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PubMed2003

Mouse preimplantation embryos developed from oocytes injected with round spermatids or spermatozoa have similar but distinct patterns of early messenger RNA expression.

Quantitative real-time polymerase chain reaction assay was used to compare the temporal transcriptional activation and mRNA removal for a number of genes in mouse embryos derived by round spermatid injection (ROSI) or intracytoplasmic sperm injection. A number of marker genes with widely different cellular functions were analyzed. Similar patterns of activation were found for the transcription factor Oct 4, the translation initiation factor eukaryotic initiation factor 1A, the L1 ribosomal protein, the chromatin modifying protein histone deacetylase 1, the enzyme hypoxanthine phosphoribosyl transferase, the murine endogenous retrovirus-like element, and the repetitive DNA LINE retrotransposons. Expression of the retrovirus-like mobile element intracisternal A particle, however, was markedly elevated from the two-cell to the blastocyst stages in ROSI embryos. Analyses performed for various paternal mRNAs introduced into the oocyte by the round spermatid, including protamines 1 and 2, transition protein 2, ropporin, and glyceraldehydes 3-phosphate dehydrogenase, revealed all were removed from the preimplantation embryos, albeit with distinct temporal patterns.

Animals↗
PubMed2003

Highly organized structure in the non-coding region of the psbA minicircle from clade C Symbiodinium.

The chloroplast genes of dinoflagellates are distributed among small, circular dsDNA molecules termed minicircles. In this paper, we describe the structure of the non-coding region of the psbA minicircle from Symbiodinium: DNA sequence was obtained from five Symbiodinium strains obtained from four different coral host species (Goniopora tenuidens, Heliofungia actiniformis, Leptastrea purpurea and Pocillopora damicornis), which had previously been determined to be closely related using LSU rDNA region D1/D2 sequence analysis. Eight distinct sequence blocks, consisting of four conserved cores interspersed with two metastable regions and flanked by two variable regions, occurred at similar positions in all strains. Inverted repeats (IRs) occurred in tandem or "twin" formation within two of the four cores. The metastable regions also consisted of twin IRs and had modular behaviour, being either fully present or completely absent in the different strains. These twin IRs are similar in sequence to double-hairpin elements (DHEs) found in the mitochondrial genomes of some fungi, and may be mobile elements or may serve a functional role in recombination or replication. Within the central unit (consisting of the cores plus the metastable regions), all IRs contained perfect sequence inverses, implying they are highly evolved. IRs were also present outside the central unit but these were imperfect and possessed by individual strains only. A central adenine-rich sequence most closely resembled one in the centre of the non-coding part of Amphidinium operculatum minicircles, and is a potential origin of replication. Sequence polymorphism was extremely high in the variable regions, suggesting that these regions may be useful for distinguishing strains that cannot be differentiated using molecular markers currently available for Symbiodinium.

Animals↗
PubMed1980

Isolation and characterization of a new family of mobile dispersed genetic elements, mdg3, in Drosophila melanogaster.

The properties of a new family of mobile dispersed genetic elements, mdg3, are described. Mdg3 is represented by a DNA fragment of about 5.5 kb long which is framed with two repetitive sequences 300-500 base pairs in length. Virtually the whole region of mdg3 including the repetitive sequences is transcribed and, as the result, 26S poly(A)+RNA is formed. The repetitive sequence is present at least at the 3'-end of a major 26S transcript. Both strands of mdg3 are transcribed, but one direction is predominant. Besides 26S RNA, a minor transcript, 15S poly(A)+RNA, can be observed. 15S RNA dose not contain sequences corresponding to the middle of mdg3. Possibly it is formed from 26S RNA by means of splicing. About 15 copies of mdg3 are present in the genome of embryonic cells and polytene chromosomes. Different copies of mdg3 are identical but surrounded with different DNA sequences. In culture cells, the gene is amplified and the number of copies is increased approximately 13 times. Mdg3 is localized in 15-17 sites on different chromosomes of D. melanogaster. Its location varies from one animal to another. The properties and possible nature of mobile dispersed genetic elements are discussed.

Animals↗
PubMed1997

Novel testis-specific protein-DNA interactions activate transcription of the mouse protamine 2 gene during spermatogenesis.

The mouse protamines are expressed exclusively in postmeiotic male germ cells and are crucial for the compaction of chromatin during the late stages of spermatogenesis. The temporal expression of the two mouse protamines is transcriptionally regulated in the testis. Recent studies have demonstrated that ubiquitous and testis-specific proteins bind to the promoter of the mouse protamine 2 (mP2) gene. We have performed in vitro transcription and mobility shift assays to characterize the functional significance of the protein-DNA interactions within 180 base pairs upstream of the mP2 transcription start site. Deletion and mutational analyses reveal two positive regulatory sequences for mP2 transcription at positions -59/-47 and -83/-72 of the mP2 promoter. The proximal element at -59/-47 binds to a novel testis-specific protein we name protamine-activating factor 1 (PAF-1). PAF-1 reaches high levels in round spermatids at the time of mP2 transcription. Deletion of the -59/-47 sequence results in about a 3-fold reduction of mP2 transcription in vitro. Although the PAF-1 binding site (PAF-responsive element, PAF-RE), contains the sequence GTCA present in the cAMP-responsive element and is very similar to the estrogen-responsive element, mobility shift assays revealed that neither the cAMP-responsive element modulator nor the estrogen receptor is the protein(s) binding to PAF-RE. Competition mobility shift assays reveal that the second positive regulatory element at -83/-72 binds a Y-box-binding protein. Using in vitro transcription assays, a 5-fold decrease in mP2 transcription is seen when both the PAF-RE and this Y-box are deleted. These data suggest that the testis-specific PAF-1 and a Y-box-binding protein are needed to activate mP2 transcription in postmeiotic male germ cells.

Aging↗
PubMed1996

The Escherichia coli retrons Ec67 and Ec86 replace DNA between the cos site and a transcription terminator of a 186-related prophage.

Retrons are unusual, reverse transcriptase-encoding elements found in bacteria. Although there are a number of indications that retrons are mobile elements, their transposition has not been observed. The Escherichia coli retrons Ec67 and Ec86 are different retrons inserted at the same site and we have further characterized this site in search of clues to the mechanism of retron transposition. We confirm, by extending previous sequence analysis, that Ec67 and Ec86 are inserted into prophages related to coliphage 186. Comparison with the recently published sequence of the 186 96-2% region indicates that the retrons have replaced approximately 180 bp of DNA between the phage cohesive end site (cos) and the transcription terminator of a phage DNA-packaging gene. These features--DNA replacement at the insertion site and the location of retron junctions near transcription terminators or DNA cleavage sites--are shared with other retrons and suggest ways in which retron transposition might have occurred.

Amino Acid Sequence↗
PubMed1990

HeT DNA: a family of mosaic repeated sequences specific for heterochromatin in Drosophila melanogaster.

HeT DNA is a complex family of repeated DNA found only in pericentric and telomeric heterochromatin. In contrast to other DNA families that have been specifically associated with heterochromatin, HeT DNA is not principally a family of tandemly repeated elements. Much of the HeT DNA family appears to be a mosaic of several different classes of large sequence elements arranged in a scrambled array; however, some elements of the family can be found in tandem repeats. In spite of the variable order of the different elements in HeT DNA, the sequence homology between different members of each class of element is extremely high, suggesting that the members are evolving in a concerted fashion. Sequence analysis suggests that some elements in the HeT family may make up a novel family of heterochromatin-specific transposable elements and that the mosaic organization of the elements may be produced by retroposition and other mechanisms involved in the transposition of mobile elements. We suggest that such mechanisms may be a general feature for the maintenance of chromosome structure.

Animals↗
PubMed2005

A comparative radiological assessment of five European biosphere systems in the context of potential contamination of well water from the hypothetical disposal of radioactive waste.

In the framework of the BioMoSA project for the development of biosphere assessment models for radioactive waste disposal the Reference Biosphere Methodology developed in the IAEA programme BIOMASS was applied to five locations, situated in different European countries. Specific biosphere models were applied to assess the hypothetical contamination of a range of agricultural and environmental pathways and the dose to individuals, following contamination of well water. The results of these site-specific models developed by the different BioMoSA partners, and the individual normalised dose to the exposure groups were compared against each other. Ingestion of drinking water, fruit and vegetables were found to be among the most important pathways for almost all radionuclides. Stochastic calculations revealed that consumption habits, transfer factors, irrigation rates and distribution coefficients (Kd(s)) were the most important parameters that influence the end results. Variations in the confidence intervals were found to be higher for sorbing elements (e.g. (36)Cl, (237)Np, (99)Tc, (238)U, (129)I) than for mobile elements (e.g. (226)Ra, (79)Se, (135)Cs, (231)Pa, (239)Pu). The influence of daughter products, for which the distribution into the biosphere was calculated individually, was also shown to be important. This paper gives a brief overview of the deterministic and stochastic modelling results and the parameter sensitivity. A screening methodology was introduced to identify the most important pathways, simplify a generic biosphere tool and refine the existing models.

Adult↗
PubMed2005

Tandem insertions of Alu elements.

Alu elements are non-autonomous, non-LTR retroposons that represent the most abundant mobile elements in the human genome (1.1 x 10(6) copies/genome). They preferentially insert adjacent to existing Alu elements. It has been proposed that Alu elements utilize LINE-1 machinery for their retroposition. The LINE-1 endonuclease cleaves at a loose consensus sequence. We have utilized a bioinformatics approach to show the order of insertion of pairs of young (Y) and old (S or J) Alu subfamily members. Our data suggest that the consensus LINE-1 endonuclease cleavage site used for insertion of the old Alu elements can be reused for integration of the younger ones inserting adjacent to them. However, there is also a preference at the 3' end of Alu into a non-ideal cleavage site that may represent unique properties of the A-tail for integration. Alu elements inserting adjacent to one another may suggest the saturation of the optimal integration sites with existing Alu elements, rather than any innate preference for Alu elements to integrate adjacent to other Alus.

Alu Elements↗
PubMed1988

[Repetitive sequences of the human genome].

A review of literature data on different families of repetitive sequences of human genome is presented. Both tandemly organized (classical satellite DNA, alpha satellite DNA, "minisatellites" etc.) and interspersed repetitive elements are characterized in detail. Special attention is paid to description of human genome mobile elements.

DNA↗
PubMed1991

Sequences homologous to Tc(s) transposable elements of Caenorhabditis elegans are widely distributed in the phylum nematoda.

To have a better understanding of the evolutionary history of mobile elements within the nematodes, we examined the distribution and the conservation of homologues to transposable elements from Caenorhabditis elegans (Tc1, Tc2, Tc3, Tc4, Tc5, and FB1) in 19 nematode species belonging to the class Secernentea. Our results show that Tc1 elements display a distribution restricted to the family Rhabditidae with poor conservation. The Tc2 and FB1 homologous elements have the same patchy distribution within the Rhabditidae. They were only found in Caenorhabditis and in Teratorhabditis. The Tc3 element is widely distributed among nematode species. Tc3 homologous elements are present in the majority of the Rhabditidae but also in two genera within the family Panagrolaimidae, and in Bursaphelenchus, which belongs to the order Aphelenchida. Tc4 and Tc5 homologues show the most limited distribution of all tested elements, being strictly limited to C. elegans. These data indicate that in some cases, the distribution of transposable elements in the nematode cannot be explained by strict vertical transmission. The distribution of Tc3, Tc4, and Tc5 suggests that horizontal transmission may have occurred between reproductively isolated species during their evolutionary history.

Animals↗
PubMed1993

P-element-induced interallelic gene conversion of insertions and deletions in Drosophila melanogaster.

We studied the process by which whd, a P-element insertion allele of the Drosophila melanogaster white locus, is replaced by its homolog in the presence of transposase. These events are interpreted as the result of double-strand gap repair following excision of the P transposon in whd. We used a series of alleles derived from whd through P-element mobility as templates for this repair. One group of alleles, referred to collectively as whd-F, carried fragments of the P element that had lost some of the sequences needed in cis for mobility. The other group, whd-D, had lost all of the P insert and had some of the flanking DNA from white deleted. The average replacement frequencies were 43% for whd-F alleles and 7% for the whd-D alleles. Some of the former were converted at frequencies exceeding 50%. Our data suggest that the high conversion frequencies for the whd-F templates can be attributed at least in part to an elevated efficiency of repair of unexpanded gaps that is possibly caused by the closer match between whd-F sequences and the unexpanded gap endpoints. In addition, we found that the gene substitutions were almost exclusively in the direction of whd being replaced by the whd-F or whd-D allele rather than the reverse. The template alleles were usually unaltered in the process. This asymmetry implies that the conversion process is unidirectional and that the P fragments are not good substrates for P-element transposase. Our results help elucidate a highly efficient double-strand gap repair mechanism in D. melanogaster that can also be used for gene replacement procedures involving insertions and deletions. They also help explain the rapid spread of P elements in populations.

Alleles↗
PubMed1987

Evolution of P transposable elements: sequences of Drosophila nebulosa P elements.

P elements have been cloned and sequenced from Drosophila nebulosa. Their sequences have diverged less than 6% from P elements of Drosophila melanogaster. However D. nebulosa P elements have nucleotide changes that close all four open reading frames found in the D. melanogaster P element. Microinjection experiments show that D. nebulosa P elements cannot provide transposase function for D. melanogaster P elements, nor are D. nebulosa P elements mobilized by the transposase provided by a D. melanogaster P factor. Three D. nebulosa P elements appear to have integrated into the same position of a complex, centromeric repeated sequence. Comparison of nucleotide sequences suggests that D. nebulosa P elements have diverged upon different pathways from a common ancestor that was 99% homologous to the P elements of D. melanogaster.

Base Sequence↗
PubMed1980

Mobile dispersed genetic element MDG1 of Drosophila melanogaster: transcription pattern.

Virtually the whole region of the mobile dispersed genetic element mdg1 including the direct repeats that frame mdg1 /1/ is transcribed. The end of the transcriptional unit is located within the direct repeat. Although the transcription of mdg1 is symmetric, one direction is transcribed preferentially and is a full-length transcript represented by approximately 29S poly(A)+RNA. Besides it, approximately 15S poly(A)+RNA is present in the cytoplasm of culture cells which corresponds to the 3'-part of 29S RNA and possibly to a small region near the 5'-end of the latter. The major fraction of mdg1 transcripts is present in the fraction of free cytoplasmic RNP particles while only 10-20% are recovered in polysomes. In this respect, mdg1 is similar to mdg3 and quite different from two single-copy genes transcripts of which are almost completely recovered in polysomes. The relationship between mobile dispersed genetic elements and endogeneous viral genomes is discussed.

Animals↗
PubMed1983

An unusual transposon encoding heat shock inducible and developmentally regulated transcripts in Dictyostelium.

We have isolated and characterized a transposable element from Dictyostelium discoideum denoted Tdd-1. There are approximately 50 complete copies of the element per haploid genome and approximately 100-150 partial elements. Southern blots of DNA from different Dictyostelium discoideum strains show that Tdd-1 is a mobile element. Tdd-1 is 4.9 kb long, with 313 bp inverted repeats. These repeats lie near the termini, but unlike other transposable elements one end of Tdd-1 extends 36 bp past the repeat and the other extends 1 bp. Tdd-1 encodes a series of developmentally regulated transcripts, all with the same polarity, that increase dramatically in abundance after approximately 10 hr of development. We have also identified a heat shock inducible transcript of the opposite polarity.

Animals↗
PubMed2005

Prophage-like elements in bifidobacteria: insights from genomics, transcription, integration, distribution, and phylogenetic analysis.

So far, there is only fragmentary and unconfirmed information on bacteriophages infecting the genus Bifidobacterium. In this report we analyzed three prophage-like elements that are present in the genomes of Bifidobacterium breve UCC 2003, Bifidobacterium longum NCC 2705, and Bifidobacterium longum DJO10A, designated Bbr-1, Bl-1, and Blj-1, respectively. These prophagelike elements exhibit homology with genes of double-stranded DNA bacteriophages spanning a broad phylogenetic range of host bacteria and are surprisingly closely related to bacteriophages infecting low-G+C bacteria. All three prophage-like elements are integrated in a tRNA(Met) gene, which appears to be reconstructed following phage integration. Analysis of the distribution of this integration site in many bifidobacterial species revealed that the attB sites are well conserved. The Blj-1 prophage is 36.9 kb long and was induced when a B. longum DJO10A culture was exposed to mitomycin C or hydrogen peroxide. The Bbr-1 prophage-like element appears to consist of a noninducible 28.5-kb chimeric DNA fragment composed of a composite mobile element inserted into prophage-like sequences, which do not appear to be widely distributed among B. breve strains. Northern blot analysis of the Bbr-1 prophage-like element showed that large parts of its genome are transcriptionally silent. Interestingly, a gene predicted to encode an extracellular beta-glucosidase carried within the Bbr-1 prophage-like element was shown to be transcribed.

Base Sequence↗
PubMed1991

[Ectopic interactions of Drosophila melanogaster polytene chromosomes in the H-E system of hybrid dysgenesis].

Analysis of salivary gland polytene chromosomes of Drosophila melanogaster age III larvae has demonstrated that inversions make up high percentage of aberrations induced by transposition of the hobo element. The frequency of inversions increases upon irradiation. In view of the fact that transpositions of mobile elements and irradiation can considerably affect the homology of associating regions, ectopic chromosome contacts were analysed. On the one hand, this analysis has revealed general features for all types of crosses, such as the prevalence of intrachromosomal contacts over interchromosomal ones, predominant localization of both types of contacts in telomeric regions of chromosomes and lower frequency of their occurrence on X chromosome in males as compared with females. On the other hand, the specificity of ectopic conjugation in different types of crosses has been determined. Given a constant average frequency of ectopic contacts in the D. melanogaster genome, differences in their distribution in chromosomes have been detected. Chromosomes of pure lines differ from their homologues in dysgenic hybrids by distribution of ectopic conjugation peaks and by localization of a number of unique events. On the basis of our own experiments and literature data, the role of ectopic contacts as structural formations connecting chromosome regions similar in their functional activity, rather than in nucleic-protein characteristics, is discussed.

Animals↗
PubMed1997

Repetitive elements and their genetic applications in zebrafish.

Repetitive elements provide important clues about chromosome dynamics, evolutionary forces, and mechanisms for exchange of genetic information between organisms. Repetitive sequences, especially the mobile elements, have many potential applications in genetic research. DNA transposons and retroposons are routinely used for insertional mutagenesis, gene mapping, gene tagging, and gene transfer in several model systems. Once they are developed for the zebrafish, they will greatly facilitate the identification, mapping, and isolation of genes involved in development as well as the investigation of the evolutionary processes that have been shaping eukaryotic genomes. In this review repetitive elements are characterized in terms of their lengths and other physical properties, copy numbers, modes of amplification, and mobilities within a single genome and between genomes. Examples of how they can be used to screen genomes for species and individual strain differences are presented. This review does not cover repetitive gene families that encode well-studied products such as rRNAs, tRNAs, and the like.

Animals↗
PubMed2004

Microbial acidification and pH effects on trace element release from sewage sludge.

Leaching of sludge-borne trace elements has been observed in experimental and field studies. The role of microbial processes in the mobilization of trace elements from wastewater sludge is poorly defined. Our objectives were to determine trace element mobilization from sludge subjected to treatments representing microbial acidification, direct chemical acidification and no acidification, and to determine the readsorption potential of mobilized elements using calcareous sand. Triplicate columns (10-cm diameter) for incubation and leaching of sludge had a top layer of digested dewatered sludge (either untreated, acidified with H2SO4, or limed with CaCO3; all mixed with glass beads to prevent ponding) and a lower glass bead support bed. Glass beads in the sludge layer, support layer or both were replaced by calcareous sand in four treatments used for testing the readsorption potential of mobilized elements. Eight sequential 8-day incubation and leaching cycles were operated, each consisting of 7.6 d of incubation at 28 degrees C followed by 8 h of leaching with synthetic acid rain applied at 0.25 cm/h. Leachates were analyzed for trace elements, nitrate and pH, and sludge layer microbial respiration was measured. The largest trace element, nitrate and S losses occurred in treatments with the greatest pH depression and greatest microbial respiration rates. Cumulative leaching losses from both microbial acidification and direct acidification treatments were > 90% of Zn and 64-80% of Cu and Ni. Preventing acidification with sludge layer lime or sand restricted leaching for all trace elements except Mo. Results suggested that the primary microbial role in the rapid leaching of trace elements was acidification, with results from direct acidification being nearly identical to microbial acidification. Microbial activity in the presence of materials that prevented acidification mobilized far lower concentrations of trace elements, with the exception of Mo. Trace elements mobilized by acidification were readsorbed by calcareous sand when present.

Calcium↗