Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “repetitive elements”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 559 records · Page 31Linked to original sources
PubMed1992

Complex formation of nuclear proteins with the RNA polymerase I promoter and repeated elements in the external transcribed spacer of Cucumis sativus ribosomal DNA.

Complex repetitive structures are located downstream of the transcription initiation site in the intergenic spacer (IGS) of the rRNA genes in Cucumis sativus (cucumber). In order to show that these repetitive elements of the 5'external transcribed spacer (ETS) are probably involved in transcriptional regulation as protein binding sites DNA-protein binding assays were carried out. The same proteins that recognize two binding sites in the promoter region analysed (upstream binding element between -164 and -105, and core promoter between -41 and +16) show binding affinity to the complex structures of the 5'external transcribed spacer. These proteins also seem to interact with the single strands of the respective DNA regions suggesting an effect on transcriptional regulation while the DNA is transcribed and, therefore, is single-stranded. Three proteins were isolated by affinity column chromatography; these proteins turned out to be much smaller (16, 22, and 24 kDa, respectively) than promoter and enhancer binding proteins in animal systems. Additionally, a 70-kDa protein could be characterized cooperating with a small segment of the repeated elements but not with the promoter.

Base Sequence↗
PubMed1985

Extrachromosomal DNA forms of copia-like transposable elements, F elements and middle repetitive DNA sequences in Drosophila melanogaster. Variation in cultured cells and embryos.

Drosophila melanogaster embryos and cells in culture were screened for the presence of unintegrated covalently closed circular DNA forms that hybridize to copia-like transposable elements, the F element and uncharacterized dispersed middle repetitive DNA elements. Our results indicate that the majority of copia-like elements (including copia, 297, 412, mdg1, mdg3 and gypsy), the F elements, and 9 of 12 middle repetitive DNA elements are present as free DNA forms in cultured cells and embryos. An 18 base-pair inverted repeat has been reported to flank the long direct repeat of mdg3, implying that mdg3 is not an orthodox copia-like element; however, we have sequenced two independently isolated mdg3 clones and shown that the inverted repeat is not part of the element. The relative abundance with which free DNA forms are found varies between the cultured cells used, and between cultured cells and embryos. This variation, which can be up to 20-fold for some elements, does not correlate well with either the amount of element-specific poly(A)+ RNA present per cell or the number of element-specific sequences integrated in the genome.

Animals↗
PubMed1998

Identification of enhancer-like elements in the ribosomal intergenic spacer of Odontophrynus americanus 2n and 4n (Amphibia, Anura).

Repetitive elements are found in the ribosomal intergenic spacer (IGS) of most organisms. A particularly complex pattern of internal repetition occurs in the IGSs of O. americanus 2n and 4n, which are composed of several types of BamHI subrepeats (B-SRs). The most repetitive one is approximately 87 bp long, and is highly represented in the IGS variants of these amphibians. Sequence analyses of six diploid and two tetraploid B-SRs show 87% and 86% homology, respectively, and related secondary structure predictions. The comparison of the 2n and 4n B-SR sequences aligned with the 81 bp enhancer of Xenopus laevis reveals 36% homology. Furthermore, other B-SR features like size, number, and secondary structures resemble those of Xenopus enhancers, suggesting that B-SRs may function as regulators of O. americanus rDNA transcription. The present data also corroborate the close evolutionary relationship between 2n and 4n O. americanus species.

Animals↗
PubMed1986

ISH51: a large, degenerate family of insertion sequence-like elements in the genome of the archaebacterium, Halobacterium volcanii.

We describe a new family of repetitive elements in the genome of the archaebacterium Halobacterium volcanii. There are some 20-30 copies of this element, which we designate ISH51. Sequenced copies show typical insertion sequence characteristics (terminal inverted repeats, direct flanking repeats of "target site" DNA). However, members of the ISH51 family are highly heterogeneous, showing on average only 85% primary sequence homology; and some genomic copies appear to be severely truncated. Some ISH51 elements are clustered together in regions of relatively AT-rich DNA. There are at least five such AT-rich "islands" in the H. volcanii genome. Repetitive sequences homologous to ISH51 are found in the genomes of most Halobacterium and Halococcus species.

Base Sequence↗
PubMed1980

Thalamocortical transformation of responses to complex auditory stimuli.

In unanesthetized guinea pigs, thalamic (CGM), and cortical (auditory I) neurons were recorded simultaneously. Nine of 69 neuron pairs showed a positive cross-correlation of their spontaneous activities, with increased discharge probability of the cortical neuron beginning 2--5 ms after the discharge of the CGM-neuron. The individual neurons of such pairs had an identical CF and the same spectral responsiveness. The responses of cortical neurons to pure tones were much more phasic than those of the corresponding CGM-neurons. Thalamic neurons could be driven up to much higher AM- and FM-modulation frequencies (100 Hz) than cortical neurons, which usually ceased to follow AM-frequencies above 20 Hz. Stronger or weaker suppression of tonic response components in cortical and thalamic neurons and the lower AM-range of cortical neurons is related to stronger or weaker intracortical and intrathalamic inhibition respectively. Response characteristics to FM-stimuli are similar to those of AM-stimuli. All CGM and cortical neurons responded to a variety of natural calls of the same or of other species. Responses of CGM-cells represented more components of a call than cortical cells even if the two cells were synaptically connected. In cortical cells, repetitive elements of a call were not represented if the repetition rate was too high. High modulation frequencies within a call, such as those of the fundamental frequency, could still be separated in the response of some CGM-neurons, but never in those of cortical neurons. Both CGM and cortical cells responded essentially to transients (amplitude or frequency modulations) within a call, if spectral components of such elements were within the spectral sensitivity of the cell. Spectral components outside the spectral sensitivity range could result in suppression of spontaneous discharge rate. Responses of cortical and CGM-cells, and thus the representation of call elements by neuronal responses, varied with the intensity of a call. It is suggested that, at higher levels of the auditory system, essential information about the temporal features of complex sounds may be represented by neural responses to transients in various spectral regions.

Animals↗
PubMed1984

Rat prostatic steroid binding protein: characterisation of the Alu element upstream of the C3 genes.

We have characterised an Alu-like repetitive element found about 400 bp upstream of the gene encoding the C3 component of rat prostatic steroid binding protein and suggest, from comparisons with other published sequences, that it is an example of a third class of rodent Alu-equivalent sequences. Members of this class are 80-90 bp long, share greater than 90% sequence homology, and contain sequences resembling the RNA polymerase III bipartite promoter. The Alu type III element within the C3 gene was found to be expressed in cell-free systems and within heterologous cells stably transfected with the C3 gene, but these transcripts were not detectable in rat ventral prostate. It therefore seems unlikely that expression of this sequence plays a role in expression from the adjacent C3 gene.

Androgen-Binding Protein↗
PubMed1994

Exploiting the informativity of 'meaningless' simple repetitive DNA from indirect gene diagnosis to multilocus genome scanning.

Most eukaryotic genomes are characterized by excessively large amounts of non-coding DNA sequences among which redundant (repetitive) elements constitute a sizable portion. The functional role of an abundant subclass of repetitive sequences--simple, tandemly arranged repeats--remained mysterious so far. Even the biological meaning of most of these elements appears quite refractory to present-day techniques in molecular genetics. Notwithstanding simple repetitive sequences have been developed into superb tools for various aspects of eukaryotic genome research: Using oligonucleotide probes carrying simple repeat motifs multilocus DNA fingerprinting can be applied for individual identification and genetic relationship analyses in plants, animals and humans. Microsatellite analyses via polymerase chain reaction of simple repeat blocks allow for efficient investigations of such divers subject matters as criminal stains, detailed genome maps and indirect gene diagnoses.

Communicable Diseases↗
PubMed1993

An Alu element retroposition in two families with Huntington disease defines a new active Alu subfamily.

Alu repetitive elements represent the most common short interspersed elements (SINEs) found in primates, with an estimated 500,000 members in the haploid human genome. Considerable evidence has accumulated that these elements have dispersed in the genome by active transcription followed by retroposition, and that this process is ongoing. Sequence variation between the individual elements has lead to the hierarchical classification of Alu repeats into families and subfamilies. Young subfamilies that are still being actively transposed are of considerable interest, and the identification of one such subfamily (designated 'PV') has lead to the hypothesis that the most recent retroposition events are due to a single master Alu source gene. In the course of our search for the gene causing Huntington disease, we have detected an Alu retroposition event in two families. Sequence analysis demonstrates that this Alu element is not a member of the PV subfamily, but is similar to 5 other Alu elements in the GenBank database. Together, these Alu elements, all of which contain a 7 base-pair internal duplication, define a distinct subfamily, designated as the Sb2 subfamily, providing evidence for a second actively retroposing Alu source gene. These data provide support for multiple source genes for Alu retroposition in the human genome.

Base Sequence↗
PubMed1993

Characterization of the 130-bp repeat enhancer element of the rat ribosomal gene: functional interaction with transcription factor E1BF.

The 130-bp repetitive element (RE) of the rat rDNA (ribosomal RNA-encoding gene) intergenic spacer stimulated the synthesis of rRNA four- to sixfold, in comparison with that of the promoter alone, both in vivo and in vitro, when ligated to the rat rDNA promoter. The addition of increasing amounts of highly purified E1BF (enhancer-1 binding factor), which binds to the rat rDNA promoter and an upstream nonrepetitive enhancer element [Zhang and Jacob, Mol. Cell. Biol. 10 (1990) 5177-5186], to an in vitro transcription system resulted in enhancement of rDNA transcription from the recombinant plasmids containing the promoter or promoter-RE. However, E1BF-mediated stimulation of transcription under the influence of the RE continued at higher concentrations of E1BF than did the control transcription from the promoter alone. The binding affinity of E1BF for the RE was comparable to its affinity for the nonrepetitive far upstream enhancer element previously characterized in our laboratory. The sequences protected by E1BF in the RE differed from those protected by UBF (upstream control element-binding factor), a well characterized pol I transcription factor. These data suggest that E1BF belongs to a class of transcription factors which interact with the promoter and spacer cis-acting RE to modulate rDNA transcription.

Animals↗
PubMed2000

Glider and Vision: two new families of miniature inverted-repeat transposable elements in Xenopus laevis genome.

We have characterised from Xenopus laevis two new short interspersed repetitive elements, we have named Glider and Vision, that belong to the family of miniature inverted-repeat transposable elements (MITEs). Glider was first characterised in an intronic region of the alpha-tropomyosin (alpha-TM) gene and database search has revealed the presence of this element in 10 other Xenopus laevis genes. Glider elements are about 150 bp long and for some of them, their terminal inverted repeats are flanked by potential target-site duplications. Evidence for the mobility of Glider element has been provided by the presence/absence of one element at corresponding location in duplicated alpha-TM genes. Vision element has been identified in the promoter region of the cyclin dependant kinase 2 gene (cdk2) where it is boxed in a Glider element. Vision is 284bp long and is framed by 14-bp terminal inverted repeats that are flanked by 7-bp direct repeats. We have estimated that there are about 20,000 and 300 copies of Glider and Vision respectively scattered throughout the Xenopus laevis genome. Every MITEs elements but two described in our study are found either in 5' or in 3' regulatory regions of genes suggesting a potential role in gene regulation.

Animals↗
PubMed1989

The effect of E. coli host strain on the consensus sequence of regions of the human L1 transposon.

We have used highly methylation tolerant host strains to clone hyper- and hypo-methylated genomic elements from different regions of the same family of long interspersed repetitive elements from human DNA, specifically the 1.8 kilobase (kb) and 1.2kb KpnI fragments from members of the L1 family of transposable elements in which respectively some 18% and 2.7% of cytosines are methylated in vivo in human spleen DNA. The consensus of the DNA sequences of the ends of 13 clones from the hypomethylated region of human L1 agreed exactly with the consensus derived previously from clones made using conventional host strains. However the sequences of 18 of our clones from the 5' end of the hypermethylated region differed significantly from the sequences of clones made using conventional hosts (P less than 0.0001). The 5' region of the 1.8kb L1 region is a CpG island which, in human somatic tissue, appears to be maintained in a highly methylated state, including methylation at sites other than CpG dinucleotides. The consensus sequence of this region also has features suggestive of a previously unrecognized open reading frame.

Base Sequence↗
PubMed2025

Chromosome-level Genome Assembly of the Halophytic Turfgrass Zoysia macrostachya.

Zoysia macrostachya Franch. & Sav. is a halophytic perennial turfgrass in the Poaceae family, commonly found in the coastal regions of Korea, Japan, and East Asia. Z. macrostachya thrives in high-salinity environments, making it an excellent model for studying abiotic stress resilience. In this study, we present a chromosome-level genome assembly of Z. macrostachya, constructed using Oxford Nanopore long reads, Illumina short reads, and Omni-C sequencing data. The assembly spans 329.78 Mb across 20 chromosomes, with a scaffold N50 of 19.24 Mb, and includes complete telomeric sequences at both ends. The assembly showed 97.8% complete BUSCOs, indicating high genome completeness. Repeat element and gene annotation identified 44.03% of the genome as repetitive elements and 33,474 protein-coding genes. The gene annotation showed 97.1% complete BUSCOs and 86.92% functionally characterized genes. Macrosynteny analysis highlighted highly collinear relationships with related species, providing a foundational understanding of the Z. macrostachya genomic structure. This high-quality genome serves as a valuable resource for advancing salinity tolerance research and improving the genetic diversity of Zoysia species.

Genome, Plant↗
PubMed1988

A yeast sigma composite element, TY3, has properties of a retrotransposon.

Sigma is a 340- or 341-base pair repetitive element which is located almost exclusively within 19 base pairs of the 5' ends of various tRNA genes in the Saccharomyces cerevisiae genome. Although most sigma elements characterized to date are isolated insertions, a few of the elements occur relatively closely spaced. One of these pairs is a direct repeat of the sigma element separated by an internal domain 4.7 kilobase pairs in length. Not only does this structure resemble a composite transposable element, but regions within the sigma elements and intervening domain are homologous to conserved regions in retroviruses and retrotransposons of yeast and other organisms. Two features suggest that the sigma elements and intervening DNA transposed in a concerted event: only one of the two sigma elements is associated with a tRNA gene, and only the outside ends of the two elements are flanked by the 5-base pair direct repeats that usually flank individual sigma insertions. Examination of genomic DNA from five laboratory strains indicates that the 4.7 kilobase pair internal domain is present in one to four copies per haploid genome and that the genomic location of this domain differs from strain to strain. In addition, Northern blot analysis showed the presence of a 5.2 kilobase poly(A) transcript which hybridizes to both sigma and internal domain-specific probes. The existence of this composite element may suggest new ways to consider the mechanisms by which retrotransposons select their targets.

Base Sequence↗
PubMed1999

Complete sequence determination of the mouse and human CTLA4 gene loci: cross-species DNA sequence similarity beyond exon borders.

CTLA4 (CD152), a receptor for the B7 costimulatory molecules (CD80 and CD86), is considered a fundamental regulator of T-cell activation. In this paper, we present the complete primary structure of the mouse and human CTLA4 gene loci. Sequence comparison between the mouse and the human CTLA4 gene loci revealed a high degree of sequence conservation both for homologous noncoding regions (65-78% identity) and for coding regions (72-98% identity), with an overall score of 71% over the entire length of the two genes. Of the CTLA4 genomic regions aligned, five simple repetitive elements were found in the mouse locus, whereas two simple repetitive sequences were localized on the human locus. RNA blot analysis of mouse and human primary tissues indicated that both CTLA4 and T-cell receptor transcripts were found in most organs with generally higher levels in lymphoid tissues. The conservation of CTLA4 gene patterning raises the possibility that constrained gene evolution of CTLA4 may be linked to conserved transcriptional control of this locus.

Abatacept↗
PubMed2004

Non-recurrent 17p11.2 deletions are generated by homologous and non-homologous mechanisms.

Several recurrent common chromosomal deletion and duplication breakpoints have been localized to large, highly homologous, low-copy repeats (LCRs). The mechanism responsible for these rearrangements, viz., non-allelic homologous recombination between LCR copies, has been well established. However, fewer studies have examined the mechanisms responsible for non-recurrent rearrangements with non-homologous breakpoint regions. Here, we have analyzed four uncommon deletions of 17p11.2, involving the Smith-Magenis syndrome region. Using somatic cell hybrid lines created from patient lymphoblasts, we have utilized a strategy based on the polymerase chain reaction to refine the deletion breakpoints and to obtain sequence data at the deletion junction. Our analyses have revealed that two of the four deletions are a product of Alu/Alu recombination, whereas the remaining two deletions result from a non-homologous end-joining mechanism. Of the breakpoints studied, three of eight are located in LCRs, and five of eight are within repetitive elements, including Alu and MER5B sequences. These findings suggest that higher-order genomic architecture, such as LCRs, and smaller repetitive sequences, such as Alu elements, can mediate chromosomal deletions via homologous and non-homologous mechanisms. These data further implicate homologous recombination as the predominant mechanism of deletion formation in this genomic interval.

Base Sequence↗
PubMed1988

Nucleotide sequence and transcription of a rat tRNA(Phe) gene and a neighboring Alu-like element.

A bacteriophage gamma Ch4A clone containing a 22-kb rat DNA insert was isolated and found to contain a solitary tRNA(Phe)GAA gene and, 436 bp downstream of it, an Alu-like element. The nucleotide sequence of a 1141-bp DNA fragment containing these genes was determined. The rat tRNA(Phe)GAA gene, with the exception of an additional A in the extra arm, has a sequence identical to that of a rabbit liver tRNA(Phe). The Alu-like element belongs to the rodent B2 family of short interspersed repetitive nucleotide sequences. This repetitive element, B2Phe, is flanked by 12-bp direct repeats, contains an internal split promoter (block A and block B) for RNA polymerase III and is devoid of an A-rich segment at the 3' end. Like other members of the B2 family, the B2Phe element presents 64% sequence homology with rat serine tRNA and contains a serine (GCT) anticodon. Both tRNA(Phe)GAA gene and B2Phe element were found to be transcriptionally active in HeLa cell and Xenopus oocyte nuclear extracts. The tRNA(Phe) gene transcripts were processed during the course of transcription to form mature-size tRNA(Phe). The transcription efficiency of the B2Phe element was found to be an order of magnitude higher than that of the tRNA(Phe) gene. Competition experiments demonstrate that the B2Phe DNA can form a more stable transcription complex than the tRNA(Phe) gene and compete with it for binding of transcription factors.

Animals↗
PubMed1996

Virtually the entire Xenopus laevis rDNA multikilobase intergenic spacer serves to stimulate polymerase I transcription.

The promoter-distal half of the spacer separating the tandem Xenopus laevis rRNA genes consists of "0" and "1" repetitive elements that have been considered unimportant in polymerase I transcriptional activation. Utilizing oocyte microinjection, we now demonstrate that the 0/1 region, as well as its component 0 and 1 repeats, substantially stimulate transcription from a ribosomal promoter in cis and inhibit transcription when located in trans. Both the cis and trans responses increase linearly with increasing numbers of 0 or 1 repeats until saturation is approached. The 0/1 block and its component elements stimulate transcription in both orientations, over distances, and when placed downstream of the initiation site, properties for which the 60/81-base pair (bp) repeats have been defined as polymerase I enhancers. In their natural promoter-distal rDNA location, the 0/1 repeats can stimulate transcription from the rRNA gene promoter, above the level afforded by the intervening 60/81-bp repeats and spacer promoter. In addition, as with the 60/81-bp repeats, the 0/1 repeats bind a factor in common with the rDNA promoter. Thus, the entire X. laevis rDNA intergenic spacer (the 0 repeats, 1 repeats, spacer promoter repeats, and 60/81-bp repeats) acts together to enhance ribosomal transcription.

Animals↗
PubMed1991

Characterization of the IS895 family of insertion sequences from the cyanobacterium Anabaena sp. strain PCC 7120.

A family of repetitive elements from the cyanobacterium Anabaena sp. strain PCC 7120 was identified through the proximity of one element to the psbAI gene. Four members of this seven-member family were isolated and shown to have structures characteristic of bacterial insertion sequences. Each element is approximately 1,200 bp in length, is delimited by a 30-bp inverted repeat, and contains two open reading frames in tandem on the same DNA strand. The four copies differ from each other by small insertions or deletions, some of which alter the open reading frames. By using a system designed to trap insertion elements, one of the elements, denoted IS895, was shown to be mobile. The target site was not duplicated upon insertion of the element. Two other filamentous cyanobacterial strains were also found to contain sequences homologous to IS895.

Amino Acid Sequence↗