomes. Melting-temperature analysis showed that the GC content of the fire ant genomic DNA is 34.8%, similar to that of most eukaryotic organisms. The results reveal that the fire ant genome is much larger and more complex than those of a number of hymenopteran insects studied to date. Our study provides a foundation for further analysis and genetic manipulation of the S. invicta genome.

Animals↗
PubMedDate not supplied

[Alu repeats in the human genome].

Highly repetitive DNA sequences account for more than 50% of the human genome. The L1 and Alu families harbor the most common mammalian long (LINEs) and short (SINEs) interspersed elements. Alu elements are each a dimer of similar, but not identical, fragments of total size about 300 bp, and originate from the 7SL RNA gene. Each element contains a bipartite promoter for RNA polymerase III, a poly(A) tract located between the monomers, a 3'-terminal poly(A) tract, and numerous CpG islands, and is flanked by short direct repeats. Alu repeats comprise more than 10% of the human genome and are capable of retroposition. Possibly, these elements played an important part in genome evolution. Insertion of an Alu element into a functionally important genome region or other Alu-dependent alterations of gene functions cause various hereditary disorders and are probably associated with carcinogenesis. In total, 14 Alu families differing in diagnostic mutations are known. Some of these, which are present in the human genome, are polymorphic and relatively recently inserted into new loci. Alu copies transposed during ethnic divergence of the human population are useful markers for evolutionary genetic studies.

Alu Elements↗
PubMed1981

Molecular structure of maternal RNA.

The presence of a stable maternal mRNA population in mature oocytes of many species is well established. In this paper we show that the mature egg contains, in addition to these mature mRNAs, a structurally more complex population of RNA transcripts. This latter class of RNA consists of polyadenylated transcripts of repetitive and nonrepetitive DNA elements covalently linked into long interspersed molecules. As much as seventy percent of the polyadenylated egg RNA of Xenopus laevis and Strongylocentrotus purpuratus is represented in this interspersed population. Most of the nonrepetitive DNA sequences represented in the mature mRNA population are also present in the interspersed RNA. These transcripts have an organization similar to that of somatic cell nuclear RNA. Data are presented that suggests some of these interspersed maternal transcripts are unprocessed precursor-like molecules. Some possible functions of this novel class of RNA during early development are discussed.

Animals↗
PubMed2004

Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions.

Comparative sequence analysis was carried out for the regions adjacent to experimentally validated transcriptional start sites (TSSs), using 3324 pairs of human and mouse genes. We aligned the upstream putative promoter sequences over the 1-kb proximal regions and found that the sequence conservation could not be further extended at, on average, 510 bp upstream positions of the TSSs. This discontinuous manner of the sequence conservation revealed a "block" structure in about one-third of the putative promoter regions. Consistently, we also observed that G+C content and CpG frequency were significantly different inside and outside the blocks. Within the blocks, the sequence identity was uniformly 65% regardless of their length. About 90% of the previously characterized transcription factor binding sites were located within those blocks. In 46% of the blocks, the 5' ends were bounded by interspersed repetitive elements, some of which may have nucleated the genomic rearrangements. The length of the blocks was shortest in the promoters of genes encoding transcription factors and of genes whose expression patterns are brain specific, which suggests that the evolutional diversifications in the transcriptional modulations should be the most marked in these populations of genes.

Animals↗
PubMed1988

Genes with specific functions in the ovarian follicles of Calliphora erythrocephala (Diptera).

Working with the large dipteran Calliphora erythrocephala, we have performed differential screening to identify genes actively expressed in the previtellogenic and early vitellogenic stages of oogenesis but silent during the early stages of embryogenesis. Clones containing sequences homologous to four such genes have been characterized. Two clones are homologous to the yolk protein 1 gene of Drosophila melanogaster. These two clones are expressed not only in the columnar follicle cells surrounding the oocyte but also in the border cells--a highly specialized subgroup of the follicle cells. This indicates a new function for these cells though previously to contribute mainly in the formation of the micropyle. A third clone, which is related to the D. melanogaster vitelline membrane protein genes of the cluster at chromosomal locus 26A, is expressed only in the perioocyte follicle cells and not the border cell population. The fourth clone encodes a sequence of unknown function which is abundantly expressed in the germ line cells of the follicle. Transcripts homologous to this clone persist into the mature follicle and initially appear concentrated at the anterior pole of the oocyte. The distribution of repetitious DNA within these four clones indicates that the C. erythrocephala genome has a short interspersion arrangement of repetitive DNA.

Animals↗
PubMed1996

The structure of the semenogelin gene locus--nucleotide sequence of the intergenic and the flanking DNA.

The sequence of 15.7 kb from the human semenogelin gene locus has been determined. Together with previously published sequences, this gives the structure of a 28-kb region encompassing the two semenogelin genes. The two transcription units are separated by 11616 bp intergenic DNA comprising more than 40% repetitive DNA sequences, predominantly located to a 4-kb block of L1 and Alu repeats. Two more blocks of L1 sequences are present in the DNA flanking the genes, so that approximately 20% of the completed sequence consists of long interspersed repeated sequences, so called LINES. A comparison of the SgI gene and the SgII gene suggests that they evolved by the duplication of an approximately 8 kb DNA segment about 61 million years ago, probably by a mechanism involving recombination between L1 elements.

Base Sequence↗
PubMed1996

Genomic simple repetitive DNAs are targets for differential binding of nuclear proteins.

The biological meaning of abundant simple repetitive DNA sequences in eukaryote genomes is obscure. Therefore, (GAA)n, (GT)n, and composite (GT)n(GA)m, blocks were characterized for protein binding in the repeat and flanking sequences of cloned genomic DNA fragments. In gel mobility shift and competition assays the binding of nuclear proteins to the repeats was specific (including some flanking single copy sequences). DNase footprinting revealed the target sequences within and adjacent to the repeats. Chemical modifications (OsO4, DEPC) demonstrated non-B DNA structures in the polypurine blocks. The binding of nuclear proteins in and around simple repeat sequences refute biological insignificance of all of these ubiquitously interspersed elements.

Animals↗
PubMed1987

Two families of repeated DNA sequences in Thiobacillus ferrooxidans.

The genome of Thiobacillus ferrooxidans ATCC 19859 is about 2.8 X 10(6) base pairs as determined by analysis of reassociation kinetics of sheared DNA. This is 70% of the size of the genome of Escherichia coli. About 6% of the genome of T. ferrooxidans consists of moderately repetitive DNA sequences that are repeated an average of 20 times per genome. Two distinct repeated sequences, designated family 1 and family 2, have been analyzed in more detail. Both families are approximately 1 kilobase in length and are repeated 20 to 30 times per genome. Preliminary evidence from restriction enzyme analysis, Southern blotting experiments, and thermal melting analysis indicates that members of both families are conserved and are interspersed with single-copy DNA. Six copies of one family are present on the 45-kilobase-pair plasmid of strain ATCC 19859.

Chromosome Mapping↗
PubMed2003

The 62-kb upstream region of Bombyx mori fibroin heavy chain gene is clustered of repetitive elements and candidate matrix association regions.

We sequenced an 80 kb DNA region containing the complete sequence of the silkworm Bombyx mori fibroin gene and its flanking, especially the upstream, regions (-62 kb). About 30% of the 62 kb upstream region is composed of repetitive elements including short interspersed elements Bm1, long interspersed elements L1Bm and mariner-like elements Bmmar1 which are widespread over the silkworm genome. This 62 kb region is also enriched of commonly considered matrix association region (MAR) motifs. A total of 25 individual MAR recognition signatures (MRSs) were identified, with 24 at the upstream and one at the downstream region. Combining two newly developed MAR prediction programs (MAR-finder and Chrclass), ten candidate MARs were predicted, with five containing MRS and seven related to the repetitive elements. The wide distribution of nested repetitive elements, candidate MARs, DNase I hypersensitive sites and other potential regulatory factors recognition sites indicates this region is probably a unique huge cis-acting element contributing to the regulation of the spatial and temporal specificity and efficiency of fibroin gene expression.

5' Flanking Region↗
PubMed1994

Junctions between repetitive DNAs on the PSR chromosome of Nasonia vitripennis: association of palindromes with recombination.

The Paternal-Sex-Ratio (PSR) chromosome of Nasonia vitripennis contains several families of repetitive DNAs that show significant sequence divergence but share two palindromic regions. This study reports on the analysis of junctions between two of these repetitive DNA families (psr2 and psr18). Three lambda clones that hybridized to both repeat families were isolated from PSR-genomic DNA libraries through multiple screenings and analyzed by Southern blots. Analysis of clones showed a region in which the two repeat types are interspersed, flanked by uniform blocks of each repeat type. PCR amplification of genomic DNA confirmed the contiguous arrangement of psr2 and psr18 on PSR and identified an additional junction region between these repeats that was not present in the lambda inserts. We isolated and sequenced 41 clones from the lambda inserts and genomic PCR products containing junction sequences. Sequence analysis showed that all transitions between psr2 and psr18 repeats occurred near one of the two palindromes. Based on the inheritance pattern of PSR, recombination between repeats on this chromosome must be mitotic (rather than meiotic) in origin. The occurrence of exchanges near the palindromes suggests that these sequences enhance recombination between repeat units. Rapid amplification of repetitive DNA may have been an important factor in the evolution of the PSR chromosome.

Animals↗