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PubMed2003

Transposable elements and vertebrate protein diversity.

Interspersed repetitive sequences are major components of eukaryotic genomes. Repetitive elements comprise about 50% of the mammalian genome. They interact with the whole genome and influence its evolution. Repetitive elements may serve as recombination hot spots or acquire specific cellular functions such as RNA transcription control or become part of protein coding regions. The latter is a subject of presented analysis. We searched all currently available vertebrate protein sequences, including human proteome complement for the presence of transposable elements. It appears that insertion of TE-cassettes into open reading frames is a general phenomena. They can be found in all vertebrate lineages and originate in all types of transposable elements. It seems that genomes use those cassettes as 'ready to use' motifs in their evolutionary experiments. Most of TE-cassettes are used to create alternative forms of a message and usually the other form, without TE-cassette, is expressed in a cell. Tables listing vertebrate messages with TE-cassettes are available at http://warta.bio.psu.edu/ScrapYard/.

Animals↗
PubMed1982

The human pro-opiomelanocortin gene: organization, sequence, and interspersion with repetitive DNA.

The human pro-opiomelanocortin (POMC) gene has been characterized by molecular cloning and DNA sequence analysis. Although this gene codes for several different polypeptide hormones, only a single intron interrupts the protein coding region. The DNA in this intron, and in a second intron found in the region of the gene homologous to the mRNA 5'-untranslated sequence, contains repetitive DNA sequences. At least some of these sequences belong to the Alu family of transcribed middle repetitive DNA. The determination of the complete nucleotide sequence of the coding regions of the gene demonstrates that the pattern of homologous and variable regions seen in the POMC protein between different species is reflected at the DNA level. DNA sequences encoding the highly conserved regions of POMC are 90-95% homologous between species while the coding sequences for the variable regions of the protein are approximately 70% homologous. The very high degree of homology in the amino terminal portion of POMC is consistent with an important physiological role for this peptide.

Amino Acid Sequence↗
PubMed1982

Comparative DNA/DNA reassociation kinetics in three hamster species.

1. Three major DNA repetition classes can be distinguished in the genomes of three hamster species Mesocricetus auratus, Cricetulus griseus, and Phodopus sungorus sungorus: A very fast reassociating fraction of about 13% of the DNA, a fast reassociating fraction comprising 10-23% of the DNA, and a slowly reassociating fraction containing single-copy sequences of 63-78% of hamster DNA. 2. In the DNA of the Syrian and Djungarian hamster 43%-53%, and in the DNA of the Chinese hamster 80% of the single-copy sequences are interspersed with repetitive sequences. 3. The lengths of repetitive DNA sequences, vary between more than 3 kb and 0.3 kb, with the majority of sequences having a length of 0.3 kb to 0.5 kb. 4. The findings suggest that the genomes of the hamster species studied are organized in a short period interspersion pattern. 5. Unlike other vertebrate and invertebrate genomes, moderately repetitive sequences exhibit a high degree of intraspecific homology in the hamster genome.

Animals↗
PubMed2004

Comparative sequence and x-inactivation analyses of a domain of escape in human xp11.2 and the conserved segment in mouse.

We have performed X-inactivation and sequence analyses on 350 kb of sequence from human Xp11.2, a region shown previously to contain a cluster of genes that escape X inactivation, and we compared this region with the region of conserved synteny in mouse. We identified several new transcripts from this region in human and in mouse, which defined the full extent of the domain escaping X inactivation in both species. In human, escape from X inactivation involves an uninterrupted 235-kb domain of multiple genes. Despite highly conserved gene content and order between the two species, Smcx is the only mouse gene from the conserved segment that escapes inactivation. As repetitive sequences are believed to facilitate spreading of X inactivation along the chromosome, we compared the repetitive sequence composition of this region between the two species. We found that long terminal repeats (LTRs) were decreased in the human domain of escape, but not in the majority of the conserved mouse region adjacent to Smcx in which genes were subject to X inactivation, suggesting that these repeats might be excluded from escape domains to prevent spreading of silencing. Our findings indicate that genomic context, as well as gene-specific regulatory elements, interact to determine expression of a gene from the inactive X-chromosome.

Actins↗
PubMed2003

Mobile genetic elements colonizing the genomes of metazoan parasites.

A substantial fraction of the genome of most eukaryotes, including those of metazoan parasites, is predicted to comprise repetitive sequences. Mobile genetic elements (MGEs) will make up much of these repetitive sequences, particularly the interspersed sequences. This article reviews information on MGEs that have colonized the genomes of metazoan parasites (i.e. parasites of parasites). Helminth and mosquito genomes, in particular, are compared with those of better-understood model organisms. MGEs from the genomes of metazoan parasites can be expected to have practical uses in transgenesis and epidemiological studies.

Animals↗
PubMed1988

Molecular studies on interspersed repetitive and unique sequences in the region of the complementation group uncoordinated on the X chromosome of Drosophila melanogaster.

The technique of chromosome walking was used to isolate approximately 60 kb of DNA from the region containing the complementation group uncoordinated of Drosophila melanogaster, located in that part of the X chromosome which spans the euchromatin-heterochromatin junction. The cloned DNA can be divided into two distinct regions. The first contains sequences that are low copy number or unique and are largely conserved between strains. The second region is characterized by units repeated in tandem arrays and is polymorphic within, and between, strains. Each repetitive unit is separated by a member of an abundant sequence family, part of which is homologous to the ribosomal type 1 insertion sequence of D. melanogaster. The molecular organization of the cloned DNA was compared with that of sequences isolated from regions of intercalary heterochromatin and also with genes which have been characterized from more conventional euchromatic regions.

Animals↗
PubMed1980

An abundant cytoplasmic 7S RNA is complementary to the dominant interspersed middle repetitive DNA sequence family in the human genome.

Evidence is presented that a homogeneous cytoplasmic species known as 7S RNA is the only abundant RNA in uninfected HeLa cells which can form strong hybrids with the dominant family of middle repetitive DNA sequences in the human genome. These DNA sequences are known collectively as the Alu family, because most of them share a common Alu I restriction site. When purified 7S RNA was hybridized to three different genomic clones containing Alu family DNA sequences, a specific region (or regions) comprising at most half the RNA sequence was protected from mild digestion with T1 ribonuclease; moreover, the hybrids between 7S RNA and cloned Alu family DNA wer imperfect, since T1 RNAase was able to nick the protected 7S RNA sequences under conditions where a true RNA: DNA duplex would have been resistant. This suggests that 7S RNA is encoded either by a small subset of the 300,000 Alu family sequences in the human genome or by an entirely different family of genes. The sequence of 7S RNA has been highly conserved through recent evolution, and in both avian and murine cells the RNA is selectively incorporated into oncornavirus particles during productive infection. The cellular function of 7S RNA is unknown.

Cytoplasm↗
PubMed1987

Short, interspersed, and repetitive DNA sequences in Spiroplasma species.

Small fragments of DNA from an 8-kbp plasmid, pRA1, from a plant pathogenic strain of Spiroplasma citri were shown previously to be present in the chromosomal DNA of at least two species of Spiroplasma. We describe here the shot-gun cloning of chromosomal DNA from S. citri Maroc and the identification of two distinct sequences exhibiting homology to pRA1. Further subcloning experiments provided specific molecular probes for the identification of these two sequences in chromosomal DNA from three distinct plant pathogenic species of Spiroplasma. The results of Southern blot hybridization indicated that each of the pRA1-associated sequences is present as multiple copies in short, dispersed, and repetitive sequences in the chromosomes of these three strains. None of the sequences was detectable in chromosomal DNA from an additional nine Spiroplasma strains examined.

Chromosome Mapping↗
PubMed1989

The L1 family of long interspersed repetitive DNA in rabbits: sequence, copy number, conserved open reading frames, and similarity to keratin.

The L1 family of long interspersed repetitive DNA in the rabbit genome (L1Oc) has been studied by determining the sequence of the five L1 repeats in the rabbit beta-like globin gene cluster and by hybridization analysis of other L1 repeats in the genome. L1Oc repeats have a common 3' end that terminates in a poly A addition signal and an A-rich tract, but individual repeats have different 5' ends, indicating a polar truncation from the 5' end during their synthesis or propagation. As a result of the polar truncations, the 5' end of L1Oc is present in about 11,000 copies per haploid genome, whereas the 3' end is present in at least 66,000 copies per haploid genome. One type of L1Oc repeat has internal direct repeats of 78 bp in the 3' untranslated region, whereas other L1Oc repeats have only one copy of this sequence. The longest repeat sequenced, L1Oc5, is 6.5 kb long, and genomic blot-hybridization data using probes from the 5' end of L1Oc5 indicate that a full length L1Oc repeat is about 7.5 kb long, extending about 1 kb 5' to the sequenced region. The L1Oc5 sequence has long open reading frames (ORFs) that correspond to ORF-1 and ORF-2 described in the mouse L1 sequence. In contrast to the overlapping reading frames seen for mouse L1, ORF-1 and ORF-2 are in the same reading frame in rabbit and human L1s, resulting in a discistronic structure. The region between the likely stop codon for ORF-1 and the proposed start codon for ORF-2 is not conserved in interspecies comparisons, which is further evidence that this short region does not encode part of a protein. ORF-1 appears to be a hybrid of sequences, of which the 3' half is unique to and conserved in mammalian L1 repeats. The 5' half of ORF-1 is not conserved between mammalian L1 repeats, but this segment of L1Oc is related significantly to type II cytoskeletal keratin.

Animals↗
PubMedDate not supplied

[Distribution of repeating nucleotide sequences in the macronucleus DNA of Tetrahymena infusoria].

The genome of Tetrahymena pyriformis macronucleus contain less than 10% of repetitive sequences. About half of them consist of long, more than 2000 base pairs, moderately repeated sequences. Short repetitive sequences (200--300 base pairs) represent 4--5% of the genome. We assume, that the short repetitive sequences are interspersed with single copy sequences of about 1000 base pairs. In this case less than 15% of the Tetrahymena DNA should consist of interspersed repetitive and single copy sequences.

Base Sequence↗
PubMed2002

PCR detection of DNAs of animal origin in feed by primers based on sequences of short and long interspersed repetitive elements.

PCR primers for the detection of materials derived from ruminants, pigs, and chickens were newly designed on the basis of sequences of the Art2 short interspersed repetitive element (SINE), PRE-1 SINE, and CR1 long interspersed repetitive element (LINE), respectively. These primers amplified the SINE or LINE from total DNA extracted from the target animals and from test feed containing commercial meat and bone meal (MBM). With the primers, detection of Art2, PRE-1, or CR1 in test feed at concentrations of 0.01% MBM or less was possible. This method was suitable for the detection of microcontamination of feed by animal materials.

Animal Feed↗
PubMedDate not supplied

[A new class of RNP particles containing small RNA homologous to short dispersed DNA repetitive sequences].

Here we show that small RNAs homologous to short interspersed repetitive DNA sequences: ID, B1, B2--in rat cells and Alu in human cells are complexed with specific proteins to form small nuclear and cytoplasmic RNP particles (alpha RNP) with common properties. alpha-RNP differ from other ribonucleoproteins by composition and properties. alpha RNA molecules are apparently transcribed by RNA polymerase III. alpha-RNAs are capable of stable antisense hybridization with specific messenger RNAs. Expression of alpha-RNA is specifically regulated by gene regulatory factors. The data obtained support the suggestion that alpha-RNA may belong to the group of regulatory eukaryotic RNAs and that alpha-RNP might be involved in the coordinative control of the expression of the sets of genes with SINE-homologous sequences in regulatory regions.

Animals↗
PubMed1976

DNA sequence arrangement and preliminary evidence on its evolution.

Some recent measurements of the sequence arrangement and evolution of the eukaryotic genome are reviewed. The range of genome sizes and extent of sequence transcribed into nuclear and messenger RNA indicate that the majority of the single copy DNA is not made up of structural genes. The rate of base substitution in the single copy DNA among the primates is similar to that of the codons for certain rapidly changing amino acid residues. This leads to the hypothesis that there is a "basal" rate of change in the genome not strongly affected by selection. The DNA of most higher animals shows a large amount of short period interspersion of repetitive and single copy DNA sequences and a smaller amount of long repetitive regions. The sequence divergence among the short interspersed repetitive sequences is greater than that of the sequences in long repetitive regions. The long repetitive regions are most probably recent additions to the genome and the short interspersed repetitive sequences result from a history of base substitution and translocation. The process of sequence rearrangement appears to be a significant part of the evolution of the genome and may have a much greater effect on the evolution of the phenotype than sequence alteration by base substitution.

Alleles↗
PubMed1986

Characterization of a member of the highly repeated long interspersed rat DNA family with long open reading frames.

A highly repetitive long interspersed sequence from rat DNA has been isolated and partly characterized. This sequence comprises at least a 1300 base-pair and a 2400 base-pair EcoRI fragment and probably additional elements. The 2400 base-pair segment has been analyzed in detail. It appears to be part of the chromosomal DNA in rat cells. The 2400 base-pair repeat is likely to be distributed over several regions in the rat genome. The 2400 base-pair segment has been cloned, mapped for restriction sites, and part of its nucleotide sequence has been determined. The 2400 base-pair sequence is a member of a typical highly repetitive long interspersed sequence with high copy number and restriction site polymorphism. There are sequence homologies to mouse and human DNA. A striking homology has been detected to the flanking sequences of a repetitive mouse DNA sequence that has been described to be located adjacent to one of the kappa-immunoglobulin variable genes. Elements in the 2400 base-pair rat repeat are transcribed in cells from most rat organs and from several continuous rat cell lines. This RNA from rat cell lines was found polyadenylated or not polyadenylated. The nucleotide sequence of parts of the 2400 base-pair DNA segment revealed open reading frames for polypeptide sequences. Such open reading frames have been detected in two different segments of the 2400 base-pair DNA repeat. Open reading frames exist in the two complementary strands in the same DNA segment. The hypothetical polypeptide whose sequence has been determined in toto has a length of 190 amino acid residues and is enriched in hydrophobic amino acids, reminiscent of the amino acid composition in membrane proteins. Hence, it is conceivable that the 2400 base-pair repeat sequence from rat DNA, at least in part, encodes messenger RNAs that might be translated into functional proteins.

Amino Acid Sequence↗
PubMed2001

Characterization of the genomic structure of the human vitamin C transporter SVCT1 (SLC23A2).

Vitamin C (L-ascorbic acid), a critical cofactor for intracellular enzymatic reactions, functions as a scavenger of free oxygen radicals and is an essential micronutrient. Vitamin C is actively transported into cells by one of two closely related sodium-dependent transporters, SVCT1 or SVCT2. In this paper, we report the complete sequencing and gene structure of SLC23A2, the gene encoding SVCT1. The1797-bp cDNA sequence (open reading frame) of the SLC23A2 gene was derived from a compact genomic sequence of 7966 bp [translation initiation codon (ATG) to poly A tail], which is divided into 14 exons. Furthermore, repetitive or masked elements constituted 17.98% of the gene; there were 4 Alu sequences and 5 MIR (Mammalian Interspersed Repetitive element) sequences. A search for common variants in SLC23A2, using current bioinformatic tools and direct resequencing of control populations, failed to identify common single nucleotide polymorphisms. The start of transcription was mapped to a position -47 relative to the ATG; the immediate 5' sequence was determined and analyzed for possible consensus binding sites for known transcription factors. Our findings will serve as the foundation for investigation of the regulation and expression of the tissue-specific sodium-dependent vitamin C transporter, SLC23A2.

Base Sequence↗
PubMed2000

Repetitive A-T rich DNA sequences from the Y chromosome of the Mediterranean fruit fly, Ceratitis capitata.

Copies of a repetitive DNA sequence distributed over 90% of the length of the long arm of the Y chromosome of the Mediterranean fruit fly, Ceratitis capitata (medfly), have been characterized. Sequencing reveals that these repeats, ranging in size from approximately 1.3 to 1.7 kb, are A-T rich overall (67%). In most cases the repeat units appear to occur in tandemly linked arrays. The repeat copies also all contain a highly similar internal region, approximately 200 bp in length, with a more extreme A-T content bias. This internal region, designated as the AT element, exhibits an A-T content of at least 83%. This exceeds what has been described for any comparable element among invertebrates. Using primers designed from the DNA sequence, PCR amplification of an internal region encompassing the AT element also reveals that these sequences are present only in the male genome in different strains of the medfly.

AT Rich Sequence↗