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PubMed2001

Non-autonomous mobile elements in the crenarchaeon Sulfolobus solfataricus.

The genome of the archaeon Sulfolobus solfataricus P2 contains at least four types of short sequence elements lacking open reading frames which are similar to eukaryal non-autonomous mobile elements. The most- conserved elements SM1 (79-80 bp) and SM2 (183-186 bp), with 95 % sequence identity, are present in 40 and 25 copies, respectively. The less-conserved elements SM3 (127-139 bp) and SM4 (160-168 bp), with 75-97 % identity, occur in 44 and 34 copies, respectively. In total, the 143 SM elements constitute about 0.6 % of the genome. The wide distribution of each class of conserved element throughout the genome, and their precise locations, indicate that they are mobile. Direct evidence arises from the presence of SM1 and SM2 in only a fraction of genomic copies of a given class of insertion element, and within copies of open reading frames that are conserved in sequence. SM1 to SM4 are likely to be mobilized by transposases encoded by insertion elements ISC1048, ISC1217, ISC1058 and ISC1173, respectively. Furthermore, the occurrence of clusters of interwoven SM and insertion elements, in potentially mobile units, suggests a mechanism for the transfer of SM elements to other organisms.

Amino Acid Sequence↗
PubMed1999

The alpha1-microglobulin/bikunin gene: characterization in mouse and evolution.

The 129Sv mouse gene coding for the alpha1-microglobulin/bikunin precursor has been isolated and characterized. The 11kb long gene contains ten exons, including six 5'-exons coding for alpha1-microglobulin and four 3'-exons encoding bikunin. Exon 7 also codes for the tribasic tetrapeptide RARR which connects the alpha1-microglobulin and bikunin parts. The sixth intron, which separates the alpha1-microglobulin and bikunin encoding parts, was compared in the human, mouse and a fish (plaice) gene. The size of this intron varies considerably, 6.5, 3.3 and 0.1kb in man, mouse and plaice, respectively. In all three genes, this intron contains A/T-rich regions, and retroposon elements are found in the first two genes. This indicates that this sixth intron is an unstable region and a hotspot for recombinational events, supporting the concept that the alpha1-microglobulin and bikunin parts of this gene are assembled from two ancestral genes. Finally, the nonsynonymous nucleotide substitution rate of the gene was determined by comparing coding sequences from ten vertebrate species. The results indicate that the alpha1-microglobulin part of the gene has evolved faster than the bikunin part.

Animals↗
PubMed2004

Origins of recently gained introns in Caenorhabditis.

The genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae both contain approximately 100,000 introns, of which >6,000 are unique to one or the other species. To study the origins of new introns, we used a conservative method involving phylogenetic comparisons to animal orthologs and nematode paralogs to identify cases where an intron content difference between C. elegans and C. briggsae was caused by intron insertion rather than deletion. We identified 81 recently gained introns in C. elegans and 41 in C. briggsae. Novel introns have a stronger exon splice site consensus sequence than the general population of introns and show the same preference for phase 0 sites in codons over phases 1 and 2. More of the novel introns are inserted in genes that are expressed in the C. elegans germ line than expected by chance. Thirteen of the 122 gained introns are in genes whose protein products function in premRNA processing, including three gains in the gene for spliceosomal protein SF3B1 and two in the nonsense-mediated decay gene smg-2. Twenty-eight novel introns have significant DNA sequence identity to other introns, including three that are similar to other introns in the same gene. All of these similarities involve minisatellites or palindromes in the intron sequences. Our results suggest that at least some of the intron gains were caused by reverse splicing of a preexisting intron.

Amino Acid Sequence↗
PubMed1998

Characterization of a double homeodomain protein (DUX1) encoded by a cDNA homologous to 3.3 kb dispersed repeated elements.

Target genes for the helicase-like transcription factor (HLTF), a member of the SNF/SWI family, were immunoprecipitated from HeLa chromatin fragments with an anti-HLTF antibody. A 182 bp fragment ( HEFT1 ) presented 87% sequence identity with 3.3 kb dispersed repeats from the 4q35 D4Z4 locus linked to facioscapulohumeral muscular dystrophy (FSHD). The HEFT1 loci were, however, not genetically linked to FSHD. Transfection and in vitro binding studies identified within HEFT1 a promoter whose basal activity required a GC box activated by Sp1 or Sp3. A 4.4 kb homologous transcript was found mostly in human skeletal muscle and heart. A 1.2 kb cDNA fragment was cloned that encoded a 170 amino acid protein (DUX1) with two paired-type homeodomains. In vitro translated DUX1 specifically interacted in electrophoretic mobility shift assay (EMSA) with a P5 oligonucleotide (5'-GATCTGAGTCTAATTGAGAATTACTGTAC-3'). DUX1 co-expression activated up to 5-fold transient expression in insect cells of a minimal promoter-luciferase construct fused to P5. The presence of 20 kDa DUX1 in vivo in rhabdomyosarcoma TE671 cell extracts was shown by western blotting with a rabbit antiserum raised against a DUX1 peptide. This antiserum suppressed a TE671 protein-P5 complex in EMSA with identical migration as the in vitro translated DUX1-P5 complex. Genomic PCR experiments could not identify a gene fragment linking the HEFT1 and DUX1 sequences, which present one mismatch in their overlapping region. However, a similar gene was found in another 3.3 kb element comprising the HEFT1 promoter and a DUX1 -like open reading frame. In addition, homologous gene sequences were identified in 3.3 kb elements of the D4Z4/FSHD locus, considered until now 'junk' DNA.

Amino Acid Sequence↗
PubMed2001

Comparative sequence analysis of the imprinted Dlk1-Gtl2 locus in three mammalian species reveals highly conserved genomic elements and refines comparison with the Igf2-H19 region.

The Dlk1-Gtl2 domain on mouse chromosome 12 contains reciprocally imprinted genes with the potential to contribute to our understanding of common features involved in imprinting control. We have sequenced this conserved region in the mouse and sheep and included the human sequence in a three species comparison. This analysis resulted in a precise conservation map and identification of highly conserved sequence elements, some of which we have shown previously to be differentially methylated in the mouse. Additionally, this analysis facilitated identification of a CpG-rich tandem repeat array located approximately 13-15 kb upstream of Gtl2. Furthermore, we have identified a third imprinted transcript that overlaps with the last Dlk1 exon in the mouse. This transcript lacks a conserved open reading frame and is probably generated by cleavage of extended Dlk1 transcripts. Because Dlk1 and Gtl2 share many of the imprinting properties of the well-characterized Igf2-H19 domain, it has been proposed that the two regions may be regulated in the same way. Comparative genomic examination of the two domains indicates that although there are similarities, other features are very different, including the location of conserved CTCF-binding sites, and the level of conservation at regulatory regions.

Animals↗
PubMed2002

The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeats.

Chlamydomonas reinhardtii is a unicellular eukaryotic alga possessing a single chloroplast that is widely used as a model system for the study of photosynthetic processes. This report analyzes the surprising structural and evolutionary features of the completely sequenced 203,395-bp plastid chromosome. The genome is divided by 21.2-kb inverted repeats into two single-copy regions of approximately 80 kb and contains only 99 genes, including a full complement of tRNAs and atypical genes encoding the RNA polymerase. A remarkable feature is that >20% of the genome is repetitive DNA: the majority of intergenic regions consist of numerous classes of short dispersed repeats (SDRs), which may have structural or evolutionary significance. Among other sequenced chlorophyte plastid genomes, only that of the green alga Chlorella vulgaris appears to share this feature. The program MultiPipMaker was used to compare the genic complement of Chlamydomonas with those of other chloroplast genomes and to scan the genomes for sequence similarities and repetitive DNAs. Among the results was evidence that the SDRs were not derived from extant coding sequences, although some SDRs may have arisen from other genomic fragments. Phylogenetic reconstruction of changes in plastid genome content revealed that an accelerated rate of gene loss also characterized the Chlamydomonas/Chlorella lineage, a phenomenon that might be independent of the proliferation of SDRs. Together, our results reveal a dynamic and unusual plastid genome whose existence in a model organism will allow its features to be tested functionally.

Amino Acid Sequence↗
PubMed2000

[REP and ERIC repetitive DNA sequences in bacteria--diagnostic significance].

Main part of eukaryotic genomes is build of unique sequences coding proteins and RNAs, but they contain as well numerous repeats interspersed with single-copy fragments. Existence of repetitive sequences were also demonstrated in prokaryotic genomes. They are found in different species of Gram-negative and Gram-positive bacteria. Interspersed repetitive sequence elements called REP and ERIC sequences are present in different species of Enterobacteriaceae family, including Escherichia coli and Salmonella typhimurium. Their functions are not completely clear, probably they play important role in regulation of gene expression. Nevertheless, REP and ERIC elements are widely use in identification and genetic analysis of bacteria. For example, using rep-PCR technique it is possible to discriminate between closely related serovars of the same species, which enables to analyze phylogenetic and epidemiological relations among them.

Animals↗
PubMed2001

Characterization of a human gene encoding nucleosomal binding protein NSBP1.

We characterize the cDNA and genomic structure of NSBP1, and demonstrate that it is a nuclear protein and the homologue of mouse Nsbp1, which is known to encode a nucleosomal binding and transcriptional activating protein related to the HMG-14/-17 chromosomal proteins. The encoded NSBP1 protein has 86% amino acid similarity to Nsbp1, including identity in nucleosomal binding domains of the HMG-14/-17 proteins. Our radiation hybrid data localize NSBP1 and Nsbp1 to homologous regions of chromosome X, with NSBP1 in Xq13.3 between DXS983 and DXS995 and Nsbp1 in the interval DXMit65 and DXMit39. Although Nsbp1 produces one mRNA transcript, NSBP1 produces three transcripts with alternate polyadenylated sites. The 3' untranslated region (UTR) of NSPB1 mRNA also contains several AU-rich elements (AREs), which are associated with rapid mRNA turnover. Northern analysis of NSBP1/Nsbp1 shows differences in transcript abundance among adult and fetal tissues, with predominant expression in liver, kidney, trabecular bone, and bone marrow stromal cells. However, a reverse transcriptase-PCR analysis shows nearly ubiquitous expression of the three NSBP1 transcripts in all tissues examined, although the abundance of each transcript was not quantified. NSBP1 is encoded by six exons and has exon-intron boundaries identical to the HMG-14/-17 genes. The last exon and the 3' UTR of NSBP1 contain retrotransposon sequences of HAL1, HERV-H, and L1MB7, suggesting that these retrotransposons were involved in the origin of NSPB1 from an ancestral-like HMG-14/-17 gene. The similarities among NSBP1, Nsbp1, and the HMG-14/-17 proteins suggest that NSBP1 may function as a nucleosomal binding and transcriptional activating element. Further, the AREs in the 3' UTR of NSPB1 suggest that alternate poly(A) site selection may mediate the mRNA stability of this gene.

3' Untranslated Regions↗
PubMed2001

Degeneration of a homing endonuclease and its target sequence in a wild yeast strain.

Mobile introns and inteins self-propagate by 'homing', a gene conversion process initiated by site-specific homing endonucleases. The VMA intein, which encodes the PI-SceI endonuclease in Saccharomyces cerevisiae, is present in several different yeast strains. Surprisingly, a wild wine yeast (DH1-1A) contains not only the intein(+) allele, but also an inteinless allele that has not undergone gene conversion. To elucidate how these two alleles co-exist, we characterized the endonuclease encoded by the DH1-1A intein(+) allele and the target site in the intein(-) allele. Sequence analysis reveals seven mutations in the 31 bp recognition sequence, none of which occurs at positions that are individually critical for activity. However, binding and cleavage of the sequence by PI-SceI is reduced 10-fold compared to the S.cerevisiae target. The PI-SceI analog encoded by the DH1-1A intein(+) allele contains 11 mutations at residues in the endonuclease and protein splicing domains. None affects protein splicing, but one, a R417Q substitution, accounts for most of the decrease in DNA cleavage and DNA binding activity of the DH1-1A protein. Loss of activity in the DH1-1A endonuclease and target site provides one explanation for co-existence of the intein(+) and intein(-) alleles.

Alleles↗
PubMed2002

Isolation of A/D and C genome specific dispersed and clustered repetitive DNA sequences from Avena sativa.

DNA gel-blot and in situ hybridization with genome-specific repeated sequences have proven to be valuable tools in analyzing genome structure and relationships in species with complex allopolyploid genomes such as hexaploid oat (Avena sativa L., 2n = 6x = 42; AACCDD genome). In this report, we describe a systematic approach for isolating genome-, chromosome-, and region-specific repeated and low-copy DNA sequences from oat that can presumably be applied to any complex genome species. Genome-specific DNA sequences were first identified in a random set of A. sativa genomic DNA cosmid clones by gel-blot hybridization using labeled genomic DNA from different Avena species. Because no repetitive sequences were identified that could distinguish between the A and D gneomes, sequences specific to these two genomes are refereed to as A/D genome specific. A/D or C genome specific DNA subfragments were used as screening probes to identify additional genome-specific cosmid clones in the A. sativa genomic library. We identified clustered and dispersed repetitive DNA elements for the A/D and C genomes that could be used as cytogenetic markers for discrimination of the various oat chromosomes. Some analyzed cosmids appeared to be composed entirely of genome-specific elements, whereas others represented regions with genome- and non-specific repeated sequences with interspersed low-copy DNA sequences. Thus, genome-specific hybridization analysis of restriction digests of random and selected A. sativa cosmids also provides insight into the sequence organization of the oat genome.

Avena↗
PubMed2001

Comparative genomics for identification of clone-specific sequence blocks in Streptococcus pneumoniae.

The partial genome sequences of a serotype 3 and a serotype 2 pneumococcal strain were compared to the complete type 4 pneumococcal genome. Over 500000 and 150000 base pairs of the partial genome data, obtained from published patents, were analysed respectively. Global alignment showed that nearly the whole genome is highly conserved in accordance with data of multilocus sequence typing of housekeeping genes. The search for clone-specific genes revealed 17 new open reading frames in the type 3 strain, while no new open reading frame was detected in the type 2 strain. Allelic variation of genes was restricted by the use of crude sequence data, but still permitted identification of some new alleles and the observation that all surface proteins present in the partial genome data were highly conserved. In both strains we observed also a variety of chromosomal rearrangements and variations due to mobile genetic elements. All together, this comparative genomic approach gives a genome-based overview of strain relatedness and a prospective on what could be expected when sequencing other pneumococcal strains.

Alleles↗
PubMedDate not supplied

[Tandem and interspersed repeats contribute to the mosaic structure of segmented duplications in the human genome].

Intrachromosomal and interchromosomal segmental duplications account for more than 5% of the human genome. To analyze the processes resulting in the complex mosaic structure of duplicons, a draft human genome sequence was searched for duplicated segments of a genomic fragment of the pericentric region of the chromosome 21 short arm. The duplicons found consist of modules having paralogs in various genome regions. Module ends are flanked with various tandem or interspersed repeats, which are more unstable as compared with unique sequences. In most cases, the boundaries of duplicated segments exactly coincide with or are in close proximity to hot spots of various rearrangements within repeats or boundaries between repeats and unique sequences or between two different repeats. Homologous recombination between repetitive elements was assumed to be the major mechanism contributing to the mosaic structure of duplicons.

Chromosomes, Human, Pair 21↗
PubMed1981

Nucleotide sequences of mouse genomic loci including a gene or pseudogene for U6 (4.8S) nuclear RNA.

We have isolated four clones which hybridize with U6 (4.8S) nuclear RNA, a mammalian small nuclear RNA(nRNA), from DNA of BALB/C mouse liver. Their restriction maps are totally different from each other, indicating that they derived from different loci in the mouse genome. The nucleotide sequences around the hybridizing region in the three clones have been determined. One clone gives a gene that is co-linear with the U6 RNA. There is a sequence TATAAAT beginning 31 nucleotides upstream of the gene, which may suggest that the U6 RNA is transcribed by RNA polymerase II. The other two clones contain a pseudogene for the U6 RNA which has 7 or 9 nucleotide changes from the RNA. The pseudogenes are surrounded by radically different sequences from those surrounding the gene, and they are closely linked to a pseudogene for another snRNA, 4.5S-I RNA, or a part of highly repetitive an interspersed sequence B1.

Animals↗
PubMed2003

Ero1-L, an ischemia-inducible gene from rat brain with homology to global ischemia-induced gene 11 (Giig11), is localized to neuronal dendrites by a dispersed identifier (ID) element-dependent mechanism.

Many changes in neuronal gene expression occur in response to ischemia, and these may play a role in determining the fate of ischemic neurons. To identify genes induced in the rat brain following cerebral ischemia, a strategy was used that combines subtractive hybridization and differential screening. Among the genes identified was one referred to as global ischemia-inducible gene 11(Giig11). Sequence analysis indicated that Giig11 exhibited 97% and 91% identity to the known Ero1-L (S. cereviseae ero1-like oxidoreductase) of mouse and human origin, which is involved in oxidative endoplasmic reticulum protein folding. Rat Ero1-L/Giig11 also contains a l07-bp sequence that is nearly identical (> 95%) to the known dispersed repetitive identifier (ID), but which is lacking in mouse and human Ero1-L. Northern blotting showed that expression of the ID element and Ero1-L/Giig11 mRNA increased after global cerebral ischemia. In situ hybridization demonstrated increased expression of Ero1-L/Giig11 in the brain following ischemic injury, with the highest levels in the vulnerable hippocampal CA1 pyramidal neurons. Transfection of cultured primary hippocampal neurons with a plasmid containing green fluorescent protein (gfp) and Ero1-L/Giig11 cDNA (with and without the ID element) produced a gfp-Ero1-L/Giig11 fusion protein, and more fusion protein was localized into dendrites in the presence of the ID element, suggesting that the ID element promotes Ero1-L/Giig11 protein localization to dendrites. Therefore, Ero-1L/Giig11 may have a role in ischemia-induced neuronal repair or survival mechanisms directed at counteracting abnormalities in protein folding, maturation and distribution.

Amino Acid Sequence↗
PubMed2006

Inviting instability: Transposable elements, double-strand breaks, and the maintenance of genome integrity.

The ubiquity of mobile elements in mammalian genomes poses considerable challenges for the maintenance of genome integrity. The predisposition of mobile elements towards participation in genomic rearrangements is largely a consequence of their interspersed homologous nature. As tracts of nonallelic sequence homology, they have the potential to interact in a disruptive manner during both meiotic recombination and DNA repair processes, resulting in genomic alterations ranging from deletions and duplications to large-scale chromosomal rearrangements. Although the deleterious effects of transposable element (TE) insertion events have been extensively documented, it is arguably through post-insertion genomic instability that they pose the greatest hazard to their host genomes. Despite the periodic generation of important evolutionary innovations, genomic alterations involving TE sequences are far more frequently neutral or deleterious in nature. The potentially negative consequences of this instability are perhaps best illustrated by the >25 human genetic diseases that are attributable to TE-mediated rearrangements. Some of these rearrangements, such as those involving the MLL locus in leukemia and the LDL receptor in familial hypercholesterolemia, represent recurrent mutations that have independently arisen multiple times in human populations. While TE-instability has been a potent force in shaping eukaryotic genomes and a significant source of genetic disease, much concerning the mechanisms governing the frequency and variety of these events remains to be clarified. Here we survey the current state of knowledge regarding the mechanisms underlying mobile element-based genetic instability in mammals. Compared to simpler eukaryotic systems, mammalian cells appear to have several modifications to their DNA-repair ensemble that allow them to better cope with the large amount of interspersed homology that has been generated by TEs. In addition to the disruptive potential of nonallelic sequence homology, we also consider recent evidence suggesting that the endonuclease products of TEs may also play a key role in instigating mammalian genomic instability.

Animals↗
PubMed1988

Microcloning reveals a high frequency of repetitive sequences characteristic of chromosome 4 and the beta-heterochromatin of Drosophila melanogaster.

Microdissection and microcloning of the euchromatin-heterochromatin transition region of the Drosophila melanogaster polytene X chromosome and part of the euchromatin of chromosome 4 reveals that they share certain features characteristic of beta-heterochromatin, which is morphologically defined as the loosely textured material at the bases of some polytene chromosome arms. Both are mosaics of many different middle-repetitive DNA sequences interspersed with single-copy DNA sequences. Sixty percent of cloned inserts derived from division 20 and about 40 percent from subdivisions 19EF of the X chromosome harbor at least one repetitive DNA sequence in an average insert of 4.5 kilobases. No repeats have significant cross-hybridization to any of the eleven satellite DNAs, or to the clustered-scrambled sequences present in pDm1. The repetitive elements are, in general, confined to the beta-heterochromatic regions of polytene chromosomes, but some are adjacent to nomadic elements. Chromosome 4, however, has some repeats spread throughout its entire euchromatin. These data have implications for the structure of transition zones between euchromatin and heterochromatin of mitotic chromosomes and also provide a molecular basis for reexamining some of the unusual classical properties of chromosome 4.

Animals↗
PubMed2000

Intronic GIY-YIG endonuclease gene in the mitochondrial genome of Podospora curvicolla: evidence for mobility.

Endonuclease genes encoded in invasive introns are themselves supposed to be mobile elements which, during evolution, have colonized pre-existing introns converting them into invasive elements. This hypothesis is supported by numerous data concerning the LAGLI-DADG subclass of intronic endonucleases. Less is known about the GIY-YIG ORFs which constitute another family of endonucleases. In this paper we describe the presence of one optional GIY-YIG ORF in the second intron of the mitochondrial cytochrome b gene in the fungus Podospora curvicolla. We show that this GIY-YIG ORF is efficiently transferred from an ORF-containing intron to an ORF-less allele. We also show that the products of both the GIY-YIG ORF and the non-canonical LAGLI-DADG-GIY-YIG ORF, which is generated by its integration, have endonuclease activities which recognize and cut the insertion site of the optional sequence. This constitutes the first direct evidence for potential mobility of an intronic GIY-YIG endonuclease. We discuss the role that such a mobile sequence could have played during evolution.

Alleles↗