Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Inverted Repeat Sequences”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,567 records · Page 87Linked to original sources
PubMed1983

Structure and expression of mouse VL30 genes.

DNA sequencing and blot hybridization analyses have been used to study the structure of a mouse VL30 gene and the molecular nature of VL30-related RNA which is induced upon the stimulation of cultured AKR mouse embryo cells with defined peptide growth factors. An integrated mouse VL30 gene was found to contain identical 601-base-pair long terminal repeats (LTRs) which were themselves terminated in short inverted repeats. The entire VL30 gene was flanked by a 4-base-pair direct repeat of cellular DNA. Thus, VL30 genes are structurally analogous to integrated forms of retrovirus proviruses and certain other classes of mobile genetic elements. The LTR sequence was found to contain putative promoter and polyadenylation signals and generally exhibited little sequence homology to murine leukemia virus proviral LTRs. Certain short regions of sequence conservation, however, were evident, including the inverted terminal repeat, LTR-adjacent regions corresponding to origins of murine leukemia virus proviral DNA synthesis, and a 36-base-pair direct repeat bearing homology to the 72-base-pair direct repeat (enhancer sequence) of the murine leukemia virus-related Moloney sarcoma virus. Upon mitogenic stimulation of quiescent cells with epidermal growth factor and insulin, a major 5.5-kilobase VL30-specific RNA complementary to both LTR and non-LTR sequences was rapidly induced. We conclude that a complete VL30 gene(s) is highly regulated by peptide growth factor binding to specific membrane receptors in these cells.

Animals↗
PubMed1991

Identification of Bordetella pertussis regulatory sequences required for transcriptional activation of the fhaB gene and autoregulation of the bvgAS operon.

Transcription of numerous virulence genes in Bordetella pertussis is positively regulated by the products of the bvgAS genes. In this study a series of lacZYA fusions containing deletions in either the fhaB or bvgA promoter regions was used to identify cis-acting regulatory regions required for bvg activation of these two genes. Gel retardation and DNase I protection analyses have shown that specific protein-DNA interactions occur at these regulatory regions and that these interactions require the transcriptional activator protein BvgA. The regulatory regions found upstream of fhaB and bvgA which are involved in protein binding both contain the sequence TTTCCTA. This sequence is part of an inverted repeat upstream of fhaB and a direct repeat upstream of bvgA. Homologous repeats are not apparent upstream of other bvg-activated genes, such as ptx and cyaA. These data suggest that the mechanism for transcriptional regulation of the other bvg-activated genes is complex and may require regulatory factors in addition to the bvgAS gene products.

Base Sequence↗
PubMed2000

Cloning and characterization of an extremely conserved satellite DNA family from the root-knot nematode Meloidogyne arenaria.

A new satellite DNA family, named pMaE, has been cloned from the genome of the phytoparasitic nematode, Meloidogyne arenaria (Nematoda: Tylenchida). It is represented as tandemly repeated sequences with a monomeric unit of 172 bp. The monomers are present at approximately 15700 copies per haploid genome, and represent about 5.3% of the total genomic DNA. Twenty-seven independent monomers have been cloned and sequenced. The deduced consensus sequence is 70.9% A + T rich, with frequent stretches of A and (or) T. Several direct or inverted sub-repeats are present in the sequence, which may allow the formation of a dyad structure, suggesting some potential role of this repetitive sequence in heterochromatin condensation. The monomers are very homogeneous in sequence, showing on average 1.8% divergence from their consensus sequence. Moreover, Southern blot experiments and sequence analysis of homologous monomers from the genome of geographically distinct M. arenaria populations have shown that this satellite DNA is uniformly distributed and highly conserved within the species. Therefore, it is hypothesized that this unusually low level of variability, either within the genome of a given population or between populations, could be achieved as the result of some highly effective homogenization mechanism acting upon the nematode genome.

Animals↗
PubMed1992

Binding of the IS903 transposase to its inverted repeat in vitro.

We have purified the transposase of IS903 in three different ways. We find that transposase expressed as a fusion protein with either glutathione-S-transferase or maltose-binding protein is soluble and can be purified rapidly using affinity chromatography. The third purification requires extracting the native transposase from an insoluble pellet using an alkaline pH buffer. All three proteins bind specifically to the ends of IS903 and give identical patterns of protection when challenged with DNase I. We have used the more stable fusion proteins to examine transposase--DNA interactions in vitro. Methylation interference experiments have identified critical bases for transposase binding; methylated purines that inhibit binding all lie within the inner part of the 18 bp inverted repeat (bp 7-16). Moreover, the positions and identities of these purines suggest that the transposase interacts with base pairs in adjacent major and minor grooves. Binding assays with mutant inverted repeats confirm that transposase binding is sensitive to sequence changes only within this inner region. We propose that the transposase binding site is limited to this domain of the inverted repeat. These data are consistent with our previous analysis of the behaviour of mutant ends in vivo, from which we postulated that the inverted repeat was composed of two functional domains; an inner binding domain (bp 6-18), which included a region of minor groove interactions, and an outer domain that was involved in a step subsequent to transposase binding.

Base Sequence↗
PubMedDate not supplied

[Structural features of the integration site of foreign DNA in the transgenic mouse genome].

The structure of the transgenic mouse DNA region containing an integrated transgene (fragment of pBR322 sequence) was analysed. In one of the sequences flanking the transgene, short direct and inverted overlapping repeats were revealed at a distance of 60 bp from the integration site. In the same flanking sequence, there is an extended sequence (3.5 kbp) 0.3-1 kbp away from the transgene. It repeats 100-300 times in the mouse genome and is highly conservative (the homologs of the repeat have been revealed in other mammalian, bird, fish and insect genomes). This up-to-date unknown family of highly-conserved dispersed repeats has been denoted by T1. We believe that both the revealed short inverted repeats capable of forming hairpins with loops and the T1 repeat are structures involved in the process of non-homologous insertion of foreign DNA into the region of the transgenic mouse genome.

Animals↗
PubMed1987

Rearranged coding segments, separated by a transfer RNA gene, specify the two parts of a discontinuous large subunit ribosomal RNA in Tetrahymena pyriformis mitochondria.

In the mitochondria of Tetrahymena pyriformis ST, the large subunit ribosomal RNA (LSU rRNA) is discontinuous, consisting of two species, alpha (280 nucleotides in length) and beta (approximately equal to 2.45 kilobases long). LSU alpha is the 5'-terminal portion (i.e. a 5.8 S-like rRNA), and LSU beta constitutes the rest of this LSU rRNA, as judged by both primary and secondary structure homology to other LSU rRNAs. Remarkably, LSU alpha is encoded downstream of LSU beta, the two genes being separated by a tRNALeu gene. This is the first demonstration of a discontinuous rRNA whose coding sequences are rearranged, deviating from the conventional, highly conserved, 5'----3' order of sequence domains in the LSU rRNA gene. This novel gene organization (5'-LSU beta-2-base pair spacer-tRNALeu-10-base pair spacer-LSU alpha) is identical in both copies of the subterminal inverted repeat in the linear T. pyriformis mitochondrial genome. Sequence heterogeneity in the LSU alpha transcript and its genes, together with Northern hybridization data, suggest that both copies of the inverted repeat are expressed.

Animals↗
PubMed1984

The nucleotide sequence of the leftmost XhoI fragment (6%) of simian adenovirus SA7P.

The DNA of simian adenovirus SA7P was cloned in pBR322. The nucleotide sequences of the leftmost 2238 bp and the rightmost 188 bp of the viral genome were determined. SA7P DNA has an inverted terminal repeat of 183 bp. The sequence at the left terminus exhibits extensive homology with that of the E1 regions of human adenovirus 5, 7 and 12 DNAs. Based on this homology, the RNA coordinates and coding regions could be deduced. The sequenced SA7P DNA contains the entire E1A and part of the E1B region.

Adenoviridae↗
PubMed1988

Structural analysis of a hepatitis B virus genome integrated into chromosome 17p of a human hepatocellular carcinoma.

Hepatitis B virus (HBV) is clearly a factor in the development of hepatocellular carcinoma, but its mechanism of action remains obscure. One possibility is that the HBV integration event alters the expression of a nearby growth-regulatory cellular gene. A 9-kilobase (kb) DNA fragment containing an HBV insert plus flanking cellular sequences was cloned from a hepatoma specimen from Shanghai, People's Republic of China. Restriction mapping of the insert revealed a large inverted repeat structure consisting of both viral sequences (encompassing all of the core and pre-S regions and portions of the X and S genes) and at least 3 kb of unique cellular sequences. The virus-cell junction mapped 11 nucleotides from the DR1 region, in a position within the HBV X gene and included in the cohesive overlap region. A probe generated from 1.0 kb of the flanking cellular DNA mapped the viral insert to chromosome 17 in the region designated 17p11.2-17p12, which is near the human proto-oncogene p53. Sequence data from a portion of the flanking cellular DNA revealed a stretch of approximately 70 base pairs that showed highly significant homology with a conserved region of a number of functional mammalian DNAs, including the human autonomously replicating sequence 1 (ARS1).

Base Sequence↗
PubMed1988

Characterization of a highly repeated satellite DNA from the cyprinid fish Notropis lutrensis.

1. A highly repeated, satellite DNA family from the North American cyprinid fish, Notropis lutrensis, was identified as a fragment band following restriction endonuclease enzyme digestion and agarose gel electrophoresis of genomic DNA; evidence of a tandem arrangement of the satellite in the genome was demonstrated by the formation of "ladders" in partial restriction endonuclease digests. 2. The satellite family was estimated densitometrically to comprise 7-8% of the N. lutrensis genome; mapping experiments using isolated and purified monomer repeat units of the satellite uncovered nine sites for seven different restriction enzymes. 3. A monomeric repeat unit of the satellite was cloned and sequenced, and found to be 174 base pairs in length and to have a base composition of 47% G + C (guanine + cytosine); computer analysis of the sequence revealed 13 new restriction sites for 12 additional enzymes. 4. Computer analysis also revealed that a large degree of internal redundancy in the monomer unit exists in the form of both direct and inverted repeating units, and that the entire sequence, starting with one base in either orientation, constitutes an open reading frame. In all but the last characteristic, the N. lutrensis satellite DNA is very similar to satellite DNAs in other eukaryotes.

Animals↗
PubMed2003

Solution structure and DNA binding of the effector domain from the global regulator PrrA (RegA) from Rhodobacter sphaeroides: insights into DNA binding specificity.

Prr/RegA response regulator is a global transcription regulator in purple bacteria Rhodobacter sphaeroides and Rhodobacter capsulatus, and is essential in controlling the metabolic changes between aerobic and anaerobic environments. We report here the structure determination by NMR of the C-terminal effector domain of PrrA, PrrAC. It forms a three-helix bundle containing a helix-turn-helix DNA binding motif. The fold is similar to FIS protein, but the domain architecture is different from previously characterised response regulator effector domains, as it is shorter than any characterised so far. Alignment of Prr/RegA DNA targets permitted a refinement of the consensus sequence, which contains two GCGNC inverted repeats with variable half-site spacings. NMR titrations of PrrAC with specific and non-specific DNA show which surfaces are involved in DNA binding and suggest residues important for binding specificity. A model of the PrrAC/DNA complex was constructed in which two PrrAC molecules are bound to DNA in a symmetrical manner.

Bacterial Proteins↗
PubMed1999

Gene stability in transgenic aspen (Populus). I. Flanking DNA sequences and T-DNA structure.

The stability of transgenes in the genome of transformed plants depends strongly on their correct physical integration into the host genome as well as on flanking target DNA sequences. For long-lived species like trees, however, no information is available so far concerning inactivation or loss of transgenes due to gene silencing or somatic genome rearrangement events. In this study, four independently transformed 35S-rolC transgenic hybrid aspen plants (Populus tremula L. x tremuloides Michx.), each harbouring one copy of the transgene, were investigated during continuous growth in the greenhouse. In one of these transgenic lines (Esch5:35S-rolC-#1) individuals frequently show phenotypic reversions, while in the remaining three lines (Esch5:35S-rolC-#3, -#5, -#16) the gene was essentially stable. Molecular analysis including PCR, Southern and Northern assays clearly showed that the transgene had been lost in the revertant tissue of the unstable line. Sequencing of T-DNA right and left borders, and flanking DNA regions, in all four transgenic aspen lines revealed no differences either in the type of flanking DNA (G-C to A-T ratio) or with respect to the presence of enhancers or MAR (matrix associated repeats)-like structures. Primers located within the left and right flanking regions in the three stable lines could be used to recover the target sites from the untransformed plants. This was not possible, however, with the unstable line, indicating that at least one flanking sequence does not derive from the plant target DNA but is of unknown origin. PCR using other primer pairs, and inverse PCR analysis, revealed an additional truncated T-DNA copy of 1050 nucleotides adjacent to the left border of the complete copy in this line. Sequencing of this truncated T-DNA revealed that it represented an inverted copy of part of the right half of the original construct. This special feature would allow the inverted repeat to pair with right border sequences of the complete copy. This would explain the frequently observed reversion resulting in transgene loss as due to intrachromosomal base-pairing leading to double-stranded loops of single-stranded DNA during mitotic cell divisions.

Bacterial Proteins↗
PubMed2003

Inferences on the evolutionary history of the S-element family of Drosophila melanogaster.

The S-element family of transposable elements has been characterized in D. melanogaster. Attempts to find it in other Drosophila-related species have failed, suggesting that this element family may have recently invaded the D. melanogaster genome by horizontal transfer. In order to investigate its evolutionary history, we analyzed the patterns of DNA polymorphism among the S-element copies present in a sample genome (Drosophila Genome Project). The observed levels of nucleotide diversity are significantly lower than theoretical expectations based on the neutral model. This is consistent with evidence for ongoing gene conversion among copies and for purifying selection on the elements' sequences, particularly on the terminal inverted repeats. A phylogenetic analysis revealed that the members of the S-element family can be grouped into at least two genetically differentiated clusters. The level of divergence between these clusters suggests that the S elements invaded the genome of the ancestor of D. melanogaster before the speciation of the D. melanogaster complex. However, other relevant scenarios are also discussed.

Amino Acid Sequence↗
PubMed2003

Hoppel, a P-like element without introns: a P-element ancestral structure or a retrotranscription derivative?

An in silico search for P-transposable-element-related sequences in the Drosophila melanogaster genome allowed us to detect sequences that are similar to P-element transposases. These sequences are located in the central region of 3.4-kb Hoppel elements, a class II transposon. Polymerase chain reaction (PCR) analysis of the insertional polymorphism revealed that these elements are mobile. The 3.4-kb elements are the longest copies of this family ever found. They contain an open reading frame that is long enough to encode a transposase, suggesting that the 3.4-kb elements are the full-length copies of the Hoppel family. Multiple alignments of several P-element transposases from different species and the Hoppel-element-encoded peptide showed that all of the P-element introns and the 5' region of the transposase are absent from the Hoppel sequence. Sequence analysis combined with reverse transcriptase PCR analysis showed that the 3.4-kb Hoppel elements are intronless. P and Hoppel not only share similar amino acid sequences but also have terminal inverted repeats of the same length (31 bp), and their excision footprints present a similar structure, which suggests that their transposases are functionally very similar. Thus, we propose that the Hoppel element family be included in the P-element superfamily. Two evolutionary scenarios are discussed considering the presence /absence of introns within the P-element superfamily.

Amino Acid Sequence↗
PubMed1985

Inverted terminal repeats and terminal proteins of the genomes of pneumococcal phages.

The nucleotide (nt) sequence at the ends of the genomes of the Streptococcus pneumoniae phages Cp-5 and Cp-7 has been determined and compared with the corresponding sequence of phage Cp-1. The genomes of phages Cp-5 and Cp-7 have inverted terminal repeats (ITRs) 343 and 347 bp long, respectively. In Cp-1 DNA the ITR is 236 bp long and the following 116 bp are 93% homologous. Some regions within the ITRs are conserved in the three genomes although the complete sequence of the ITRs is no more conserved than the rest of their genomes. The chromatographic behavior of their tryptic peptides suggests that the terminal proteins (TPs) of at least two of the phages are similar and that the TPs of the three pneumococcal phages differ markedly from that of the Bacillus subtilis phage psi 29.

Bacteriophages↗
PubMed1983

Organization of Achlya mtDNA: a population with two orientations and a large inverted repeat containing the rRNA genes.

We have investigated mtDNA organization in the oömycetous water mold; Achlya, and report here that this primitive organism contains a circular mitochondrial genome of 49.8 kilobase pairs. Extensive restriction endonuclease analysis indicates that a significant portion of the genome is present as an inverted repeat. Of 52 restriction sites for 14 enzymes thus far mapped, 28 sites cluster in two 9.6-kilobase-pair regions; within these regions, the sequence of sites is inverted but the spacing between analogous sites is identical. The repeat arms have a maximum length of 12.1 kilobase pairs and are separated by 4.6-8.4 and 21.0-22.3 kilobase pairs of unique sequences. Transfer hybridization experiments show that genes for both the large and the small rRNAs are contained within each repeat. Restriction endonuclease analysis shows that the unique regions between the inverted repeats are present in both possible orientations with respect to each other and in approximately equal proportions. These orientational, or "flip-flop," isomers of the unique regions are postulated to occur by intramolecular homologous recombination between the repeated regions.

Base Sequence↗
PubMed1981

Inserted sequences in bovine satellite DNA's.

The nucleotide sequence of the 1413-base-pair repeat unit of bovine 1.711a satellite DNA (density in cesium chloride, 1.711 grams per cubic centimeter) has been determined. The repeat unit contains two segments consisting of variants of a basic 23-base-pair sequence that is closely related to sequences of bovine 1.706 satellite DNA. A third segment of the repeat unit contains an unrelated 611-base-pair sequence that is not internally repetitive. This segment is flanked by inverted repeats of 8 base pairs and, on one side, by a direct repeat of the terminal sequence. A related segment is present in bovine 1.711b satellite DNA and is inserted into sequences derived from the 1.715 satellite. These nucleotide sequences suggest the timing of some of the stages in the evolution of these complex, closely related satellite DNA's and indicate the mechanisms inherent in their divergence from a common ancestor.

Animals↗
PubMed1985

The endpoints of an inversion in wheat chloroplast DNA are associated with short repeated sequences containing homology to att-lambda.

The endpoints of an inversion in wheat chloroplast DNA are shown to be associated with copies of a short repeated sequence. Recombination across the repeats in an inverted configuration may have been responsible for the inversion, although they are currently in a direct orientation owing to a second inversion. The repeated sequence contains an element homologous to the core of the bacteriophage lambda att-site, which can function as such in vivo.

Bacteriophage lambda↗
PubMed1992

Site-specific recombinase, R, encoded by yeast plasmid pSR1.

The R gene product (R protein) of Zygosaccharomyces rouxii plasmid pSR1 catalyzes site-specific recombination within a 58 base-pair (bp) sequence present in the 959 bp inverted repeats of this plasmid. The R protein was produced in Escherichia coli and partially purified. The partially purified protein catalyzed site-specific recombination in vitro without the supply of an energy source. Recombination resulted in intramolecular inversion or deletion, depending on whether the orientations of the two recombination sites on the substrate plasmid were the same or opposite. Presumably, R protein is the only protein required for the recombination reaction. A circular DNA molecule appears to be a better substrate than a linear molecule in R-mediated in vitro intramolecular recombination. The R protein binds to a set of six 12 bp elements within the inverted repeats of pSR1. Two of these 12 bp elements are arranged in an inverted configuration with a 7 bp spacer in the 58 bp sequence. The R protein mediates strand cleavage in vitro at the junction between the 12 bp elements and the 7 bp spacer. The cleavage sites on the top and bottom strands are staggered and flanked by polypurine tracts that form part of the 12 bp elements.

Base Sequence↗