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Results for “Interspersed Repetitive Sequences”

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PubMed2006

Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats.

A unique feature of late-flowering fwa epigenetic mutations is that the phenotype is caused by ectopic expression of the homeobox gene FWA. During normal development the FWA gene is expressed specifically in the endosperm in an imprinted manner. Ectopic FWA expression and disruption of imprinting can be induced in mutants of a CG methyltransferase MET1 (methyltransferase 1) or a chromatin-remodeling gene DDM1 (decrease in DNA methylation 1), suggesting that the proper FWA expression depends on cytosine methylation. However, critical methylated residues controlling FWA silencing are not pinpointed. Nor is it understood how the FWA gene is initially methylated and silenced in wild-type plants. Here we mapped sequences critical for FWA silencing by application of RdDM (RNA-directed DNA methylation) to a ddm1-induced stable fwa epiallele. Transcription of double-stranded RNA corresponding to the tandem direct repeats around the FWA transcription start site induced de novo DNA methylation, transcriptional suppression and phenotypic reversion. The induced changes were heritable even without the transgene, which correlates with inheritance of CG methylation in the direct repeats. The newly silenced FWA allele was transcribed in an endosperm-specific and imprinted manner, as is the case for the wild-type FWA gene. The results indicate that methylation of the direct repeats, which presumably originated from a short interspersed nuclear element (SINE), is sufficient to induce proper epigenetic control of the FWA gene.

Arabidopsis↗

PubMed1984

Methylation of a middle repetitive DNA sequence class during differentiation in Friend erythroleukemia cells.

We have examined the methylation patterns within middle repetitive sequences in Friend erythroleukemia cells. Mouse-interspersed-family-1 (MIF-1) and a group characterized by a 1350-bp Eco-Bam fragment cloned into pBR322 as plasmid pFS-13, are both less modified in Friend cell DNA than in normal tissue DNA. The pattern of methylation present in pFS-13 homologous sequences was found to be stable during cell division, i.e., somatically inherited, and stable during differentiation induced by HMBA.

Acetamides↗

PubMedDate not supplied

Low-frequency velocity correlation spectrum of fluid in a porous media by modulated gradient spin echo.

In addition to the fast correlation for local stochastic motion, the molecular velocity correlation function in a fluid enclosed within the pore boundaries features a slow long time-tail decay. Here we present its study by the NMR modulated gradient spin-echo method (MGSE) [1] on a system of water trapped in the space between the closely packed polystyrene beads. With MGSE pulse sequence, a repetitive train of RF pulses with interspersed gradient pulses periodically modulates the spin phase. It gives the spin echo attenuation proportional to a value of the molecular velocity correlation spectrum at the modulation frequency. Covering the frequency range between Hz and MHz, it is a complement to the quasi-elastic neutron scattering, and so a suitable technique for the investigation of low frequency molecular dynamics in fluids. In our experiment, it enables to extract the low frequency correlation spectrum of water molecules confined in porous media. The function exhibits a negative long time-tail characteristic (a low frequency decay of the spectrum), which can be interpreted as a molecular back scattering on boundaries. The results can be well fitted with the spectrum calculated from the solution of the Langevin equation for restricted diffusion (which exhibits an exponential decay) [2] as well as with the spectrum obtained when simulating the hydrodynamics of molecular motion constrained by capillary walls (which gives an algebraic decay) [3]. Despite much work on theories and simulation, which predict slow negative long time tail of molecular velocity correlation dynamics in confined fluids, the obtained velocity correlation spectrum is the first experimental evidence to confirm these effects. The obtained dependence of spin echo attenuation on time, gradient strength and modulation frequency is also the first experimental verification of the recently developed approach to the spin echo in porous media, that uses the spin phase average with the cumulant expansion to get the attenuation as a discord of spin spatial coherence [4].

Magnetic Resonance Spectroscopy↗

PubMed1992

Characterisation of a boundary between satellite III and alphoid sequences on human chromosome 10.

Alphoid and satellite III sequences are arranged as large tandem arrays in the centromeric regions of human chromosomes. Several recent studies using in situ hybridisation to investigate the relative positions of these sequences have shown that they occupy adjacent but non-overlapping domains in metaphase chromosomes. We have analysed the DNA sequence at the junction between alphoid and satellite III sequences in a cosmid previously mapped to chromosome 10. The alphoid sequence consists of tandemly arranged dimers which are distinct from the known chromosome 10-specific alphoid family. Polymerase chain reaction experiments confirm the integrity of the sequence data. These results, together with pulsed field gel electrophoresis data place the boundary between alphoid and satellite III sequences in the mapping interval 10 centromere-10q11.2. The sequence data shows that these repetitive sequences are separated by a partial L1 interspersed repeat sequence less than 500bp in length. The arrangement of the junction suggests that a recombination event has brought these sequences into close proximity.

Base Sequence↗

PubMed2000

Sequence, structure, and evolution of a complete human olfactory receptor gene cluster.

The olfactory receptor (OR) gene cluster on human chromosome 17p13.3 was subjected to mixed shotgun automated DNA sequencing. The resulting 412 kb of genomic sequence include 17 OR coding regions, 6 of which are pseudogenes. Six of the coding regions were discovered only upon genomic sequencing, while the others were previously reported as partial sequences. A comparison of DNA sequences in the vicinity of the OR coding regions revealed a common gene structure with an intronless coding region and at least one upstream noncoding exon. Potential gene control regions including specific pyrimidine:purine tracts and Olf-1 sites have been identified. One of the pseudogenes apparently has evolved into a CpG island. Four extensive CpG islands can be discerned within the cluster, not coupled to specific OR genes. The cluster is flanked at its telomeric end by an unidentified open reading frame (C17orf2) with no significant similarity to any known protein. A high proportion of the cluster sequence (about 60%) belongs to various families of interspersed repetitive elements, with a clear predominance of LINE repeats. The OR genes in the cluster belong to two families and seven subfamilies, which show a relatively high degree of intermixing along the cluster, in seemingly random orientations. This genomic organization may be best accounted for by a complex series of evolutionary events.

Base Sequence↗

PubMedDate not supplied

[Genome of the pogonophore Siboglinum fiordicum: organizational characteristics and divergence with respect to the genomes of representatives of certain types of invertebrates].

DNA of Pogonophora Siboglinum fiordicum was studied. DNA was isolated from ethanol fixed animals. It contains 40.5% GC according to the melting temperature and 39.3% GC as estimated by cation-exchange chromatography. From the reassociation kinetic data with a [125I] tracer 400 nucleotide long it is clear that 70% of the genome consists of repetitive sequences. The fast component (C0t less than 0.04) constitutes 11% of the genome, the intermediate (C0t 1/2 = 1.5, repetition frequency 1600)--59%. The unique sequences comprise about 30% of the genome. Experiments where [125I]tracers of increasing length were reassociated with driver DNA fragments 300 nucleotides long point out that at least 80% of the genome contains repetitive sequences, part of them being organized in short-period interspersion patterns. The hybridization of Pogonophora [125I]DNA fragments with DNA of invertebrates of other types--Echinodermata, Ascidia, Mollusca, Annelida--did not show any measurable homology between their DNAs neither in repetitive, nor in the unique fraction.

Animals↗

PubMed1994

DNA class organization on maize Adh1 yeast artificial chromosomes.

The organization of higher plant genomes is poorly understood. These genomes are typified by their large size and extensive repetitive DNA component. To further our understanding of the composition and arrangement of genomic DNA sequences, we have performed a detailed analysis of a contiguous interval of 280 kb surrounding the Adh1 locus of maize. A series of overlapping lambda subclones was isolated, and individual fragments were characterized with respect to their genomic copy number. Cross-hybridization analyses were used to define a minimum of 37 repetitive DNA classes within the 280-kb interval. Hybridizations with highly repetitive DNAs cloned from other regions of the maize genome suggested that > 50% of all highly repetitive elements in maize are represented on this single yeast artificial chromosome. These repeated sequences were found in an organizational pattern not previously observed; individual repetitive elements are interspersed with one another in an apparently random fashion and are spatially separate from single copy number sequences. Extensive tandem arrays were not found. Sequences from one end of the 280-kb interval were used to isolate overlapping yeast artificial chromosome clones, representing the first step in a chromosome walk.

Alcohol Dehydrogenase↗

PubMed1994

Molecular characterization and clinical use of a polymorphic tandem repeat in an intron of the human alanine:glyoxylate aminotransferase gene.

The autosomal recessive disease primary hyperoxaluria type 1 (PH1) is caused by a deficiency of the liver-specific peroxisomal enzyme alanine:glyoxylate amino-transferase (AGT). This paper concerns the identification, characterization and clinical use of an unusual discretely polymorphic tandem repeat sequence in the fourth intron of the human AGT gene (gene locus designation AGXT). In a random Caucasian population, three alleles could be clearly recognized that consisted of either 12 (type III), 17 (type II) or approximately 38 (type I) tandemly repeated copies of a highly conserved 29/32-bp sequence with frequencies of 33%, 7% and 60%, respectively. In a random Japanese population, the allelic frequencies were markedly different (i.e. 31%, 45% and 19%, respectively). In addition, a fourth allele was identified, consisting of approximately 32 repeats (type IV), with an allelic frequency of approximately 5% in Japanese. The repetitive sequence was similar to previously identified mammalian sequences with homology to the Epstein-Barr virus IR3 repetitive element involving a 12/15-bp region GCA(GGN)GGAGGAGGG within the repeat unit. This IR3-like sequence was interspersed with a 17-bp sequence with no similarity to any currently known repetitive element. The type I and type III alleles were judged to be equivalent to a previously identified TaqI polymorphism. Two polymorphisms previously shown to be associated with the peroxisome-to-mitochondrion mistargeting of AGT in PH1 (a C154-->T point substitution in exon 1 and a 74-bp duplication in intron 1) were found to segregate exclusively with the type I intron 4 polymorphism in Caucasians, but not in Japanese. The polymorphic nature of the intron 4 tandem repeats makes them of potential use in the prenatal diagnosis of PH1, especially when coupled with the exon 1 C154-->T substitution or intron 1 duplication polymorphisms. A PH1 family, in which a fetus had been predicted previously to be either normal or a carrier by AGT enzymic analysis of a fetal liver biopsy, but who had been shown to be only partially informative with respect to the C154-->T/intron 1 polymorphisms, was analysed retrospectively. The family was completely informative for the intron 4 tandem repeat polymorphism and the carrier status of the fetus was confirmed.

Alanine Transaminase↗

PubMed1987

Repeated immunogenic amino acid sequences of Plasmodium species share sequence homologies with proteins from humans and human viruses.

The use of recombinant peptides based upon the repeated amino acid sequences of Plasmodium has been proposed for malaria vaccines. By reducing homologies of such peptide vaccines to host proteins, the possibility of autoimmune complications may be reduced, and the effective immune response may be enhanced. The Wilbur and Lipman Wordsearch algorithm was used to identify homologous amino acid sequences between tandemly repeated Plasmodium amino acid sequences and the human and human viral sequences compiled in the National Biomedical Research Foundation database. Six published repetitive immunogenic amino acid sequences from the circumsporozoite (CS) antigen, ring-infected erythrocyte surface antigen (RESA), soluble (S) antigen, and falciparum interspersed repetitive antigen (FIRA) of P. falciparum, and the CS protein of P. vivax, were analyzed by computer. Matches of at least 4 amino acids were found for all sequences. In the database, 29 matches were found for human proteins and 26 matches were found for human viruses with the 6 antigen sequences. Most of the matched proteins, and many of the matched human viruses, are found in blood. The biological significance of these matches remains to be clarified.

Amino Acid Sequence↗

PubMed1988

[Repetitive sequences of the human genome].

A review of literature data on different families of repetitive sequences of human genome is presented. Both tandemly organized (classical satellite DNA, alpha satellite DNA, "minisatellites" etc.) and interspersed repetitive elements are characterized in detail. Special attention is paid to description of human genome mobile elements.

DNA↗

PubMed1990

Tissue-specific and age-related variations in repetitive sequences of mouse extrachromosomal circular DNAs.

Extrachromosomal circular (ecc) DNA was isolated from mouse brain, liver, and heart tissues at different ages. To determine the abundance of repetitive sequences in eccDNAs, preparations were probed for short-interspersed (B1 and B2), long-interspersed (L1), endogenous retroviral-like (IAP), and tandemly repeated satellite sequences (SAT) of the mouse genome. Together these sequence families comprise approximately 15% of the mouse genome. The hybridization results showed that each tissue had a characteristic pattern of repetitive sequence elements in eccDNAs, and the abundance of repetitive sequences changed as a function of age. Repetitive sequences decreased in liver and brain eccDNAs from 1 month to 8 months of age but appeared to remain stable thereafter. In contrast, repetitive sequence families in heart eccDNAs were constant from 1 month to 16 months of age but declined in 24-month-old mice. The present studies indicate that extrachromosomal sequences exhibit greater flexibility than chromosomal sequences.

Aging↗

PubMed1986

A highly reiterated family of transcribed oligo(A)-terminated, interspersed DNA elements in the genome of Bombyx mori.

A library of low Cot DNA (Cot is the molar concentration of DNA times the incubation time in seconds) from Bombyx mori was used to isolate five independent clones of highly reiterated sequences from the genome of this organism. Sequence analysis revealed that all five clones belong to a single family of repetitive DNA elements, which we have named Bm1, and whose reiteration frequency is approximately 2.3 X 10(4) copies per haploid genome. Probing of a Bombyx genomic library (in lambda phage) with a Bm1 clone reveals that this repetitive sequence is dispersed throughout the genome. The pattern of interspersion was confirmed by Southern blot mapping of a large (270 X 10(3) base-pairs) domain of the chorion locus of Bombyx, where at least 13 independent regions were found to hybridize to Bm1. Four additional Bm1 elements have been sequenced from a 4.8 X 10(3) base-pair genomic fragment containing an early chorion gene. Two of these four elements are bounded by short (4 to 12 base-pairs) direct repeats. The nine Bm1 elements which have been sequenced are greater than 88% homologous to each other, and tend to fall in at least two size classes (253 base-pairs and 450 base-pairs). Seven of the nine Bm1 elements have a short 6 to 10 base-pair oligo(A) sequence at the 3' end. A sequence of about 29 base-pairs at the 3' end, including the oligo(A), shows 86% homology to the equivalent 3'-terminal domain of human Alu family repetitive elements. A 129 base-pair domain at the 5' end of Bm1 shows 66% homology to a Drosophila valine transfer RNA gene; thus the 5' end of Bm1 may contain the split internal RNA polymerase III promoter that is characteristic of most transcribed tRNA-like retroposons. Dot-blot analysis of Bombyx RNA shows that Bm1 DNA is indeed transcribed, and that the transcripts are well-represented in the total RNA of an ovarian-derived permanent cell line and posterior silk glands early in the fifth instar, but are less abundant in the RNA of pupae or silk glands late in the fifth instar.

Animals↗

PubMedDate not supplied

[Nucleotide sequence of the repetitive B2 region of the mouse genome].

Mouse genome contains two major families of short interspersed repeats in more than 10(5) copies and scattered throughout the whole genome. They were named as B1 and B2 sequences since they were first isolated from the genome library by means of a dsRNA-B probe. Three copies of B2 family were sequenced and compared with previously sequenced B1 repeat. B2 ubiquitous repeat is of ca. 180 bp long. The members of the family deviate by 5% of nucleotides from the consensus sequence. B2 contains the regions of homology to RNA polymerase III split promoter and to 4.5 S snRNA I. In contrast to B1, it does not contain clear homologies to exon-intron junctions, papova replication origins and human Alu-sequence. One side of B2 repeat is represented by a very AT-rich sequence (30 bp long) followed with an oligo(A) stretch 10-15 nucleotides long. This region of the repeat is the most variable one. The unit is flanked by 15-16 bp direct repeats different in sequenced copies of B2. The same is true for some copies of B1 family. The properties of B1 and B2 repeats suggest that they represent a novel class of transposon-like elements of eukaryotic genome. The possible role of B-type repeats in genome reorganization, DNA replication and pre-mRNA processing is discussed.

Animals↗

PubMed1977

Sequence relationship between long and short repetitive DNA of the rat: a preliminary report.

Long and short repetitive sequences of rat DNA can be isolated and characterized. Long [greater than 1.5 kilobases (kb)] sequences can be separated from short (0.2-0.4 kb) sequences by exclusion chromatography after renaturation of 4-kb DNA fragments to a repetitive Cot and digestion with the single-strand-specific S1 nuclease. (Cot is the initial concentration of DNA in mol of nucleotides/liter multiplied by time in sec.) Long repetitive DNA can be driven by an excess of whole rat DNA can also be used to drive tracer quantities of either long (self-renaturation) or short repetitive DNA. Both the extent and the rate of the renaturations are found to be similar, suggesting that long and short DNA fragments share sequences. When long repetitive DNA is used to drive whole DNA tracers of various lengths, a 3.2-kb interspersion period is found. These data are consistent with the concept that short repetitive sequences are present within long repetitive DNA sequences in the rat genome.

Animals↗

PubMed1981

Locations of three repetitive sequence families found in BALB/c adult beta-globin clones.

Three different repeat sequences have been mapped within the cloned EcoRI fragments that contain the adult beta-globin genes from the BALB/c (Hddd) mouse. One sequence, "a", occurs 1.5-2 kb 3' to the beta-major gene. A second, "b", is found 4kb 5' and 7.5kb 3' to the beta-minor gene. The 14kb EcoRI fragment bearing the beta-minor gene carries at least one additional repetitive element, "c". Probing a BALB/c DNA library with each repeat has demonstrated that these sequences are moderately to highly repetitive and are extensively interspersed with each other throughout the genome. In addition, repeats "a" and "b" are preferentially found in satellite and main-band DNa, respectively. The occurrence of these repeats elsewhere in the beta-globin cluster was demonstrated by probing the non-adult globin clones with each repeat. The arrangement of these repeats around the non-adult genes is 5'-"b"-"b"-epsilon y-beta hl-beta h2-"c"-beta h3-3'. Probing the C57BL/10 (Hbbs) adult gene clones with these repeats demonstrated that the distribution of these sequences in the adult region of these two haplotypes is essentially the same.

Animals↗

PubMed1976

Structural organization and processing of the genetic transcript in the cellular slime mold Dictyostelium discoideum.

The organization of the genome and the synthesis and processing of heterogeneous nuclear RNA (HNRNA) in the cellular slime mold Dictysotelium discoideum have been analyzed. Approximately 60-70% of the genome of Dictyostelium consists of interspersed reiterated and single-copy sequences. The interspersed reiterated sequences have an average length of 250-400 nucleotides. Approximately 50% of the reiterated DNA sequences consist of long noninterspersed sequences. The results of analyses of ynRNA synthesis and processing have been incorporated into a model. According to the model the primary genetic transcript of Dictyostelium is synthesized as a molecule that is 25% larger than mRNA. The bulk of the hnRNA is synthesized from a unit consisting of a short reiterated DNA sequence transcript at the 5' end of the molecule and a single-copy sequence of approximately 1,200 nucleotides in length. In the processing of the mRNA precursor, there appears to be a loss of the majority of the repetitive sequence at the 5' end. The genome contains interspersed sequences of poly (dT)25. These sequences, which appear to be at the 3' terminus of the transcription unit, are transcribed directly into the heterogenous nuclear RNA and are contained within the messenger RNA. During the processing of the heterogeneous nuclear RNA, a poly (A) sequence of approximately 125 nucleotides in length is added posttranscriptionally to the 3' end of the molecule.

Base Sequence↗

PubMed2001

RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse.

In mouse brain cDNA libraries generated from small RNA molecules we have identified a total of 201 different expressed RNA sequences potentially encoding novel small non-messenger RNA species (snmRNAs). Based on sequence and structural motifs, 113 of these RNAs can be assigned to the C/D box or H/ACA box subclass of small nucleolar RNAs (snoRNAs), known as guide RNAs for rRNA. While 30 RNAs represent mouse homologues of previously identified human C/D or H/ACA snoRNAs, 83 correspond to entirely novel snoRNAS: Among these, for the first time, we identified four C/D box snoRNAs and four H/ACA box snoRNAs predicted to direct modifications within U2, U4 or U6 small nuclear RNAs (snRNAs). Furthermore, 25 snoRNAs from either class lacked antisense elements for rRNAs or snRNAS: Therefore, additional snoRNA targets have to be considered. Surprisingly, six C/D box snoRNAs and one H/ACA box snoRNA were expressed exclusively in brain. Of the 88 RNAs not belonging to either snoRNA subclass, at least 26 are probably derived from truncated heterogeneous nuclear RNAs (hnRNAs) or mRNAS: Short interspersed repetitive elements (SINEs) are located on five RNA sequences and may represent rare examples of transcribed SINES: The remaining RNA species could not as yet be assigned either to any snmRNA class or to a part of a larger hnRNA/mRNA. It is likely that at least some of the latter will represent novel, unclassified snmRNAS:

Animals↗

PubMed1996

Sporadic amplification of ID elements in rodents.

ID sequences are members of a short interspersed element (SINE) repetitive DNA family within the rodent genome. The copy number of individual ID elements varies by up to three orders of magnitude between species. This amplification has been highly sporadic in the order Rodentia and does not follow any phylogenetic trend. Using library screening and dot-blot analysis, we estimate there are 25,000 copies of ID elements in the deer mouse, 1,500 copies in the gerbil (both cricetid rodents), and 60,000 copies of either ID or ID-like elements in a sciurid rodent (squirrel). By dot-blot analysis, we estimate there are 150,000, 4,000, 1,000, and 200 copies of ID elements in the rat, mouse, hamster, and guinea pig, respectively (which is consistent with previous reports) and 200 copies in the hystricognath rodent, nutria. Therefore, a rapid amplification took place not only after the divergence of rat and mouse but also following the deer mouse (Peromyscus) and hamster split, with no evidence of increased amplifications in hystricognath rodents. No notable variations of sequences from the BC1 genes of several myomorphic rodents were observed that would possibly explain the varied levels of ID amplification. We did observe subgenera and species-group-specific variation in the ID core sequence of the BC1 gene within the genus Peromyscus. Sequence analysis of cloned ID elements in Peromyscus show most ID elements in this genus arose prior to Peromyscus subgenus divergence. Correspondence of the consensus sequence of individual ID elements in gerbil and deer mouse further confirms BC1 as a master gene in ID amplification. Several possible mechanisms responsible for the quantitative variations are explored.

Animals↗