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Results for “Repetitive Sequences, Nucleic Acid”

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PubMed1996

Two chicken repeat one (CR1) elements lacking a silencer-like region upstream of the chicken avidin-related genes Avr4 and Avr5.

Two repetitive elements of the chicken CR1 family, each located in the 5' flanking region of the avidin-related genes Avr4 and Avr5, have been cloned and sequenced. Both elements are 721 bp in length with 72% identity to a CR1 consensus sequence. They had a 191 bp deletion in a region corresponding to the functional silencer regions previously detected within the CR1 elements upstream of the chicken lysozyme and apoVLDLII genes.

Animals↗

PubMed1993

The third human homolog of a murine gene encoding an inhibitor of stem cell proliferation is truncated and linked to a CpG island-containing upstream sequence.

The murine gene, MIP1 alpha, encodes a cytokine (macrophage inflammatory protein 1 alpha) that inhibits the proliferation of bone marrow stem cells. Two human homologs have been characterized, G0S19-1 and G0S19-2. Like MIP1 alpha, these genes contain three exons, the first of which encodes a hydrophobic signal sequence. The existence of a third human G0S19 gene, present in one in four individuals, has been predicted from restriction enzyme analyses. This paper reports that a previously identified human genomic clone containing a G0S19 sequence (G0S19-3), corresponds to the third gene. However, the first G0S19 exon is missing. The sequence differs from those of G0S19-1 and G0S19-2 upstream of a point 31 nucleotides from the junction of the first intron with the second exon. This upstream sequence contains a CpG island and is named "CpG island-containing upstream sequence," CUS. Apart from the G0S19-3-associated copy found only in individuals with the third G0S19 gene, all individuals have one DNA species hybridizing strongly to a CUS-specific probe and at least two less strongly hybridizing species. The CUS has potential binding sites for transcription factors AP-1, AP-2, AP-3, AP-4, and Sp1, a Donehower conserved repetitive element, and motifs characteristic of cytokine, oncogene, and retroviral promoters. Thus, the CUS might promote the transcription of sequences with which it became associated. We suggest that the CUS-G0S19-3 sequence was generated by recombination between a G0S19-2 gene and a member of a novel CUS-associated gene family.

Base Sequence↗

PubMed1993

Identification of a functional role for the 3' region of the human oestrogen receptor gene.

A well-conserved feature of the steroid receptor gene family is the presence of an exceptionally long 3' untranslated region (UTR). Analysis of this sequence from the human oestrogen receptor (hER) gene showed the presence of a number of AT-rich regions that included thirteen repeats of the ATTTA motif, an element known to have a destabilizing effect in other systems. In the region 3' of the gene there were a further eight copies of this pentamer. Also located in this sequence were two members of the Alu repetitive family in inverse orientation and in a tandem arrangement. Transfection experiments in which the 3' UTR and 3' flanking sequence were included in chloramphenicol acetyltransferase expression vectors revealed a large destabilization effect with several different fragments. This inherent instability appears to be determined by the primary nucleotide sequence but may act in conjunction with other factors. This post-transcriptional regulatory mechanism may contribute to the control of the level of the hER mRNA.

Base Sequence↗

PubMed1991

Identification of regulatory building blocks in Escherichia coli genome.

The nucleotide sequences of extragenic regions in the Escherichia coli genome are statistically analyzed. Sequence elements with high occurrence frequencies are identified; these elements are: (1) extragenic palindromic sequences, which are markedly distinguishable from the already identified repetitive extragenic palindromic sequences; (2) promoter sequences of purine biosynthetic genes; and (3) rho-independent terminator sequences. The repetitious occurrence and extensive sequence similarities suggest that these elements share common evolutionary origins. Copies of one sequence element would have become distributed to various positions on the genome during evolution and have been fixed at locations that provide a selective advantage. The extragenic regions of the E. coli genome seem to consist of various regulatory 'building blocks', similar to a protein which consists of modules or domains.

Base Sequence↗

PubMed2002

Suppression of 15-lipoxygenase synthesis by hnRNP E1 is dependent on repetitive nature of LOX mRNA 3'-UTR control element DICE.

Cytidine-rich 15-lipoxygenase differentiation control element (15-LOX DICE) is a multifunctional cis-element found in the 3'-UTR of numerous eukaryotic mRNAs. It binds KH domain proteins of the type hnRNP E and K, thus mediating mRNA stabilization and translational control. Translational silencing is caused by formation of a simple binary complex between DICE and recombinant hnRNP E1 (E1). Electromobility shift assays and sucrose gradient centrifugation demonstrate that rabbit 15-LOX DICE, which is composed of ten subunits of the sequence (CCCCPuCCCUCUUCCCCAAG)10=10R, is able to bind up to ten molecules of E1. Protein/RNA interaction was studied with different subunits and submotifs of the 10R structure. Binding appears to be dependent on the degree of polymerization of the C-clusters (1R<2R<4R<10R), but not on their order. The minimal motif, which still functioned in E1 binding, contained two C-clusters (CCCCPuCCCUCUU). For efficient translational control, E1 binding is a necessary, but not sufficient, condition. Translational inhibition by E1 is only observed when at least a dimeric 2R configuration of the DICE is present in the 3'-UTR of a reporter mRNA. We conclude that binding of at least two E1 molecules activate or expose a binding site to enable the complex to interact with the 5'-end of the mRNA and the translational machinery. DICE-motifs are widely distributed in nature. The UTR database UTRnr contains 78 entries of mRNAs with 15-LOX DICEs. Most DICEs were two- to fourfold repetitive, but also highly repetitive structures were found, as in quail myelin protein mRNA (31 repeats) and hyperglycemic hormone mRNA of two crayfish species (nine and 11 repeats).

3' Untranslated Regions↗

PubMed1993

The complete sequence of the gene encoding bovine alpha s2-casein.

From a bovine genomic library, five overlapping clones, spanning some 50 kb, have been isolated. These clones contain the complete alpha s2-casein-encoding gene (alpha s2ca) and its 5' and 3' flanking regions. The nucleotide (nt) sequence of the complete gene including 2510 bp of the 5' flanking region and 276 bp of the 3' region has been determined. The total length of alpha s2ca appears to be 18483 bp and, therefore, it is the longest of the four bovine casein-encoding genes. The alpha s2ca gene is comprised of 18 exons ranging in size from 21 to 266 nt. There are 16 Alu-like artiodactyla retroposons inserted at ten different locations within the gene. About 14% of the gene is composed of these repetitive sequences. Although the organization of alpha s2ca appears to be similar to that of the alpha s1-casein-encoding gene (alpha s1ca), sequence comparisons and the length of the exons indicate that it is more closely related to the beta-casein-encoding gene. Furthermore, it is shown that both genes could have evolved from a common ancestor by means of internal duplications.

Animals↗

PubMed1996

Variability in the upstream promoter and intron sequences of the human, mouse and chick type X collagen genes.

The type X collagen gene is specifically expressed in hypertrophic chondrocytes during endochondral ossification. Transcription of the type X collagen gene by these differentiated cells is turned on at the same time as transcription of several other cartilage specific genes is switched off and before mineralization of the matrix begins. Analysis of type X collagen promoters for regulatory regions in different cell culture systems and in transgenic mice has given contradictory results suggesting major differences among species. To approach this problem, we have determined the nucleotide sequences of the two introns and upstream promoter sequences of the human and mouse type X collagen genes and compared them with those of bovine and chick. Within the promoter regions, we found three boxes of homology which are nearly continuous in the human gene but have interruptions in the murine gene. One of these interruptions was identified as a complex 1.9 kb repetitive element with homology to LINE, B1, B2 and long terminal repeat sequences. Regulatory elements of the human type X collagen gene are located upstream of the region where the repetitive element is inserted in the mouse gene, making it likely that the repetitive element is inserted between the coding region and regulatory sequences of the murine gene without interfering with its expression pattern. We also compared the sequences of the introns of both genes and found strong conservation. Comparisons of the mammalian sequences with promoter and first intron sequences of the chicken type X collagen gene revealed that only the proximal 120 nucleotides of the promoter were conserved, whereas all other sequences displayed no obvious homology to the murine and human sequences.

Animals↗

PubMed1997

Exon 2 of human cathepsin B derives from an Alu element.

Transcripts for the cysteine protease cathepsin B are alternatively spliced in the untranslated regions (UTRs). We show that a cathepsin B probe containing 5'-UTR sequences hybridized to an RNA of approximately 300 nt in addition to the typical 2.2 and 4.0 kbp mRNAs. Within this 5'-UTR, exon 2 was found to be homologous to Alu repetitive elements. Specifically, exon 2 was part of an Alu element interspersed with the cathepsin B gene. The approximately 300 nt band that hybridized to our cathepsin B probe likely corresponds to Alu transcripts, which are known to accumulate in human cells. Indeed, a similarly migrating band was detected with an authentic Alu probe. Thus, we suggest that primary transcripts for cathepsin B contain Alu sequences which are preserved as exon 2 in some fully spliced mRNAs.

Alternative Splicing↗

PubMed1991

Transfer RNA genes from Dictyostelium discoideum are frequently associated with repetitive elements and contain consensus boxes in their 5' and 3'-flanking regions.

A total of 68 different tRNA genes from the cellular slime mold Dictyostelium discoideum have been isolated and characterized. Although these tRNA genes show features common to typical nuclear tRNA genes from other organisms, several unique characteristics are apparent: (1) the 5'-proximal flanking region is very similar for most of the tRNA genes; (2) more than 80% of the tRNA genes contain an "ex-B motif" within their 3'-flanking region, which strongly resembles characteristics of the consensus sequence of a T-stem/T-loop region (B-box) of a tRNA gene; (3) probably more than 50% of the tRNA genes in certain D. discoideum strains are associated with a retrotransposon, termed DRE (Dictyostelium repetitive element), or with a transposon, termed Tdd-3 (Transposon Dictyostelium discoideum). DRE always occurs 50 (+/- 3) nucleotides upstream and Tdd-3 always occurs 100 (+/- 20) nucleotides downstream from the tRNA gene. D. discoideum tRNA genes are organized in multicopy gene families consisting of 5 to 20 individual genes. Members of a particular gene family are identical within the mature tRNA coding region while flanking sequences are idiosyncratic.

Animals↗

PubMed1995

Comparison of the inverted terminal repetition sequences from five porcine adenovirus serotypes.

The nucleotide sequences of the region of inverted terminal repetition from representative strains of all five porcine adenovirus (PAV) serotypes were determined and analyzed. The first 17 nucleotides of this region were identical in PAV-1 to 3 and PAV-5, and 10 bp of identical sequence was found in all the PAVs. The closest relationships were among PAV-1 to 3, which shared more common sequences than the other serotypes. PAV-4 had the longest inverted terminal repeat reported for any adenovirus. The proximal 54-bp AT-rich region was partially conserved and the distal GC-rich region was less well conserved among all five serotypes.

Animals↗

PubMed1992

A bipartite suppressor: conjunction of two distinct factor-binding sites is essential for down-regulation in rat epoxide hydrolase gene expression.

We describe a novel transcriptional suppressor element found in the control region of the gene that encodes rat microsomal epoxide hydrolase (mEH), an inducible xenobiotic metabolizing enzyme. This element consists of the juxtaposition of two distinct factor-binding regions. The first region is composed of a series of five tandemly repeated factor-binding sequences, and the second region is an unique AT-rich factor-binding sequence. Although each region binds its cognate factor(s) in vitro, a single region does not function as a suppressor independently of the other. Transcriptional suppression was observed only when the two regions were combined. Thus, we propose that this regulatory element is a bipartite suppressor, requiring two distinct factor-binding regions for its function. The element displayed position-independent but orientation-dependent suppressor activity. The level of suppressor activity was proportional to the number of repetitive sites in region 1. We speculate that this region could mediate the dose-response behavior of mEH gene expression induced by chemical carcinogens in vivo. A qualitative difference in the region 2 binding factor(s) was observed between normal liver cells and a hepatoma cell line or carcinogen-treated liver cells. The possible relationship between this observation and the deregulation of mEH gene expression during the course of hepatocarcinogenesis is discussed.

Animals↗

PubMed1990

Characterization of the Alu-rich 5'-flanking region of the human prothrombin-encoding gene: identification of a positive cis-acting element that regulates liver-specific expression.

The nt sequence of 6127 bp of sequence upstream of the human prothrombin-encoding gene (F2) has been determined. Since we previously characterized 417 bp of DNA immediately upstream from the transcription start point (tsp), 6544 bp of continuous flanking sequence are known. Eleven Alu repeat sequences present in this region comprise 45% of the sequence; other repetitive sequences were identified by searching GenBank. The tsp was found to be heterogeneous by exon mapping and primer extension analysis. To localize the cis-acting sequences responsible for the liver-specific expression of F2, hybrid cat genes were constructed with various lengths of F2 5'-flanking region cloned upstream from a promoterless cat gene. After transfection into HepG2 and HeLa cells, it was inferred that the region between nt -1101 and -798 was required for synthesis in HepG2 cells; no synthesis was observed using these constructs in HeLa cells. Two sequences for known liver-specific or regulatory cis-acting sequences were identified in this region.

Amino Acid Sequence↗

PubMed1998

A novel repetitive sequence of sugar cane, SCEN family, locating on centromeric regions.

Tandem repetitive sequences consisting of 140-bp repetitive units were cloned from sugar cane genomic DNA and designated the SCEN family. In situ hybridization revealed that they were located on the centromeric region of almost all of the chromosomes of sugar cane. The 140-bp sequence included three CENP-B box-like sequences. Phylogenetic analysis of the members of the SCEN family revealed that the sequences had 75% homology with each other, on average, and that the sequences could not be further classified into smaller subfamilies. The copy number of the sequence was estimated to be 2.6 x 10(5) per haploid sugar cane genome and, therefore, 4.6 x 10(3) or 630 kb per chromosome on average.

Autoantigens↗

PubMed1987

A composite transposon 3' to the cow fetal globin gene binds a sequence specific factor.

Two unusual sequence organizations were found within the beta-globin locus of the cow. Each was a composite, consisting of closely linked Alu-type repeats with a short stretch of genomic non-repetitive sequence, called a lagan, sandwiched between. One lagan was found 3' to the fetal globin gene, while the second lay between the adult globin gene and a globin pseudogene. Southern blot analysis indicated that both lagans appeared twice within the cow haploid genome, with the second copies lying outside the cow beta-globin locus. One of these non-globin locus homologues was cloned and subjected to sequence analysis. Comparison of the DNA sequence data showed that the lagan-Alu composite was transposed as a unit. The lagan 3' to the cow fetal globin gene contains the recognition site for a sequence specific DNA binding factor. This factor was present in extracts from fetal, but not from adult cow tissues.

Animals↗

PubMed1995

The human myelin oligodendrocyte glycoprotein (MOG) gene: complete nucleotide sequence and structural characterization.

Human myelin oligodendrocyte glycoprotein (MOG), a myelin component of the central nervous system, is a candidate target antigen for autoimmune-mediated demyelination. We have isolated and sequenced part of a cosmid clone that contains the entire human MOG gene. The primary nuclear transcript, extending from the putative start of transcription to the site of poly(A) addition, is 15,561 nucleotides in length. The human MOG gene contains 8 exons, separated by 7 introns; canonical intron/exon boundary sites are observed at each junction. The introns vary in size from 242 to 6484 bp and contain numerous repetitive DNA elements, including 14 Alu sequences within 3 introns. Another Alu element is located in the 3'-untranslated region of the gene. Alu sequences were classified with respect to subfamily assignment. Seven hundred sixty-three nucleotides 5' of the transcription start and 1214 nucleotides 3' of the poly(A) addition sites were also sequenced. The 5'-flanking region revealed the presence of several consensus sequences that could be relevant in the transcription of the MOG gene, in particular binding sites in common with other myelin gene promoters. Two polymorphic intragenic dinucleotide (CA)n and tetranucleotide (TAAA)n repeats were identified and may provide genetic marker tools for association and linkage studies.

Base Sequence↗

PubMed1989

Phase variation of gonococcal protein II: regulation of gene expression by slipped-strand mispairing of a repetitive DNA sequence.

Expression of outer membrane protein II (P.II) of Neisseria gonorrhoeae is subject to reversible phase variation at a rate of 10(-3)-10(-4)/cell/generation. The signal peptide coding regions of P.II genes contain variable numbers of tandem repeats of the sequence CTCTT. Changes in the number of CTCTT units, leading to frameshifting within the gene, are responsible for changes in P.II expression. Phase variation mediated by the CTCTT repeat also occurred in E. coli, as assayed with a P.II-alkaline phosphatase (phoA) gene fusion. Phase variation in both the gonococcus and E. coli was recA-independent, occurred at similar rates, and involved insertions or deletions of one or more repeat units. The characteristics of the phase variation process were consistent with a model in which expression of P.II genes is regulated by slipped-strand mispairing of the DNA in the CTCTT repeat region.

Bacterial Outer Membrane Proteins↗

PubMed1995

Two cis elements collaborate to spatially repress transcription from a sea urchin promoter.

The expression pattern of many territory-specific genes in metazoan embryos is maintained by an active process of negative spatial regulation. However, the mechanism of this strategy of gene regulation is not well understood in any system. Here we show that reporter constructs containing regulatory sequence for the SM30-alpha gene of Stronglyocentrotus purpuratus are expressed in a pattern congruent with that of the endogenous SM30 gene(s), largely as a result of active transcriptional repression in cell lineages in which the gene is not normally expressed. Chloramphenicol acetyl transferase assays of deletion constructs from the 2600-bp upstream region showed that repressive elements were present in the region from -1628 to -300. In situ hybridization analysis showed that the spatial fidelity of expression was severely compromised when the region from -1628 to -300 was deleted. Two highly repetitive sequence motifs, (G/A/C)CCCCT and (T/C)(T/A/C)CTTTT(T/A/C), are present in the -1628 to -300 region. Representatives of these elements were analyzed by gel mobility shift experiments and were found to interact specifically with protein in crude nuclear extracts. When oligonucleotides containing either sequence element were co-injected with a correctly regulated reporter as potential competitors, the reporter was expressed in inappropriate cells. When composite oligonucleotides, containing both sequence elements, were fused to a misregulated reporter, the expression of the reporter in inappropriate cells was suppressed. Comparison of composite oligonucleotides with oligonucleotides containing single constituent elements show that both sequence elements are required for effective spatial regulation. Thus, both individual elements are required, but only a composite element containing both elements is sufficient to function as a tissue-specific repressive element.

Animals↗

PubMed1991

The rat vitamin D binding protein (Gc-globulin) gene. Structural analysis, functional and evolutionary correlations.

The complete rat vitamin D binding protein (DBP) gene has been cloned and characterized. Genomic mapping suggests that there is only one copy of this gene in the haploid genome. The gene spans 35 kilobase pairs and contains 13 exons. All exons, exon/intron borders, and 2196 base pairs of 5'-flanking region have been sequenced. The transcription cap site, determined by primer extension analysis, is 62 base pairs upstream from the start of translation and predicts that an unusual TGTAAA motif may serve as a surrogate TATA. The promoter region contains about 50% nucleotide sequence similarity to the corresponding region of the partially characterized human DBP gene and is uniquely interrupted by a repetitive element. Although lacking in overall sequence similarity to the albumin (ALB) and alpha-fetoprotein (AFP) genes, the 5'-flanking region of the DBP gene contains a number of conserved segments which may correspond to critical proximal promoter elements in this gene family. The location of the introns in the coding region of the DBP gene is highly conserved when compared with the ALB and AFP genes. Detailed comparison of exon size and content confirms the previous prediction that the smaller size of the DBP protein results from loss of internal exons 12 and 13 from the DBP progenitor gene during its evolutionary divergence from ALB and AFP.

Amino Acid Sequence↗