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PubMed1991

Evolution and sequence analysis of a human Y-chromosomal DNA fragment.

A Y-chromosomal DNA fragment has been isolated from a human Y-Charon 21A recombinant library. Evolutionary analysis of 1F5 indicates that the size and sequence of this fragment have been conserved in higher primates. Deletion mapping and in situ hybridization analysis have localized 1F5 to the middle euchromatic portion of the long arm of the human Y chromosome at Yq11.2. Sequence analysis revealed the presence of an atypical Alu element and two regions rich in polypyrimidine-polypurine residues.

Base Sequence↗
PubMed1988

Sensitive detection and typing of human papillomavirus DNA in gynecological cell scrapings by slot-blot hybridization.

A rapid and sensitive method for detecting and typing human papillomaviruses (HPVs) in cell scrapings is presented. DNA from scrapings is extracted and bound to nitrocellulose filters (Slot-Blot). By DNA-DNA hybridization with specific 32P-labelled HPV-probes (types 6/11 or 16/18) the patient's DNA is then analyzed for the presence of, and for the type of, HPV DNA sequences. A parallel hybridization with a human repetitive element (Alu sequence) allows quantitation of the different hybridization results. Experiments with HeLa cell DNA show that as little as 10(4) HPV sequences can be detected and typed specifically with this test. Evaluation of this test is completed within 6 to 7 days after cell collection. This Slot-Blot method was used to analyse 1330 specimens taken at the Bernese Dysplasia Outpatient Clinic. The results reveal a very high percentage (90%) of HPV-positive cases in the patient group examined.

Autoradiography↗
PubMed1998

The BC200 RNA gene and its neural expression are conserved in Anthropoidea (Primates).

The gene encoding BC200 RNA arose from a monomeric Alu element. Subsequently, the RNA had been recruited or exapted into a function of the nervous system. Here we confirm the presence of the BC200 gene in several primate species among the Anthropoidea. The period following the divergence of New World monkeys and Old World monkeys from their common ancestor is characterized by a significantly higher substitution rate in the examined 5' flanking region than in the BC200 RNA coding region itself. Furthermore, the conservation of CpG dimers in the RNA coding region (200 bp) is drastically increased compared to the 5' flanking region (approximately 400 bp) over all 12 species examined. Finally, the brain-specific expression pattern of BC200 RNA and its presence as a ribonucleoprotein particle (RNP) are conserved in Old World and New World monkeys. Our studies indicate that the gene encoding BC200 RNA was created at least 35-55 million years ago and its presence, mode of expression, and association with protein(s) as an RNP are under selective pressure.

Animals↗
PubMed2002

The association between HLA-A alleles and young Alu dimorphisms near the HLA-J, -H, and -F genes in workshop cell lines and Japanese and Australian populations.

At least two polymorphic Alu insertions have been previously identified and characterized within the class I region of the major histocompatibility complex (MHC). We have identified another two new polymorphic Alu insertions, AluyHJ and AluyHF, located near HLA-J and HLA-F, respectively, within the a block of the MHC. Here we report on (1). the haplotypic relationships between the Alu dimorphisms and the HLA-A locus within a panel of 51 IHW homozygous cell lines representing at least 36 HLA class I haplotypes, (2). the Alu genotype, allele, and haplotype frequencies present in the Australian Caucasians and Japanese populations, and (3). the frequency of association between the different Alu dimorphisms and the HLA-A alleles in 109 Australian Caucasians and 99 Japanese. PCR was used to detect the presence or absence of insertion for AluyHJ, AluyHG, and AluyHF within the DNA samples prepared from the cell lines and the two population groups that had been previously typed for HLA-A. In the homozygous cell lines, all three Alu insertions were found in only one HLA class I haplotype (HLA-A1, -B57, -Cw6), no Alu insertions were detected in six HLA class I haplotypes and one or more of the Alu insertions were found in 29 HLA class I haplotypes. At least one of the Alu insertions was found in about 86% of the Japanese and Australian individuals, with the AluyHJ generally related inversely to AluyHG and/or AluyHF. The gene frequency of the AluyHJ and AluyHF insertions was significantly different (p <0.05) between Japanese and Australians, whereas there was no difference (P > 0.05) between the frequencies of AluyHG in the two populations. The Alu haplotype frequencies were also significantly different between the Japanese and the Australians. In the cell lines and the population groups, the AluyHJ insertion was most frequently found associated with HLA-A1 or A24, AluyHG with HLA-A2, and AluyHF with HLA-A2, -A10, or -A26. This study suggests that the three polymorphic Alu elements have been inserted into the a block of the MHC in different progenitor groups and therefore will be useful lineage and linkage markers in human population studies and for elucidating the evolution of HLA class I haplotypes.

Alleles↗
PubMed2001

Structure and origin of a novel dimeric retroposon B1-diD.

Here we describe a new short retroposon family of rodents. Like the primate Alu element consisting of two similar monomers, it is dimeric, but the left and right monomers are different and descend from B1 and ID short retroposons, respectively. Such elements (B1-dID) were found in the genomes of Gliridae, Sciuridae, Castoridae, Caviidae, and Hystricidae. Nucleotide sequences of this retroposon can be assigned to several structural variants. Phylogenetic analysis of B1-dID and related sequences suggests a possible scenario of B1-dID evolution in the context of rodent evolution.

Animals↗
PubMed1997

Differential display analysis of RNA accumulation in arbuscular mycorrhiza of pea and isolation of a novel symbiosis-regulated plant gene.

Differential RNA display was used to analyze gene expression during the early steps of mycorrhiza development on Pisum sativum following inoculation with Glomus mosseae. Seven out of 118 differentially displayed cDNA fragments were subcloned and sequenced. One fragment corresponded to part of the fungal 25S ribosomal RNA gene and a second one showed similarity to a human Alu element. The others were derived from plant genes of unknown function. One of the fragments was used for the isolation of a full-length cDNA clone. It corresponded to a single-copy gene (psam1) which is induced during early symbiotic interactions, and codes for a putative transmembrane protein. Northern and RNA dot blot analyses revealed enhanced accumulation of psam1 RNA after inoculation with G. mosseae of wild-type pea and an isogenic mutant deficient for nodule development (Nod-, Myc+).

Base Sequence↗
PubMed1999

Isolation, characterization, and mapping of four novel polymorphic markers and an H3.3B pseudogene to chromosome 9p21-22.

Alterations in chromosomal region 9p21-22 are among the most frequently encountered cytogenetic changes present in a number of human malignancies. In addition, the causative genes of a number of hereditary cancers have been genetically mapped to this region. We describe the isolation and precise localization of four novel polymorphic markers and a previously identified marker, D9S1846, from this region. Moreover, we have identified a retroposon-rich area within this oncogenic region containing a processed H3.3B pseudogene flanked by an L1 sequence and an Alu element. Together, these finely mapped and ordered reagents should prove useful for genetic mapping, sequencing, and loss of heterozygosity studies of the 9p21-22 region.

Base Sequence↗
PubMed2005

Screening for exonic copy number mutations at MSH2 and MLH1 by MAPH.

BACKGROUND: Exonic deletions in MSH2 and MLH1 are significant contributors to the mutation spectrum in HNPCC, and heterozygous changes in exon copy number are not detected by conventional mutation screening methods. AIMS: We aimed to develop methods for screening copy number changes in all the exons of the MLH1 and MSH2 genes using a single multiplex amplifiable probe hybridisation (MAPH) assay. METHODS: We developed a probe set consisting of probes from the 19 exons of MLH1 and 16 exons of MSH2, and 3 control probes, and applied it to screening for deletions and duplications using fluorescent detection of amplified fragments. RESULTS: We tested 73 DNA samples from controls and 50 from HNPCC patients in whom no point mutations had been found, and detected 10 copy number changes among the patient samples. A deletion of about 1.4 kb including exon 3 of MSH2 was confirmed by amplification of a junction fragment, and was shown to be the result of an unequal recombination between intronic Alu elements. CONCLUSIONS: MAPH can detect exonic copy number changes in MLH1 and MSH2 in DNA from HNPCC patients. Since finding an exonic deletion or duplication makes full sequence analysis unnecessary, it may be most cost-effective to pre-screen samples by MAPH or MLPA before screening for point mutations.

Adaptor Proteins, Signal Transducing↗
PubMed1990

Insulin-resistant diabetes associated with partial deletion of insulin-receptor gene.

The insulin-receptor genes from a 16-year-old girl with type A insulin resistance, who presented with fasting hyperinsulinaemia, acanthosis nigricans, and reduced insulin binding, and from her family were examined. One allele of her insulin-receptor gene inherited from her mother contained a 1.2 kb deletion arising from a recombination between two Alu elements. The deletion removed the 14th exon in the beta subunit and altered the reading frame, to produce a stop codon after aminoacid 867. Pedigree analysis indicated that this mutation alone will not cause diabetes, and the proband is possibly a compound heterozygote. 4 other members of her family were heterozygous for the same mutation; all 4 had a decrease in insulin binding and slight impairment of glucose tolerance. Perhaps the same mutation is an underlying feature of some cases of non-insulin-dependent diabetes mellitus.

Adolescent↗
PubMed1993

Conservative evolution of the Mbc-DP region in anthropoid primates.

To determine the organization of the DP region in the Mbc of anthropoid primates, we constructed contig maps from cosmid clones of the chimpanzee and orangutan, representatives of the infraorder Catarrhini, as well as of the cotton-top tamarin, a representative of the infraorder Platyrrhini. We found the maps to be remarkably similar to each other and to the previously published map of the human DP region. In each of the four species, the DP region consists of four loci arranged in the same order (DPB2 . . . DPA2 . . . DPB1 . . . DPA1) and in the same transcriptional orientation (tail-to-tail). The regions in the four species are of approximately the same length and many of the restriction sites are shared between species. The inserts of most Alu elements, of a ribosomal protein pseudogene, and of an IgC epsilon-like pseudogene are found in corresponding positions in all four species. The data indicate that the human-type organization of the DP region was established before the divergence of the Catarrhini and Platyrrhini lines more than 37 million years ago and that it has remained principally intact since that time. This conservation of the DP region is in striking contrast to the evolutionary instability of certain other Mbc regions, in particular those occupied by the DRB or C4 and CYP21 loci. We interpret the stability of the DP region as an indication that the region is being phased out functionally.

Animals↗
PubMed1989

Human ribosomal DNA: novel sequence organization in a 4.5-kb region upstream from the promoter.

We have investigated the molecular organization of a portion of the human ribosomal nontranscribed spacer, by determining the sequence of 4580 bp of DNA upstream from the promoter. This region contains two pairs of oppositely oriented Alu elements, each of which is separated by dA (or dT)-rich stretches. One dT-rich region extends over 800 bp and is of variable length in different ribosomal genes. This and other portions of the spacer consist of simple sequences reiterated many times: for instance, (TACAA)26, (TTTC)117, and (TTGC)47. We are able to position the distal junction of the ribosomal repeat and sequences that have the propensity to form alternate structures, such as Z-DNA and bent DNA. A complex DNA methylation pattern and the influence on transcription of analogous regions in other species, suggest that this upstream area may be important to the expression of the human gene.

Base Composition↗
PubMed1990

Organization and sequence of the human gene encoding cytokeratin 8.

Among the various intermediate filament (IF) proteins, cytokeratin 8 (CK8) is especially remarkable as it is produced early in embryogenesis, is the only type-II CK occurring in many simple epithelial cells, and can also be synthesized in certain non-epithelial cells. Using a cDNA probe specific for human CK8 we have isolated an approx. 14-kb genomic clone (in phage lambda EMBL3) which contains the gene encoding human CK8. The gene comprising a total of 7766 nucleotides (nt) from the transcription start point, determined by primer extension analysis, to the polyadenylation site, determined from cDNA sequencing, and a 1030-nt 5' upstream region have been sequenced. The sequence of 485 amino acids (aa) deduced from the exon sequences (Mr 53,532) shows strong homology with the corresponding gene products of bovine, murine and amphibian (Xenopus laevis) origins. Surprisingly, the ck8 gene contains only seven introns instead of eight as found in all other genes of the same (type-II) CK subfamily; while all seven introns occur in identical positions as in the other type-II CK-encoding genes, intron V of these genes is missing in the ck8 gene. Intron I of ck8 is remarkably long (2534 nt) and contains a cluster of potential regulatory sequences, including three Sp1 sites, and an extended Alu-element. In Southern-blot analyses, we found only one intron-containing gene encoding CK8 in the human genome, and by heterologous transfection experiments we showed that this gene is correctly transcribed in non-human cells expressing the orthologous gene.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1993

Analysis of a viral integration event in a CG-rich region at the 1p36 human chromosomal site.

The preinsertion site of an adenovirus-5/simian virus 40 recombinant construct (Ad5/SV40) has been cloned and sequenced. Our data suggest that viral integration has occurred in a genomic region which has been the target of multiple events of Alu element retropositions within a TAA minisatellite. Extensive homologies between the left viral end and the host cellular DNA were also observed. The compositional similarity between Adenoviridae and the region of viral integration is consistent with the observed insertion of exogenous DNA in isochores of similar composition [G. Bernardi, Annu. Rev. Genet. 23 (1989) 637-661].

Base Sequence↗
PubMed1992

Survey of human and rat microsatellites.

Length variations in simple sequence tandem repeats (microsatellite DNA polymorphisms) are finding increasing usage in mammalian genetics. Although every variety of short tandem repeat that has been tested has been shown to exhibit length polymorphisms, little information on the relative abundance of the different repeat motifs has been collected. In this report, summaries of GenBank searches for all possible human and rat microsatellites ranging from mononucleotide to tetranucleotide repeats are presented. In humans, the five most abundant microsatellites with total lengths for the runs of repeats of greater than or equal to 20 nucleotides contained repeat sequences of A, AC, AAAN, AAN, and AG, in order of decreasing abundance, where N is C, G, or T. These five groups comprised about 76% of all microsatellites. Many other human simple sequence repeats were found at low frequency. In the 745 kb of human genomic DNA surveyed, one microsatellite of greater than or equal to 20 nucleotides in length was found, on average, every 6 kb. Only 12% of the human microsatellites had total lengths greater than or equal to 40 nucleotides. Roughly 80% of the A, AAN, and AAAN microsatellites and 50% of the AT microsatellites, but few of the other human microsatellites, were found to be associated with interspersed, repetitive Alu elements. In rats, the five most abundant microsatellites contained AC, AG, A, AAAN, and AAGG sequences, respectively. Rat microsatellites were generally longer than human microsatellites, with 43% of the rat sequences greater than or equal to 40 nucleotides.

Animals↗
PubMed2005

Identification of differentially expressed genes in primary varicose veins.

BACKGROUND: A number of changes in protein expression have been described in primary varicose veins, but the altered gene expressions in this disease are unknown. The aim of this study was to identify differentially expressed genes in primary varicose veins. MATERIALS AND METHODS: Total RNAs were isolated from two groups of greater saphenous veins (four primary varicose veins and three normal) and then were reverse transcribed into cDNAs. We used the differential display reverse transcription-polymerase chain reaction technique to screen the differences in the mRNA expression profiles of the groups. RESULTS: We found that three cDNAs showed differences in expression patterns between normal and diseased saphenous veins. The cDNAs are prominently expressed only in patients with varicose veins. We identified that the cDNAs had significant similarities to the L1M4 repeat sequence of clone RP11-57L9, clone RP11-299H13, and Alu repetitive sequence of human tropomyosin 4 mRNA. CONCLUSIONS: Our results suggest that the screened cDNA clones are useful disease markers in the genetic diagnosis of primary varicose vein and that the L1 and Alu elements possibly participated in the development of primary varicose veins through their expression patterns in genes encoded with structural proteins, such as collagen, elastin, and tropomyosin. Further studies are required to elucidate the potential relationship between repeat sequences and primary varicose veins.

Collagen↗
PubMed2006

DNA methylation and targeting of LINE retrotransposons in Entamoeba histolytica and Entamoeba invadens.

In this study, we have isolated by affinity chromatography, using anti-m5C antibody as a ligand, a DNA encoding reverse transcriptase of LINE retrotransposon (RT LINE) in both Entamoeba invadens and Entamoeba histolytica. RT LINE transcripts were detected in E. histolytica but were absent from E. invadens. The methylation status of genomic copies of E. invadens RT LINE was confirmed by bisulfite analysis. In contrast, all the genomic copies of the E. histolytica RT LINE analyzed in this study were not methylated. Many of these genomic copies diverge from the RT LINE isolated by m5C affinity chromatography by a number of mutations that includes conversion of C to T and G to A. These mutations are reminiscent of the conversion of C to T (and G to A on the complementary DNA strand) that occurred during primate evolution in Alu elements following accelerated deamination of methylated cytosines. E. invadens and E. histolytica RT LINEs isolated by affinity chromatography were cloned in a pEhAct Neo vector, amplified in E. coli GM2163 (dam-dcm) and transformed into E. histolytica. Bisulfite analysis of transfected amoeba showed the presence of m5C in E. invadens RT LINE replicated in E. histolytica, but not in E. histolytica RT LINE or in the neomycine phosphotransferase gene, which is also carried by the pEhAct Neo vector. These results suggest the existence of a specific mechanism based on DNA methylation that controls retrotransposons in these parasites.

Animals↗
PubMed2004

A newly identified chromosomal microdeletion of the rapsyn gene causes a congenital myasthenic syndrome.

The objective is mutation analysis of the RAPSN gene in a patient with sporadic congenital myasthenic syndrome (CMS). Mutations in various genes encoding proteins expressed at the neuromuscular junction may cause CMS. Most mutations affect the epsilon subunit gene of the acetylcholine receptor (AChR) leading to endplate AChR deficiency. Recently, mutations in the RAPSN gene have been identified in several CMS patients with AChR deficiency. In most patients, RAPSN N88K was identified, either homozygously or heteroallelic to a second missense mutation. A sporadic CMS patient from Germany was analyzed for RAPSN mutations by RFLP, long-range PCR and sequence analysis. Clinically, the patient presents with an early onset CMS, associated with arthrogryposis multiplex congenita, recurrent episodes of respiratory insufficiency provoked by infections, and a moderate general weakness, responsive to anticholinesterase treatment. The mutation RAPSN N88K was found heterozygously to a large deletion of about 4.5 kb disrupting the RAPSN gene. Interestingly, an Alu-mediated unequal homologous recombination may have caused the deletion. We hypothesize that numerous interspersed Alu elements may predispose the RAPSN locus for genetic rearrangements.

Child, Preschool↗
PubMed2004

Crystal structure of the targeting endonuclease of the human LINE-1 retrotransposon.

The human L1 endonuclease (L1-EN) is encoded by the non-LTR retrotransposon LINE-1 (L1). L1 is responsible for more than 1.5 million retrotransposition events in the history of the human genome, contributing more than a quarter to human genomic DNA (L1 and Alu elements). L1-EN is related to the well-understood human DNA repair endonuclease APE1, and its nicking specificity is a major determinant for retrotransposon integration site selection. The crystal structure of human L1 endonuclease is the first of a retrotransposon-encoded protein and a prototype for retrotransposon-encoded endonucleases involved in target-primed reverse transcription. Structure-based endonuclease alignments reveal a conserved threonine in addition to previously identified invariant residues and suggest that DNA recognition proceeds via the accommodation of an extrahelical nucleotide within a pocket of the enzyme. The present analysis will help to refine phylogenetic and functional relationships among metal-dependent phosphohydrolases and provides a basis for manipulating non-LTR retrotransposon integration site selection.

Amino Acid Sequence↗