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Technical note: A quick and more sensitive method to identify pork in processed and unprocessed food by PCR amplification of a new specific DNA fragment.

We developed and evaluated a PCR procedure to detect pork in heated and unheated meat, sausages, canned food, cured products, and pâtés using a faster, more specific, and more sensitive method than others previously described. Isolation of a new DNA-specific porcine repetitive element was performed by nonspecific PCR amplification. After analyzing this repetitive sequence, a pair of primers were synthesized. To confirm the effectiveness and specificity of this fragment, 55 pig blood DNA samples (from differents breeds) were tested and positive results were obtained. With 200 samples tested from other species, the specific pork amplification was not detected. Using this method, we can partially quantify degree of contamination, depending on the PCR amplification cycles, detecting up to 0.005% pork in beef and 1% pork in duck pâté using 30 and 20 PCR amplification cycles, respectively. The amount of porcine DNA detected in cattle DNA was 1.25 and 250 pg when using 30 and 20 amplification cycles, respectively. Pork has been identified in both heated and unheated meat products, sausages, canned food, hamburgers, and pâtés. In conclusion, specific PCR amplification of a repetitive DNA element seems to be a powerful technique for the identification of pork in processed and unprocessed food, because of its simplicity, specificity, and sensitivity (with 30 amplification cycles we can detect 0.005% pork). Furthermore, it is a very fast method, because 1% pork contamination can be detected with 20 PCR cycles. The procedure is also much cheaper than other methods based on RFLP-PCR, immunodiffusion, or other techniques that need expensive equipment.

Animals↗

Mapping the clonally unstable recombinogenic PRM1-->PRM2-->TNP2 region of human 16p13.2.

We have isolated a human cosmid clone encompassing approximately 40 kb of the chromosome 16p13.2 region. This region contains the protamine genes PRM1 and PRM2 and the transition protein gene TNP2. To facilitate the characterization of this under represented region of the chromosome 16 physical map, a detailed map of this cosmid clone was constructed. Analysis revealed that this gene cluster was nestled amid numerous repetitive elements. Under representation of this segment may be attributed to these repetitive sequence elements scattered throughout this region rendering this locus clonally unstable. Verification of the map by cosmid and genomic Southern analysis resolved discrepancies within the literature and showed that this highly repetitive DNA sequence containing cosmid was representative of this region of the human genome. This dynamic and recombinogenic region continues to evolve.

Blotting, Southern↗

Structural analysis of the entire proopiomelanocortin gene of Xenopus laevis.

In the pars intermedia of the pituitary the prohormone proopiomelanocortin (POMC) is tissue-specifically processed to, among other peptides, alpha-melanotropin (alpha MSH). In the South African clawed toad Xenopus laevis this hormone mediates the process of background adaptation: release of alpha-MSH causes darkening of the animal, while inhibition of alpha-MSH release results in a pale toad. Elevated release of alpha-MSH coincides with a higher rate of POMC gene transcription. The present study aims to find possible transcriptional regulatory elements in the Xenopus POMC gene. For that purpose the complete nucleotide sequence of the POMC gene and its 5'- and 3'- flanking regions were determined and analyzed. The Xenopus POMC gene promoter contains several regions which may be regulatory DNA elements in view of their similarity with corresponding regions of mammalian POMC gene promoters. In the rat POMC gene promoter, many of these regions represent protein-binding sequences. Besides the promoter sequence and the protein-coding sequences, no other segments with significant identity between the Xenopus and human POMC genes were found. Intron A of the Xenopus POMC gene contains a simple sequence, (TATC)76, and a JH12 repetitive element, while the 3'-flanking region contains a repetitive-EcoRI-monomer-2 element. Comparison of the JH12 sequence of the POMC gene with JH12 sequences from other Xenopus genes revealed a 335-bp consensus sequence which is flanked by a 30-bp inverted repeat. This JH12 consensus sequence is significantly larger than the previously reported JH12 core region. Alignment of intron B of the Xenopus POMC gene with database sequences revealed a consensus sequence of a novel Xenopus repetitive element of 330 bp flanked by a nearly perfect inverted repeat, indicating that this element may be a transposon-like element.

Animals↗

Active Alu elements are passed primarily through paternal germlines.

Repetitive elements are distributed non-randomly in the human genome but, as reviewed in this paper, biological processes underlying the observed patterns appear to be complex and remain relatively obscure. Recent findings indicate that chromosomal distribution of Alu retroelements deposited in the past is different from the distribution of Alu elements that continue to be inserted in human population. These active elements from AluY sub(sub)families are the major focus of this paper. In particular, we analyzed chromosomal proportions of 19 AluY subfamilies, of which nine are reported for the first time in this paper. These 19 subfamilies contain over 80% of Alu elements that are polymorphic in the human genome. The chromosomal density of these most recent Alu insertions is around three times higher on chromosome Y than on chromosome X and over two times higher than the average density for all human autosomes. Based on this observation and other data we propose that active Alu elements are passed through paternal germlines. There is also some evidence that a small fraction of active Alu elements from less abundant subfamilies can be retroposed in female germlines or in the early embryos. Finally, we propose that the origin of Alu subfamilies in human populations may be related to evolution of chromosome Y.

Base Sequence↗

Recruitment to the cytoplasm of a cellular lamin-like protein from the nucleus during a poxvirus infection.

Monoclonal antibodies (Mabs) directed against core proteins of rabbit poxvirus (RPV) have proven effective in the identification of host cell proteins such as RNA polymerase II (Pol II) that may play a role in the infectious process (D. K. Morrison and R. W. Moyer, 1986, Cell 44, 587-596). In this article we describe a Mab that has allowed the detection and characterization of a lamin-like protein derived from the nucleus of the infected cell, which like Pol II is recruited to the cytoplasm following RPV infection. A portion of the gene encoding this protein has been isolated through the screening of a lambda gt11 expression vector library. Sequence analysis of the gene shows it to be derived from a member of the HindIII 1.9-kb repetitive element, a family of mammalian repetitive sequences that are highly conserved. Immunoblot analysis and sequence analysis of the open reading frame show divergent relatedness to certain nuclear lamins. The protein is not, however, one of the three principal lamins characterized to date, but instead appears to be a perinuclear protein related to the highly conserved nuclear lamins that is recruited to the cytoplasm during the infectious process.

Amino Acid Sequence↗

Characterization of pre-insertion loci of de novo L1 insertions.

The human Long Interspersed Element-1 (LINE-1) and the Short Interspersed Element (SINE) Alu comprise 28% of the human genome. They share the same L1-encoded endonuclease for insertion, which recognizes an A+T-rich sequence. Under a simple model of insertion distribution, this nucleotide preference would lead to the prediction that the populations of both elements would be biased towards A+T-rich regions. Genomic L1 elements do show an A+T-rich bias. In contrast, Alu is biased towards G+C-rich regions when compared to the genome average. Several analyses have demonstrated that relatively recent insertions of both elements show less G+C content bias relative to older elements. We have analyzed the repetitive element and G+C composition of more than 100 pre-insertion loci derived from de novo L1 insertions in cultured human cancer cells, which should represent an evolutionarily unbiased set of insertions. An A+T-rich bias is observed in the 50 bp flanking the endonuclease target site, consistent with the known target site for the L1 endonuclease. The L1, Alu, and G+C content of 20 kb of the de novo pre-insertion loci shows a different set of biases than that observed for fixed L1s in the human genome. In contrast to the insertion sites of genomic L1s, the de novo L1 pre-insertion loci are relatively L1-poor, Alu-rich and G+C neutral. Finally, a statistically significant cluster of de novo L1 insertions was localized in the vicinity of the c-myc gene. These results suggest that the initial insertion preference of L1, while A+T-rich in the initial vicinity of the break site, can be influenced by the broader content of the flanking genomic region and have implications for understanding the dynamics of L1 and Alu distributions in the human genome.

Alu Elements↗

Identification of distal KIR promoters and transcripts.

A more complete understanding of the transcriptional control of the human and murine class I MHC receptors will help to shed light on the mechanism of selective, stochastic, gene activation that operates in these gene families. Studies of the murine Ly49 class I MHC receptor genes have revealed an important role for distal transcripts originating upstream of the proximal promoter. To date, there have been no reports of distal promoters within the functionally analogous human KIR family of class I MHC receptors. In the current study, reverse transcriptase-polymerase chain reaction (RT-PCR) and RNase protection assays were used to reveal the presence of distal KIR transcripts initiating upstream of the previously characterized proximal KIR promoter. The intergenic promoter elements detected were associated with repetitive elements of the Alu and L1 families. Unlike the proximal KIR promoter, the distal promoter regions were not NK cell-specific. KIR genes expressed in a variegated manner produced a low level of distal transcripts containing a large 5' untranslated region. In contrast, the highly expressed KIR2DL4 gene possessed a higher level of spliced distal transcripts that were capable of producing KIR2DL4 protein. The identification of distal KIR promoter elements suggests that intergenic transcripts may influence the expression of KIR genes.

Cell Line↗

Conserved nucleotide differences and subfamily structure of porcine short interspersed elements.

Interspersed elements are ubiquitous in the genomes of higher eukaryotes and account for over a third of the genomic DNA (Smit 1996). In swine the short interspersed elements, SINEs or PREs (porcine repetitive elements), have been found in a number of introns and 3' untranslated regions of different genes. However, compared to human Alu repeats the number of available PRE DNA sequences is still limited. In this study we have compared 85 PREs selected from DNA sequence database entries. The PREs were aligned and for each nucleotide position the relative frequencies of the four bases were calculated. A consensus sequence was derived from the first base usage. Similar to studies of SINEs in other species, the analysis showed that most mutations in PREs occur at CpG dinucleotide hot spots. The position variability for the two most frequent bases shows a bimodal distribution. The analysis suggests that the porcine SINEs can be divided into three major subfamilies sharing conserved nucleotide similarities.

Animals↗

Alu RNP and Alu RNA regulate translation initiation in vitro.

Alu elements are the most abundant repetitive elements in the human genome; they emerged from the signal recognition particle RNA gene and are composed of two related but distinct monomers (left and right arms). Alu RNAs transcribed from these elements are present at low levels at normal cell growth but various stress conditions increase their abundance. Alu RNAs are known to bind the cognate proteins SRP9/14. We purified synthetic Alu RNP, composed of Alu RNA in complex with SRP9/14, and investigated the effects of Alu RNPs and naked Alu RNA on protein translation. We found that the dimeric Alu RNP and the monomeric left and right Alu RNPs have a general dose-dependent inhibitory effect on protein translation. In the absence of SRP9/14, Alu RNA has a stimulatory effect on all reporter mRNAs. The unstable structure of sRight RNA suggests that the differential activities of Alu RNP and Alu RNA may be explained by conformational changes in the RNA. We demonstrate that Alu RNPs and Alu RNAs do not stably associate with ribosomes during translation and, based on the analysis of polysome profiles and synchronized translation, we show that Alu RNP and Alu RNA regulate translation at the level of initiation.

Alu Elements↗

The colanic acid gene cluster of Salmonella enterica has a complex history.

The colanic acid gene cluster of Salmonella enterica LT2 was sequenced and compared with that of Escherichia coli K-12. The two clusters are similar with divergence slightly higher than average for genes of the two species. The cluster was divided into four blocks by GC content and seems likely to have transferred from a higher GC content species to the ancestor of E. coli and S. enterica. All 19 genes of K-12 and 13 genes of LT2 appear to have undergone random genetic drift with amelioration of the GC content. However, in the case of S. enterica, we believe that the six genes of the GDP-fucose pathway group were replaced relatively recently by genes closely related to those of the original donor species. Two repetitive elements were observed: a bacterial interspersed mosaic element in the intergenic region between wzx and wcaK in K-12 only and a RSA (repetitive sequence element) sequence between wcaJ and wzx in LT2 only.

Bacterial Proteins↗

A naturally occurring T14A11 tract blocks nucleosome formation over the human neurofibromatosis type 1 (NF1)-Alu element.

The nature of chromatin organization over Alu repetitive elements is of interest with respect to the maintenance of their transcriptional silencing as well as their potential to influence local chromatin structure. We previously demonstrated that the pattern of nucleosomal organization over Alu elements in native chromatin is specific and similar to the pattern observed with an in vitro reconstituted Alu template. This pattern, distinguished by a nucleosome centered over the 5 -end of the Alu element, is associated with repression of polymerase III-dependent transcription in vitro (Englander, E. W., Wolffe, A. P., and Howard, B. H. (1993) J. Biol. Chem. 268, 19565-19573; Englander, E. W., and Howard, B. H. (1995) J. Biol. Chem. 270, 10091-10096). In the current study, additional templates representing both evolutionarily old and young Alu subfamilies were found to direct a similar pattern of nucleosome assembly, consistent with the view that nucleosome positioning in vitro is shared by a majority of Alus. We discovered however, that the specific nucleosome positioning pattern was disrupted over one member of a young Alu subfamily, which recently transposed immediately downstream to a T14A11 sequence in the neurofibromatosis type 1 locus (Wallace, M. R., Andersen, L. B., Saulino, A. M., Gregory, P. E., Glover, T. W., and Collins, F. S. (1991) Nature 353, 864-866). Upon removal of this sequence motif, the expected pattern of assembly was restored to the neurofibromatosis type 1-Alu template. This finding indicates that, at least in vitro, certain sequences can override the propensity for positioning nucleosomes that is inherent to Alu elements. The finding also raises the possibility that a similar situation may occur in vivo, with potential implications for understanding mechanisms by which certain Alu elements may evade chromatin-mediated transcriptional silencing.

Animals↗

Natural genetic variation caused by transposable elements in humans.

Transposons and transposon-like repetitive elements collectively occupy 44% of the human genome sequence. In an effort to measure the levels of genetic variation that are caused by human transposons, we have developed a new method to broadly detect transposon insertion polymorphisms of all kinds in humans. We began by identifying 606,093 insertion and deletion (indel) polymorphisms in the genomes of diverse humans. We then screened these polymorphisms to detect indels that were caused by de novo transposon insertions. Our method was highly efficient and led to the identification of 605 nonredundant transposon insertion polymorphisms in 36 diverse humans. We estimate that this represents 25-35% of approximately 2075 common transposon polymorphisms in human populations. Because we identified all transposon insertion polymorphisms with a single method, we could evaluate the relative levels of variation that were caused by each transposon class. The average human in our study was estimated to harbor 1283 Alu insertion polymorphisms, 180 L1 polymorphisms, 56 SVA polymorphisms, and 17 polymorphisms related to other forms of mobilized DNA. Overall, our study provides significant steps toward (i) measuring the genetic variation that is caused by transposon insertions in humans and (ii) identifying the transposon copies that produce this variation.

DNA Transposable Elements↗

Dynamics of mobile element activity in chalcone synthase loci in the common morning glory (Ipomoea purpurea).

Mobile element dynamics in seven alleles of the chalcone synthase D locus (CHS-D) of the common morning glory (Ipomoea purpurea) are analyzed in the context of synonymous nucleotide sequence distances for CHS-D exons. By using a nucleotide sequence of CHS-D from the sister species Ipomoea nil (Japanese morning glory [Johzuka-Hisatomi, Y., Hoshino, A., Mori, T., Habu, Y. & Iida, S. (1999) Genes Genet. Syst. 74, 141-147], it is also possible to determine the relative frequency of insertion and loss of elements within the CHS-D locus between these two species. At least four different types of transposable elements exist upstream of the coding region, or within the single intron of the CHS-D locus in I. purpurea. There are three distinct families of miniature inverted-repeat transposable elements (MITES), and some recent transpositions of Activator/Dissociation (Ac/Ds)-like elements (Tip100), of some short interspersed repetitive elements (SINEs), and of an insertion sequence (InsIpCHSD) found in the neighborhood of this locus. The data provide no compelling evidence of the transposition of the mites since the separation of I. nil and I. purpurea roughly 8 million years ago. Finally, it is shown that the number and frequency of mobile elements are highly heterogeneous among different duplicate CHS loci, suggesting that the dynamics observed at CHS-D are locus-specific.

Acyltransferases↗

A novel abundant family of retroposed elements (DAS-SINEs) in the nine-banded armadillo (Dasypus novemcinctus).

About half of the mammalian genome is composed of retroposons. Long interspersed elements (LINEs) and short interspersed elements (SINEs) are the most abundant repetitive elements and account for about 21% and 13% of the human genome, respectively. SINEs have been detected in all major mammalian lineages, except for the South American order Xenarthra, also termed Edentata (armadillos, anteaters, and sloths). Investigating this order, we discovered a novel high-copy-number family of tRNA derived SINEs in the nine-banded armadillo Dasypus novemcinctus, a species that successfully crossed the Central American land bridge to North America in the Pliocene. A specific computer algorithm was developed, and we detected and extracted 687 specific SINEs from databases. Termed DAS-SINEs, we further divided them into six distinct subfamilies. We extracted tRNA(Ala)-derived monomers, two types of dimers, and three subfamilies of chimeric fusion products of a tRNA(Ala) domain and an approximately 180-nt sequence of thus far unidentified origin. Comparisons of secondary structures of the DAS-SINEs' tRNA domains suggest selective pressure to maintain a tRNA-like D-arm structure in the respective founder RNAs, as shown by compensatory mutations. By analysis of subfamily-specific genetic variability, comparison of the proportion of direct repeats, and analysis of self-integrations as well as key events of dimerization and deletions or insertions, we were able to delineate the evolutionary history of the DAS-SINE subfamilies.

Animals↗

Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B.

Bread wheat (Triticum aestivum) is one of the most important crops worldwide. However, because of its large, hexaploid, highly repetitive genome it is a challenge to develop efficient means for molecular analysis and genetic improvement in wheat. To better understand the composition and molecular evolution of the hexaploid wheat homoeologous genomes and to evaluate the potential of BAC-end sequences (BES) for marker development, we have followed a chromosome-specific strategy and generated 11 Mb of random BES from chromosome 3B, the largest chromosome of bread wheat. The sequence consisted of about 86% of repetitive elements, 1.2% of coding regions, and 13% remained unknown. With 1.2% of the sequence length corresponding to coding sequences, 6000 genes were estimated for chromosome 3B. New repetitive sequences were identified, including a Triticineae-specific tandem repeat (Fat) that represents 0.6% of the B-genome and has been differentially amplified in the homoeologous genomes before polyploidization. About 10% of the BES contained junctions between nested transposable elements that were used to develop chromosome-specific markers for physical and genetic mapping. Finally, sequence comparison with 2.9 Mb of random sequences from the D-genome of Aegilops tauschii suggested that the larger size of the B-genome is due to a higher content in repetitive elements. It also indicated which families of transposable elements are mostly responsible for differential expansion of the homoeologous wheat genomes during evolution. Our data demonstrate that BAC-end sequencing from flow-sorted chromosomes is a powerful tool for analysing the structure and evolution of polyploid and highly repetitive genomes.

Base Sequence↗

A retrotransposable element from the mosquito Anopheles gambiae .

A family of middle repetitive elements from the African malaria vector Anopheles gambiae is described. Approximately 100 copies of the element, designated T1Ag, are dispersed in the genome. Full-length elements are 4.6 kilobase pairs in length, but truncation of the 5' end is common. Nucleotide sequences of one full-length, two 5'-truncated, and two 5' ends of T1Ag elements were determined and aligned to define a consensus sequence. Sequence analysis revealed two long, overlapping open reading frames followed by a polyadenylation signal, AATAAA, and a tail consisting of tandem repetitions of the motif TGAAA. No direct or inverted long terminal repeats (LTRs) were detected. The first open reading frame, 442 amino acids in length, includes a domain resembling that of nucleic acid-binding proteins. The second open reading frame, 975 amino acids long, resembles the reverse transcriptases of a category of retrotransposable elements without LTRs, variously termed class II retrotransposons, class III elements or non-LTR retrotransposons. Similarity at the sequence and structural levels places T1Ag in this category.

Amino Acid Sequence↗

Putative target sites for mobile G + C rich clusters in yeast mitochondrial DNA: single elements and tandem arrays.

GC clusters constitute the major repetitive elements in the mitochondrial (mt) genome of the yeast Saccharomyces cerevisiae. Many of these clusters are optional and thus contribute much to the polymorphism of yeast mtDNAs. We have made a systematic search for polymorphic sites by comparing mtDNA sequences of various yeast strains. Most of the 26 di- or polymorphic sites found differ by the presence or absence of a GC cluster of the majority class, here referred to as the M class, which terminate with an AGGAG motif. Comparison of sequences with and without the GC clusters reveal that elements of the subclasses M1 and M2 are inserted 3' to a TAG, flanked by A + T rich sequences. M3 elements, in contrast, only occur in tandem arrays of two to four GC clusters; they are consistently inserted 3' to the AGGAG terminal sequence of a preexisting cluster. The TAG or the terminal AGGAG, therefore, are regarded as being part of the target sites for M1 and M2 or M3 elements, respectively. The dinucleotide AG is in common to both target sites; it also occurs at the 3' terminus (AGGAG). This suggests its duplication during GC cluster insertion. This notion is supported by the observation that GC clusters of the minor classes G and V similarily repeat at their 3' terminus a GT or an AA dinucleotide, respectively, from their putative target sites.

Base Sequence↗

"Retroposon" insertion into the cellular oncogene c-myc in canine transmissible venereal tumor.

We examined by Southern blotting the state of the cellular oncogene c-myc in the dog transmissible venereal tumor. The tumor DNA contains a 16.8-kilobase pair (kbp) rearranged c-myc fragment in addition to the normal 15-kbp and 7.5-kbp fragments. We compared the structure of the cloned rearranged c-myc (re-myc) with that of a cloned normal c-myc and found that the rearrangement was due to the insertion of a 1.8-kbp DNA upstream to the first exon of c-myc. The inserted DNA is flanked by 10-base-pair direct repeats and contains a dA-rich tail, suggesting its origin from mRNA. Partial sequence of the inserted element showed 62% homology with the primate interdispersed Kpn I repetitive element. These results provide an example for the behavior of repetitive DNA sequences like the Kpn I family, as movable elements that can transpose nearby to oncogenes or other structural genes and perhaps affect their activity.

Animals↗