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A repetitive element containing a critical tyrosine residue is required for transcriptional activation by the EWS/ATF1 oncogene.

Chromosomal fusion of the N-terminal region of the Ewings Sarcoma Oncogene (EWS-activation-domain, EAD) to the DNA-binding domains of a variety of cellular transcription factors produce oncogenic proteins (EWS-fusion proteins (EFPs)) that cause distinct malignancies. In EFPs, the EAD acts as a potent transcriptional activation domain and this ability is repressed in the context of normal, non-tumorigenic, EWS. Trans-activation by the EAD is therefore a specific characteristic of EFPs and it is thought that EFPs induce tumorigenesis via improper transcriptional activation of cellular genes. Functional elements required for transcriptional activation are dispersed throughout the EAD, as are thirty-one copies of a Degenerate Hexapeptide Repeat (DHR, consensus SYGQQS). This suggests that the EAD contains a highly reiterated functional element related to DHRs. Here we show that in the context of EWS/ATF1, the EFP that causes malignant melanoma of soft parts, trans-cooperation by small regions of the EAD ( approximately 30 residues) results in potent transcriptional activation dependent on the conserved tyrosine residues present in DHRs. These findings provide the first evidence for a role of DHRs in EAD-mediated trans-activation and demonstrate that the EAD represents a novel tyrosine-dependent transcriptional activation domain.

Amino Acid Sequence↗

The gene encoding the MOK-2 zinc-finger protein: characterization of its promoter and negative regulation by mouse Alu type-2 repetitive elements.

The mouse gene MOK-2 encodes a protein with seven highly similar zinc fingers. The MOK-2 transcripts are preferentially detected in transformed cell lines, brain and testis tissues. The characterized 5'-flanking sequence differs from those of tissue-specific genes previously described. DNA sequence analysis shows that the promoter region lacks TATA and CCAAT boxes. Two short interspersed mouse genomic repeats (B2 sequences) found in this region exert a negative cis-acting effect on MOK-2 promoter activity.

Amino Acid Sequence↗

Repetitive element sequence based polymerase chain reaction for typing of Brucella strains.

A collection of 40 Brucella strains, including 19 clinical B.canis isolates, was analyzed using ERIC-PCR and REP-PCR. PCR amplification using primers REP 1R-I and REP 2-I provided distinct patterns for Brucella spp. All Brucella strains could be discriminated at least to the species level. ERIC-PCR, employing ERIC 1R and ERIC 2 as primers was less discriminative for Brucella, only allowing a discrimination to the genus level with occasional discrimination between individual strains. It can be concluded that rep PCR is a promising fingerprinting method for the evaluation of an outbreak.

Animals↗

Sequence organization and developmental expression of an interspersed, repetitive element and associated single-copy DNA sequences in Dictyostelium discoideum.

We have examined the genomic organization and developmental expression pattern of a short, transcribed, interspersed repeat element and its associated single-copy sequences. We have previously shown that 1% of the polyadenylated [poly(A)+] RNA from vegetative cells contains sequences that hybridize to this repeat. The complementary RNA is heterogeneous in size, and 90% of its mass hybridizes to single-copy DNA. In this study, we examined a series of genomic DNAs and cDNAs derived from poly(A)+ RNAs which are complementary to the repeat. Comparisons of sequence data from various genomic and cDNA clones indicated that (AAC)n X (GTT)n is the common sequence element. The tandem repeat occurred in approximately 100 short segments (approximately 35 to 150 base pairs) per haploid genome interspersed with single-copy DNA. Probes from regions adjacent to this element hybridized to unique restriction fragments on DNA blots and unique poly(A)+ RNA species on RNA blots. The (AAC)n X (GTT)n sequence was asymmetrically transcribed with only (AAC)n sequences represented in RNA. The repeat was localized within the transcribed regions of several genes and 70 base pairs 5' to the transcription initiation site of another gene. Individual (AAC)n-containing RNAs exhibited a developmental pattern of expression suggestive of the coordinate expression of many AAC gene family members.

Base Sequence↗

Nucleotide sequence analysis of the spacer regions flanking the rat rRNA transcription unit and identification of repetitive elements.

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.

Animals↗

A repetitive element in the genome of Atlantic salmon, Salmo salar.

When Atlantic salmon (Salmo salar) genomic DNA is digested with the restriction endonuclease BglI and the fragments separated by agarose-gel electrophoresis, bands corresponding to approximately 430 and 923 bp are visualized after EtdBr staining. The 923-bp band was excised from a preparative gel and used to screen a salmon genomic library for recombinant phage (re-phage) containing the repeat. The BglI repeat element is tandemly arrayed, and an array from one re-phage has been sequenced. The BglI repeats comprise 2.3% of the S. salar genome and have been found in the vicinity of rDNA genes (encoding ribosomal RNA). Southern blot hybridization detects a homologue of the Atlantic salmon BglI repeat in the brown trout (Salmo trutta) genome, but not in other salmonids. However, a DNA fragment with sequence homology to part of the BglI repeat has recently been isolated from Arctic charr (Salvelinus alpinus; S.E. Hartley and W.S.D., unpublished data). In addition, the BglI repeat detects RFLPs in Atlantic salmon.

Animals↗

Restriction polymorphisms and fingerprint patterns from an interspersed repetitive element of Plasmodium falciparum DNA.

A recombinant DNA clone, pC4.H32, identifies distinguishable restriction fragment patterns from different Plasmodium falciparum clones. Analysis of these DNA fingerprint patterns from parasites cultivated over several years and from progeny of a P. falciparum cross showed the fingerprints to be mitotically and meiotically stable. Restriction fragments from the parents of the cross possessed sufficient polymorphism and number to generate 14 unique fingerprint patterns in 16 independent recombinant progeny. The pC4.H32 insert contains a 0.5-kb imperfectly repeated sequence found in subtelomeric regions of multiple chromosomes. Restriction site variations both within and outside of the 0.5-kb repeat contribute to the fingerprint polymorphisms. Fingerprint analysis can serve to type P. falciparum clones and can detect mislabeling and cross-contamination of parasite stocks.

Animals↗

Quantitative PCR for DNA identification based on genome-specific interspersed repetitive elements.

We have designed and evaluated a series of class-specific (Aves), order-specific (Rodentia), and species-specific (equine, canine, feline, rat, hamster, guinea pig, and rabbit) polymerase chain reaction (PCR)-based assays for the identification and quantitation of DNA using amplification of genome-specific short and long interspersed elements. Using SYBR Green-based detection, the minimum effective quantitation levels of the assays ranged from 0.1 ng to 0.1 pg of starting DNA template. Background cross-amplification with DNA templates derived from sixteen other species was negligible prior to 30 cycles of PCR. The species-specificity of the PCR amplicons was further demonstrated by the ability of the assays to accurately detect known quantities of species-specific DNA from mixed (complex) sources. The 10 assays reported here will help facilitate the sensitive detection and quantitation of common domestic animal and bird species DNA from complex biomaterials.

Animals↗

Analysis of two different tandem repetitive elements within the human apolipoprotein B gene.

A large number of copies of the sequence (dTG-dAC)n, where n is between 10 and 60, exist in the human genome, and many are useful as polymorphic markers. One of these sequences occurs about 3 kilobases 5' of the human apolipoprotein (apo) B gene as seven distinguishable alleles containing from (TG)12 to (TG)18. This repeat is also present in the DNA of other primates. A second alternating purine-pyrimidine sequence with nine dinucleotide repeats and located in intron 4 is not polymorphic. Together with the apoB hypervariable repeat immediately 3' of the gene, the (TG)n sequence will provide a useful haplotype marker capable of distinguishing a large number of human apoB alleles, some of which may be associated with disease states.

Animals↗

The uteroglobin gene region: hormonal regulation, repetitive elements and complete nucleotide sequence of the gene.

Differential uteroglobin induction represents an appropriate model for the molecular analysis of the mechanism by which steroid hormones control gene expression in mammals. We have analyzed the structure and hormonal regulation of a 35 Kb region of genomic DNA in which the uteroglobin gene is located. The complete sequence of 3,700 nucleotides including the uteroglobin gene and its flanking regions has been determined, and the limits of the gene established by S1 nuclease mapping. Several regions containing repeated sequences were mapped by blot hybridization, one of which is located within the large intron in the uteroglobin gene. Analysis of the RNAs extracted from endometrium, lung and liver, after treatment with estrogen and/or progesterone shows that within the 35 Kb region, the uteroglobin gene is the only DNA segment whose transcription into stable RNA is induced by progesterone.

Amino Acid Sequence↗

Interspersed repetitive element polymerase chain reaction product mapping using a mouse interspecific backcross.

We have developed a rapid method of generating and simultaneously mapping interrepeat polymerase chain reaction products using DNA from interspecific backcross animals derived from mating C57BL/6J and Mus spretus mice. This method is based on the high degree of B1, B2, and L1 dispersed repeat position polymorphism found between these two species of mouse. We have mapped 13 new loci to 9 different chromosomes and have found no evidence of clustering among these loci. The advantages of this approach are that no prior knowledge of sequence is required, a single PCR reaction generates many markers which can be mapped simultaneously, and only 50 ng of each backcross DNA (a finite resource) is required. We anticipate that many more markers remain to be characterized in this valuable new source of polymorphism.

Animals↗

Biased distribution of repetitive elements: a landmark for neo-Y chromosome evolution in Drosophila miranda.

It is generally assumed that the sex chromosomes developed from a pair of homologs. Over evolution, the proto-Y chromosome, with a very short differential segment, matured in its final stage into a heterochromatic and, for the most part, genetically eroded Y chromosome. The constraints on the evolution of the proto-Y chromosome have been speculated upon since the sex chromosomes were discovered. Several models have been suggested. Drosophila miranda has proved to be a unique and potent model system to study Y-chromosome evolution. We use selected test genes distributed along the neo-Y chromosome as entry gates to analyze the molecular mechanisms involved in the process of Y-chromosome evolution. Here, we report our findings on the Krüppel gene (Kr), which is located distally on the neo-sex chromosome pair.

Animals↗

The sequence of the 3.3-kilobase repetitive element from Dipodomys ordii suggests a mechanism for its amplification and interspersion.

DNA from the kangaroo rat, Dipodomys ordii, contains a 3.3-kb, highly repeated sequence that is interspersed throughout the genome in small tandem clusters. One 3.3-kb unit has been cloned into pBR322 and the nucleotide sequence determined. The clone used was shown to be representative of the bulk of such sequences found in the genomic DNA. The sequence contains 10 homologous subunits each ca. 260 bp in length. Comparison of these to one another yielded a 258-bp consensus sequence containing a 35-bp terminal inverted repeat. Two unique stretches also occur. One of these contains a region that could serve as a promoter for RNA polymerase III; the other contains a sequence related to the ARS sequences of yeast. It is proposed that an ancestral sequence similar to the consensus sequence was amplified to 10 or more units, and that, subsequently, two other sequences were inserted. The properties of these insertions may have led to the dispersal of the sequence throughout the genome.

Animals↗

Species-specific amplification of tRNA-derived short interspersed repetitive elements (SINEs) by retroposition: a process of parasitization of entire genomes during the evolution of salmonids.

Fourteen members of the Hpa I subfamilies of tRNA-derived SINEs in particular salmonid species were isolated from genomic libraries of chum salmon, kokanee, coho salmon, masu salmon, and steelhead. Alignment of the sequences of these 14 members, together with those of 4 members already published, 3 of which were previously demonstrated to have been amplified specifically in certain lineages, revealed the presence of five subfamilies with particular diagnostic nucleotides. The amplification of members of the same subfamily in different salmonid lineages and the amplification of members of different subfamilies in the same salmonid lineage suggest that multiple dispersed loci were responsible for amplification or, alternatively, that SINEs were transmitted horizontally between species. These two possibilities are not mutually exclusive. Our results also indicate that the Hpa I SINEs in salmonids behave like parasites. The amplification of these SINEs is ongoing and continues to shape the evolution of salmonid genomes.

Animals↗

Repetitive elements sequence (REP/ERIC)-PCR based genotyping of clinical and environmental strains of Yersinia enterocolitica biotype 1A reveal existence of limited number of clonal groups.

REP- and ERIC-PCR genotyping were used to assess genetic heterogeneity among 81 strains of Yersinia enterocolitica biotype 1A isolated from India, Germany, France and the USA. Although both gave comparable results, ERIC fingerprints discriminated the strains better. The rep- (REP and ERIC) PCR genotyping showed that strains having different serotypes produced identical rep-profiles indicating their limited genetic diversity. The concatenated dendrogram of REP- and ERIC-PCR fingerprints clustered the biotype 1A strains into two major groups. In each group, majority of the Indian, European and American strains exhibited similarities ranging from 85% to >95%. Similarity of rep-PCR fingerprints amongst strains isolated from widely separated geographical regions revealed existence of a limited number of clonal groups of Y. enterocolitica biotype 1A. The present study failed to reveal unequivocal relationships between rep-PCR genotypes and the source of isolation. However, the clinical serotype O:6,30-6,31 strains formed a tight cluster and the aquatic O:6,30-6,31 strains formed a yet another tight cluster.

Animals↗

The mouse transition protein 1 gene contains a B1 repetitive element and is located on chromosome 1.

The gene for mouse transition protein 1 (mTP1) was isolated, sequenced, and chromosomally mapped. The nucleotide sequence of 1895 bp of a 6.4-kb mTP1 genomic subclone was determined to include 788 bp of 5' flanking region, 564 bp of coding region including a 396-bp intron and a TAA stop codon, and 543 bp of 3' flanking region. The mTP1 gene contains a B1 repeat sequence within the only intron of the gene. The transcriptional start site of the mTP1 mRNA was determined to be located 31 bases upstream of the ATG translational start codon. Southern blot analysis demonstrated the presence of sequences homologous to the mTP1 cDNA in the genomes of the rat, hamster, bull, boar, dog, horse, ram, human, and two marsupials (the American opossum and Monodelphis), suggesting that the mTP1 gene sequence is widely conserved. The TP1 gene has been mapped by analysis of restriction fragment length variants (RFLV) in an interspecific backcross to a position 0.7 +/- 0.4 cM telomeric of Mylf and 1.2 +/- 0.5 cM centromeric of Vil on mouse chromosome 1.

Amino Acid Sequence↗

Aberrant class switching juxtaposes c-myc with a middle repetitive element (LINE) and an IgH intron in two spontaneously arising rat immunocytomas.

Our previous studies of spontaneously arising rat immunocytomas of the Lou/Wsl strain have shown that Ig switch regions are frequently the targets for c-myc recombination. In several tumors, however, we were unable to show recombination of the c-myc with Ig switch regions. We have cloned the rearranged c-myc fragments from 2 of these tumors, IR209 and IR223, and found that the c-myc recombines with a LINE region in the IR209 and with intron 1 of the epsilon locus in the IR223. Although switch regions are not found at the breakpoints, the sequences at the breakpoints share limited homology with Ig switch recognition sequences. This suggests that the switch recombinase enzymes are able to recognize sequences in addition to the defined switch recombination sites. At the same time, both the LINE and epsilon intron 1 sequences are located within the Ig cluster, providing further evidence for the selection of c-myc activation by Ig sequences in the pathogenesis of rat immunocytoma, mouse plasmacytoma, and Burkitt's lymphoma.

Animals↗

Several short interspersed repetitive elements (SINEs) in distant species may have originated from a common ancestral retrovirus: characterization of a squid SINE and a possible mechanism for generation of tRNA-derived retroposons.

Using labeled transcripts generated in vitro from squid total genomic DNA as a probe, we isolated and characterized a SINE that is present in the squid genome. The squid SINE appears to be derived from a tRNA(Lys). When the consensus sequences of five different SINEs with a tRNA(Lys)-like structure from distantly related species, including squid, were aligned, we found in the tRNA-unrelated region two sequence motifs that were almost identical among these five SINEs. This observation suggests a common evolutionary origin for these SINEs and/or some function(s) for these motifs. Similar sequences were unexpectedly found to be present in sequences complementary to the U5 regions of several mammalian retroviruses whose primer is a tRNA(Lys). On the basis of these findings, we present a model for the generation of SINEs. We propose that they are derived from a "strong-stop DNA" with a primer tRNA(Lys) that is an intermediate in the reverse transcription of certain retroviruses. Our model suggests that a certain group of SINEs may have been generated by horizontal transmission, although it is not clear whether information was transmitted via a similar retrovirus or via an RNA or DNA of a SINE.

Animals↗