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Results for “Interspersed Repetitive Sequences”

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PubMed1980

Interspersion of repetitive with repetitive sequences in an amphibian, Rana berlandieri.

When conventional genome arrangement analyses performed on R. berlandieri DNA at a normal (60 degrees C) and a high (75 degrees C) reassociation temperature were compared, an additional interspersion pattern was detected which indicates that different classes of repetitive sequences are closely interspersed with each other. Our results further suggest that the genomic abundance of purified (or cloned) repetitive sequences can be accurately determined by solution hybridization with genomic DNA only when the reassociation is performed at a relatively high temperature (Tm - 10 degrees C).

Ambystoma↗

PubMed1988

A long, nontranslatable poly(A) RNA stored in the egg of the sea urchin Strongylocentrotus purpuratus.

Nontranslatable transcripts containing interspersed repetitive sequence elements constitute a major fraction of the poly(A) RNA stored in the cytoplasm of both the sea urchin egg and the amphibian oocyte. We report the first complete sequence of a representative interspersed maternal RNA transcript, called ISp1. The transcript is about 3.7 kb in length [including poly(A) tail]; and the 5' half consists of a cluster of repetitive sequences, whereas the 3' half is single copy. Other repetitive sequences occur in the 5' and 3' regions flanking the transcription unit. In several cloned alleles, the flanking repetitive and single-copy sequences differ, indicating a high degree of insertional and deletional rearrangement around, as well as within, the transcription unit. No significant open reading frames exist in any region of the ISp1 transcript, nor is it spliced to give rise to translatable mRNA in egg or embryo. A 620-nucleotide repetitive sequence element at the 5' end of the ISp1 transcript is also represented in a large number of other long interspersed maternal poly(A) RNAs. In addition, this sequence appears in a prevalent set of small polyadenylated RNAs about 600-nucleotides in length, which disappear almost completely by the gastrula stage of development. The structural features of the ISp1 RNA uncovered in this work exclude several hypotheses of interspersed maternal poly(A) RNA origin and function.

Animals↗

PubMed1991

Structural analysis of repetitive DNA sequences in the goat growth hormone gene region.

Two clones that contain goat growth hormone (gGH) genes were isolated from goat genomic library using goat growth hormone cDNA as a probe. One clone CgGH contained gGH1 gene, and another clone, EgGH, contained gGH2 and gGH3 genes. The clone EgGH contained 491 bp inserted sequence, just upstream of the gGH3 gene, which was not present in the clone CgGH. From the sequencing data of the flanking regions of these gGH genes, short interspersed repetitive sequences (SINES) were found. Four SINES's existed in the CgGH clone and eight SINES's existed in the EgGH clone. The number of the repetitive DNA sequences in the goat genome was estimated about 10(2) copies from the analysis of the reassociation rate. As the number of gGH genes (gGH1, gGH2, and gGH3) per genome was different among individual goats, DNA fragments containing gGH1 gene, and that containing gGH2 and gGH3 genes, were estimated to be allelic on the goat chromosome.

Animals↗

PubMed1987

Size and structure of the bird genome. II. Repetitive DNA and sequence organization.

1. Highly repetitive, middle repetitive and single copy DNA were evaluated in 19 species of birds, belonging to nine orders, by means of a reassociation kinetics method. 2. A rather uniform pattern is present in all the species studied (single copy = 60-75%; middle repetitive = 13-20% and highly repetitive 10-20%). 3. Reassociation kinetics of fragments of different length confirms the presence of a long period interspersion pattern. 4. Among different orders, no significant differences are observed. 5. DNA sequence organization seems to be related to genome size, with an inverse correlation between DNA nuclear content and amount of interspersed repetitive sequences.

Animals↗

PubMed1986

Polite DNA: functional density and functional compatibility in genomes.

Certain as yet poorly defined functions of DNA appear to involve collectively domain-sized sequences. It is proposed that most sequence segments within a domain may be either functionally superfluous or instrumental, depending on how many related sequences are present in the domain. When redundant and functionally dispensable, such DNA segments presumably still have to conform to compositional or sequence-motif patterns that characterize the domain. In its relations with neighboring sequences, such DNA is required to be "polite." Polite DNA is DNA that, without being crucially involved in function, is subject to constraints of conformity and, through its base composition, respects a function for which it is not required. This concept is developed by contrasting the distribution of specific and general functions over DNA with this distribution as found in proteins and by distinguishing functional compatibility from pivotal functionality. The sequence constraints to which heterochromatin as well as, apparently, long interspersed repetitive sequences are known to be subject seem to imply that DNA, even when it does not carry out a pivotal function, is indeed, at the very least, required to be polite.

Animals↗

PubMed1984

A DNA sequence of Drosophila melanogaster with a differential telomeric distribution.

A DNA sequence (8-19T) of 2.3 kilobase pairs (kb) of Drosophila melanogaster was localized by in situ hybridization to the extreme ends of polytene chromosomes and to the chromocenter. The relative abundance of this sequence at the ends of polytene chromosomes X:2L:2R:3L:3R is 1:3.4:1.9:0:2.7. This differential distribution is probably due to different copy numbers at the individual telomeric regions. Restriction enzyme analysis of genomic DNA shows that 8-19T sequences are interspersed with other sequences. The clone 8-19T, which contains most of this interspersed repetitive sequence, is itself not internally repetitive but has a complex sequence composition. Some of these sequences are transcribed into poly(A)+RNA. We suggest that the ends of Drosophila chromosomes are of a complex arrangement with some sequences common to all ends.

Animals↗

PubMed1982

Molecular characterization of small polydisperse circular deoxyribonucleic acid from an African green monkey cell line.

Several size classes of small polydisperse circular (spc) DNA from the African green monkey cell line BSC1 have been cloned into the bacterial plasmid pBR322. Analysis of the cloned spc DNA fragments as well as total spc DNA reveals that (a) most or all cloned spc DNAs share homologies with chromosomal sequences, (b) both unique and repetitive chromosomal sequences are represented in spc DNA, (c) the repetitive sequences in spc DNA include two known major repeat families (the alpha and the Alu) as well as a third, as yet unidentified, set of interspersed repetitive sequences, and (d) the alpha-like sequences are present in an oligomeric series of circular DNA molecules within the spc DNA population. The organizational features of repetitive DNA sequence-carrying circles suggest a mechanism for their generation.

Animals↗

PubMed1980

Sequence organization of animal nuclear DNA.

Animal nuclear genomes contain DNA sequences of various degrees of repetition. These sequences are organized in highly ordered fashions; repetitive and nonrepetitive sequences either alternate in short periods, i.e., short [0.2-0.4 kilobases (kb) long] repeats are flanked by nonrepetitive sequences less than 2 kb long, or in longer periods, with repetitive and/or nonrepetitive sequences extending for several kilobases. There are two main categories of genome organization, namely those exhibiting short-period interspersion and those that do not. There are arguments for and against a regulatory role of short interspersed repetitive sequences. Besides the merely 'statistical' kinetic approach by conventional reassociation kinetics, sequence organization has been studied by restriction endonuclease mapping and nucleotide sequencing. Such studies have revealed some general features of the organization of the eukaryotic gene and its transcripts, namely possible 'promoters', 'leaders', 'introns', 'exons', 'flanking sequences', 'caps', ribosome-binding sites, and poly(A) sequences. This paper discusses how these elements of a gene might serve regulatory roles in its expression.

Animals↗

PubMed1990

Spatial organization of repetitive DNA sequences in the bovine sperm nucleus.

During spermatogenesis, DNA in the sperm head becomes more tightly condensed as histones are replaced by protamine-like molecules. In this article, the question is asked whether, during the production of this highly differentiated cell, controls are imposed on the spatial organization of DNA within the nucleus. Heads from bull spermatozoa were isolated by a technique that removed the plasma membrane and acrosomal contents, and the DNA was induced to decondense by addition of 2-mercaptoethanol and trypsin. Under these conditions, decondensation was induced in all regions of the head. To determine whether there was any spatial restraint on packaging of the genome, three DNA probes were used (pl.709-512, containing an interspersed repetitive sequence; pCSIH, containing a copy of the major bovine centromeric statellite sequence; p18 s and p28 s, containing the 18 S and 28 S ribosomal genes) that might be expected to hybridize to different regions. Results showed that the interspersed repetitive probe hybridized to all regions of the head, whereas the ribosomal and centromeric probes hybridized to sequences that were largely confined to the equatorial region of the sperm. We conclude that organization of the genome in the bovine sperm nucleus is not random.

Animals↗

PubMed1990

Alumorphs--human DNA polymorphisms detected by polymerase chain reaction using Alu-specific primers.

The simultaneous analysis of multiple loci could substantially increase the efficiency of mapping studies. Toward this goal, we used the polymerase chain reaction to amplify multiple DNA fragments originating from dispersed genomic segments that are flanked by Alu repeats. Analysis of different human DNA samples revealed numerous amplification products distinguishable by size, some of which vary between individuals. A family study demonstrated that these polymorphic fragments are inherited in a Mendelian fashion. Because of the ubiquitous distribution of Alu repeats, these markers, called "alumorphs," could be useful for linkage mapping of the human genome. A major advantage of alumorphs is that no prior knowledge of DNA sequence of marker loci is required. This approach may find general application for any genome where interspersed repetitive sequences are found.

Base Sequence↗

PubMed1980

The sequence organization of bovine DNA.

The organization of repetitive DNA sequences has been investigated in bovine DNA. Repetitive sequences of all kinds constitute 25% to 30% of the total. Five density satellites constitute about 20% of the genome, and most of the remainder consists of alternating repeating and nonrepeating sequences. The nonrepeating sequences have a very broad size distribution averaging 4,000 nucleotide paris in length with the longest exceeding 10,000 nucleotide pairs. The interspersed repetitive sequences are much more nearly homogeneous in size, averaging 350 nucleotide pairs in length, and are divided into 8 to 14 sequence families.

Animals↗

PubMedDate not supplied

[Glucocorticoids specifically regulate the expression of dispersed repeating sequences in liver cells. Detection of small ID-like antisense RNA].

Differential regulation of the expression of various families of the rat genome interspersed repetitive sequences by glucocorticoid hormones in liver has been demonstrated. Small ID-like RNA complementarily associated with high-molecular-weight cytoplasmic poly(A)-containing RNAs has been identified. The results obtained indicate that glucocorticoids hormones induce expression of the B2, ID, and L1 families in rat liver. The content of the transcripts of these repetitive elements is increased by the hormones in the molecules of heterogeneous nuclear RNA. In the molecules of high-molecular-mass poly(A)-containing cytoplasmic RNA glucocorticoids increase the content of the ID-homologous sequences. In the population of the small specific RNA the content of the ID-homologous transcripts is also increased. A suggestion is put forward about the involvement of the ID-like element in the hormonal posttranscriptional regulation of gene expression at the mRNA level.

Animals↗

PubMed1996

The origin of interspersed repeats in the human genome.

Over a third of the human genome consists of interspersed repetitive sequences which are primarily degenerate copies of transposable elements. In the past year, the identities of many of these transposable elements were revealed. The emerging concept is that only three mechanisms of amplification are responsible for the vast majority of interspersed repeats and that with each autonomous element a number of dependent non-autonomous sequences have co-amplified.

Animals↗

PubMed1987

The MT family of mouse DNA is made of short interspersed repeated elements.

In certain mouse cells transformed by polyomavirus (Py), viral DNA is excised from the chromosome together with a defined mouse component, which has been designated Ins [Bourgaux et al., Virology 122 (1982) 84-97]. Ins carries a sequence which anneals with the DNA at many sites in the mouse genome, while displaying no detectable homology with well-characterized SINEs and LINEs [Sylla et al., Gene 29 (1984) 343-350]. Recently, others have reported that this sequence belongs to a newly discovered family of repetitive mouse DNA, designated MT for Mouse Transcript [Heinlein et al., Nucl. Acids Res. 14 (1986) 6403-6416]. We demonstrate here that the MT family consists of short interspersed repetitive sequences (SINEs) with structural features of retroposons. Using cloned fragments of Ins as probes, we have identified recombinants carrying MT sequences in a genomic library of mouse DNA. Regions of homology to the probes were subcloned twice from the DNA of lambda phage using plasmids pAT153 and pUC13, and characterized in detail by heteroduplex mapping and by sequencing. The three distinct elements thus studied were highly homologous over 400 bp, terminated in 3' with a short sequence rich in A residues, and were flanked by a short direct repeat. On the basis of these complete elements, a 400-bp consensus sequence was established for the MT family.

Animals↗

PubMed1990

Painting of human chromosomes with probes generated from hybrid cell lines by PCR with Alu and L1 primers.

Specific amplification of human sequences of up to several kb length has recently been accomplished in man-hamster and man-mouse somatic hybrid cell DNA by IRS-PCR (interspersed repetitive sequence - polymerase chain reaction). This approach is based on oligonucleotide primers that anneal specifically to human Alu- or L1-sequences and allows the amplification of any human sequences located between adequately spaced, inverted Alu- or L1-blocks. Here, we demonstrate that probe pools generated from two somatic hybrid cell lines by Alu- and L1-PCR can be used for chromosome painting in normal human lymphocyte metaphase spreads by chromosomal in situ suppression (CISS-) hybridization. The painted chromosomes and chromosome subregions directly represent the content of normal and deleted human chromosomes in the two somatic hybrid cell lines. The combination of IRS-PCR and CISS-hybridization will facilitate and improve the cytogenetic analysis of somatic hybrid cell panels, in particular, in cases where structurally aberrant human chromosomes or human chromosome segments involved in interspecies translocations cannot be unequivocally identified by classical banding techniques. Moreover, this new approach will help to generate probe pools for the specific delineation of human chromosome subregions for use in cytogenetic diagnostics and research without the necessity of cloning.

Animals↗

PubMed1992

The beta globin gene cluster of the prosimian primate Galago crassicaudatus: nucleotide sequence determination of the 41-kb cluster and comparative sequence analyses.

The nucleotide sequence of the beta globin gene cluster of the prosimian Galago crassicaudatus has been determined. A total sequence spanning 41,101 bp contains and links together previously published sequences of the five galago beta-like globin genes (5'-epsilon-gamma-psi eta-delta-beta-3'). A computer-aided search for middle interspersed repetitive sequences identified 10 LINE (L1) elements, including a 5' truncated repeat that is orthologous to the full-length L1 element found in the human epsilon-gamma intergenic region. SINE elements that were identified included one Alu type I repeat, four Alu type II repeats, and two methionine tRNA-derived Monomer (type III) elements. Alu type II and Monomer sequences are unique to the galago genome. Structural analyses of the cluster sequence reveals that it is relatively A+T rich (about 62%) and regions with high G+C content are associated primarily with globin coding regions. Comparative analyses with the beta globin cluster sequences of human, rabbit, and mouse reveal extensive sequence homologies in their genic regions, but only human, galago, and rabbit sequences share extensive intergenic sequence homologies. Divergence analyses of aligned intergenic and flanking sequences from orthologous human, galago, and rabbit sequences show a gradation in the rate of nucleotide sequence evolution along the cluster where sequences 5' of the epsilon globin gene region show the least sequence divergence and sequences just 5' of the beta globin gene region show the greatest sequence divergence.

Amino Acid Sequence↗

PubMed1998

Identification of a novel bone morphogenetic protein-responsive gene that may function as a noncoding RNA.

Bone morphogenetic proteins (BMPs)/osteogenic proteins (OPs), members of the transforming growth factor-beta superfamily, have a wide variety of effects on many cell types including osteoblasts and chondroblasts, and play critical roles in embryonic development. BMPs transduce their effects through binding to two different types of serine/threonine kinase receptors, type I and type II. Signaling by these receptors is mediated by the recently identified Smad proteins. Despite the rapid progress in understanding of the signaling mechanism downstream of BMP receptors, the target genes of BMPs are poorly understood in mammals. Here we identified a novel gene, termed BMP/OP-responsive gene (BORG), in C2C12 mouse myoblast cell line which trans-differentiates into osteoblastic cells in response to BMPs. Expression of BORG was dramatically induced in C2C12 cells by the treatment with BMP-2 or OP-1 within 2 h and peaked at 12-24 h, whereas transforming growth factor-beta had a minimal effect. BMP-dependent expression of BORG was also detected in other cell types which are known to respond to BMPs, suggesting that BORG is a common target gene of BMPs. Cloning and sequence analysis of BORG cDNA and the genomic clones revealed that, unexpectedly, the transcript of BORG lacks any extensive open reading frames and contains a cluster of multiple interspersed repetitive sequences in its middle part. The unusual structural features suggested that BORG may function as a noncoding RNA, although it is spliced and polyadenylated as authentic protein-coding mRNAs. Together with the observation that transfection of antisense oligonucleotides of BORG partially inhibited BMP-induced differentiation in C2C12 cells, it is possible that a new class of RNA molecules may have certain roles in the differentiation process induced by BMPs.

Animals↗

PubMed1990

The primary structure of the rat guanylyl cyclase A/atrial natriuretic peptide receptor gene.

We have isolated and characterized three genomic clones and a genomic fragment amplified by the polymerase chain reaction that contain the rat guanylyl cyclase-A (GC-A)/atrial natriuretic peptide receptor gene. The gene spans about 17.5 kilobases and includes 22 exons and 21 introns. All of the exon-intron junction sequences coincide with the GT/AG consensus. GC-A consists of at least the following four distinguishable domains: extracellular ligand binding, transmembrane, kinase-like, and cyclase catalytic. Exon 7 encodes the putative transmembrane domain. The kinase-like and catalytic domains are encoded by exons 8-15 and 16-22, respectively. The 5' end of the transcript, estimated by primer extension and S1 mapping, is 370 nucleotides upstream of the methionine initiation codon. The initiator sequence (-3 to +5) of CACACTCC has two mismatches when compared with a consensus initiator sequence of CTCANTCT. The 5'-flanking region contains three potential Sp1-binding sites and an inverted CCAAT box, but no apparent TATA box. Three different and short interspersed, repetitive sequences are found within intervening sequences and within the 5'- and 3'-flanking regions of the gene (five rat identifier, two rat type 2 Alu equivalent, and seven Alu-like sequences). They fall between the four major domains suggestive that these may be sites for frequent recombination events. This first reported structure of a gene for a member of this new enzyme/receptor family should facilitate the search for new family members, as well as allow studies to progress on the mechanisms by which the gene is regulated.

Amino Acid Sequence↗