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Results for “Interspersed Repetitive Sequences”

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PubMed2005

Distribution and intensity of constraint in mammalian genomic sequence.

Comparisons of orthologous genomic DNA sequences can be used to characterize regions that have been subject to purifying selection and are enriched for functional elements. We here present the results of such an analysis on an alignment of sequences from 29 mammalian species. The alignment captures approximately 3.9 neutral substitutions per site and spans approximately 1.9 Mbp of the human genome. We identify constrained elements from 3 bp to over 1 kbp in length, covering approximately 5.5% of the human locus. Our estimate for the total amount of nonexonic constraint experienced by this locus is roughly twice that for exonic constraint. Constrained elements tend to cluster, and we identify large constrained regions that correspond well with known functional elements. While constraint density inversely correlates with mobile element density, we also show the presence of unambiguously constrained elements overlapping mammalian ancestral repeats. In addition, we describe a number of elements in this region that have undergone intense purifying selection throughout mammalian evolution, and we show that these important elements are more numerous than previously thought. These results were obtained with Genomic Evolutionary Rate Profiling (GERP), a statistically rigorous and biologically transparent framework for constrained element identification. GERP identifies regions at high resolution that exhibit nucleotide substitution deficits, and measures these deficits as "rejected substitutions". Rejected substitutions reflect the intensity of past purifying selection and are used to rank and characterize constrained elements. We anticipate that GERP and the types of analyses it facilitates will provide further insights and improved annotation for the human genome as mammalian genome sequence data become richer.

Animals↗

PubMed1993

SIRE-1, a long interspersed repetitive DNA element from soybean with weak sequence similarity to retrotransposons: initial characterization and partial sequence.

Gm776 is a 776-bp subregion of a member of an interspersed family of relatively homogeneous repetitive DNA elements from soybean (Glycine max). The fragment was originally amplified from soybean DNA by the polymerase chain reaction using a single 22-nucleotide primer, and consequently terminates in an inverted repeat. The elements defined by Gm776 are at least 10.6 kb in length and constitute a family of 500-800 members per haploid genome. The family has been designated SIRE-1 (soybean interspersed repetitive element 1). Overlapping regions of Gm776 exhibit suggestive DNA sequence similarity to Ta1 and Ty1, copia-like retrotransposons from Arabidopsis thaliana and Saccharomyces cerevisiae, respectively. However, there are no similarities at the amino acid level, and the regions of similarity are not functionally related.

Base Sequence↗

PubMed1974

Interspersion of repetitive and single-copy sequences in nuclear ribonucleic acid of high molecular weight.

Nuclear RNA of high molecular weight, approximately 15 to 30 x 10(3) nucleotides long, isolated from rat ascites cells, has been shown previously to contain both middle repetitive and single-copy sequences. However, it was not known whether these sequences were located on separate molecules or whether they were interspersed within the same molecule. The present communication distinguishes between these possibilities and shows that a large proportion of nuclear RNA of high molecular weight consists of interspersed middle repetitive and single-copy sequences.

Animals↗

PubMed2003

Comparative analysis of vertebrate dystrophin loci indicate intron gigantism as a common feature.

The human DMD gene is the largest known to date, spanning > 2000 kb on the X chromosome. The gene size is mainly accounted for by huge intronic regions. We sequenced 190 kb of Fugu rubripes (pufferfish) genomic DNA corresponding to the complete dystrophin gene (FrDMD) and provide the first report of gene structure and sequence comparison among dystrophin genomic sequences from different vertebrate organisms. Almost all intron positions and phases are conserved between FrDMD and its mammalian counterparts, and the predicted protein product of the Fugu gene displays 55% identity and 71% similarity to human dystrophin. In analogy to the human gene, FrDMD presents several-fold longer than average intronic regions. Analysis of intron sequences of the human and murine genes revealed that they are extremely conserved in size and that a similar fraction of total intron length is represented by repetitive elements; moreover, our data indicate that intron expansion through repeat accumulation in the two orthologs is the result of independent insertional events. The hypothesis that intron length might be functionally relevant to the DMD gene regulation is proposed and substantiated by the finding that dystrophin intron gigantism is common to the three vertebrate genes.

Amino Acid Sequence↗

PubMed1998

Expression of transposon LINE-1 is relatively human-specific and function of the transcripts may be proliferation-essential.

A new 1.7-kb LINE (L1) transcript has been discovered from the cDNA library of human small-cell lung cancer. The nucleotide sequence of 1.7-kb L1 transcript is 98.4% similar to that of open reading frame 2 (ORF2) found in consensus complete 6.5-kb L1. Although L1 DNA segments could be detected from both genomic DNAs of human and rodent cells by PCR, these L1 transcripts were not detectable from cellular RNA of rodent cells by RT-PCR and northern hybridization, implying that the expression of L1 was relatively human-specific. The functions of L1 transcripts in cells are not yet clear. This paper shows that L1 transcripts are essential for cell proliferation when determined by antisense oligonucleotides. Alternately, L1 transcripts exhibit in all human cells we have examined so far, and they map to all the human chromosomes. A sequence-similarity search in the GenBank database indicates that the major sequence of 1.7-kb L1 is integrated in human retinoblastoma (Rb), IL-2, and factor VIII genes. Since Rb and factor VIII genes have displayed high frequency of chromosomal deletions in various cancers and haemophilia A, the universal integration of long and homologous L1 segments in the genes and all chromosomes may be liable to promote abnormal DNA rearrangement.

Base Sequence↗

PubMed2003

Development of a gene expression vector for Thermus thermophilus based on the promoter of the respiratory nitrate reductase.

A specific expression system for Thermus spp. is described. Plasmid pMKE1 contains replicative origins for Escherichia coli and Thermus spp., a selection gene encoding a thermostable resistance to kanamycin, and a 720 bp DNA region containing the promoter (Pnar), and the regulatory sequences of the respiratory nitrate reductase operon of Thermus thermophilus HB8. Two genes, encoding a thermophilic beta-galactosidase and an alkaline phosphatase were cloned in pMKE1 as cytoplasmic and periplasmic reporters, respectively. The expression of the reporters was specifically induced by the combined action of nitrate and anoxia in facultative anaerobic derivatives of T. thermophilus HB27 to which the gene cluster for nitrate respiration was transferred by conjugation. Overexpressions in the range of approximately 200-fold were obtained for the cytoplasmic reporter, whereas that of the periplasmic reporter was limited to approximately 20-fold, with respect to their intrinsic respective activities.

Alkaline Phosphatase↗

PubMed1998

Nonhomologous recombination between the cytochrome b558 heavy chain gene (CYBB) and LINE-1 causes an X-linked chronic granulomatous disease.

We cloned and characterized a genomic DNA fragment including the deletion junction of a chronic granulomatous disease patient with a 25-kb deletion extending to the 5' two-thirds of CYBB. The 3' breakpoint of the deletion exists in exon 7 of CYBB. A LINE-1 element lies at 5 kb upstream of CYBB in normal persons, and the 5' breakpoint of the deletion in the patient is in the LINE-1 element. There are no significant homologies between corresponding normal 5' and 3' regions flanking the breakpoint of the patient, so a nonhomologous recombination is the most possible mechanism for this 25-kb deletion. The analysis also reveals that the patient has a novel 30-bp duplication in the 5' flanking region of the deletion point, which was transmitted by his mother with the deletion. Furthermore we suggest that the deletion occurred in his grandfather.

Base Sequence↗

PubMed2006

Complete sequence of the large virulence plasmid pSFO157 of the sorbitol-fermenting enterohemorrhagic Escherichia coli O157:H- strain 3072/96.

The large virulence plasmid pSFO157 of sorbitol-fermenting E. coli O157:H(-) strain 3072/96 has a size of 121,239bp and contains 96 open reading frames >50bp. It is therefore 29,162bp larger (ca. 32%) than plasmid pO157 of E. coli O157:H7 strain EDL933. Major differences between the plasmids are the absence of katP, espP, and toxB in pSFO157 and, instead of these, the presence of the sfp fimbriae gene cluster and a large part of an F-plasmid transfer region, the latter accounting for most of the additional DNA. The differences in the order of the genes and their composition, as well as the presence of a number of replication-associated genes and mobile genetic elements suggests that the large E. coli O157 virulence plasmids have a complex evolutionary origin.

Bacterial Proteins↗

PubMed2004

Molecular evolutionary characterization of the mussel Mytilus histone multigene family: first record of a tandemly repeated unit of five histone genes containing an H1 subtype with "orphon" features.

The present work represents the first characterization of a clustered histone repetitive unit containing an H1 gene in a bivalve mollusk. To complete the knowledge on the evolutionary history of the histone multigene family in invertebrates, we undertake its characterization in five mussel Mytilus species, as an extension of our previous work on the H1 gene family. We report the quintet H4-H2B-H2A-H3-H1 as the major organization unit in the genome of Mytilus galloprovincialis with two 5S rRNA genes with interspersed nontranscribed spacer segments linked to the unit, which is not justified by their cotranscription with histone genes. Surprisingly, 3' UTR regions of histone genes show two different mRNA termination signals, a stem-loop and a polyadenylation signal, both related to the evolution of histone gene expression patterns throughout the cell cycle. The clustered H1 histones characterized share essential features with "orphon" H1 genes, suggesting a common evolutionary origin for both histone subtypes which is supported by the reconstructed phylogeny for H1 genes. The characterization of histone genes in four additional Mytilus species revealed the presence of strong purifying selection acting among the members of the family. The chromosomal location of most of the core histone genes studied was identified by FISH close to telomeric regions in M. galloprovincialis. Further analysis on nucleotide variation would be necessary to assess if H1 proteins evolve according to the birth-and-death model of evolution and if the effect of the strong purifying selection maintaining protein homogeneity could account for the homologies detected between clustered and "orphon" variants.

Amino Acid Sequence↗

PubMed2002

The human ribosomal protein genes: sequencing and comparative analysis of 73 genes.

The ribosome, as a catalyst for protein synthesis, is universal and essential for all organisms. Here we describe the structure of the genes encoding human ribosomal proteins (RPs) and compare this class of genes among several eukaryotes. Using genomic and full-length cDNA sequences, we characterized 73 RP genes and found that (1) transcription starts at a C residue within a characteristic oligopyrimidine tract; (2) the promoter region is GC rich, but often has a TATA box or similar sequence element; (3) the genes are small (4.4 kb), but have as many as 5.6 exons on average; (4) the initiator ATG is in the first or second exon and is within plus minus 5 bp of the first intron boundaries in about half of cases; and (5) 5'- and 3'-UTRs are significantly smaller (42 bp and 56 bp, respectively) than the genome average. Comparison of RP genes from humans, Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae revealed the coding sequences to be highly conserved (63% homology on average), although gene size and the number of exons vary. The positions of the introns are also conserved among these species as follows: 44% of human introns are present at the same position in either D. melanogaster or C. elegans, suggesting RP genes are highly suitable for studying the evolution of introns.

Animals↗

PubMed2006

Regulated expression of glutamyl-tRNA synthetase is directed by a mobile genetic element in the cyanobacterium Tolypothrix sp. PCC 7601.

The genome of Tolypothrix sp. PCC 7601 carries two copies of a novel insertion sequence, ISTosp1. One of the two copies is located upstream of the gene encoding glutamyl-tRNA synthetase, an enzyme playing a key role in protein and pigment synthesis. The tnpA gene of the IS element and gltX were co-transcribed and their expression was transiently upregulated upon retrieval of the ammonium source irrespective of whether nitrate or no nitrogen source were available. The second copy is also transcribed and shows a similar regulatory pattern. Structural elements of the promoter (-10 and -35 sequences) directing the expression of the tnpA-gltX operon have been localized within the IS. Regulatory sequences involving the NtcA transcription factor in the control of tnpA-gltX expression were found both within and in sequences upstream of the insertion element. The expression of gltX in a closely related cyanobacterium, Nostoc sp. PCC 7120, which lacks the insertion upstream of gltX, decreased upon ammonium retrieval, a regulatory pattern that markedly differs from that observed in Tolypothrix sp. PCC 7601. ISTosp1 constitutes a good example of how cells can make use of a transposable element to evolve an original regulatory mechanism.

Bacterial Proteins↗

PubMed2005

Human subtelomere structure and variation.

Work towards completion of the human reference genome sequence has revealed a great deal of complexity and plasticity in human subtelomeric regions. The highly variable subtelomeric repeat regions are filled with recently shuffled genomic segments, many of which contain sequences matching transcripts and transcript fragments; the rapid duplication and combinatorial evolution of these regions has generated an extremely diverse set of subtelomeric alleles in the human species, the complexity and potential significance of which is only beginning to be understood. This review summarizes recent progress in analyzing human subtelomeric sequence assemblies and large-scale variation in human subtelomere regions.

Genetic Variation↗

PubMed2001

Architecture and anatomy of the genomic locus encoding the human leukemia-associated transcription factor RUNX1/AML1.

The RUNX1 gene on human chromosome 21q22.12 belongs to the 'runt domain' gene family of transcription factors (also known as AML/CBFA/PEBP2alpha). RUNX1 is a key regulator of hematopoiesis and a frequent target of leukemia associated chromosomal translocations. Here we present a detailed analysis of the RUNX1 locus based on its complete genomic sequence. RUNX1 spans 260 kb and its expression is regulated through two distinct promoter regions, that are 160 kb apart. A very large CpG island complex marks the proximal promoter (promoter-2), and an additional CpG island is located at the 3' end of the gene. Hitherto, 12 different alternatively spliced RUNX1 cDNAs have been identified. Genomic sequence analysis of intron/exon boundaries of these cDNAs has shown that all consist of properly spliced authentic coding regions. This indicates that the large repertoire of RUNX1 proteins, ranging in size between 20-52 kDa, are generated through usage of alternatively spliced exons some of which contain in frame stop codons. The gene's introns are largely depleted of repetitive sequences, especially of the LINE1 family. The RUNX1 locus marks the transition from a ~1 Mb of gene-poor region containing only pseudogenes, to a gene-rich region containing several functional genes. A search for RUNX1 sequences that may be involved in the high frequency of chromosomal translocations revealed that a 555 bp long segment originating in chromosome 11 FLI1 gene was transposed into RUNX1 intron 4.1. This intron harbors the t(8;21) and t(3;21) chromosomal breakpoints involved in acute myeloid leukemia. Interestingly, the FLI1 homologous sequence contains a breakpoint of the t(11;22) translocation associated with Ewing's tumors, and may have a similar function in RUNX1.

3' Untranslated Regions↗

PubMedDate not supplied

The closely related neuropeptide genes encoding adipokinetic hormones I and II have very different 5'-flanking regions.

Adipokinetic hormones I and II are 10- and 8-amino-acid grasshopper neuropeptides that are derived from 63- and 61-amino-acid peptide precursors, respectively. Each precursor is encoded by a separate gene consisting of three very small exons separated by two large introns. The identical exon structure of the two genes suggests that they evolved through duplication of a common ancestral gene. Despite the precise conservation of exon structure and the similarity of the coding sequences, the two genes have very different 5'-flanking regions, suggesting that they are differentially regulated. For example, sequences similar to the vertebrate insulin enhancer elements NIR and FAR are present upstream of the promoter region of the adipokinetic hormone II gene, but not in the adipokinetic hormone I gene. Both of these insect genes contain short interspersed repetitive DNA sequences in their introns that may have facilitated a gene duplication event.

Amino Acid Sequence↗

PubMed2002

Clonality of Fusobacterium nucleatum in root canal infections.

Fusobacterium nucleatum is a gram-negative non-spore-forming, non-motile, obligate anaerobic rod that is normally isolated from the oral cavity. Several studies have reported a significant heterogeneity within the F. nucleatum species. The aim of the present study was to analyze the clonal diversity of F. nucleatum strains isolated from intracanal infections and to evaluate the presence of Enterobacterial Repetitive Intergenic Consensus (ERIC)-like sequences in the genome of F. nucleatum. Samples were collected from 13 single-root teeth from adult patients, all having carious lesions, necrotic pulps and radiographic evidence of periradicular bone loss. F. nucleatum was isolated from two different patients (subjects 5 and 7) by culture. Amplification of 19 colonies from subject 5 and 15 colonies from subject 7 using ERIC primers resulted in four clonal types, two per subject. An intense amplicon of approximately 700 bp was generated by ERIC-PCR for all F. nucleatum isolates and F. nucleatum ssp. polymorphum ATCC 10953. The amplification reaction using primer 1254 confirmed the results obtained with the ERIC primer. Our findings indicate that DNA fingerprints provided by ERIC- and Arbitrarily Primed (AP)-PCR may constitute a powerful tool for investigating F. nucleatum clonal diversity.

Adult↗

PubMed1999

Molecular characterization of In50, a class 1 integron encoding the gene for the extended-spectrum beta-lactamase VEB-1 in Pseudomonas aeruginosa.

A clinical isolate of Pseudomonas aeruginosa, JES, was resistant to extended-spectrum cephalosporins with a marked synergistic effect with clavulanic acid on a routine antibiogram. Preliminary PCR analysis revealed the presence of blaVEB-1, an integron-located gene encoding an extended-spectrum beta-lactamase previously identified in Escherichia coli MG-1. Using class 1 integron primers and blaVEB-1 intragenic primers, the insert region of the blaVEB-1 containing integron along with some flanking sequence from P. aeruginosa JES was amplified and subsequently sequenced. In50 contains within its variable region, in addition to qacE delta 1 and sull genes commonly found in class 1 integrons, two gene cassettes, veb1 and aadB. In50 is peculiar since its attI1 site is interrupted by two novel insertion sequences, IS1999 and IS2000. P. aeruginosa JES and Escherichia coli MG-1 strains were isolated from patients previously hospitalized in south east Asian countries. The finding of blaVEB-1 in these strains and on different integrons underlines the interspecies spread of this integron-located extended-spectrum beta-lactamase gene.

Amino Acid Sequence↗

PubMed2005

[Molecular typing of the Mycobacterium tuberculosis strains circulating in central Russia: efficiency of spoligotyping and VNTR-MIRU].

Current problems of molecular epidemiology of the Mycobacterium tuberculosis strains circulating in Samara Region, Russia are discussed. A total of 190 isolates of Mycobacterium tuberculosis were typed using two PCR-based molecular methods. The cultures were isolated from civil and prison patients with pulmonary tuberculosis recruited from different tuberculosis institutions across the Samara region. The usefulness of spoligotyping and 15-locii VNTR-MIRU was assessed for genotyping of Mycobacterium in population with high prevalence of Beijing strains (67.9%) using statistical analyses that included calculation of Hunter-Gaston index. The VNTR-MIRU method was demonstrated to be more efficient and was characterized by higher discrimination (index 0.747) compare to spoligotyping (index 0.572). VNTR-MIRU loci 10, 26, 31, 39, 40 and ETR-A were mostly polymorphic and therefore recommended for use in screening. It could be performed by manual electrophoresid, provided that automated sequencing is not available.

Bacterial Typing Techniques↗

PubMed2003

Structure of gene flanking regions and functional analysis of sequences upstream of the rat hsp70.1 stress gene.

We present structural and comparative analysis of the flanking regions of the rat hsp70.1 stress gene. Several repetitive sequences, microsatellites and short interspersed repetitive elements (SINEs) were found, as well as a significant gap in the 3' UTR, as compared to the orthologous mouse gene. We also show that the complex microsatellite region composed of partially overlapping inverted repeat and long homopurine-homopyrimidine sequence, which is localized 1.8 kbp upstream of the transcription start site, is capable to adopt non-B DNA structures (an H-DNA and a cruciform structure) in vitro. Functional analysis performed with the use of various fragments of the 5'end flanking regions ligated to the chloramphenicol acetyltransferase (CAT) reporter gene revealed a crucial role of cooperation between heat shock element (HSE) regulatory sequences, while none of the three HSEs alone is able to drive efficient heat induced transcription of the reporter gene. We also found that the microsatellite region does not influence transcription by itself, however, it abolishes the effect of the adjacent putative silencing element. To our knowledge, this is a first extensive structural and functional analysis of the promoter region of the mammalian heat inducible hsp70i gene localized distally to the hsp70-related spermatid-specific gene in the major histocompatibility complex III.

3' Flanking Region↗