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PubMed1992

Isolation of telomere junction fragments by anchored polymerase chain reaction.

We describe a simple polymerase chain reaction (PGR)-based method for isolating short stretches of nontelomeric DNA adjacent to arrays of telomere repeat units, in principle applicable to any species for which the telomere repeat sequence is known. Application of this approach to human DNA resulted in the isolation of many candidate telomere junction clones, at least some of which were shown to be derived from telomere-adjacent regions. Most of the isolated clones detect multiple sequences in the human genome which represent one or a few sequence families present at the ends of most or all autosomes and variably truncated before the start of the telomere repeat array. Substantial sequence divergence between different members of these sequence families suggests a low rate of sequence homogenization by telomere exchange processes. The pseudoautosomal telomere junction has also been isolated and contains a shortened version of a recently described family of short interspersed repetitive elements (SINEs), only 14 base pairs (b.p.) from the start of the telomere.

Base Sequence↗
PubMed1981

Repeated DNA sequences near the 5'-end of the silk fibroin gene.

Four different repeated sequence elements have been found in cloned silk moth DNA, extending from 5700 base pairs upstream from the silk fibroin gene to 600 base pairs within its intervening sequence. Only 2 of the 12 overlapping restriction fragments examined, ranging from 164 to 1800 base pairs in length, do not contain a repeated sequence. The 830 base pairs adjoining the 5'-end of the fibroin gene hybridize with only one sequence in the Bombyx mori genome. Fibroin gene transcription initiates within this single-copy DNA at least 500 base pairs downstream from any repeated DNA sequence. The data show that repeated sequences comprise a major portion of the DNA flanking this developmentally regulated gene but not the DNA immediately 5' to it; that an intervening sequence can contain a repeated element; and that repeated sequences can be interspersed with one another as well as with single-copy DNA in a typical animal genome. In addition, filter transfer hybridization can be used to quantitate repetition frequency and sequence divergence and to distinguish patterns of repeated sequence organization.

Animals↗
PubMed1995

Cloning and characterization of the majority of repetitive DNA in cotton (Gossypium L.).

Repetitive DNA elements representing 60-70% of the total repetitive DNA in tetraploid cotton (Gossypium barbadense L.) and comprising 30-36% of the tetraploid cotton genome were isolated from a genomic library of DNA digested with a mixture of four blunt-end cutting restriction enzymes. A total of 313 clones putatively containing nuclear repetitive sequences were classified into 1103 families, based on cross hybridization and Southern blot analysis. The 103 families were characterized in terms of genome organization, methylation pattern, abundance, and DNA variation. As in many other eukaryotic genomes, interspersed repetitive elements are the most abundant class of repetitive DNA in the cotton genome. Paucity of tandem repeat families with high copy numbers (>10(4)) may be a unique feature of the cotton genome as compared with other higher plant genomes. Interspersed repeats tend to be methylated, while tandem repeats seem to be largely unmethylated in the cotton genome. Minimal variation in repertoire and overall copy number of repetitive DNA elements among different tetraploid cotton species is consistent with the hypothesis of a relatively recent origin of tetraploid cottons.

Base Sequence↗
PubMed2006

Evidence of influence of genomic DNA sequence on human X chromosome inactivation.

A significant number of human X-linked genes escape X chromosome inactivation and are thus expressed from both the active and inactive X chromosomes. The basis for escape from inactivation and the potential role of the X chromosome primary DNA sequence in determining a gene's X inactivation status is unclear. Using a combination of the X chromosome sequence and a comprehensive X inactivation profile of more than 600 genes, two independent yet complementary approaches were used to systematically investigate the relationship between X inactivation and DNA sequence features. First, statistical analyses revealed that a number of repeat features, including long interspersed nuclear element (LINE) and mammalian-wide interspersed repeat repetitive elements, are significantly enriched in regions surrounding transcription start sites of genes that are subject to inactivation, while Alu repetitive elements and short motifs containing ACG/CGT are significantly enriched in those that escape inactivation. Second, linear support vector machine classifiers constructed using primary DNA sequence features were used to correctly predict the X inactivation status for >80% of all X-linked genes. We further identified a small set of features that are important for accurate classification, among which LINE-1 and LINE-2 content show the greatest individual discriminatory power. Finally, as few as 12 features can be used for accurate support vector machine classification. Taken together, these results suggest that features of the underlying primary DNA sequence of the human X chromosome may influence the spreading and/or maintenance of X inactivation.

Base Sequence↗
PubMed1988

Discontinuous transcription in Leptomonas seymouri: presence of intact and interrupted mini-exon gene families.

Mature mRNAs of trypanosomatid protozoa result from the joining of at least two exons, which are initially transcribed as separate RNAs. In all trypanosomatids examined to date, the first exon (mini-exon) is encoded by approximately 200 tandemly reiterated genes. In characterizing the mini-exon genes of Leptomonas seymouri, we identified two predominant size classes of repetitive sequences that hybridized strongly to the L. seymouri mini-exon sequence. These two sequences are arranged as interspersed clusters. DNA sequence analysis of a clone representing the smaller size class demonstrated that these sequences have the capacity to encode a mini-exon donor (med)RNA corresponding to the 86 nt component seen in Northern blots of L. seymouri RNA. The larger size class comprises a family of related sequences, some of which contain DNA inserted into the mini-exon portion of the medRNA gene. The specific insert identified here (LINS 1) is exclusively associated with medRNA sequences, and is present in approximately 20% of the larger size class of L. seymouri medRNA genes. Disregarding the insertion, the sequences of the smaller bona fide mini-exon genes and the gene copy containing the insert were almost identical. The insert sequence is transcribed in the same direction as medRNA to yield at least four small non-polyadenylated RNAs, which appeared not to be linked to medRNA sequences.

Animals↗
PubMed2001

Preattentive voice discrimination by the human brain as indexed by the mismatch negativity.

The goal of the present study was to determine whether the mismatch negativity (MMN), a component of the auditory event-related potential (ERPs) indexing perceptual difference between any two sounds, could be used as an objective measure of speaker discriminability and similarity/dissimilarity. ERPs were recorded in response to natural speech sounds from subjects watching a silent video. The stimuli consisted of a sequence of repetitive 'standard' sounds (the vowel /e/ pronounced by a female voice), which was infrequently interspersed with 'deviant' stimuli; the same /e/vowel pronounced by different speakers (one male and three females). Voice intensity and duration were matched between all the voices used. A separate behavioural discrimination task measured the perceptual distance of each deviant voice from the standard voice through pair-wise dissimilarity ratings. The MMN was elicited by all deviant voices. Furthermore, the dissimilarity ratings on the behavioural task paralleled the preattentive discrimination as indexed by the MMN amplitude. These results suggest that the MMN could be used as an objective measure of voice similarity/dissimilarity, and thus could serve objective speaker recognition.

Acoustic Stimulation↗
PubMed1999

A complex population of RNAs exists in human ejaculate spermatozoa: implications for understanding molecular aspects of spermiogenesis.

The presence of mRNAs in human ejaculate spermatozoa is well established, yet little is known of the representation or function of these transcripts. To address these issues, the complexity of spermatozoal RNA was examined. As expected, testis-expressed mRNAs were detected by RT-PCR in mature human spermatozoa. Interestingly, when a testis cDNA library was probed with total spermatozoal RNA, less than 2% of plaques gave a strong hybridization signal, suggesting a rather unique sperm-derived population. To further define the sequence distribution, 18 strongly hybridizing clones were selected at random for end-sequence analysis. Twelve matched unique sequences in the EST, STS and NR databases, whereas five showed no similarity to any of the sequences in the databases. In addition, one clone belonged to the SINE repetitive element family. As demonstrated by sequencing randomly primed cloned inserts, short (SINE/MER) or long (LINE/ORF2) interspersed repeat-like sequences are also contained as part of the spermatozoal RNA fraction. It is now evident that human spermatozoa contain a rich repertoire of both known and unknown protein-encoding and non-coding RNAs. This provides a unique opportunity to identify and investigate the many genes responsible for the structure and function/dysfunction of the male gamete using spermatozoal RNA as the template.

Amino Acid Sequence↗
PubMed1988

The Drosophila mobile element jockey belongs to LINEs and contains coding sequences homologous to some retroviral proteins.

A detailed investigation of the Drosophila melanogaster mobile dispersed repetitive element jockey was performed. This is similar in its structural organization and coding potential to the long interspersed elements (LINEs) of various organisms. A complete copy of jockey (approx. 5 kb) is terminated with an oligodeoxynucleotide (dA) sequence preceded by two long open reading frames (ORFs) overlapping with a frameshift-1. Judging by the sequence homologies, ORF1 codes for a nucleic-acid-binding protein, and ORF2 for a reverse transcriptase which is most similar in its sequence to putative reverse transcriptase of other LINEs. As demonstrated by sequencing two deleted jockey copies, they contain only a small part of ORF2; however, other regions, including the terminal sequences, are highly conservative. The existence of a large number of jockey copies with a deletion in the second frame may indicate that they can use reverse transcriptase in trans.

Amino Acid Sequence↗
PubMed1990

Characterization of a tandemly repeated DNA from the fleshfly Sarcophaga bullata.

In studies on the highly repetitive DNA sequences of the flesh fly Sarcophaga bullata, a 279 bp tandem repeat was cloned and sequenced. A 17 bp stretch within the clone was identical to a motif repeated five times in the satellite DNA of the Bermuda land crab. Southern DNA blotting showed the tandem repeat had a high degree of conservation of MboI sites, but had divergence for EcoRI sites; thus, all repeat units were not identical. The cloned DNA localized to the quinacrine-bright centromeric heterochromatin of the C and E autosomes and to sites on the chromosomal arms. In cases of asynapsis of homologs, the probe localized to euchromatic sites on both homologs or sometimes only on one homolog. The probe also localized near, to, or at a major developmental puff (B9). We conclude that blocks of this short interspersed repetitive DNA occur throughout the Sarcophaga genome in both heterochromatin and euchromatin, and also that the variable position of these sequences suggests they possess a degree of instability.

Animals↗
PubMed2005

Heterogeneous duplications in patients with Pelizaeus-Merzbacher disease suggest a mechanism of coupled homologous and nonhomologous recombination.

We describe genomic structures of 59 X-chromosome segmental duplications that include the proteolipid protein 1 gene (PLP1) in patients with Pelizaeus-Merzbacher disease. We provide the first report of 13 junction sequences, which gives insight into underlying mechanisms. Although proximal breakpoints were highly variable, distal breakpoints tended to cluster around low-copy repeats (LCRs) (50% of distal breakpoints), and each duplication event appeared to be unique (100 kb to 4.6 Mb in size). Sequence analysis of the junctions revealed no large homologous regions between proximal and distal breakpoints. Most junctions had microhomology of 1-6 bases, and one had a 2-base insertion. Boundaries between single-copy and duplicated DNA were identical to the reference genomic sequence in all patients investigated. Taken together, these data suggest that the tandem duplications are formed by a coupled homologous and nonhomologous recombination mechanism. We suggest repair of a double-stranded break (DSB) by one-sided homologous strand invasion of a sister chromatid, followed by DNA synthesis and nonhomologous end joining with the other end of the break. This is in contrast to other genomic disorders that have recurrent rearrangements formed by nonallelic homologous recombination between LCRs. Interspersed repetitive elements (Alu elements, long interspersed nuclear elements, and long terminal repeats) were found at 18 of the 26 breakpoint sequences studied. No specific motif that may predispose to DSBs was revealed, but single or alternating tracts of purines and pyrimidines that may cause secondary structures were common. Analysis of the 2-Mb region susceptible to duplications identified proximal-specific repeats and distal LCRs in addition to the previously reported ones, suggesting that the unique genomic architecture may have a role in nonrecurrent rearrangements by promoting instability.

Base Sequence↗
PubMed1977

Purification and characterization of two transcribed repetitive DNA fractions from the pigeon genome.

Two fractions of the repeats belonging to intermediate frequency repetitive DNA were isolated from the total pigeon nuclear DNA fragmented to about 450 nucleotides. One fraction was designated as "rare repeats" (repetition frequency about 35 per haploid genome) and another termed as "moderate repeats" (repetition frequency about 2500 per haploid genome). The rare repeats, which constitute about 7% of the total DNA, include at least 75% of the repetitive DNA sequences transcribed into the high molecular fraction (greater than 45S) of HnRNA in erythroid cells. These repeats have properties compatible with the characteristics of the class of low frequency interspersed DNA found in genomes of many other Metazoan species. The moderate repeats contribute only about 10-20% of the total repetitive DNA copies present in greater than 45S HnRNA and differ from the rare repeats in some other properties.--The possible role of the rare repeats in the genome is discussed.

Animals↗
PubMedDate not supplied

Methylation patterns of long interspersed repeated DNA and alphoid repetitive DNA from human cell lines and tumors.

The methylation status of CCGG sites has been determined in long interspersed repeated (L1Hs sequences) DNA and in alphoid satellite DNA extracted from human cell lines and also from pathological specimens. Southern blot experiments were performed using a cloned 1.2 kb KpnI fragment of L1Hs DNA and a cloned 680 bp tetrameric unit of alphoid satellite. DNA as probes for these sequences. In vitro transformation of human lymphocytes by Esptein-Barr virus is correlated with a progressive hypomethylation of L1 Hs DNA sequences. This loss of modification of L1 sequences is also observed in DNA isolated directly from colon adenocarcinoma and in chronic lymphocytic leukemia. Therefore, alteration of the level of methylation of L1 sequences seems not to be due solely to in vitro cultivation of human cells but is associated with the immortalization of these cells. In addition, these sequences are preferentially hypomethylated when compared to alpha-satellite DNA in several lymphoblastoid cell lines and pathological specimens.

Cell Line↗
PubMed1986

Organization and chromosomal distribution of a novel repetitive DNA component from Muntiacus muntjak vaginalis with a repeat length of more than 40 kb.

The organization and chromosomal distribution of the repetitive DNA component IB from Muntiacus muntjak vaginalis (MMV) was investigated. DNA fragments of component IB were cloned in cosmids and their structure analysed using restriction nucleases and blot-hybridization experiments. Two cosmids were found to be practically identical by restriction enzyme mapping. The repeat unit of component IB DNA is more than 40 kb and contains the 11 and 18 kb Bam HI fragments, which have previously been shown to cross-hybridize with MMV satellite IA. In addition, the repeat unit contains long stretches of DNA sequences which are unique to component IB. In situ hybridization experiments showed that component IB has the properties characteristic of long interspersed repetitive DNA rather than tandemly repeated satellite DNA. Consistent with this conclusion, only a minor fraction of component IB is located on the X chromosome as demonstrated by the analysis of somatic cell hybrids. This is in marked contrast to satellite IA that is specific for the X chromosome. These results have interesting implications for the evolution of the component I DNA family of the MMV genome.

Animals↗
PubMed2002

Gamera, a family of LINE-like repetitive sequences widely distributed in medaka and related fishes.

A family of repetitive sequences, designated Gamera, has been identified in the genome of the Hainan medaka fish Oryzias curvinotus, a closely related species to the common medaka fish O. latipes. Sequencing and Southern blot analyses of this family revealed: (1) amino acid sequence similarity to reverse transcriptase domains of long interspersed nuclear elements (LINEs); (2) 5' truncation of dispersed copies; and (3) the disruption of another genetic element, indicating a past transposition event. These results suggest that Gamera belongs to the LINE superfamily. Gamera is widely distributed in the genus Oryzias, and the phylogenetic relationship might indicate its presence in the common ancestor of the genus.

Amino Acid Sequence↗
PubMed1985

Complete nucleotide sequence of mRNA for caerulein precursor from Xenopus skin: the mRNA contains an unusual repetitive structure.

The complete nucleotide sequence of mRNA for caerulein precursor in the skin of Xenopus laevis was determined. The sequence was composed of 705 bp of coding region, accounting for 234 amino acids, 58 bp of 5'-untranslated region and 158 bp of 3'-untranslated region containing two putative poly(A) signals. It coded for four caerulein peptides interspersed with three 147 bp segments (intercaerulein segment; ICS). Analyses of several caerulein encoding cDNAs revealed some interesting features of caerulein mRNA species, which were highly heterogeneous and consisted of a repetition of two fundamental RNA sequences, a 45-nucleotide caerulein fragment and a 147-nucleotide ICS. The result of Northern blotting indicated that caerulein mRNA was only present in frog skin, not in stomach, upper intestine or liver. It appears that caerulein has different physiological function(s) from mammalian gastrin and cholecystokinin-pancreozymin (CCK). The relationship of caerulein to mammalian gastrointestinal hormones is discussed.

Amino Acid Sequence↗
PubMed2000

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↗
PubMed1999

Analysis of major repetitive DNA sequences in the dog (Canis familiaris) genome.

A systematic screening and analysis of repeated DNA sequences from a dog genomic library composed of small DNA inserts enabled us to characterize abundant canine repetitive DNA families. Four main families were identified: i) a group of highly repeated tRNA-derived short interspersed repetitive DNA elements (tRNA-SINEs); ii) another type of SINE-like element that was mainly found inserted into long interspersed repetitive elements (LINEs); iii) LINEs of the L1 type; and iv) satellite or satellite-like DNA. Surprisingly, no SINEs derived from 7SL RNA were found in the dog genome. These data should help in the analysis of canine DNA sequences and in the design of canine genome mapping reagents.

Animals↗