==================================BSR51================================== 51. Repetitive sequences in eucaryotic DNA. 1 UI - 87112728 AU - Satchwell SC ; Drew HR ; Travers AA TI - Sequence periodicities in chicken nucleosome core DNA. AB - The rotational positioning of DNA about the histone octamer appears to be determined by certain sequence-dependent modulations of DNA structure. To establish the detailed nature of these interactions, we have analysed the sequences of 177 different DNA molecules from chicken erythrocyte core particles. All variations in the sequence content of these molecules, which may be attributed to sequence-dependent preferences for DNA bending, correlate well with the detailed path of the DNA as it wraps around the histone octamer in the crystal structure of the nucleosome core. The sequence-dependent preferences that correlate most closely with the rotational orientation of the DNA, relative to the surface of the protein, are of two kinds: ApApA/TpTpT and ApApT/ApTpT, the minor grooves of which face predominantly in towards the protein; and also GpGpC/GpCpC and ApGpC/GpCpT, whose minor grooves face outward. Fourier analysis has been used to obtain fractional variations in occurrence for all ten dinucleotide and all 32 trinucleotide arrangements. These sequence preferences should apply generally to many other cases of protein-DNA recognition, where the DNA wraps around a protein. In addition, it is observed that long runs of homopolymer (dA) X (dT) prefer to occupy the ends of core DNA, five to six turns away from the dyad. These same sequences are apparently excluded from the near-centre of core DNA, two to three turns from the dyad. Hence, the translational positioning of any single histone octamer along a DNA molecule of defined sequence may be strongly influenced by the placement of (dA) X (dT) sequences. It may also be influenced by any aversion of the protein for sequences in the "linker: region, the sequence content of which remains to be determined. MH - Animal ; Base Sequence ; Chickens ; Cloning, Molecular ; *DNA ; Erythrocytes/ANALYSIS ; Fourier Analysis ; Nucleosomes/*ANALYSIS ; Oligodeoxyribonucleotides ; *Repetitive Sequences, Nucleic Acid ; Support, U.S. Gov't, P.H.S. SO - J Mol Biol 1986 Oct 20;191(4):659-75 2 UI - 87106850 AU - Hollis M ; Hindley J TI - Human Sau3A repeated DNA is enriched in small polydisperse circular DNA from normal lymphocytes. AB - Representatives of the Sau3A family of short human repeated sequences [Meneveri et al., J. Mol. Biol. 186 (1985) 483-489] have been isolated from the small polydisperse circular DNA (spcDNA) of peripheral human lymphocytes. The prototype repeat is a 72-bp element which is at least partially tandemly repeated in spcDNA and human genomic DNA. In comparison with three major families of human repeated DNA, the Sau3A repeats are enriched in spcDNA. The function of spcDNA in normal and transformed eukaryotic cells is not understood and most studies have attempted to resolve this problem by molecular analysis of circular DNA isolated from cells in culture [see Rush and Misra, Plasmid 14 (1985) 177-191 for references]. We have studied the spcDNA present in normal uncultured human lymphocytes and present data pointing to the selective accumulation of the Sau3A family of repeated DNA within this population. The sequences of twelve of these repeats, the consensus sequence for this family and the sequence of a genomic repeat, are presented. MH - Base Sequence ; Cloning, Molecular ; DNA, Circular/*GENETICS ; Genes, Reiterated ; Human ; Lymphocytes/ANALYSIS ; *Repetitive Sequences, Nucleic Acid ; Support, Non-U.S. Gov't SO - Gene 1986;46(2-3):153-60 3 UI - 87091560 AU - Suzuki N ; Fujiyoshi T ; Maehara Y ; Takahashi K ; Yamamoto M ; Endo H TI - A new family of LTR-like sequences abundantly expressed in rat tumors. AB - We report the identification of two genome DNA fragments containing middle repetitive sequences abundantly expressed in various rat tumors but rarely in normal tissues. These fragments included homologous regions which belonged to a new family of long terminal repeat (LTR) like sequences, designated RAL elements; one displayed the solitary type and the other a provirus structure. The element was transcribed in a strand specific fashion and started from the presumptive cap site within the RAL element. The presumptive polyA addition site within the element was also utilized as evidence of the analysis of a cDNA clone containing the RAL element. This evidence suggested that transcriptional control signals within the element were functioning. Run on assay revealed that expression of the element was regulated at the transcriptional level. MH - Animal ; DNA/ANALYSIS ; DNA, Neoplasm/*ANALYSIS ; Gene Expression Regulation ; Neoplasms, Experimental/*FAMILIAL & GENETIC ; Nucleic Acid Hybridization ; Poly A/ANALYSIS ; Rats ; Rats, Inbred Strains ; *Repetitive Sequences, Nucleic Acid ; Retroviridae/GENETICS ; RNA/ ANALYSIS ; Sequence Homology, Nucleic Acid ; Support, Non-U.S. Gov't ; Transcription, Genetic SO - Nucleic Acids Res 1986 Dec 9;14(23):9271-89 4 UI - 87064883 AU - Perler FB ; Karam M TI - Cloning and characterization of two Onchocerca volvulus repeated DNA sequences. AB - Two repeated sequences, plasmids pOV8 and pOV26, were cloned and characterized from the filarial parasite Onchocerca volvulus. Both clones can be used to distinguish O. volvulus DNA from other Onchocerca species or other nematodes by restriction fragment length polymorphisms, but neither clone can differentiate between DNA from savanna (Mali) or forest (Ivory Coast) O. volvulus isolates. DNA from one O. volvulus infective larva can be detected by both clones in dot blot hybridization assays. Neither clone cross hybridizes with DNA from host or vector species (human or simuliid, respectively). pOV26 is a member of an interspersed repeated DNA family composed of at least 100 members, and is only observed in the genus Onchocerca. Repeated DNA clone pOV8 cross reacts with DNA from other parasitic filarial nematodes, and is also present in at least 100 copies per O. volvulus genome. pOV26 is a potential tool in the diagnosis of human onchocerciasis, since it is specific for the genus Onchocerca. In the future, we plan to look for regions of these repeated sequences which may serve as a basis for the development of probes to discriminate among Onchocerca species and strains using a simple dot hybridization test. MH - Animal ; Cloning, Molecular ; Comparative Study ; DNA/*ANALYSIS ; DNA Restriction Enzymes ; Electrophoresis, Agar Gel ; Genes ; Ivory Coast ; Larva ; Mali ; Nucleic Acid Hybridization ; Onchocerca/CLASSIFICATION/ *GENETICS ; Onchocerciasis/DIAGNOSIS ; Plasmids ; *Repetitive Sequences, Nucleic Acid ; Simuliidae ; Species Specificity SO - Mol Biochem Parasitol 1986 Nov;21(2):171-8 5 UI - 87064877 AU - Chambers AE ; Almond NM ; Knight M ; Simpson AJ ; Parkhouse RM TI - Repetitive DNA as a tool for the identification and comparison of nematode variants: application to Trichinella isolates. AB - DNA prepared from four isolates of Trichinella was compared by genomic DNA cross-hybridisation, by electrophoresis following restriction endonuclease digestion and by hybridisation studies using a cloned repetitive DNA sequence from T. spiralis. The DNA from T. spiralis, T. nelsoni and T. pseudospiralis isolates was distinct and the interrelationships of these isolates were inferred. In contrast to previous work on T. nativa and T. spiralis, our work suggests that these two isolates are very similar. MH - Animal ; Cloning, Molecular ; Comparative Study ; DNA/*ANALYSIS ; DNA Restriction Enzymes ; Electrophoresis, Agar Gel ; Genes ; Nucleic Acid Hybridization ; *Repetitive Sequences, Nucleic Acid ; Sequence Homology, Nucleic Acid ; Support, Non-U.S. Gov't ; Trichinella/CLASSIFICATION/ *GENETICS/ISOLATION & PURIFICATION SO - Mol Biochem Parasitol 1986 Nov;21(2):113-20 6 UI - 87055269 AU - Shore SK ; Bacheler LT ; de Riel JK ; Barrows LR ; Lynch M TI - Cloning and characterization of a rat-specific repetitive DNA sequence. AB - A 2.1-kb EcoRI fragment of rat DNA has been cloned and sequenced. This fragment contained a repetitive element which was highly specific for rat DNA and widely dispersed throughout the rat genome. The repetitive element is homologous to a sequence found in the 3' end of the rat LINE family. Because of its high degree of species specificity and its heterodisperse distribution, this sequence provided a useful marker for rat DNA in DNA transfection experiments into mouse host cells. MH - Animal ; Cloning, Molecular ; Comparative Study ; DNA, Recombinant/ *ANALYSIS ; Human ; Mammals/GENETICS ; Rats ; Rats, Inbred Strains/ *GENETICS ; *Repetitive Sequences, Nucleic Acid ; Species Specificity ; Support, Non-U.S. Gov't ; Support, U.S. Gov't, P.H.S. SO - Gene 1986;45(1):87-93 7 UI - 87029657 AU - McDermid HE ; Duncan AM ; Higgins MJ ; Hamerton JL ; Rector E ; Brasch KR ; White BN TI - Isolation and characterization of an alpha-satellite repeated sequence from human chromosome 22. AB - We constructed a library in lambda L47.1 with DNA isolated from flow-sorted human chromosome 22. Over 50% of the recombinants contained the same highly repetitive sequence. When this sequence was used to probe Southern blots of EcoRI-digested genomic DNA, a ladder of bands with increments of about 170 bp was observed. This sequence comigrates with satellite III in Ag+/Cs2SO4 gradients and may account for at least part of the 170 bp Hae III ladder seen in isolated satellite III DNA. Partial sequence analysis revealed homology to the 171 bp monomeric repeat unit of alpha-R1-DNA and the X specific alpha-satellite consensus sequence. After low stringency in situ hybridization, silver grains were found over the centromeres of a number of chromosomes. Under high stringency conditions, however, the labeling was concentrated over the centromeric region of chromosome 22. This localization was confirmed using DNA from a panel of human/hamster cell lines which showed that the homologous 2.1 and 2.8 kb EcoR1 restriction fragments were chromosome 22 specific. These clones therefore contain chromosome 22 derived alpha-satellite sequences analogous to other chromosome-specific satellite sequences described previously. MH - Animal ; Chromosomes, Human, Pair 22/*ANALYSIS ; DNA, Recombinant/ ANALYSIS ; DNA, Satellite/*ISOLATION & PURIFICATION ; Hamsters ; Human ; Hybrid Cells/ANALYSIS ; Nucleotide Mapping ; *Repetitive Sequences, Nucleic Acid ; Support, Non-U.S. Gov't SO - Chromosoma 1986;94(3):228-34 8 UI - 87026681 AU - Sol K ; Lapointe M ; MacLeod M ; Nadeau C ; DuBow MS TI - A cloned fragment of HeLa DNA containing consensus sequences of satellite II and III DNA hybridizes with the Drosophila P-element and with the 1.8 kb family of human KpnI fragments. AB - We have cloned a repetitive EcoRI fragment from the human genome which displays weak homologies with the Drosophila melanogaster transposable P-element. This cloned DNA appeared not to be a mobile element but, instead, a divergent member of human satellite II or III DNAs. We present here the first complete nucleotide sequence of a 1.797 kilobase pair (kb) satellite-like DNA. Moreover, this EcoRI satellite monomer contains a unique sequence of 49 basepairs (bp) that is devoid of the satellite consensus repeat 5'TTCCA3'. Southern hybridization analysis revealed that the cloned insert is closely related to a highly repetitive 1.8 kb KpnI family of tandemly organized satellite DNAs. Thus, the relationships among these satellite DNA families appear to be complex and may be a factor in their copy number, position and spatial organization. MH - Animal ; Base Sequence ; Cloning, Molecular ; Drosophila Melanogaster/ GENETICS ; DNA Restriction Enzymes ; *DNA, Satellite ; Hela Cells ; Human ; Nucleic Acid Hybridization ; *Repetitive Sequences, Nucleic Acid ; Sequence Homology, Nucleic Acid ; Support, Non-U.S. Gov't SO - Biochim Biophys Acta 1986 Nov 13;868(2-3):128-35 9 UI - 87004658 AU - Landolt P ; Tobler H TI - Characterization of inverted repeated sequences in Ascaris nuclear DNA. AB - The inverted repeated sequences of the chromatin-eliminating nematode Ascaris lumbricoides var. suum have been examined by electron microscopy and by hydroxyapatite chromatography, both in the germ-line and in the somatic DNA. 38% of the inverted repeats of the germ-line DNA analysed in the electron microscope have a single-stranded loop, in comparison to about 50% of looped structures in the somatic DNA. The loops are on average 2.3 X 10(3) base pairs (bp) long. The rest of the foldback DNA consists of simple hairpins. The average length of looped and unlooped inverted repeats is of the order of 300-400 bp in the germ-line and in the somatic DNA. The content of S1-resistant foldback duplexes isolated by hydroxyapatite chromatography amounts to 1.3% in spermatids, with an average length of 350 bp, and to 1.1% in intestinal or larval cell nuclei, with a length of about 320 bp. We estimate by two different methods that there exist approximately 12500 inverted repeats per haploid germ-line genome and approximately 8000 in the haploid somatic genome. A statistical analysis of the data indicates that the great majority of the foldback sequences are randomly distributed in the Ascaris genome, with a spacing of about (40-80) X 10(3) bp, both in the germ-line and in the somatic DNA. MH - Animal ; Ascaris/*GENETICS ; Chromatography/METHODS ; *DNA/ULTRASTRUCTURE ; Hydroxyapatites ; Microscopy, Electron ; Nucleic Acid Conformation ; *Repetitive Sequences, Nucleic Acid ; Support, Non-U.S. Gov't SO - Eur J Biochem 1986 Sep 15;159(3):435-42 10 UI - 87002455 AU - Morin GB ; Cech TR TI - The telomeres of the linear mitochondrial DNA of Tetrahymena thermophila consist of 53 bp tandem repeats. AB - We have cloned and sequenced the telomeric DNA of the linear mitochondrial DNA (mtDNA) of T. thermophila BVII. The mtDNA telomeres consist of a 53 bp sequence tandemly repeated from 4 to 30 times, with most molecules having 15 +/- 4 repetitions. The previously recognized terminal heterogeneity of the mtDNA is completely accounted for by the variability in the number of repeats. The 53 bp repeat does not resemble known telomeric DNA in sequence, repeat size, or number of repetitions. The termini occur at heterogeneous positions within the 53 bp repeat. The junction of the telomeric repeat with the internal DNA is at a different position within the telomeric repeat on each end of the mtDNA. We propose a model for the maintenance of the mtDNA ends involving unequal homologous recombination. MH - Animal ; Base Sequence ; Cloning, Molecular ; DNA Restriction Enzymes/ DIAGNOSTIC USE ; DNA, Mitochondrial/*GENETICS ; Hydrogen Bonding ; Nucleic Acid Conformation ; *Repetitive Sequences, Nucleic Acid ; Support, U.S. Gov't, P.H.S. ; Tetrahymena/*GENETICS SO - Cell 1986 Sep 12;46(6):873-83 11 UI - 86304423 AU - Haydock PV ; Dale BA TI - The repetitive structure of the profilaggrin gene as demonstrated using epidermal profilaggrin cDNA. AB - Filaggrin is the histidine-rich basic protein that aggregates keratin filaments in fully differentiated cells of the epidermis. Filaggrin is synthesized in the granular cell layer as a high molecular weight precursor protein (profilaggrin) that consists of multiple repeated copies of filaggrin. cDNA clones for rat and mouse epidermal profilaggrin have been constructed from sucrose gradient-enriched RNA in order to study the repetitive structure of profilaggrin. These clones hybridize to high molecular weight epidermal mRNA (23 kilobase pairs, rat and 19 kilobase pairs, mouse) and exhibit limited cross-hybridization between species. Several rat clones direct the synthesis of a portion of rat profilaggrin in bacteria. One of these, rat profilaggrin cDNA clone R4D6, is 2400 base pairs in length. The R4D6 cDNA is shown to contain repetitive sequence by restriction mapping and southern hybridization analysis of restriction digests of this plasmid, using subfragments of the plasmid as hybridization probes. Southern hybridization analysis of rat genomic DNA, digested to completion with several restriction enzymes, reveals a simple hybridization pattern of fragments equal in size to those of the cDNA. Partial digestion of rat genomic DNA results in a ladder of bands based on a 1200-base pair repeat, equal to the size of the repeating unit of the cDNA clone, and consistent with the expected repeating size of profilaggrin. Together, these results show that the profilaggrin mRNA and gene have repetitive structure and that the gene apparently lacks introns in the coding region. MH - Amino Acid Sequence ; Animal ; Base Sequence ; Cloning, Molecular ; DNA/ *ANALYSIS ; Electrophoresis, Agar Gel ; Epidermis/ANALYSIS ; Intermediate Filament Proteins/*GENETICS ; Mice ; Protein Precursors/*GENETICS ; Rats ; *Repetitive Sequences, Nucleic Acid ; Support, Non-U.S. Gov't ; Support, U.S. Gov't, P.H.S. SO - J Biol Chem 1986 Sep 25;261(27):12520-5 12 UI - 86273614 AU - Sch:afer R ; B:oltz E ; Becker A ; Bartels F ; Epplen JT TI - The expression of the evolutionarily conserved GATA/GACA repeats in mouse tissues. AB - Simple repeated GATA and GACA sequences were initially identified in sex-specific snake satellite DNA. The organization of these sequences in the mouse genome is described in Sch:afer et al. 1986. The expression of these simple repeats was studied here in several mouse tissues using a variety of different probes: oligonucleotides and "single-stranded: as well as nick-translated DNA. The transcription of discrete RNA species was found to be differentially regulated in several organs but sex differences in transcription were not observed. GATA- and GACA-containing cDNA clones were isolated and sequenced and a genomic clone was characterized with respect to the transcription of GATA flanking sequences. Functional aspects of GATCA simple DNA repeats are discussed in terms of internally repetitive, hydrophobic translation products. MH - Animal ; Base Sequence ; Cloning, Molecular ; DNA/ANALYSIS ; DNA, Satellite/*GENETICS ; *Evolution ; Female ; Liver/METABOLISM ; Male ; Mice ; Mice, Inbred C57BL ; Nucleic Acid Hybridization ; *Repetitive Sequences, Nucleic Acid ; Sex Factors SO - Chromosoma 1986;93(6):496-501 13 UI - 86245066 AU - Saris CJ ; Tack BF ; Kristensen T ; Glenney JR Jr ; Hunter T TI - The cDNA sequence for the protein-tyrosine kinase substrate p36 (calpactin I heavy chain) reveals a multidomain protein with internal repeats. AB - We have isolated and sequenced a full-length cDNA clone for the protein-tyrosine kinase substrate p36 (calpactin I heavy chain). This sequence predicts a 339 amino acid (Mr 38,493) protein containing an N-terminal region of 20 amino acids, known to interact with a 10 kd protein (light chain), and a C-terminal region, found to contain two Ca2+/phospholipid-binding sites, that can be aligned as four 70 amino acid repeats. A single p36 gene was detected in the mouse genome, and a major p36 mRNA of 1.6 kb was found to be expressed in different mouse tissues. Unexpectedly, p36 and the phospholipase A2 inhibitor lipocortin I were found to be 50% identical in sequence over the C-terminal 300 residues. The function of p36 and its relation to other proteins are discussed. MH - Amino Acid Sequence ; Animal ; Base Sequence ; Calcium-Binding Proteins/ *GENETICS ; Cloning, Molecular ; DNA/*GENETICS ; DNA Restriction Enzymes ; Mice ; Molecular Weight ; Protein-Tyrosine Kinase/*GENETICS ; *Repetitive Sequences, Nucleic Acid ; RNA, Messenger/GENETICS ; Support, U.S. Gov't, P.H.S. SO - Cell 1986 Jul 18;46(2):201-12 14 UI - 86302779 AU - Ohno S ; Ohno M TI - The all pervasive principle of repetitious recurrence governs not only coding sequence construction but also human endeavor in musical composition. AB - Organisms which have evolved on this earth are governed by multitudes of periodicities; tomorrow is another today, and the next year is going to be much like this year. Accordingly, the principle of repetitious recurrence pervades every aspect of life on this earth. Thus, individual genes in the genome have been duplicated and triplicated often to the point of redundancy, and each coding sequence consists of numerous variously truncated as well as variously base-substituted copies of the original primordial building block base oligomers and their allies. This principle even appears to govern the manifestations of human intellect; musical compositions also rely on this principle of repetitious recurrence. Accordingly, coding base sequences can be transformed into musical scores using one set rule. Conversely, musical scores can be transcribed to coding base sequences of long open reading frames. MH - Animal ; DNA/*GENETICS ; Evolution ; Genes, Structural ; Human ; Mice ; *Music ; Phosphoglycerate Kinase ; Protein Conformation ; *Repetitive Sequences, Nucleic Acid ; RNA Polymerase II/GENETICS SO - Immunogenetics 1986;24(2):71-8 15 UI - 86273615 AU - Sch:afer R ; Ali S ; Epplen JT TI - The organization of the evolutionarily conserved GATA/GACA repeats in the mouse genome. AB - Simple repeated GATA and GACA sequences which were originally isolated from sex-specific snake satellite DNA have been found subsequently in all eukaryotes studied. The organization of these sequences within the mouse genome was investigated here by using synthetic oligonucleotide probes as a novel tool in comparison with conventional hybridization probes. Southern blot hybridization showed sex-specific patterns with both the (GATA)4 and (GACA)4 oligonucleotide probes, as previously described with conventional probes. The quantitative analysis of two mouse DNA phage libraries and of 25 isolated GATA-positive phage clones revealed intensive interspersion of GATA sequences with GACA, and with other repetitive and single-copy sequences. Ubiquitous interspersion and homogeneous genomic distribution of GATA and GACA sequences were confirmed by hybridization in situ of the oligonucleotide probes to metaphase chromosomes. The lengths of the GATA and GACA stretches were found to vary considerably in the individual phage clones. DNA inserts from 20 phages were assigned to autosomes and sex chromosomes and three genomic fragments were found to be confined to the Y chromosome. The organization of GATA and GACA sequences is discussed in the context of their evolutionary potential and possible conservation mechanisms. MH - Animal ; Bone Marrow/CYTOLOGY ; Chromosome Banding ; DNA, Satellite/ *GENETICS ; *Evolution ; Genes ; Karyotyping ; Metaphase ; Mice ; Mice, Inbred C57BL ; Nucleic Acid Hybridization ; *Repetitive Sequences, Nucleic Acid ; Support, Non-U.S. Gov't ; Translation, Genetic SO - Chromosoma 1986;93(6):502-10 16 UI - 86268997 AU - Simmen FA ; Mandel M ; Humphreys T TI - Length and sequence polymorphisms in the ribosomal gene spacer of the Hawaiian sea urchin, T. gratilla. AB - Blot-hybridization of sea urchin (Tripneustes gratilla) genomic DNA with a cloned rDNA probe revealed individual variation in the length of the rDNA repeat unit and also in the non-transcribed spacer sequences. The number of distinct rDNA repeat subclasses distinguishable within any one sea urchin was limited and usually 2 to 3. However, examination of a number of sea urchins indicated a large number of distinct rDNA repeat types in the population as a whole; all of the rDNA repeat types in nine individuals were different. The presence of limited heterogeneity in the rDNA repeats of single individuals, with may different repeat types in the population as a whole, suggests that rDNA variants can be rapidly and selectively propagated within a chromosomal lineage. MH - Animal ; Cloning, Molecular ; DNA/*ANALYSIS ; *Genes, Structural ; Nucleic Acid Hybridization ; *Polymorphism (Genetics) ; *Repetitive Sequences, Nucleic Acid ; Ribosomes/*METABOLISM ; Sea Urchins/*GENETICS ; Support, U.S. Gov't, P.H.S. ; Transcription, Genetic SO - Biochem Biophys Res Commun 1986 Jun 13;137(2):834-40 17 UI - 86230917 AU - Hattori M ; Kuhara S ; Takenaka O ; Sakaki Y TI - L1 family of repetitive DNA sequences in primates may be derived from a sequence encoding a reverse transcriptase-related protein. AB - Primate and rodent genomes contain a family of highly repetitive, long interspersed sequences, designated the L1 family or LINE-1. Characteristic features of the L1 family sequences such as an A-rich stretch at the 3' end, a truncated 5' end, the existence of significantly long open reading frames (ORFs) and the presence of L1 family transcripts in various types of cells, including pluripotential embryonic cells, suggest that the L1 family is derived from a sequence encoding a protein(s) and dispersed in the genome through an RNA-mediated process. These features of the L1 family are believed to be due to reverse transcription beginning at the 3' end of the L1 transcript and terminating prematurely and to the site duplication caused by the insertion of the complementary DNA. It is likely that this type of transcript is converted to cDNA and inserted into the chromosome through a process similar to that of the formation of processed pseudogenes. The above model, however, does not necessarily explain why the L1 family should produce the extraordinarily large number of copies (more than 10(4) per haploid genome) seen during evolution. It seems likely that the progenitor of the L1 family itself carries (or carried) a function which promotes the active dispersion of the L1 family sequence. We reasoned that such a function, if present, must be conserved during evolution and may be shown by comparative analysis of L1 family sequences from evolutionarily distant species. We show here that the L1 family sequence contains an ORF possessing significant sequence homology to several RNA-dependent DNA polymerases of viral and transposable element origins.(ABSTRACT TRUNCATED AT 250 WORDS) MH - Amino Acid Sequence ; Animal ; DNA/*GENETICS ; Evolution ; Human ; Lorisidae/*GENETICS ; Rats ; *Repetitive Sequences, Nucleic Acid ; Reverse Transcriptase/*GENETICS ; Sequence Homology, Nucleic Acid ; Support, Non-U.S. Gov't SO - Nature 1986 Jun 5-11;321(6070):625-8 18 UI - 86200462 AU - Chiu IM ; Skuntz SF TI - Nucleotide sequence analysis of squirrel monkey retrovirus reveals a novel primer-binding site for tRNALys1,2. AB - Nucleotide sequences of a DNA fragment containing the long terminal repeat (LTR) of squirrel monkey retrovirus (SMRV) were determined. Sequence analysis showed that the SMRV LTR is 456 base pairs (bp) long and is bounded by 2-bp inverted repeats. Within the U3 region, there are two 43-bp repeats and two 42-bp repeats which are homologous to each other. These repeats are likely to provide enhancer activities commonly observed in other enhancer sequences. Following the repeats are transcriptional regulatory sequences including a CAT box, a Goldberg-Hogness box, and a polyadenylation signal, all positioned within the U3 region of SMRV LTR. A 22-nucleotide sequence immediately downstream from the LTR was found to be complementary to tRNALys1,2, suggesting that tRNALys1,2 serves as the primer for the reverse transcription of SMRV viral RNA. MH - Animal ; Binding Sites ; Cebidae/*MICROBIOLOGY ; DNA, Viral/*ANALYSIS ; Enhancer Elements (Genetics) ; *Repetitive Sequences, Nucleic Acid ; Retroviridae/*GENETICS ; RNA, Transfer, Amino Acyl/*METABOLISM ; Saimiri/ *MICROBIOLOGY ; Transcription, Genetic SO - J Virol 1986 Jun;58(3):983-7 19 UI - 86214059 AU - Shaw DR ; Khandekar P ; Siddiqui MA ; Ennis HL TI - The 3'-noncoding region of the chick myosin light-chain gene hybridizes to a family of repetitive sequences in the slime mold Dictyostelium discoideum. AB - During studies aimed at isolating myosin-specific genomic clones in Dictyostelium, we probed a lambda genomic library with a chicken myosin light-chain sequence (pML10). Many lambda recombinant Dictyostelium clones hybridized to the pML10 cDNA insert, indicating that this sequence was reiterated in the Dictyostelium genome. It was found that the 3'-noncoding region (pML10-NC) alone was responsible for these results. Dictyostelium DNA contained approximately 65 copies of a sequence(s) similar but not identical to that of pML10-NC. Southern blot analysis showed that pML10-NC hybridized to many Dictyostelium genomic DNA fragments of varying sizes generated by digestion with EcoRI, HindIII, or AluI. In addition, each of the Dictyostelium clones was different in its size, restriction map, and flanking sequences. It seems likely, therefore, that the sequences which hybridized to pML10-NC are scattered throughout the Dictyostelium genome and similar but not identical to each other or to pML10-NC. Thus, probing with pML10-NC has allowed us to select a family of closely related but not identical sequences. These D. discoideum sequences are not found in other slime mold species. No RNA complementary to pML10-NC was found in vegetative cells, 18 h culmination stage, spores, or 1- and 2-h germinating spores. pML10-NC-related sequences were present in two other Dictyostelium species but were absent in the related genus Polysphondylium. MH - Animal ; Chickens ; Cloning, Molecular ; Dictyostelium/*GENETICS ; DNA ; DNA Restriction Enzymes ; *DNA, Fungal ; *Genes, Structural ; Myosin/ *GENETICS ; *Nucleic Acid Hybridization ; *Repetitive Sequences, Nucleic Acid SO - Arch Biochem Biophys 1986 May 1;246(2):829-37 20 UI - 86200213 AU - Burton FH ; Loeb DD ; Voliva CF ; Martin SL ; Edgell MH ; Hutchison CA 3d TI - Conservation throughout mammalia and extensive protein-encoding capacity of the highly repeated DNA long interspersed sequence one. AB - We report an investigation of the structure, evolutionary history, and function of the highly repeated DNA family named Long Interspersed Sequence One (L1). Hybridization studies show, first, that L1 is present throughout marsupial and placental mammalian orders. Second, L1 is more homologous within these species than between them, which suggests that it has undergone concerted evolution within each mammalian lineage. Third, on the whole L1 diverges in accordance with the fossil record. This suggests that it arose in each lineage rather by inheritance from a common ancestral family, which was present in the progenitor to mammals, than by cross-species transmission. Alignment of 1.6 X 10(3) bases of primate and mouse L1 DNA sequences shows a predominance of silent mutations within aligned long open reading frames, indicating that at least this part of L1 has produced functional protein. The observation of additional long open reading frames in further unaligned DNA sequences suggests that a minimum of 3.2 X 10(3) bases or at least half of the L1 structure is a protein-coding sequence. Thus L1, which contains about 100,000 members in mouse, is by far the most repetitive family of which a subset comprises functional protein-encoding genes. The ability of the putative protein-encoding regions of mouse L1 to hybridize to L1 homologs throughout the Mammalia implies that these sequences have been subject to conservative selection upon protein function in all mammalian lineages, rather than in a few. L1 is therefore a highly repeated family of genes with both a widespread and an ancient history of function in mammals. MH - Amino Acid Sequence ; Animal ; Base Sequence ; *DNA ; DNA Restriction Enzymes ; *Evolution ; *Genetic Code ; Human ; Mammals/*GENETICS ; Mice ; Nucleic Acid Hybridization ; Primates ; *Repetitive Sequences, Nucleic Acid ; Sequence Homology, Nucleic Acid ; Support, Non-U.S. Gov't ; Support, U.S. Gov't, P.H.S. SO - J Mol Biol 1986 Jan 20;187(2):291-304 21 UI - 86176766 AU - Yavachev LP ; Georgiev OI ; Braga EA ; Avdonina TA ; Bogomolova AE ; Zhurkin VB ; Nosikov VV ; Hadjiolov AA TI - Nucleotide sequence analysis of the spacer regions flanking the rat rRNA transcription unit and identification of repetitive elements. AB - We investigated the organization of the rat rDNA non-transcribed spacer (NTS) by determining the sequence of large NTS segments located upstream (2501 bp) and downstream (4025 bp) from the rRNA transcription unit. We identified four B2-like and two ID mobile elements. They may be grouped in three pairs with the members of each pair located in the upstream and downstream NTS. The ID sequences are identical to the consensus sequence, while the pairs of B2-like elements show 85% and 50/65% homology to the consensus B2 sequence. The proximal part of the downstream NTS contains a region of widely diverged SalI tandem repeats. A considerable part of the analyzed upstream and downstream NTS sequences is constituted by different types of simple sequences and long poly(purine) X poly(pyrimidine) tracts. These data show that the rat rDNA NTS regions flanking the rRNA transcription unit are characterized by a combination of short interspersed (B2-superfamily) and various simple sequences. MH - Animal ; Base Sequence ; DNA, Ribosomal/*GENETICS ; Linkage (Genetics) ; Rats ; *Repetitive Sequences, Nucleic Acid ; RNA, Ribosomal/*GENETICS ; Transcription, Genetic SO - Nucleic Acids Res 1986 Mar 25;14(6):2799-810 22 UI - 86174885 AU - Oquendo P ; Goman M ; Mackay M ; Langsley G ; Walliker D ; Scaife J TI - Characterisation of a repetitive DNA sequence from the malaria parasite, Plasmodium falciparum. AB - A repetitive DNA fragment cloned from the malaria parasite, Plasmodium falciparum, has been analysed. It contains a 21 base pair sequence which occurs in multiple tandem repeats. Two clusters of the same repeat are found in opposite orientations on the same DNA fragment. The repetitive DNA provides an additional way to distinguish between different strains of parasite by hybridisation to genomic blots and may serve as a species-specific probe for diagnosis. MH - Animal ; Cloning, Molecular ; DNA/*ANALYSIS/ISOLATION & PURIFICATION ; Nucleic Acid Hybridization ; Phage Lambda/GENETICS ; Plasmodium Falciparum/*GENETICS ; *Repetitive Sequences, Nucleic Acid ; Support, Non-U.S. Gov't SO - Mol Biochem Parasitol 1986 Jan;18(1):89-101 23 UI - 86166505 AU - De Stefano GF ; Romano E ; Ferrucci L TI - The Alu I-induced bands in metaphase chromosomes of orangutan (Pongo pygmaeus). Implications for the distribution pattern of highly repetitive DNA sequences. AB - Restriction endonucleases have been recently proved to be active on fixed chromosomes, thus they are useful in chromatin structure studies. Within this class of enzymes, Alu I is able to detect the presence and localization of highly repetitive DNA sequences in human and in other mammalian and dipteran species. In this paper the pattern obtained on fixed metaphase chromosomes of orangutan (Pongo pygmaeus) by Alu I digestion and Giemsa staining is shown. The results are discussed in the light of the distribution, in this species, of the I-IV human satellite DNAs. It is also suggested that in Pongo some highly repetitive sequences, different from the major human satellites, are present. MH - Animal ; Chromosome Banding ; DNA/*GENETICS ; DNA Restriction Enzymes ; Human ; Karyotyping ; Metaphase ; Pongidae/*GENETICS ; Pongo pygmaeus/ *GENETICS ; *Repetitive Sequences, Nucleic Acid ; Species Specificity ; Support, Non-U.S. Gov't SO - Hum Genet 1986 Mar;72(3):268-71 24 UI - 86144071 AU - Deiss LP ; Frenkel N TI - Herpes simplex virus amplicon: cleavage of concatemeric DNA is linked to packaging and involves amplification of the terminally reiterated a sequence. AB - Herpes simplex virus-infected cells contain large concatemeric DNA molecules arising from replication of the viral genome. The large concatemers are cleaved to generate unit-length molecules terminating at both ends with the a sequence. We have used constructed defective virus vectors (amplicons) derived from herpes simplex virus to study the mechanism of cleavage of viral DNA concatemers and the packaging of viral DNA into nucleocapsids. These studies revealed that (i) a 248-base-pair a sequence contained the signal(s) required for cleavage-packaging, (ii) the cleavage of viral DNA concatemers was coupled to packaging, (iii) the a sequence contained the information required for its own amplification, and (iv) cleavage-packaging occurred by a novel process involving the amplification of the a sequence. MH - Animal ; DNA Replication ; DNA, Viral/*METABOLISM ; *Gene Amplification ; *Genes, Viral ; Herpesvirus Hominis/*GENETICS ; Plasmids ; Rabbits ; *Repetitive Sequences, Nucleic Acid ; Support, U.S. Gov't, Non-P.H.S. ; Support, U.S. Gov't, P.H.S. ; Virus Replication SO - J Virol 1986 Mar;57(3):933-41 25 UI - 86136600 AU - Dodin G TI - Heteroduplex stabilities in highly repetitive DNA. An hypothesis for the polymorphism of Plasmodium parasite antigenic response. AB - Codon repeats encountered in DNA sequences may formally lead to several double-stranded structures of similar stabilities. This is observed in the highly repetitive sequences of some Plasmodium antigens (S-antigen, CS proteins). It is postulated that gene recombination may occur via various heteroduplex molecules thus leading to antigenic polymorphism of Plasmodium parasites. RF - REVIEW ARTICLE: 15 REFS. MH - Animal ; Antigens, Protozoan/*GENETICS ; DNA/*GENETICS ; Evolution ; Models, Biological ; *Nucleic Acid Heteroduplexes ; Plasmodium/GENETICS/ *IMMUNOLOGY ; Plasmodium Falciparum/GENETICS/IMMUNOLOGY ; Polymorphism (Genetics) ; Recombination, Genetic ; *Repetitive Sequences, Nucleic Acid ; Review SO - FEBS Lett 1986 Mar 3;197(1-2):5-8 26 UI - 86133548 AU - Arkhipova IR ; Mazo AM ; Cherkasova VA ; Gorelova TV ; Schuppe NG ; Llyin YV TI - The steps of reverse transcription of Drosophila mobile dispersed genetic elements and U3-R-U5 structure of their LTRs. AB - Reverse transcription intermediate forms (minus and plus strong-stop DNA) are detected in Drosophila melanogaster cultured cells for mobile dispersed genetic elements mdg1, mdg3, and mdg4 (gypsy). The mdg elements studied possess a common mechanism of reverse transcription, despite their structural differences, and the comparative analysis of intermediate forms proves that mdg elements pass the same stages of reverse transcription as retroviruses. The length of minus strong-stop DNA that locates the RNA start site coincides with the data obtained from S1 nuclease analysis of transcription initiation. S1 analysis has also revealed that mdg LTRs have a U3-R-U5 structure analogous to that of retroviral LTRs. Transcription of mdg1, mdg3, and mdg4 is initiated within or immediately after the same sequence TCAGTPy. Neither the TATA box nor the CAAT box can be found at their characteristic positions upstream of the 5' ends of mRNAs. MH - Animal ; Base Sequence ; Chromosome Mapping ; Drosophila Melanogaster/ *GENETICS ; DNA/*GENETICS ; *DNA Insertion Elements ; Endonucleases/ DIAGNOSTIC USE ; Genes, Regulator ; Recombination, Genetic ; *Repetitive Sequences, Nucleic Acid ; Reverse Transcriptase/*METABOLISM ; *Transcription, Genetic SO - Cell 1986 Feb 28;44(4):555-63 27 UI - 86121027 AU - McReynolds LA ; DeSimone SM ; Williams SA TI - Cloning and comparison of repeated DNA sequences from the human filarial parasite Brugia malayi and the animal parasite Brugia pahangi. AB - A 320-base-pair repeated sequence was observed when DNA samples from the filarial parasites Brugia malayi and Brugia pahangi were digested with the restriction endonuclease Hha I. A 640-base-pair dimer of the repeated sequence from B. malayi was inserted into the plasmid pBR322. When dot hybridization was used, the copy number of the repeat in B. malayi was found to be about 30,000. The 320-base-pair Hha I repeated sequences are arranged in direct tandem arrays and comprise about 12% of the genome. B. pahangi has a related repeated sequence that cross-hybridizes with the cloned B. malayi Hha I repeat. Dot hybridization with the cloned repeat shows that the sequence is present in B. malayi and in B. pahangi but not in four other species of filarial parasites. The cloned repeated DNA sequence is an extremely sensitive probe for detection of Brugia in blood samples. Hybridization with the cloned repeat permits the detection of DNA isolated from a single parasite in an aliquot of blood from animals infected with B. malayi. There are differences in the restriction sites present in the repeated sequences that can be used to differentiate between the two Brugia species. The B. malayi repeated DNA sequence is cleaved by Alu I and Rsa I but the B. pahangi sequence is not. A comparison of repeated sequences between the two species by DNA sequence analysis indicates that some regions of individual repeats are over 95% homologous, while other short regions are only 60-65% homologous. These differences in DNA sequence will allow the construction of species-specific hybridization probes. MH - Animal ; Animals, Wild ; Anthropoidea ; Base Sequence ; Brugia/*GENETICS ; Cats ; Cloning, Molecular ; Comparative Study ; Dogs ; DNA/*GENETICS ; DNA Restriction Enzymes/DIAGNOSTIC USE ; Elephantiasis, Filarial/ PARASITOLOGY/VETERINARY ; Human ; Nucleic Acid Hybridization ; *Repetitive Sequences, Nucleic Acid SO - Proc Natl Acad Sci USA 1986 Feb;83(3):797-801 28 UI - 86083147 AU - Brookfield JF TI - A model for DNA sequence evolution within transposable element families. AB - A quantitative model is proposed for the expected degree of relationship between copies of a family of transposable elements in a finite population of hosts. Special cases of the model (in which the process of homogenization of element copies either is or is not limited by transposition rate) are presented and illustrated, using data on mobile sequences from different species. It is shown that transposition will be expected, in large populations, to result in only a rather distant relationship between transposable elements at different genomic sites. Possible inadequacies of the model are suggested and quantified. MH - Animal ; Drosophila Melanogaster/GENETICS ; DNA/*GENETICS ; *DNA Insertion Elements ; *Evolution ; Genetics, Population ; *Models, Genetic ; *Repetitive Sequences, Nucleic Acid ; Statistics SO - Genetics 1986 Feb;112(2):393-407