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Results for “Interspersed Repetitive Sequences”

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PubMed1986

Chromosome-specific subfamilies within human alphoid repetitive DNA.

Nucleotide sequence data of about 20 X 10(3) base-pairs of the human tandemly repeated alphoid DNA are presented. The DNA sequences were determined from 45 clones containing EcoRI fragments of alphoid DNA isolated from total genomic DNA. Thirty of the clones contained a complete 340 base-pair dimer unit of the repeat. The remaining clones contained alphoid DNA with fragment lengths of 311, 296, 232, 170 and 108 base-pairs. The sequences obtained were compared with an average alphoid DNA sequence determined by Wu & Manuelidis (1980). The divergences ranged from 0.6 to 24.6% nucleotide changes for the first monomer and from 0 to 17.8% for the second monomer of the repeat. On the basis of identical nucleotide changes at corresponding positions, the individual repeat units could be shown to belong to one of several distinct subfamilies. The number of nucleotide changes defining a subfamily generally constitutes the majority of nucleotide changes found in a member of that subfamily. From an evaluation of the proportion of the total amount of alphoid DNA, which is represented by the clones studied, it is estimated that the number of subfamilies of this repeat may be equal to or exceed the number of chromosomes. The expected presence of only one or a few distinct subfamilies on individual chromosomes is supported by the study, also presented, of the nucleotide sequence of 17 cloned fragments of alphoid repetitive DNA from chromosome 7. These chromosome-specific repeats all contain the characteristic pattern of 36 common nucleotide changes that defines one of the subfamilies described. A unique restriction endonuclease (NlaIII) cleavage site present in this subfamily may be useful as a genetic marker of this chromosome. A family member of the interspersed Alu repetitive DNA was also isolated and sequenced. This Alu repeat has been inserted into the human alphoid repetitive DNA, in the same way as the insertion of an Alu repeat into the African green monkey alphoid DNA.

Base Sequence↗

PubMed2006

Evolutionary clues from comparative analysis of Mycobacterium tuberculosis variable-number tandem repeat sequences within genetic families.

Mycobacterium tuberculosis is one of the most successful bacterial pathogens in the history of mankind, and the study of the evolutionary and genetic behaviour of this organism is ongoing. The potential of variable-number tandem repeat (VNTR) regions to provide insight into the evolutionary past of this organism has yet to be evaluated. The aim of this study was to investigate diversity occurring within VNTR loci within established evolutionary lineages. Mycobacterial interspersed repetitive unit (MIRU) 4 and 26 nucleotide sequencing was undertaken revealing significant differences in VNTR discriminatory power and distribution of allelic types within defined sub-lineages, within a moderately discriminant and a highly discriminant locus, respectively. These findings indicate potential allele bias at these loci within the defined groups dependent on the genotype of their progenitor strain, and the patterns of distribution suggest that a step-wise contraction/expansion process is responsible for VNTR repeat evolution. The results also identified a possible incidence of genetic drift within major genetic group 2 (MGG2), which has a point mutation at locus MIRU26 in a clonal subgroup.

Amino Acid Sequence↗

PubMed2005

Abundant novel transcriptional units and unconventional gene pairs on human chromosome 22.

Novel transcriptional units (TUs) are EST-supported transcribed features not corresponding to known genes. Unconventional gene pairs (UGPs) are pairs of genes and/or TUs sharing exon-to-exon cis-antisense overlaps or putative bidirectional promoters. Computational TU and UGP discovery followed by manual curation was performed in the entire published 34.9-Mb human chromosome 22 euchromatic sequence. Novel TUs (n = 517) were as abundant as known genes (n = 492) and typically did not have nonprimate DNA and protein homologies. One hundred seventy-one (33%) of TUs, but only 13 (3%) of genes, both lacked nonprimate conservation and localized to gaps in the human-mouse BLASTZ alignment. Novel TUs were richer in exonic primate-specific interspersed repetitive elements (P = 0.001) and were more likely to rely on splice junctions provided by them, than were known genes: 19% of spliced TUs, versus 5% of spliced genes, had a splice site within a primate-specific repeat. Hence, novel TUs and known genes may represent different portions of the transcriptome. Two hundred nine (21%) of chromosome 22 transcripts participated in 77 cis-antisense and 42 promoter-sharing UGPs. Transcripts involved simultaneously in both UGP types were more common than was expected (P = 0.01). UGPs were nonrandomly distributed along the sequence: 89 (75%) clustered in distinct regions, the sum of which equaled 4.4 Mb (<13% of the chromosome). Eighty (67%) of the UGPs possessed significant locus structure differences between primates and rodents. Since some TUs may be functional noncoding transcripts and since the cis-regulatory potential of UGPs is well recognized, TUs and UGPs specific to the primate lineage may contribute to the genomic basis for primate-specific phenotypes.

Animals↗

PubMed2005

From the margins of the genome: mobile elements shape primate evolution.

As is the case with mammals in general, primate genomes are inundated with repetitive sequence. Although much of this repetitive content consists of "molecular fossils" inherited from early mammalian ancestors, a significant portion of this material comprises active mobile element lineages. Despite indications that these elements played a major role in shaping the architecture of the genome, there remain many unanswered questions surrounding the nature of the host-element relationship. Here we review advances in our understanding of the host-mobile element dynamic and its overall impact on primate evolution.

Alternative Splicing↗

PubMed1992

Characterization of a highly repeated interspersed DNA sequence of Trypanosoma cruzi: its potential use in diagnosis and strain classification.

In the present paper we report the characterization of a repetitive DNA sequence from the genome of the Maracay strain of Trypanosoma cruzi. The sequence is 1025 nucleotides long and represent about 7% of the total nuclear DNA of the parasite with a copy number of 1-2 x 10(4) copies per genome. It is also present in a high copy number in several strains of T. cruzi but absent from other trypanosomatids and from the human genome. The DNA sequence is interspersed and present on many chromosomes. We show that the different copies of this repeat present extensive endonuclease restriction polymorphisms. Using 2 conserved oligonucleotide primers derived from the repetitive sequence, together with the polymerase chain reaction technique, the presence of less than 1/30 of a single parasite can be readily detected by ethidium bromide staining.

Animals↗

PubMed1994

Genome size and organization in the ixodid tick Amblyomma americanum (L.).

We used DNA reassociation kinetics to determine genome size and organization in the ixodid tick Amblyomma americanum. We calculated the genome size of A. americanum to be approximately 1.08 pg or 1.04 x 10(9) base pairs and to consist of 35.8% unique DNA, 4.2% foldback sequences, 17.9% highly repetitive sequences, and 42.1% moderately repetitive sequences. Comparison of the reassociation kinetics of long and short fragments revealed repetitive sequences to be distributed in a pattern of long period interspersion, a feature that, to date, has been associated with arthropod genomes that lack a high percentage of repetitive DNA.

Animals↗

PubMedDate not supplied

A paradigm to measure mismatch negativity responses to phonetic and acoustic changes in parallel.

The mismatch negativity (MMN) of the event-related potential has been purported to be an objective index of central auditory processing. The present study tested a new paradigm to measure the MMN responses to phonological changes in parallel with those to simple acoustic changes. Stimulus sequences consisted of repetitive consonant-vowel syllables interspersed with infrequent phonetic changes (in place of articulation or voicing) and repetitive sinusoidal tones with occasional acoustic changes (in frequency or duration). The speech and tone stimuli were delivered to the opposite ears (right and left, respectively) at a stimulus onset asynchrony (SOA) of 300 ms. The MMNs elicited in this new paradigm were compared with those measured in a conventional paradigm, in which the speech and tone stimuli were presented in separate sequences at an identical speech-speech or tone-tone SOA (600 ms) of the new paradigm. The MMNs elicited in the two paradigms had a similar morphology and topography, although the MMNs measured with the new paradigm were slightly smaller for 3 out of 4 types of deviants. The results suggest that the new paradigm enables the measurement of reliable MMNs to phonetic changes in parallel with those to acoustic changes.

Adult↗

PubMed1988

Organization of the Euplotes crassus micronuclear genome.

Euplotes crassus, like other hypotrichous ciliated protozoa, eliminates most of its micronuclear chromosomal DNA in the process of forming the small linear DNA molecules that comprise the macronuclear genome. By characterizing randomly selected lambda phage clones of E. crassus micronuclear DNA, we have determined the distribution of repetitive and unique sequences and the arrangement of macronuclear genes relative to eliminated DNA. This allows us to compare the E. crassus micronuclear genome organization to that of another distantly related hypotrichous ciliate, Oxytricha nova. The clones from E. crassus segregate into three prevalent classes: those containing primarily eliminated repetitive DNA (Class I); those containing macronuclear genes in addition to repetitive sequences (Class II); and those containing only eliminated unique sequence DNA (Class III). All of the repetitive sequences in these clones belong to the same highly abundant repetitive element family. Our results demonstrate that the sequence organization of the E. crassus and O. nova micronuclear genomes is related in that the macronuclear genes are clustered together in the micronuclear genome and the eliminated unique sequences occur in long stretches that are uninterrupted by repetitive sequences. In both organisms a single repetitive element family comprises the majority of the eliminated interspersed middle repetitive DNA and appears to be preferentially associated with the macronuclear sequence clusters. The similarities in the sequence organization in these two organisms suggest that clustering of macronuclear genes plays a role in the chromosome fragmentation process.

Animals↗

PubMed1992

Molecular cloning of porcine soluble angiotensin-binding protein.

Soluble angiotensin-binding protein (sABP) is a 75-kDa cytosolic protein that binds angiotensins and its analogues with high affinity. In this study, the primary structure of porcine sABP is determined by cDNA cloning. Based on the partial amino acid sequences of sABP tryptic fragments, fully degenerate oligonucleotides were synthesized, and used as primers for polymerase chain reactions to amplify the corresponding sABP cDNA fragment from porcine liver first-strand cDNA. By using initially the polymerase chain reaction product and later partial cDNA clones as probes, porcine heart and liver cDNA libraries were screened, and several positive clones were obtained including one covering the entire coding region. From the cDNA sequence, an open reading frame that encodes sABP as a 704-amino acid protein with molecular mass of 80,800 daltons is predicted. No significant homology was seen between sABP and other proteins in GenBank and NBRF data bases, including the angiotensin-related proteins such as angiotensin converting enzyme, renin, and AT1 angiotensin II receptor. Northern blot analysis of poly(A)+ RNA revealed that the mRNA for sABP is expressed as 5.3- and 2.8-3.2-kilobase transcripts. These transcripts are generated by the use of alternative polyadenylation signals. Within the 3'-untranslated region of the cDNA sequence downstream from the polyadenylation signals for smaller transcripts, a porcine short interspersed repetitive element (SINE) was found; only the longer 5.3-kilobase transcript had the SINE sequence.

Amino Acid Sequence↗

PubMed2001

An Alu insert as the cause of a severe form of hemophilia A.

Alu sequences represent a specific human family of interspersed repetitive DNA, with a copy number in excess of 500,000 within the human genome. Alu repeats are rarely present in protein-coding regions of mature RNA, and only a few Alu insert mutations have been described so far. In this paper we present an Alu retroposition event in a family with a severe form of hemophilia A. The inserted Alu element belonging to the youngest Yb8 subfamily disrupts the reading frame at methionine 1224, exon 14 of the factor VIII gene, leading to a stop codon within the inserted sequence. This observation indicates that the retroposition of Alu elements is a continuing process possibly generating various human genetic defects.

Adolescent↗

PubMed1982

[Nucleotide sequence organization of nuclear DNA of wheat embryos].

The kinetic component composition of wheat embryo nuclear DNA was studied. It was shown that 32% of the genome consist of highly repetitive sequences. Intermediate repetitive sequences with repetitive frequency 1300 per genome constitute the bulk (52%) of the wheat embryo nuclear genome. The unique sequences constitute 12% of wheat embryo DNA. The individual families of intermediate repetitive and unique sequences were isolated; their reassociation kinetics were investigated and their kinetic complexity and repetition frequency were evaluated. Intermediate repetitive sequences 600-800 nucleotides in length were interspersed with unique sequences 800-1000 nucleotides long in the nuclear genome of wheat embryos. The linear relationship between the fragment length and the increasing amount of the zero-time binding DNA implies that 4% of the wheat embryos genome consists of palindromic sequences, which are clustered into groups.

Base Composition↗

PubMed1978

DNA sequence organisation in avian genomes.

By means of renaturation kinetics of DNA of the three avian species Cairina domestica, Gallus domesticus and Columba livia domestica the following major DNA repetition classes were observed: a very fast reannealing fraction comprising about 15% of the DNA, a fast or intermediate reannealing fraction that makes up 10%, and a slow reannealing fraction of about 70%, which apparently renatures with single copy properties. --Comparing the reassociation behaviour of short (0.3 kb) and long (greater than 2 kb) DNA fragments of duck and chicken it becomes apparent that only 12% (duck) and 28% (chicken) of the single copy DNA are interspersed with repetitive elements on 2 to 3 kb long fragments. The lengths of the repetitive sequences were estimated by optical hyperchromicity measurements, by agarose A-50 chromatography of S1 nuclease resistant duplexes and by electron microscopic measurements of the S1 nuclease resistant duplexes. It was found that in the case of the chicken DNA the single copy sequences alternating with middle repetitive ones are at least 2.3 kb long; the interspersed moderate repeats have a length average of at least 1.5 kb. The sequence length of the moderate repeats in duck DNA is smaller. The results show that the duck and the chicken genomes do not follow the short period interspersion pattern of genome organisation, characteristic of the eucaryotic organisms studied so far.

Animals↗

PubMed2001

Dynamics of mobile element activity in chalcone synthase loci in the common morning glory (Ipomoea purpurea).

Mobile element dynamics in seven alleles of the chalcone synthase D locus (CHS-D) of the common morning glory (Ipomoea purpurea) are analyzed in the context of synonymous nucleotide sequence distances for CHS-D exons. By using a nucleotide sequence of CHS-D from the sister species Ipomoea nil (Japanese morning glory [Johzuka-Hisatomi, Y., Hoshino, A., Mori, T., Habu, Y. & Iida, S. (1999) Genes Genet. Syst. 74, 141-147], it is also possible to determine the relative frequency of insertion and loss of elements within the CHS-D locus between these two species. At least four different types of transposable elements exist upstream of the coding region, or within the single intron of the CHS-D locus in I. purpurea. There are three distinct families of miniature inverted-repeat transposable elements (MITES), and some recent transpositions of Activator/Dissociation (Ac/Ds)-like elements (Tip100), of some short interspersed repetitive elements (SINEs), and of an insertion sequence (InsIpCHSD) found in the neighborhood of this locus. The data provide no compelling evidence of the transposition of the mites since the separation of I. nil and I. purpurea roughly 8 million years ago. Finally, it is shown that the number and frequency of mobile elements are highly heterogeneous among different duplicate CHS loci, suggesting that the dynamics observed at CHS-D are locus-specific.

Acyltransferases↗

PubMed2001

Maque, a family of extremely short interspersed repetitive elements: characterization, possible mechanism of transposition, and evolutionary implications.

Database analysis revealed a novel family of very short interspersed repetitive elements named Maque in the African malaria mosquito, Anopheles gambiae. Past mobility of Maque was demonstrated by evidence of its insertion that resulted in a target duplication. Approximately 220 copies of Maque were present in the A. gambiae genome. Although only approximately 60 bp long, Maque has the appearance of a distinct transposition unit. Eleven of the 12 Maque elements found in the database were flanked by 9-14 bp direct repeats, indicating that their transposition was relatively recent. Sequence comparison and phylogenetic analyses suggest that there are at least two subgroups within the Maque family, suggesting that they may have been originated from more than one source. Five of the 12 Maque elements had at least one other repetitive element nearby. Three of the Maque elements were found near genes. However, Maque was not found in the coding regions of genes or in any of the expressed sequence tags (ESTs), which is consistent with its significantly biased distribution toward A + T rich regions. Several characteristics of Maque indicate that it is likely a non-autonomous retro-element. The evolutionary origin of Maque and the differences between Maque and other known retro-elements including short interspersed repetitive elements (SINEs) are discussed. A hypothesis is proposed in which short sequences containing just the reverse transcriptase recognition signal (RTRS) could potentially contribute to exon shuffling and the genesis of some primordial SINEs.

Animals↗

PubMed1998

Identification of a short interspersed repetitive element in partially spliced transcripts of the bell pepper (Capsicum annuum) PAP gene: new evolutionary and regulatory aspects on plant tRNA-related SINEs.

In bell pepper, a gene encoding a major plastid-lipid associated protein is expressed as both partially and totally spliced transcripts (respectively PAP2 and PAP1). Although PAP is present as a single-copy gene in the bell pepper genome, Southern blots using PAP2 as a probe revealed multiple homologous copies. Analyses of the intronic sequence of PAP2 showed the existence of a 206bp short interspersed repetitive element (SINE) belonging to the Ts family of retrotransposons (Yoshioka et al., 1993). Comparison with PAP sequences in other Solanaceae species suggested that the structure of the gene is highly conserved: the two introns are inserted at the same position. However, the Ts insertion found in bell pepper is absent in tobacco and tomato. Studies using RT-PCR showed that in these latter species only totally spliced transcripts of PAP are present. On the other hand, RNA analyses of tobacco plants transformed with the bell pepper PAP revealed the presence of both totally and incompletely spliced transcripts. Altogether our results support the hypothesis that the Ts insertion into the first intron of PAP results in a splicing defect of the corresponding pre-mRNA. Based on the presence of peculiar, previously unidentified Ts elements, a possible horizontal transmission of Ts elements from animals to plants is discussed.

Animals↗

PubMed1995

Polymorphic human specific Alu insertions as markers for human identification.

Alu sequences represent the largest family of short interspersed repetitive elements (SINEs) in humans with 500 000 copies per genome. Recently, one Alu subfamily was found to be human specific (HS). We originally described the use of polymorphis HS Alu insertions as a tool in population studies and recently as tools in DNA fingerprinting and forensic analysis. In this report, we will use this simple polymerase chain reaction (PCR) base technique for the detection of HS Alu insertion polymorphisms. We will test the resolving power of this DNA profiling approach in both population genetics and paternity assessment. At the population level, we will describe the genotypic distribution of five polymorphic Alu insertions among 3 populations from the American continent, one of African origin, the other two Amerindians. Insight into their relationships will be provided. At the family level, we will examine one European American family of seven individuals and the same pedigree will also be characterized by way of the two systems currently and widely used to ascertain paternity: PCR-sequence specific oligonucleotide probe hybridization (PCR-SSO) and PCR-restriction fragment length polymorphism (PCR-RFLP) of human leucocyte antigen (HLA) class II molecules, and a standard RFLP protocol used in forensic casework and paternity studies. The importance and strengths of the methods as well as its perspectives for future use in filiation studies will be evaluated.

Forensic Medicine↗

PubMed2001

Typical demethylation events in cloned pig embryos. Clues on species-specific differences in epigenetic reprogramming of a cloned donor genome.

We investigated whether a genomic demethylation process occurs in pig preimplantation embryos produced by either normal fertilization or somatic cell nuclear transfer. The methylation status of the centromeric satellite and the PRE-1 short interspersed element (SINE) sequences was characterized using bisulfite-sequencing technology. Typical demethylation processes were identified in these repetitive sequences of the cloned donor genome during cleavage, the patterns of which were similar to the ones detected in fertilized counterparts. These findings are different from previous observations with cloned bovine embryos where various repeated regions of the donor genome exhibited aberrant methylation patterns. Our results indicate that species-specific differences exist in modifying the epigenetic status of cloned donor genomes.

Animals↗

PubMed2003

Unique mammalian tRNA-derived repetitive elements in dermopterans: the t-SINE family and its retrotransposition through multiple sources.

Short interspersed nuclear elements (SINEs) are dispersed repetitive DNA sequences that are major components of all mammalian genomes. They have been described in almost all lineages of Euarchontoglires (rodents, rabbits, primates, flying lemurs, and tree shrews), except in flying lemurs. Most SINE family members are composed of three distinct regions: a 5' tRNA-related region, a tRNA-unrelated region, and a short tandem repeat at the 3' end that is AT-rich. The newly discovered SINE family in Cynocephalus deviates from this common structure. All 30 SINE loci analyzed in this family lack a tRNA-unrelated region and are composed exclusively of tRNA-related elements. Therefore, this novel SINE structure, described for the first time in mammalian genomes, was designated as t-SINE. The t-SINE family exhibits a high copy number and is specific to flying lemurs. Three major t-SINE subfamilies could be distinguished on the basis of characteristic nucleotides, deletions, insertions, and duplications. These sequence-specific characteristics within subfamilies and sub-subfamilies reveal that they are derived copies of distinct progenitors. We present evolutionary relationships between subfamilies and compare relationships between the subfamilies and the isoleucine tRNA gene. t-SINE amplification occurred through multiple sources and is supposedly mobilized via the L1-encoded reverse transcriptase-dependent retrotranspositional mechanism in trans.

Animals↗