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At least 271 records · Page 15Linked to original sources
PubMed2003

Reverberation of rapid and slow trills: implications for signal adaptations to long-range communication.

Many acoustic signals in animals include trills, i.e., rapid repetitions of similar elements. Elements within these trills usually are frequency modulated and are degraded by reverberation during long-range transmission. Reverberation primarily affects consecutive elements with the same frequency characteristics and thus imposes a major constraint in the evolution of design and perception of long-range signals containing trills. Here transmission of frequency-unmodulated trills with different element repetition rates was studied. Trills were generated at different frequencies to assess frequency dependence of reverberation and then broadcast under three acoustic conditions--an open field and to assess seasonal changes in transmission properties, a deciduous forest before and after foliage had emerged. Reverberation was quantified at different positions within trills. The results show strong effects of vegetation density (season), transmission distance, frequency, element repetition rate, and element position within the trill on effects of reverberation. The experiments indicate that fast trills transmit less well than slow trills and thus are less effective in long-range communication. They show in particular that selection on trills should not act only on element repetition rate within trills but also on the trill duration as effects of reverberation increased with trill duration.

Acoustics↗
PubMed1996

Polymorphism in Brucella strains detected by studying distribution of two short repetitive DNA elements.

Thirty-four Brucella reference or field strains representing all the species and biovars were studied by repetitive element sequence-based PCR, a PCR using primers complementary to two enterobacterial short repetitive sequences: repetitive extragenic palindromic and enterobacterial repetitive intergenic consensus sequences. All the stains showed a positive amplification, suggesting that the Brucella genome contains such sequences. Repetitive extragenic palindromic PCR was less discriminating than enterobacterial repetitive intergenic consensus PCR in terms of distinguishing strains, but a combination of the two methods was able to distinguish all the isolates, except for some strains belonging to biovars 3 and 9 of Brucella abortus. Repetitive element sequence-based PCR appears to be a simple and useful method for the study of brucellosis epidemiology.

Base Sequence↗
PubMed2004

A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements.

We report a method for studying global DNA methylation based on using bisulfite treatment of DNA and simultaneous PCR of multiple DNA repetitive elements, such as Alu elements and long interspersed nucleotide elements (LINE). The PCR product, which represents a pool of approximately 15 000 genomic loci, could be used for direct sequencing, selective restriction digestion or pyrosequencing, in order to quantitate DNA methylation. By restriction digestion or pyrosequencing, the assay was reproducible with a standard deviation of only 2% between assays. Using this method we found that almost two-thirds of the CpG methylation sites in Alu elements are mutated, but of the remaining methylation target sites, 87% were methylated. Due to the heavy methylation of repetitive elements, this assay was especially useful in detecting decreases in DNA methylation, and this assay was validated by examining cell lines treated with the methylation inhibitor 5-aza-2'deoxycytidine (DAC), where we found a 1-16% decrease in Alu element and 18-60% LINE methylation within 3 days of treatment. This method can be used as a surrogate marker of genome-wide methylation changes. In addition, it is less labor intensive and requires less DNA than previous methods of assessing global DNA methylation.

Alu Elements↗
PubMed1994

The polymorphic subtelomeric regions of Plasmodium falciparum chromosomes contain arrays of repetitive sequence elements.

The human malaria parasite Plasmodium falciparum exhibits a high degree of chromosomal polymorphism, which may contribute to its ability to evade host defenses. The analysis of parasite chromosomes has revealed that these polymorphisms are confined to the subtelomeric regions, which are transcriptionally silent and contain repetitive sequence elements. Several subtelomeric repetitive elements have been isolated and mapped by using P. falciparum yeast artificial chromosome (YAC) clones. Structural analysis of parasite telomeric and subtelomeric YAC clones demonstrated that these repetitive elements are conserved between P. falciparum chromosome ends. We suggest that these subtelomeric elements promote chromosome pairing in P. falciparum and facilitate meiotic recombination and gene conversion between telomere-proximal genes.

Animals↗
PubMed1999

Characterization of repetitive DNA elements in Arabidopsis.

We have applied computational methods to the available database and identified several families of repetitive DNA elements in the Arabidopsis thaliana genome. While some of the elements have features expected of either miniature inverted-repeat transposable elements (MITEs) or retrotransposons, the most abundant class of repetitive elements, the AthE1 family, is structurally related to neither. The AthE1 family members are defined by conserved 5' and 3' sequences, but these terminal sequences do not represent either inverted or direct repeats. AthE1 family members with greater than 98% identity are easily identified on different Arabidopsis chromosomes. Similar to nonautonomous DNA-based transposon families, the AthE1 family contains members in which the conserved terminal domains flank unrelated sequences. The primary utility of characterizing repetitive sequences is in defining, at least in part, the evolutionary architecture of specific Arabidopsis loci. The repetitive elements described here make up approximately 1% of the available Arabidopsis thaliana genomic sequence.

Algorithms↗
PubMed2000

Prediction and phylogenetic analysis of mammalian short interspersed elements (SINEs).

The presence of repetitive elements can create serious problems for sequence analysis, especially in the case of homology searches in nucleotide sequence databases. Repetitive elements should be treated carefully by using special programs and databases. In this paper, various aspects of SINE (short interspersed repetitive element) identification, analysis and evolution are discussed.

Animals↗
PubMed2002

Identification of a novel repetitive DNA element and its use as a molecular marker for strain typing and discrimination of ara- from ara+ Burkholderia pseudomallei isolates.

A novel 10-bp repeat (5'-CGACGCAGGC-3')34 was identified in a strain of Burkholderia pseudomallei, the first repetitive element found in this species. A pair of primers, based on the flanking sequences of the repetitive region, was used in PCR and DNA sequence analysis to determine the genomic structure and distribution of the repetitive element in 76 arabinose- (ara-) and 7 ara+ B. pseudomallei isolates. DNA fragments of 400-700 bp were amplified in all ara- isolates. Ara+ isolates were characterised by a uniform fragment of 402 bp. Nucleotide sequence analysis of these fragments revealed broad heterogeneity of the variable-number tandem repeats with 26 distinct alleles ranging between (5'-CGACGCAGGC-3')13 and (5'-CGACGCAGGC-3')45 identified in the ara- isolates. In contrast, a novel non-repetitive sequence was identified in each of the ara+ isolates. This was confirmed by Southern blot analysis. Such biotype-specific variable-number tandem repeats may be useful as genetic markers for rapid strain differentiation of ara- isolates.

Alleles↗
PubMed2006

Repetitive DNA elements as mediators of genomic change in response to environmental cues.

There is no logical or theoretical barrier to the proposition that organismal and cell signaling could transduce environmental signals into specific, beneficial changes in primary structure of noncoding DNA via repetitive element movement or mutation. Repetitive DNA elements, including transposons and microsatellites, are known to influence the structure and expression of protein-coding genes, and to be responsive to environmental signals in some cases. These effects may create fodder for adaptive evolution, at rates exceeding those observed for point mutations. In many cases, the changes are no doubt random, and fitness is increased through simple natural selection. However, some transposons insert at specific sites, and certain regions of the genome exhibit selectively and beneficially high mutation rates in a range of organisms. In multicellular organisms, this could benefit individuals in situations with significant potential for clonal expansion: early life stages or regenerative tissues in animals, and most plant tissues. Transmission of the change to the next generation could occur in plants and, under some circumstances, in animals.

Animals↗
PubMed2005

Chromosomal translocation mechanisms at intronic alu elements in mammalian cells.

Repetitive elements comprise nearly half of the human genome. Chromosomal rearrangements involving these elements occur in somatic and germline cells and are causative for many diseases. To begin to understand the molecular mechanisms leading to these rearrangements in mammalian cells, we developed an intron-based system to specifically induce chromosomal translocations at Alu elements, the most numerous family of repetitive elements in humans. With this system, we found that when double-strand breaks (DSBs) were introduced adjacent to identical Alu elements, translocations occurred at high frequency and predominantly arose from repair by the single-strand annealing (SSA) pathway (85%). With diverged Alu elements, translocation frequency was unaltered, yet pathway usage shifted such that nonhomologous end joining (NHEJ) predominated as the translocation pathway (93%). These results emphasize the fluidity of mammalian DSB repair pathway usage. The intron-based system is highly adaptable to addressing a number of issues regarding molecular mechanisms of genomic rearrangements in mammalian cells.

Alu Elements↗
PubMedDate not supplied

Short palindromic repetitive DNA elements in enterobacteria: a survey.

We present a survey of short palindromic repetitive elements in enterobacteria. Seven families are presented. Five were already known (RSA, IRU, 29-bp repeats, BIMEs and boxC), and their properties are updated; in particular, a new composite element is shown to include the formerly identified boxC repeats. Two repetitions, YPAL1 and YPAL2, found primarily in Yersinia, are described here for the first time.

Base Sequence↗
PubMedDate not supplied

Abundance of repetitive sequence elements in the mouse testis-specific lactate dehydrogenase-C gene.

We have cloned and sequenced the entire mouse ldhc gene and mapped it physically in relation to the somatic ldha gene. The 2 genes were found to be oriented in head-to-tail fashion with about a 6-kilobase (kb) distance between the 3' end of ldha and the 5' end of ldhc. The ldhc gene is composed of 43% repetitive elements compared to only 16% in the ldha gene. Despite the close physical distance of mouse ldha and ldhc, the 2 genes have a very different content of repetitive elements, and this most likely reflects different levels of selective pressure.

Animals↗
PubMed2002

Repetitive DNA elements in fungi (Mycota): impact on genomic architecture and evolution.

Repetitive DNA elements, microsatellites or simple repeats, minisatellites, mobile elements that transpose at the level of DNA, retrotransposons and various derivatives thereof are ubiquitous constituents of all fungal genomes. Many of these elements, especially the different types of transposon, have been cloned and characterised at the sequence level. Their biological role, however, has not yet been sufficiently elucidated. We are far from understanding the selection mechanisms that tend to conserve repeated DNA at defined loci. There is also little insight into the mechanisms that provide the balance between spreading repetitive elements within genomes and control of their copy number. Depending on the fungal group, this balance can be stabilised at different levels. Asco- and basidiomycetes rarely contain more than 5% repetitive DNA, whereas the phylogenetically older division Zygomycota is characterised by typically more than 30%. The effects of repetitive DNAs on the expression of adjacent genes are only rarely understood and their role for genomic plasticity on an evolutionary time scale is still especially enigmatic. This survey summarises the main characteristics of well studied experimental systems and intends to define important open questions for stimulating future research.

Base Sequence↗
PubMed1989

Characterization of the repetitive DNA elements in the genome of fish lymphocystis disease viruses.

The complete DNA nucleotide sequence of the repetitive DNA elements in the genome of fish lymphocystis disease virus (FLDV) isolated from two different species (flounder and dab) was determined. The size of these repetitive DNA elements was found to be 1413 bp which corresponds to the DNA sequences of the 5' terminus of the EcoRI DNA fragment B (0.034 to 0.052 m.u.) and to the EcoRI DNA fragment M (0.718 to 0.736 m.u.) of the FLDV genome causing lymphocystis disease in flounder and plaice. The degree of DNA nucleotide homology between both regions was found to be 99%. The repetitive DNA element in the genome of FLDV isolated from other fish species (dab) was identified and is located within the EcoRI DNA fragment B and J of the viral genome. The DNA nucleotide sequence of one duplicate of this repetition (EcoRI DNA fragment J) was determined (1410 bp) and compared to the DNA nucleotide sequences of the repetitive DNA elements of the genome of FLDV isolated from flounder. It was found that the repetitive DNA elements of the genome of FLDV derived from two different fish species are highly conserved and possess a degree of DNA sequence homology of 94%. The DNA sequences of each strand of the individual repetitive element possess one open reading frame.

Amino Acid Sequence↗
PubMed1993

Specific interaction of IHF with RIBs, a class of bacterial repetitive DNA elements located at the 3' end of transcription units.

The prokaryotic REP (repetitive extragenic palindromes) or PU (palindromic units) sequences are often associated with other repetitive elements, forming arrangements which have been called 'BIMEs' (bacterial interspersed mosaic elements). It is estimated that the Escherichia coli chromosome carries approximately 300-500 BIMEs, whose biological role is at present unknown. We have identified a family of BIMEs consisting of two converging REP sequences flanking a 35 bp conserved segment which carries a static DNA bend and a binding site for IHF, the integration host factor of E.coli. We estimate that the E.coli genome harbors approximately 100 copies of this module, which we name 'RIB' (reiterative ihf BIME). We have analyzed by gel retardation and by footprinting the in vitro interaction of IHF with individual RIBs, and shown that the protein binds strongly and specifically to their center. We have also demonstrated binding of IHF to the chromosomal population of RIBs, using a new approach which combines two-dimensional bandshift and Southern blotting. RIB elements are at the end of transcription units, and thus define a new class of ihf sites. Possible implications for genome structure and DNA topology are discussed.

Bacterial Proteins↗
PubMed1994

Characterization of the CNRE-1 family of repetitive DNA elements in Cryptococcus neoformans.

The pathogenic yeast Cryptococcus neoformans contains 10-20 dispersed repetitive elements that hybridize to clone CNRE-1.0. Screening of a genomic library with probes derived from CNRE-1.0 identified five phages with restriction maps that overlapped CNRE-1.0 and three additional phages that belonged to two distinct groups. Sequencing of internal 3.5-kb SstI fragments from two CNRE-1-like elements revealed 95% homology, as well as a conserved open reading frame. A PCR-RFLP assay was developed that can distinguish different subfamilies of CNRE-1-like elements.

Base Sequence↗
PubMed1999

RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements.

While the significance of middle repetitive elements had been neglected for a long time, there are again tendencies to ascribe most members of a given middle repetitive sequence family a functional role--as if the discussion of SINE (short interspersed repetitive elements) function only can occupy extreme positions. In this article, I argue that differences between the various classes of retrosequences concern mainly their copy numbers. Consequently, the function of SINEs should be viewed as pragmatic such as, for example, mRNA-derived retrosequences, without underestimating the impact of retroposition for generation of novel protein coding genes or parts thereof (exon shuffling by retroposition) and in particular of SINEs (and retroelements) in modulating genes and their expression. Rapid genomic change by accumulating retrosequences may even facilitate speciation [McDonald, J.F., 1995. Transposable elements: possible catalysts of organismic evolution. Trends Ecol. Evol. 10, 123-126.] In addition to providing mobile regulatory elements, small RNA-derived retrosequences including SINEs can, in analogy to mRNA-derived retrosequences, also give rise to novel small RNA genes. Perhaps not representative for all SINE/master gene relationships, we gained significant knowledge by studying the small neuronal non-messenger RNAs, namely BC1 RNA in rodents and BC200 RNA in primates. BC1 is the first identified master gene generating a subclass of ID repetitive elements, and BC200 is the only known Alu element (monomeric) that was exapted as a novel small RNA encoding gene.

Animals↗
PubMed2005

Palindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii.

We have identified 141 novel palindromic repetitive elements in the genome of euryarchaeon Methanocaldococcus jannaschii. The total length of these elements is 14.3kb, which corresponds to 0.9% of the total genomic sequence and 6.3% of all extragenic regions. The elements can be divided into three groups (MJRE1-3) based on the sequence similarity. The low sequence identity within each of the groups suggests rather old origin of these elements in M. jannaschii. Three MJRE2 elements were located within the protein coding regions without disrupting the coding potential of the host genes, indicating that insertion of repeats might be a widespread mechanism to enhance sequence diversity in coding regions.

Amino Acid Sequence↗
PubMed1993

Coordinated posttranscriptional control of gene expression by modular elements including Alu-like repetitive sequences.

We previously reported that in rat fibroblasts, accumulation of a set of mRNAs ("pIL genes") was modulated as a function of cell growth and transformation, at a posttranscriptional stage, and by a mechanism that depends on a short nucleotide sequence containing an ID repetitive element. In mouse fibroblasts, hybridization with rat pIL probes identified mRNAs with the same pattern of expression, which did not contain ID sequences but contained a different regulatory element, encompassing a repetitive sequence of the B1 family. Expression in mouse cells of a reporter beta-globin gene carrying this element inserted in its 3' noncoding region was growth- and transformation-dependent. The nucleotide sequences of two murine and of three rat pIL cDNAs showed clear similarities in the region immediately adjacent to the ID and B1 repeats. Both the repeat and the flanking sequence were required to confer on beta-globin constructs the pattern of expression characteristic of the pIL genes. The hypothesis is presented that repetitive sequences in the eukaryotic genome might be modular parts of complex regulatory elements ensuring the coordinated expression of various mRNA species.

3T3 Cells↗