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At least 415 records · Page 23Linked to original sources
PubMed1985

Sequence of Dictyostelium DIRS-1: an apparent retrotransposon with inverted terminal repeats and an internal circle junction sequence.

The Dictyostelium discoideum transposon DIRS-1 contains long terminal repeats that are inverted (ITRs) and nonidentical. We show here that the internal sequence contains 4158 nucleotides and encodes three open reading frames (ORFs). Two of the ORFs (ORFs 2 and 3) are colinear and overlap for more than 2000 bases. Unusual sequence conservation between the two DIRS-1 elements in the overlap region is discussed. The conserved reading frame (ORF3) contains a 200 amino acid region that bears significant homology to retrovirus reverse transcriptase. Based on this homology, we classify DIRS-1 as a possible retrotransposon and propose a model by which the nearly genomic length 4.5 kb DIRS-1 RNA could be used to generate a genomic DNA copy of DIRS-1 with nonidentical inverted terminal repeats.

Base Sequence↗
PubMed1999

Pogo transposase contains a putative helix-turn-helix DNA binding domain that recognises a 12 bp sequence within the terminal inverted repeats.

Pogo is a transposable element with short terminal inverted repeats. It contains two open reading frames that are joined by splicing and code for the putative pogo transposase, the sequence of which indicates that it is related to the transposases of members of the Tc1/mariner family as well as proteins that have no known transposase activity including the centromere binding protein CENP-B. We have shown that the N-terminal region of pogo transposase binds in a sequence-specific manner to the ends of pogo and have identified residues essential for this. The results are consistent with a prediction that DNA binding is due to a helix-turn-helix motif within this region. The transposase recognises a 12 bp sequence, two copies of which are present at each end of pogo DNA. The outer two copies occur as inverted repeats 14 nucleotides from each end of the element, and contain a single base mismatch and indicate the inverted repeats of pogo are 26 nucleotides long. The inner copies occur as direct repeats, also with a single mismatch.

Amino Acid Sequence↗
PubMed2006

Sequence polymorphisms in the long terminal repeat of bovine leukemia virus: evidence for selection pressures in regulatory sequences.

Bovine leukemia virus (BLV) is an oncogenic virus widespread in cattle. It belongs to the genus Deltaretrovirus of the family Retroviridae along with human and simian T-lymphotropic viruses. The BLV transcriptional promoter is located in the proviral 5' long terminal repeat (LTR), composed of U3, R, and U5 regions. BLV LTR contains multiple cis-acting elements important for promoter activity, a short coding sequence (encoding the NH(2) terminus of the G4 regulatory protein), and non-regulatory/non-coding regions. Variation in coding sequences of BLV structural proteins has been studied extensively, but little work has been done on sequence variability of non-coding regions, mostly located in LTR. Here, we report the first study on the natural diversity of the BLV LTR, using viral isolates from 52 cattle in several different areas worldwide. Nucleotide variations from the consensus sequence were observed in most isolates and clustered phylogenetically, corresponding to the geographic distribution of donor cattle. Overall, regulatory regions were significantly more conserved than non-regulatory regions in the BLV LTR, as well as in LTR sub-regions (U3, R, and U5). Evidence of selection pressures in BLV LTR suggests that selection occurs not only in coding sequences, but may also involve regulatory sequences.

5' Untranslated Regions↗
PubMed2004

Establishing the rDNA IGS structure of Cannabis sativa.

The rDNA intergenic spacer (IGS) structure of Cannabis sativa was established and can be used for classification and identification of this species. In this study, DNA fragments of rDNA IGS were amplified by PCR from Cannabis sativa plant extracts and a 1387 bp fragment was obtained. DNA sequence analysis revealed six different repeat motifs. In the middle of the IGS sequence, there were three sequence motifs, and the same three sections of DNA were then repeated with minor variation in sequence. The terminal region of the IGS was composed of another three different repeat units; multiple copies of these terminal repeat motifs were present in no discernible order. Within six repeat motifs, point variations were observed in five. The DNA sequence of the locus was compared with all the plant sequences registered in GenBank by the Fasta program of GCG software with the result that this DNA fragment was significantly different from any other DNA sequence recorded to date. The most similar sequence was that of Hops (Humulus lupulus), but with a similarity of only 88.9% over 579 bp. These specific and complex variations of IGS may be related to the species and geographic distributions.

Base Sequence↗
PubMed1982

Long terminal repeat of murine retroviral DNAs: sequence analysis, host-proviral junctions, and preintegration site.

The nucleotide sequence of the long terminal repeat (LTR) of three murine retroviral DNAs has been determined. The data indicate that the U5 region (sequences originating from the 5' end of the genome) of various LTRs is more conserved than the U3 region (sequences from the 3' end of the genome). The location and sequence of the control elements such as the 5' cap, "TATA-like" sequences, "CCAAT-box," and presumptive polyadenylic acid addition signal AATAAA in the various LTRs are nearly identical. Some murine retroviral DNAs contain a duplication of sequences within the LTR ranging in size from 58 to 100 base pairs. A variant of molecularly cloned Moloney murine sarcoma virus DNA in which one of the two LTRs integrated into the viral DNA was also analyzed. A 4-base-pair duplication was generated at the site of integration of LTR in the viral DNA. The host-viral junction of two molecularly cloned AKR-murine leukemia virus DNAs (clones 623 and 614) was determined. In the case of AKR-623 DNA, a 3- or 4-base-pair direct repeat of cellular sequences flanking the viral DNA was observed. However, AKR-614 DNA contained a 5-base-pair repeat of cellular sequences. The nucleotide sequence of the preintegration site of AKR-623 DNA revealed that the cellular sequences duplicated during integration are present only once. Finally, a striking homology between the sequences flanking the preintegration site and viral LTRs was observed.

AKR murine leukemia virus↗
PubMed1985

Structure of genes and an insertion element in the methane producing archaebacterium Methanobrevibacter smithii.

DNA fragments cloned from the methanogenic archaebacterium Methanobrevibacter smithii which complement mutations in the purE and proC genes of E. coli have been sequenced. Sequence analyses, transposon mutagenesis and expression in E. coli minicells indicate that purE and proC complementations result from the synthesis of M. smithii polypeptides with molecular weights of 36,697 and 27,836 respectively. The encoding genes appear to be located in operons. The M. smithii genome contains 69% A/T basepairs (bp) which is reflected in unusual codon usages and intergenic regions containing approximately 85% A/T bp. An insertion element, designated ISM1, was found within the cloned M. smithii DNA located adjacent to the proC complementing region. ISM1 is 1381 bp in length, has 29 bp terminal inverted repeat sequences and contains one major ORF encoded in 87% of the ISM1 sequence. ISM1 is mobile, present in approximately 10 copies per genome and integration duplicates 8 bp at the site of insertion. The duplicated sequences show homology with sequences within the 29 bp terminal repeat sequence of ISM1. Comparison of our data with sequences from halophilic archaebacteria suggests that 5'GAANTTTCA and 5'TTTTAATATAAA may be consensus promoter sequences for archaebacteria. These sequences closely resemble the consensus sequences which precede Drosophila heat-shock genes (Pelham 1982; Davidson et al. 1983). Methanogens appear to employ the eubacterial system of mRNA: 16SrRNA hybridization to ensure initiation of translation; the consensus ribosome binding sequence is 5'AGGTGA.

Amino Acid Sequence↗
PubMed1998

Changing transcription start sites in H-type alpha(1,2)fucosyltransferase gene (FUT1) during differentiation of the human erythroid lineage.

Recent studies have suggested that at least three transcription-initiation sites were present in the human H-type alpha(1,2)fucosyltransferase gene (FUT1). In the present study, we have investigated these transcription start sites of FUT1 in undifferentiated leukemic cells (K562) that have erythroid characteristics, in erythroleukemia cells (HEL), and in bone marrow cells. K562 cells used exclusively exon 1 as the start site. While HEL cells used mainly exon 2 as the start site, the major start site for bone marrow cells was within exon 7. In addition, we investigated the transcription start site(s) in vascular endothelial cells (ECV304) as an example of mature cells and found that the start site was predominantly within exon 7. The promoter activities were found in the 5' flanking regions of these three start sites after transfection of constructs with luciferase reporter gene into K562 and HEL cells. These findings suggested that the transcription start sites of FUT1 changed during differentiation of the erythroid lineage and that the tissue-specific and stage-specific expressions of the FUT1 were regulated by three distinct promoters. We also found that the 5' flanking region of exon 2 (intron 1) consisted of repetitive sequences (chromosome 19-specific 37-bp minisatellite repeats, Alu sequence and long terminal repeat) and that the start site of exon 2 was within the long terminal repeat. Thus, these repetitive sequences may play a role in the expression of the FUT1.

Base Sequence↗
PubMed1991

Improvement of avian leukosis virus (ALV)-based retrovirus vectors by using different cis-acting sequences from ALVs.

Production and expression of double-expression vectors which transduce both Neo(r) and lacZ genes and are based on the structure of avian leukosis virus were enhanced by using cis-acting sequences (long terminal repeats and noncoding sequences) from Rous-associated virus-1 and Rous-associated virus-2 rather than those of avian erythroblastosis virus previously used in our constructs. Polyclonal producer cells obtained after transfection of these vectors into the Isolde packaging cell line gave rise to titers as high as 3 x 10(5) lacZ CFU/ml, whereas it was possible to isolate clones of producer cells giving rise to titers of more than 10(6) resistance focus-forming units per ml.

Animals↗
PubMedDate not supplied

[Universal orientation and 3'-terminal localization of repeated sequences in the B2 family of mRNA].

A cDNA library in pBR322 was prepared with cytoplasmic poly(A) + RNA from mouse liver cells. From 1 to 1.5% of clones hybridized to either B1 or B2 ubiquitous repetitive sequences. Several clones hybridizing to a B2 repeat were partially sequenced. The full-length B2 sequence was found at the 3'-end of abundant 20S poly(A) + RNA (designated as B2 + mRNA chi) within the non-coding part of it. B2 + mRNA chi is tissue-specific, concentrated in mouse liver polysomes and absent in cytoplasm of Ehrlich carcinoma cells. The B2 sequence seems to be located at the 3'-end of some other mRNAs as well. To determine the orientation of the B2 sequence in different RNAs, its two strands were labeled, electrophoretically separated, and used for hybridization with Northern blots containing nuclear, cytoplasmic and polysomal RNAs. In nuclear RNA, the B2 sequence is present in both orientations; in polysomal and cytoplasmic poly(A) + RNAs, only one ("canonical") strand of it can be detected. Low molecular weight poly(A) + B2 + RNA also contains the same strand of the B2 element. The conclusion has been drawn that only one of its strand can survive the processing. This strand contains promoter-like sequences and AATAAA blocks. The latter can be used in some cases by the cell as mRNA polyadenylation signals.

Animals↗
PubMed1983

Nucleotide sequence analysis of the long terminal repeat of murine virus-like DNA (VL30) and its adjacent sequences: resemblance to retrovirus proviruses.

VL30 DNA represents a retrovirus-like multigene family of mice whose genetic origin is unknown. We have now determined the primary nucleotide sequences and the adjacent sequences of the long terminal direct repeats (LTRs) possessed by a randomly selected VL30 unit. The LTR of the VL30 unit comprised 435 nucleotide base pairs and had an inverted repeat of five bases at its 5' and 3' termini. At the joints with flanking mouse DNA was the VL30 sequence (5')TG . . . CA(3') and a tetranucleotide direct repeat of flanking sequences. At the inner boundary of the 5' LTR was an 18-base sequence that is complementary to tRNApro, and at the inner boundary of the 3' LTR was a purine-rich tract ending with AATG. These results suggested that VL30 DNA used the same integration strategy that is exercised by retrovirus proviruses and transposable elements and that the VL30 LTR is synthesized in a similar way that the LTR of retroviruses is synthesized. The data thus reinforce the retrovirus-like nature of VL30 genetic information.

Animals↗
PubMed1987

Multiple reiteration of a 40-bp nucleotide sequence in the inverted terminal repeat of the genome of a canine adenovirus.

The DNA of a vaccine strain of canine adenovirus type 1 [ICHV vaccine; Connaught Laboratories, Ltd.; CAV-1(CLL)] has been cloned in plasmid pAT153 in the form of subgenomic BamHI digestion fragments. Analysis of the nucleotide sequences of cloned terminal fragments has revealed an inverted terminal repeat (ITR) with a minimum length of 198 nucleotides, including a tandem reiteration of the 40-bp nucleotide sequence from positions 14 to 53. The ITRs had the 5'-CATCATCAAT ... sequence typical of adenoviruses and the highly conserved sequence ATAATATAC (nucleotides 9-17) of human strains. Additionally, one BamHI A clone (left terminus) contained three sequential copies of the 40-bp sequence, and two BamHI C clones (right terminus) contained at least seven. These did not appear to be artifacts of cloning, since evidence was obtained that the multiple reiterations also occurred in DNA isolated from intact virus. By analogy with human adenoviruses, the repetitive sequence in the CAV-1(CLL) genome encompasses the entire nuclear factor I (NFI) binding site of the origin of DNA replication. Additionally, the 40-bp nucleotide sequence was found to contain the sequence AGG(N)4GCCTAA (nucleotides 27-39), which closely resembles the concensus sequence of the human adenovirus NFI binding site [TGG(N)6-7GCCAA; nucleotides 25-38]. It appears, therefore, that the Connaught CAV-1 vaccine contains reiterated copies of an essential part of the adenoviral origin of DNA replication. A mechanism is proposed for the generation of multiple reiterations of sequences in the right ITR, given an initial single tandem repeat in the left ITR.

Adenoviridae↗
PubMed1987

Sequence instability in the long terminal repeats of avian spleen necrosis virus and reticuloendotheliosis virus.

Sequence divergence between the 3' long terminal repeats (LTR) of avian reticuloendotheliosis virus (REV), deletion variant proviral clone 2-20-4, and spleen necrosis virus (SNV)-proviral clones 14-44, 60, and 70-was found to involve two classes of base substitutions: low-frequency interspersed and high-frequency clustered substitutions. Clones 2-20-4 and 14-44 have diverged 4.4% owing to low-frequency substitutions. In contrast, two high-frequency substitution segments have diverged by 30% and 29%, respectively. Clustered substitutions appear to be located either within or next to tandem repeats, suggesting their introduction concomitant with sequence deletions and duplications commonly associated with such repeats. A new 19-bp tandem repeat is found in clone 2-20-4. Its sequence could have evolved from the 26-bp repeats found in the SNV clones.

Base Composition↗
PubMed2007

Retrotransposons and tandem repeat sequences in the nuclear genomes of cryptomonad algae.

The cryptomonads are an enigmatic group of unicellular eukaryotic algae that possess two nuclear genomes, having acquired photosynthesis by the uptake and retention of a eukaryotic algal endosymbiont. The endosymbiont nuclear genome, or nucleomorph, of the cryptomonad Guillardia theta has been completely sequenced: at only 551 kilobases (kb) and with a gene density of approximately 1 gene/kb, it is a model of compaction. In contrast, very little is known about the structure and composition of the cryptomonad host nuclear genome. Here we present the results of two small-scale sequencing surveys of fosmid clone libraries from two distantly related cryptomonads, Rhodomonas salina CCMP1319 and Cryptomonas paramecium CCAP977/2A, corresponding to approximately 150 and approximately 235 kb of sequence, respectively. Very few of the random end sequences determined in this study show similarity to known genes in other eukaryotes, underscoring the considerable evolutionary distance between the cryptomonads and other eukaryotes whose nuclear genomes have been completely sequenced. Using a combination of fosmid clone end-sequencing, Southern hybridizations, and PCR, we demonstrate that Ty3-gypsy long-terminal repeat (LTR) retrotransposons and tandem repeat sequences are a prominent feature of the nuclear genomes of both organisms. The complete sequence of a 30.9-kb genomic fragment from R. salina was found to contain a full-length Ty3-gypsy element with near-identical LTRs and a chromodomain, a protein module suggested to mediate the site-specific integration of the retrotransposon. The discovery of chromodomain-containing retroelements in cryptomonads further expands the known distribution of the so-called chromoviruses across the tree of eukaryotes.

Cloning, Molecular↗
PubMed1995

A transposon-like sequence with short terminal inverted repeats in the nuclear genome of Chlamydomonas reinhardtii.

A 1.2 kb DNA sequence, flanked by a potential seven base target-site duplication, was found inserted into a TOC1 transposable element from Chlamydomonas reinhardtii. The insertion sequence, named TOC2, is a member of a family of repeated DNA sequences that is present in all the C. reinhardtii strains tested. It resembles class II transposable elements: it possesses short 14 bp imperfect terminal repeats that begin AGGAGGGT, and sub-terminal direct repeats located within 250 bp of the termini. No large open reading frames were found. The terminal bases and length of target-site duplication are important in classifying transposable elements. On this basis TOC2 does not fall readily into existing families of class II transposable elements found in plants.

Animals↗
PubMed1999

Rapid isolation of plant Ty1-copia group retrotransposon LTR sequences for molecular marker studies.

The terminal sequences of long-terminal repeat (LTR) retrotransposons are a source of powerful molecular markers for linkage mapping and biodiversity studies. The major factor limiting the widespread application of LTR retrotransposon-based molecular markers is the availability of new retrotransposon terminal sequences. We describe a PCR-based method for the rapid isolation of LTR sequences of Ty1-copia group retrotransposons from the genomic DNA of potentially any higher plant species. To demonstrate the utility of this technique, we have identified a variety of new retrotransposon LTR sequences from pea, broad bean and Norway spruce. Primers specific for three pea LTRs have been used to reveal polymorphisms associated with the corresponding retrotransposons within the Pisum genus.

Amino Acid Sequence↗