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PubMed1990

Structure and in vitro transcription of the rat CYP2A1 and CYP2A2 genes and regional localization of the CYP2A gene subfamily on mouse chromosome 7.

The CYP2A1 and CYP2A2 genes code for hepatic steroid hydroxylases and differ in their development regulation and expression in male and female rats. In order to explore the mechanism of regulation of these two genes, both genes were isolated and sequenced, their upstream regions compared, and their promoters transcribed in a cell-free system derived from liver. The CYP2A1 gene was completely sequenced and spanned 12,835 bp. The CYP2A2 gene was sequenced except for 1.5 and 12 kbp in the second and fifth introns, respectively. This gene was about 10 kbp longer than CYP2A1. Both genes possess nine exons that displayed overall 93% nucleotide similarity. DNA 4544 and 5529 bp upstream from the CYP2A1 and CYP2A2 genes, respectively, was also sequenced, and the transcription start sites were determined. Both genes had typical TATA boxes but did not contain CCAAT boxes within -100 bp of their polymerase start sites. CYP2A1, however, contained a reverse CCAAT box between -85 and -90. Search of the Gene Bank revealed a 255 bp region that lies -3 kbp upstream from the transcription start site of CYP2A1 displaying similarity with retrovirus polymerase. Two regions upstream of CYP2A2 were also found that displayed 90% sequence similarity with the consensus long interspersed middle repetitive element (LINE). In addition, an unusual 1.6 kbp inserted sequence was detected between -165 and -1779 bp upstream of the CYP2A2 gene that appears to be a retropseudogene. A nuclear extract derived from adult hepatocytes was used to direct in vitro transcription of the CYP2A1 and CYP2A2 gene promoters. Both genes were accurately transcribed in extracts derived from livers of male and female rats. This result is surprising in view of the fact that the CYP2A1 gene is expressed in adult female rats while the CYP2A2 gene is expressed exclusively in adult males. The CYP2A1 promoter was more actively expressed in both extracts than that of CYP2A2. By analyzing the segregation pattern of CYP2A genes in backcross offspring from an interspecies cross between the laboratory strain NFS/N and the wild mouse Mus musculus musculus, the Cyp2a subfamily was mapped proximal to the Gpi-1 locus near the centromere on chromosome 7.

Amino Acid Sequence↗

PubMed1982

[Mapping of 2 cloned DNA fragments containing repetitive mouse genome regions, actively transcribing into pre-mRNA].

Sequence organization of two cloned mouse genomic DNA fragments which are efficiently transcribed into pre-mRNA was studied. In both cases, the arrangement of sequences hybridizing to polysomal mRNA (or cDNA), double-stranded RNA (dsRNA-B) isolated from pre-mRNA and oligo (dT), was established. In one fragment, the regions transcribed are represented by three different repetitive mRNA (or cDNA) hybridizing sequences interspersed into the AT-rich tract, the type B-2 sequence and the unique DNA sequence which also transcribed into mRNA. Nuclear pre-mRNA of 28S is hybridized to three repetitive mRNA hybridizing regions. The significance of such a complex array of repeated sequences inside eukaryotic transcription units and their possible role in mRNA processing and splicing is discussed.

Animals↗

PubMed1988

A new family of repetitive, retroposon-like sequences in the genome of the rainbow trout.

We have identified a new family of interspersed, moderately repetitive DNA elements, termed the RSg-1 family, in the genome of the rainbow trout. Two of the elements examined here are situated upstream of sequences which code for trout nuclear proteins; a protamine gene (p101) and the clustered histone H4 gene. Sequence comparison of various RSg-1 elements indicated a high degree of nucleotide sequence homology between different members of the family. These repetitive elements exhibit well defined 3' ends which contain poly(A) segments preceded by the consensus polyadenylation signal AATAAA. Sequences flanking the 3' end of the poly(A) tract also conform to a consensus sequence. A similar sequence is also found flanking the 5' terminus of the element in the protamine clone p101, and thus may represent a target-site duplication generated upon insertion of the element into the genome. These characteristics, together with the heterogeneous nature of the 5' ends of the elements, are reminiscent of processed pseudogenes and retroposons such as the mammalian L1 family of interspersed repetitive elements.

Animals↗

PubMed2002

A technique for genome-wide identification of differences in the interspersed repeats integrations between closely related genomes and its application to detection of human-specific integrations of HERV-K LTRs.

We have developed a method of targeted genomic difference analysis (TGDA) for genomewide detection of interspersed repeat integration site differences between closely related genomes. The method includes a whole-genome amplification of the flanks adjacent to target interspersed repetitive elements in both genomic DNAs under comparison, and subtractive hybridization (SH) of the selected amplicons. The potential of TGDA was demonstrated by the detection of differences in the integration sites of human endogenous retroviruses K (HERV-K) and related solitary long terminal repeats (LTRs) between the human and chimpanzee genomes. Of 55 randomly sequenced clones from a library enriched with human-specific integration (HSI) sites, 33 (60%) represented HSIs. All the human-specific (Hs) LTRs belong to two related evolutionarily young groups, suggesting simultaneous activity of two master genes in the hominid lineage. No deletion/insertion polymorphism was detected for the LTR HSIs for 25 unrelated caucasoid individuals. We also discuss the possible research applications for TGDA research.

Animals↗

PubMed1987

The sequence of the 3.3-kilobase repetitive element from Dipodomys ordii suggests a mechanism for its amplification and interspersion.

DNA from the kangaroo rat, Dipodomys ordii, contains a 3.3-kb, highly repeated sequence that is interspersed throughout the genome in small tandem clusters. One 3.3-kb unit has been cloned into pBR322 and the nucleotide sequence determined. The clone used was shown to be representative of the bulk of such sequences found in the genomic DNA. The sequence contains 10 homologous subunits each ca. 260 bp in length. Comparison of these to one another yielded a 258-bp consensus sequence containing a 35-bp terminal inverted repeat. Two unique stretches also occur. One of these contains a region that could serve as a promoter for RNA polymerase III; the other contains a sequence related to the ARS sequences of yeast. It is proposed that an ancestral sequence similar to the consensus sequence was amplified to 10 or more units, and that, subsequently, two other sequences were inserted. The properties of these insertions may have led to the dispersal of the sequence throughout the genome.

Animals↗

PubMed1989

ATP synthase from bovine mitochondria: complementary DNA sequence of the mitochondrial import precursor of the gamma-subunit and the genomic sequence of the mature protein.

The gamma-subunit of mitochondrial ATP synthase is part of the extrinsic membrane sector of the enzyme F1-ATPase. It is a nuclear gene product. Complementary DNA clones encoding a precursor of the protein have been isolated from a bovine library. The initial partial clone was identified with a mixture of 32 synthetic oligonucleotides designed from the known protein sequence (Walker et al., 1985), and this isolate was then used to screen the library again in order to find a complete cDNA. The DNA sequence of a clone that encodes the entire mature protein has been established, and the deduced protein sequence agrees exactly with that determined by direct sequence analysis of protein isolated from bovine hearts (Walker et al., 1985). At the 3' ends of two independently isolated clones, alternative polyadenylation sites have been observed; otherwise, the DNA sequences of the clones are concordant. In common with many other mitochondrial proteins encoded in nuclear genes, the deduced protein sequence has an N-terminal extension that is absent from the mature protein. These presequences direct the protein to its appropriate mitochondrial compartment and are removed during the import process. The cDNA clone has been employed to isolate bovine genomic clones containing the gene for the gamma-subunit. From them, the DNA sequence has been established of a region encoding the mature protein and six amino acids in the presequence, but not the remainder of the proposed import sequence. This sequence extends over almost 10 kb and is divided into eight exons. Intron B between exons I and II contains a sequence that is related to long interspersed repetitive elements (LINEs) that have been described in other mammals. Human LINEs are usually flanked by directly repeated sequences with a poly(A) tract at their 3' ends, and these features are present in the bovine LINE which is truncated. This sequence contains an open reading frame encoding part of a protein that is closely related to a protein encoded in mouse LINEs, to reverse transcriptase, and to DNA binding proteins. We have also made a preliminary investigation by DNA hybridization of the number of sequences related to the bovine gene in both the bovine and human genomes. Under the experimental conditions employed, one fragment hybridized in digests of bovine DNA, and two to four bands were detected in digests of human DNA; these latter fragments have originated from either expressed genes or pseudogenes.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗

PubMed2005

Cloning and characterization of cDNAs encoding steroidogenic acute regulatory protein from freshwater stingrays (Potamotrygon spp.).

The steroidogenic acute regulatory protein (StAR) is critical to the regulated synthesis of steroids in vertebrates. We have isolated cDNA sequences encoding StAR in the freshwater stingrays Potamotrygon hystrix and P. motoro. A single P. hystrix StAR transcript (3376 bp) and two overlapping P. motoro StAR transcripts (1272 and 3365 bp) were isolated. The P. hystrix and P. motoro StAR transcripts contain open reading frames encoding proteins of 284 amino acids that are 99% identical to each other and 56-64% identical to other StAR proteins. Pregnenolone synthesis by green monkey kidney (COS-1) cells transfected with an expression construct encoding a human cholesterol side chain cleavage/adrenodoxin reductase/adrenodoxin fusion protein was increased 16-fold by coexpression with a pCMV5/P. motoro StAR expression construct. Northern blot analysis revealed a single 4000 bp StAR transcript in the P. motoro interrenal gland, but RT-PCR indicates StAR mRNA is also expressed in the brain, gonads, atria, ventricle, gill (female only) and muscle (female only). Expression in extragonadal and extraadrenocortical tissues is an indication that StAR may be critical to processes other than steroidogenesis. The longest P. motoro StAR transcript contains a sequence with great similarity to short interspersed repetitive elements found in other elasmobranchs. This study is the first to isolate and characterize elasmobranch StAR cDNA sequences and to demonstrate the activity of a nonmammalian StAR protein in a heterologous expression system.

5' Untranslated Regions↗

PubMed1990

Mouse satellite DNA is transcribed in senescent cardiac muscle.

Mouse satellite DNA consists of highly repetitive tandem sequences located in the centromeric heterochromatin. It is generally assumed that these simple sequences are not transcribed. We have analyzed total cellular RNA preparations from mouse liver, kidney, brain, and heart tissues at different ages for satellite transcripts. Using recombinant probes containing the major mouse satellite sequence, satellite transcripts were detected only in the heart RNA samples. These transcripts were not detected in the heart muscle of young adult animals (2 and 6 months), but then appeared at the age of 12 months and continued to increase over 2-fold up to the age of 32 months. The transcripts were resistant to DNase I and sensitive to RNases and alkaline treatment. Northern hybridization experiments showed a large and heterogeneous size range of satellite transcripts. Control studies using short-interspersed (B1 and B2) and long-interspersed (L1 and IAP) repetitive DNA sequence probes did not show a similar age-related pattern of transcription. These results indicate that satellite transcription does occur in mice but is highly tissue- and age-specific. The unique occurrence of satellite transcription only in adult and senescent heart tissue indicates age to be an important determinant of gene activity. An understanding of the regulatory mechanisms involved could lead to new insights in the biological role of satellite DNA, gene derepression of reiterated DNA sequences, and the aging processes of cardiac muscle.

Aging↗

PubMedDate not supplied

Identification and characterization of an interspersed repetitive DNA fragment in Plasmodium vivax with potential use for specific parasite detection.

We cloned and characterized a Plasmodium vivax repeat element of 7872bp named PvRE7.8. Several internal tandem repeats were found along the sequence. The repetitive nature of the PvRE7.8 element was confirmed by hybridization of a P. vivax YAC library. Based on the data bank analysis and the presence of two contiguous putative genes that may encode proteins related to DNA metabolism, PvRE7.8 could be considered an inactivated transposon-LINE element. By using Pv79 as probe or primers derived from Pv79-flanking sequences, P. vivax DNA Could be detected from whole blood and mosquito samples. We consider that the repeat element described here has potential for P. vivax malaria diagnosis and for epidemiological analysis of P. vivax transmission areas.

Aedes↗

PubMed2001

HIV-1 and HIV-2 LTR nucleotide sequences: assessment of the alignment by N-block presentation, "retroviral signatures" of overrepeated oligonucleotides, and a probable important role of scrambled stepwise duplications/deletions in molecular evolution.

Previous analyses of retroviral nucleotide sequences, suggest a so-called "scrambled duplicative stepwise molecular evolution" (many sectors with successive duplications/deletions of short and longer motifs) that could have stemmed from one or several starter tandemly repeated short sequence(s). In the present report, we tested this hypothesis by focusing on the long terminal repeats (LTRs) (and flanking sequences) of 24 human and 3 simian immunodeficiency viruses. By using a calculation strategy applicable to short sequences, we found consensus overrepresented motifs (often containing CTG or CAG) that were congruent with the previously defined "retroviral signature." We also show many local repetition patterns that are significant when compared with simply shuffled sequences. First- and second-order Markov chain analyses demonstrate that a major portion of the overrepresented oligonucleotides can be predicted from the dinucleotide compositions of the sequences, but by no means can biological mechanisms be deduced from these results: some of the listed local repetitions remain significant against dinucleotide-conserving shuffled sequences; together with previous results, this suggests that interspersed and/or local mononucleotide and oligonucleotide repetitions could have biased the dinucleotide compositions of the sequences. We searched for suggestive evolutionary patterns by scrutinizing a reliable multiple alignment of the 27 sequences. A manually constructed alignment based on homology blocks was in good agreement with the polypeptide alignment in the coding sectors and has been exhaustively assessed by using a multiplied alphabet obtained by the promising mathematical strategy called the N-block presentation (taking into account the environment of each nucleotide in a sequence). Sector by sector, we hypothesize many successive duplication/deletion scenarios that fit our previous evolutionary hypotheses. This suggests an important duplication/deletion role for the reverse transcriptase, particularly in inducing stuttering cryptic simplicity patterns.

Algorithms↗

PubMed1984

Structural organization of interspersed repetitive elements present in the DNA of Mus musculus.

Two-dimensional displays of the restriction fragments from the DNA of Mus musculus revealed a complex species-specific pattern produced from nonsatellite repetitive sequences. The patterns have been used as a guide in the direct purification of a group of broadly interspersed repeated DNA sequences (characterized by a 1350-bp Eco-Bam fragment) that have been studied by molecular cloning, restriction mapping and genomic Southern blotting. These studies show that the cloned representatives originate from an abundant group of sequences that share homology with about 2% of the mouse genome. The sequences do not appear to share homology with mouse-interspersed-family-1 (MIF-1) nor with the major AT-rich satellite sequences of mouse. They appear to be part of a group of larger repetitive elements that is both broadly interspersed and heavily methylated in normal mouse tissue.

Animals↗

PubMed1992

A highly repetitive DNA sequence possibly unique to canids.

A short interspersed nucleotide (nt) element (SINE) was cloned from the genomic DNA of the domestic dog, Canis familiaris. Southern-blot analysis of canine DNA digested with four restriction endonucleases indicated that the SINE is widely dispersed throughout the genome. Hybridizations also indicated that the element may be unique to canids and is absent in a variety of other mammals, including members of four closely-related carnivore families. Three examples of the SINE have been located and sequenced. The 130-bp SINE contains putative RNA polymerase III transcriptional control sequences. The SINE is flanked at the 3' end by a (TC)8-repeat region followed by a poly(A) tract of 35-65 nt. Computer database searches located two homologous sequences with approx. 80% identity to the SINE. These sequences were located in untranslated regions of the canine genes encoding interferon-omega and clotting factor IX.

Animals↗

PubMed1994

Screening of a mouse/human Y-chromosomal cosmid library for gene candidates and markers by using (short) oligonucleotide probes.

A comprehensive approach is described for the identification of sequences of interest from a human Y chromosomal cosmid library via (short) consensus oligonucleotide probes. It involves the ordering of cosmid clones grown in microtiter plates onto small filter membranes by a robot workstation. A high number of the clones are characterized by their repetitive sequence content, either by ubiquitously interspersed simple tandem blocks or by Y-specific elements. The Y chromosomal repeat (DYZ2) appears underrepresented in the library. In contrast many novel microsatellite marker systems can now be developed for the Y chromosome on the basis of the simple repeat blocks described here. Though novel genes were not yet delineated so far, a number of candidate sequences with high coding potential and other interesting characteristics are described.

Animals↗

PubMed1999

An allele of the ripening-specific 1-aminocyclopropane-1-carboxylic acid synthase gene (ACS1) in apple fruit with a long storage life.

An allele of the 1-aminocyclopropane-1-carboxylic acid (ACC) synthase gene (Md-ACS1), the transcript and translated product of which have been identified in ripening apples (Malus domestica), was isolated from a genomic library of the apple cultivar, Golden Delicious. The predicted coding region of this allele (ACS1-2) showed that seven nucleotide substitutions in the corresponding region of ACS1-1 resulted in just one amino acid transition. A 162-bp sequence characterized as a short interspersed repetitive element retrotransposon was inserted in the 5'-flanking region of ACS1-2 corresponding to position -781 in ACS1-1. The XhoI site located near the 3' end of the predicted coding region of ACS1-2 was absent from the reverse transcriptase-polymerase chain reaction product, revealing that exclusive transcription from ACS1-1 occurs during ripening of cv Golden Delicious fruit. DNA gel-blot and polymerase chain reaction analyses of genomic DNAs showed clearly that apple cultivars were either heterozygous for ACS1-1 and ACS1-2 or homozygous for each type. RNA gel-blot analysis of the ACS1-2 homozygous Fuji apple, which produces little ethylene and has a long storage life, demonstrated that the level of transcription from ACS1-2 during the ripening stage was very low.

Alleles↗

PubMed2005

Can 15-locus mycobacterial interspersed repetitive unit-variable-number tandem repeat analysis provide insight into the evolution of Mycobacterium tuberculosis?

The phylogeny and evolution of the bacterium Mycobacterium tuberculosis is still poorly understood despite the application of a variety of molecular techniques. We analyzed 469 M. tuberculosis and 49 Mycobacterium bovis isolates to evaluate if the mycobacterial interspersed repetitive units-variable-number tandem repeats (MIRU-VNTR) commonly used for epidemiological studies can define the phylogeny of the M. tuberculosis complex. This population was characterized by previously identified silent single-nucleotide polymorphisms (sSNPs) or by a macroarray based on these sSNPs that was developed in this study. MIRU-VNTR phylogenetic codes capable of differentiating between phylogenetic lineages were identified. Overall, there was 90.9% concordance between the lineages of isolates as defined by the MIRU-VNTR and sSNP analyses. The MIRU-VNTR phylogenetic code was unique to M. bovis and was not observed in any M. tuberculosis isolates. The codes were able to differentiate between different M. tuberculosis strain families such as Beijing, Delhi, and East African-Indian. Discrepant isolates with similar but not identical MIRU-VNTR codes often displayed a stepwise trend suggestive of bidirectional evolution. A lineage-specific panel of MIRU-VNTR can be used to subdivide each lineage for epidemiological purposes. MIRU-VNTR is a valuable tool for phylogenetic studies and could define an evolutionarily uncharacterized population of M. tuberculosis complex organisms.

Base Sequence↗

PubMed1984

A large interspersed repeat found in mouse DNA contains a long open reading frame that evolves as if it encodes a protein.

DNA sequence analysis of a region contained within a large, interspersed repetitive family of mice reveals a long open reading frame. This sequence extends 978 base pairs between two stop codons, creating a reading frame that is open for 326 amino acids. The DNA sequence in this region is conserved between three distantly related Mus species, as well as between mouse and monkey, in a manner that is characteristic of regions undergoing selection for protein function.

Amino Acid Sequence↗

PubMed1986

The population biology of transposable elements.

A transposable element can be defined as a DNA sequence capable of moving to new sites in the genome. Such DNA sequences have been described in a wide range of organisms. The evolutionary processes affecting transposable elements can thus be divided into two categories: changes in sequence and changes in genomic location. As with other types of evolutionary change, the nature of the evolutionary process will be reflected in the extent and type of genetic variation existing in wild populations. Quantitative models of the evolution of transposable element sequences and positions will be outlined, and related to relevant data. The extent to which models designed to describe obvious transposable elements such as the mobile sequences of Drosophila are also applicable to interspersed repetitive DNAs from other species will be discussed.

Animals↗

PubMed1976

DNA sequence organization in the lepidopteran Antheraea pernyi.

A large fraction of the genome of the lepidopteran Antheraea pernyi consists of interspersed single-copy sequences and repetitive DNA sequences of 300 nucleotide average length. Most of the single-copy sequences are about 800 nucleotides long and a minority are considerably longer. Thus, the organization of the DNA sequences of this insect is similar to that of most higher organisms and different from that of Drosophila.

Animals↗