Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Retroelements”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 703 records · Page 39Linked to original sources
PubMed2003

Ty3/gypsy-like retrotransposons in Candida albicans and Candida dubliniensis: Tca3 and Tcd3.

Ty3/gypsy retrotransposons are a widespread group of eukaryote mobile genetic elements. They are similar in structure to, and may be ancestors of, the vertebrate retroviruses. Here we describe the first Ty3/gypsy retrotransposons from the pathogenic yeasts Candida albicans and Candida dubliniensis, which we refer to as Tca3 and Tcd3, respectively. Tca3 was first identified in a variety of strains as an element lacking a large part of its coding region. Comparative analyses between C. albicans and C. dubliniensis allowed us to identify the closely related full-length Tcd3 element, and, subsequently, the full-length Tca3 elements. The full-length versions of Tca3 and Tcd3 are broadly similar in structure to other Ty3/gypsy elements, but have several features of special interest, e.g. both elements appear to have a novel mechanism for priming minus-strand DNA synthesis, probably involving conserved secondary structures adjacent to the 5' LTRs. Also, while closely related to each other, the two elements appear to be fairly distantly related to other known Ty3/gypsy-like elements. Finally, the occurrence of the internally deleted forms of Tca3 in many strains raises interesting questions concerning the evolution of these transposable elements in Candida and the evolution of Candida itself. The sequences reported in this paper have been assigned GenBank Accession Nos AF499463, AF499464 and AF510498.

Amino Acid Sequence↗
PubMed1996

Upregulation of the Drosophila 1731 retrotransposon long-terminal repeat by UV-B irradiation requires a short sequence in the U3 region.

A 1731 is a Drosophila melanogaster retrotransposon, the transcripts of which decrease in Drosophila cells after treatment by the 20-hydroxyecdysone (20-OH), the steroid-molting hormone of insects. In order to analyze the regulation of the long terminal repeat (LTR) directed transcription by UV-B, S2 Drosophila cells were transfected with various chimeric constructs carrying the LTR of 1731 linked to the bacterial chloramphenicol acetyltransferase (CAT) reporter gene and then subjected to UV-B irradiation. The results demonstrated that the 1731 LTR is activated by UV-B irradiation in a dose- and time-dependent manner. Using constructions expressing the reporter gene under the control of either the entire or deleted LTRs of 1731, we established that a sequence located in the U3 region was required for the retrotransposon to respond to UV-B. The cis-acting element is identical to the binding sequence of the dorsal transcription factors. In addition, the S2 Drosophila cell produced extracellular factor(s) in response to UV-B irradiation which activated the 1731 LTR in nonirradiated cells. This factor(s) was detected when responding cells were cocultured with inducing cells and when conditioned medium from irradiated cultures was added to the cell cultures.

Animals↗
PubMed1996

The three human cytochrome P450 lanosterol 14 alpha-demethylase (CYP51) genes reside on chromosomes 3, 7, and 13: structure of the two retrotransposed pseudogenes, association with a line-1 element, and evolution of the human CYP51 family.

The three human lanosterol 14 alpha-demethylase (CYP51) genes have been mapped to human chromosomes 3, 7, and 13 using a polychromosomal somatic cell hybrid panel. Two of the genes have been cloned from human chromosome 3-specific (CYP51P1) or from human chromosome 13-containing (CYP51P2) cell hybrids. Both were found to be processed pseudogenes, the first reported in the cytochrome P450 (CYP) gene superfamily. The functional CYP51 gene resides on human chromosome 7. CYP51P1 is 96.5% identical to the human CYP51 coding sequence and is not interrupted with introns but has six in-frame stop codons resulting from point mutations. The intronless CYP51P2 gene is 97.2% identical to the CYP51 cDNA coding region. It has a 1-bp insertion leading to a change of reading frame after codon 9 and a stop codon after amino acid 81. In addition, the CYP51P2 sequence is interrupted with a 5' truncated 131-bp LINE-1 element after nucleotide 606. The element belongs to the youngest LINE subfamily Sb and is 98.2% identical to the LINE-1 element expressed in human teratocarcinoma cells. CYP51 processed pseudogenes are the only known examples of the reverse flow of genetic information during evolution of the large (more than 480 genes) CYP superfamily, suggesting expression in the germ line and a housekeeping function of the lanosterol 14 alpha-demethylase gene. CYP51 pseudogenes evolved by two independent reverse transcription events of the human CYP51 mRNA approximately 9.5 MYR (CYP51P2) and approximately 11.7 MYR (CYP51P1) ago and were inactivated soon after the insertion. The truncated L1 element was inserted into CYP51P2 approximately 6 MYR ago.

Amino Acid Sequence↗
PubMed2001

On the problem of establishing the subcellular localization of Dictyostelium retrotransposon TRE5-A proteins by biochemical analysis of nuclear extracts.

At first sight a protein that is enriched in extracts prepared from nuclei by means of biochemical methods can be considered to be a nuclear protein in vivo. Although this assumption will hold true for most of the analyzed proteins, it could also lead to false interpretations. We analyzed the subcellular distribution of endogenous and plasmid-borne proteins derived from the retrotransposon TRE5-A of Dictyostelium discoideum. In biochemical fractionation experiments the proteins encoded by TRE5-A open reading frame 1 (ORF1p) and the putative endonuclease encoded in ORF2 (ENp) were found in the detergent-insoluble material containing the nuclei. However, salt extraction of isolated nuclei did not considerably release the TRE5-A proteins. Instead, the TRE5-A proteins were strongly enriched in a fraction that contained the chromosomal DNA after removal of most cytoskeletal and histone proteins. These observations implied that ORF1p and ENp were both attached to chromatin in vivo, but this conclusion was disproved by the expression of genetic fusions of green fluorescent protein with either ORF1p or ENp. We show conclusive evidence that both fusion proteins were located as large aggregates of native protein in the cytoplasm of D. discoideum cells.

Animals↗
PubMed1996

Efficient synthesis of a 72-kDa mitochondrial polypeptide using the yeast Ty expression system.

Using the Ty system from yeast we report the efficient expression of a heterologous eukaryotic gene encoding a 72 kDa mitochondrial polypeptide. The pFM2IIBgIII expression vector was initially modified for this purpose by inserting the factor X(a) protease cleavage site. The TyA gene, which encodes the structural component of the yeast virus-like particles (VLPs), and the eukaryotic yst1 gene, encoding a 72 kDa mitochondrial tyrosyl-tRNA synthetase from the filamentous fungus Podospora anserina, were subsequently fused to the factor X(a) cleavage site. The resulting chimeric gene, in which the two polypeptide coding sequences are separated by the factor X(a) cleavage site, was expressed in yeast. High yield expression of this foreign protein, which was isolated from yeast transformants as hybrid TyVLPs, was verified after factor X(a) treatment by SDS polyacrylamide gel electrophoresis and antibody detection. The strategy presented here should be useful for expressing a wide variety of eukaryotic genes.

Base Sequence↗
PubMed1996

A sensitive RNase protection assay to detect transcripts from potentially functional human endogenous L1 retrotransposons.

A high background of read-through transcripts from degenerate human L1 retrotransposons is present in almost all human cell types. This prevents the detection of RNA transcripts from potentially functional elements. To overcome this, we have developed an RNase protection assay based on the reconstructed consensus sequence for the 5' end of the major L1 family. In the human Ntera2D1 teratocarcinoma cell line, this assay readily detected L1 transcripts that were located primarily in the cytoplasm and where 20% were in filterable particles. By this assay, potentially functional L1 elements are also transcriptionally active in lymphocytes from some but not all normal individuals. Together with the full length protection product, there were three other discrete L1 RNAs, two of which (305 and 275 bases) were transcribed from the 5' end of the L1 element. These smaller L1 RNAs do not appear to be derived from transcripts from divergent L1 families but are either discrete shorter transcripts or specifically processed products from longer initial transcripts.

Animals↗
PubMed1998

Identification of genes differentially expressed in vascular smooth muscle cells following benzo[a]pyrene challenge: implications for chemical atherogenesis.

We have previously shown that serial passage of vascular smooth muscle cells (vSMCs) treated with a single low dose of benzo[a]pyrene (BaP) induces acquisition of highly proliferative (i.e. atherogenic) phenotypes. To define the molecular basis of this response, differential display polymerase chain reaction was used to identify early target genes in murine vSMCs challenged with 3 microM BaP for 8 hr. Of 170 differentially expressed cDNAs, 111 were re-amplified, and 64 examined for homology to known genes. Aac11 apoptosis inhibitor, aldose reductase, GalNAc transferase, TCP-1 chaperonin gene, and mouse mitochondrial gene, were downregulated in vSMCs treated with BaP. In contrast, enhanced expression of unique retrotransposon cDNAs were found in BaP-treated cells. This is the first report showing that BaP modulates the expression of these genes in mammalian cells. Of particular interest is the modulation of retrotransposon mRNAs which coupled to other genetic events, may play a significant role in the atherogenic response to this carcinogen.

Aldehyde Reductase↗
PubMed2000

The yeast retrotransposons Ty1 and Ty3 require the RNA Lariat debranching enzyme, Dbr1p, for efficient accumulation of reverse transcripts.

A mutant screen has been initiated to identify host genes important for the replication of retrotransposons in Saccharomyces cerevisiae. Two mutants were identified that undergo Ty1 and Ty3 transposition at <10% of the wild-type frequency. Both these mutants have deficiencies in the accumulation of full-length Ty1 and Ty3 cDNAs, although Ty proteins (including reverse transcriptase) accumulate at wild-type levels. The DBR1 gene, encoding the yeast debranching enzyme, complements both mutants. This suggests that Dbr1p is important for either reverse transcription or the stability of Ty cDNA, roles that have not been previously reported for this protein. The deficiency in accumulation of Ty cDNAs in dbr1 mutants is apparent when engineered Ty elements are expressed for short time periods (6-10 h) but is not apparent following long expression periods (>24 h).

Base Sequence↗
PubMed2002

A double RING-H2 domain in RNF32, a gene expressed during sperm formation.

The RING domain is a cysteine-rich zinc-binding motif, which is found in a wide variety of proteins, among which are several proto-oncogenes and the gene implicated in autosomal recessive juvenile parkinsonism, Parkin. The domain mediates binding to other proteins, either via their RING domains or other motifs. In several proteins, RING domains are found in combination with other cysteine-rich binding motifs and some proteins contain two RING domains. Recent evidence suggests that RING finger proteins function in the ubiquitin pathway as E3 ligases. A variant of the RING domain is the RING-H2 domain, in which one of the cysteines is replaced by a histidine. We have cloned and characterized a novel gene, RNF32, located on chromosome 7q36. RNF32 is contained in 37 kb of genomic DNA and consists of 9 constitutive and 8 alternatively spliced exons, most of which are alternative first exons. A long and a short transcript of the gene are expressed; the short transcript containing exons 1-4 only. This gene encodes two RING-H2 domains separated by an IQ domain of unknown function. This is the first reported gene with a double RING-H2 domain. In humans, RNF32 overlaps with a processed retroposon located on the opposite strand, C7orf13. RNF32 is specifically expressed in testis and ovary, whereas C7orf13 is testis-specific, suggesting that its expression may be regulated by elements in the RNF32 promoter region. RNF32 is expressed during spermatogenesis, most likely in spermatocytes and/or in spermatids, suggesting a possible role in sperm formation.

Alternative Splicing↗
PubMedDate not supplied

Conserved, erythropoietin-responsive VL30 promoters isolated from erythroid progenitor cells.

Virus-like 30S (VL30) elements are endogenous retro-elements of the mouse retrotransposon family. These elements are transcriptionally responsive in a temporal and tissue-specific manner due to the U3 promoter region of the elements' long terminal repeat (LTR). We have analyzed VL30 promoters from erythroid progenitor cell lines (MEL 585S and ELM-I-1) that contrasted in their response to erythropoietin (epo). Through RT-PCR-generated cDNAs, VL30 promoters were identified and showed homology to the third and fourth U3 subgroups, with GATA-1, Jak2/STAT5, and B10 RRE sites. One clone (ELM5) showed 97% homology to BVL-1, a putative epo-responsive VL30 element. In addition, a novel U3 promoter (MEL/ELM CONSTIT) showed complete sequence homology between both cell lines. Ribonuclease protection confirmed that epo-induced VL30 promoters were activated in ELM-I-1 cells, whereas the conserved VL30 MEL-ELM CONSTIT VL30 promoter showed no enhanced expression in the epo-unresponsive MEL cells. Identification of these U3 promoters suggests that VL30s are conserved and can be transcriptionally activated in an epo-specific manner.

Animals↗
PubMed2002

A germline-specific splicing generates an extended ovo protein isoform required for Drosophila oogenesis.

Most regulatory genes are employed multiple times to control different processes during development. The Drosophila Ovo/Shavenbaby (Svb) transcription factor is required both for germline and epidermal differentiation, two roles also found for its ortholog m-ovo1 in mice. In Drosophila, these two distinct functions are contributed by separate control regions directing the expression of Ovo/Svb in the germline (ovo) and soma (svb), respectively. We report here that alternative splicing represents an additional level of the regulation of Ovo/Svb functional specificity. Characterization of the ovo(D1rv23) mutation revealed that the intragenic insertion of a novel retrotransposon, romano, inactivates ovo without altering svb. We provide evidence that this insertion disrupts a germline-specific alternative exon, exon 2b, which encodes a 178-amino-acid internal extension (2B). While both isoforms, Ovo+2B and Ovo-2B, accumulate during oogenesis, only Ovo+2B is able to fulfill germinal ovo functions. Ovo-2B is unable, even when overexpressed, to fully rescue oogenic defects resulting from the absence of wild type ovo product. By contrast, either Ovo+2B or Ovo-2B germline protein can substitute for Svb in the epidermis. Our results emphasize the specific features of splicing in the germline, and reveal its functional importance for the control of ovo/svb-dependent ovarian and epidermal differentiation.

Alternative Splicing↗
PubMed1996

Genetic differentiation in the rice blast fungus revealed by the distribution of the Fosbury retrotransposon.

Repetitive DNA sequences genetically differentiate certain host-specific forms of the plant pathogenic fungus Pyricularia grisea. For example, high copy numbers of a sequence designated MGR586 are conserved in isolates that infect rice. In this report, we describe the molecular characterization of another repetitive DNA sequence designated fosbury. Restriction mapping and DNA sequence analysis show that fosbury is a member of a long terminalrepeat (LTR)-containing retrotransposon family, and gel blot hybridization analysis suggests that, like MGR586, fosbury is preferentially found in isolates that infect rice. This supports the view that rice pathogens comprise a genetically distinct form of P. grisea. We also investigated the distribution of fosbury and MGR586 and found that these elements are sometimes associated in the genome, and gel blot hybridization analysis shows that restriction sites flanking both of these elements resolve rice pathogens into similar clonal lineage groups. We conclude that the transposition of repetitive DNA sequences plays an important role in generating DNA fingerprint variation in the rice blast fungus.

Ascomycota↗
PubMed2001

Organization and distribution pattern of MGLR-3, a novel retrotransposon in the rice blast fungus Magnaporthe grisea.

A specific telomere was deleted in spontaneous, gain-of-virulence mutants derived from a rice pathogen of Magnaporthe grisea. Three different types of transposons, including Pot2, Mg-SINE, and a novel, 6-kb-long LTR (long terminal repeat)-type retrotransposon designated MGLR-3, were identified on this chromosomal end. The 114-bp-long telomeric repeat is immediately followed by the 3' LTR of MGLR-3. A truncated copy of Pot2 immediately flanks the 5' LTR, suggesting that this telomere was generated by a transposition event of MGLR-3 into this Pot2 element, causing the breakage of a chromosome. The subsequent addition of a telomeric repeat to the 3' LTR of MGLR-3 most probably repaired the broken end of the chromosome. Mg-SINE is located 25 bp away from the truncated Pot2 element. MGLR-3 exhibited strong homology to various gypsy-class retrotransposons, including grh and MAGGY in M. grisea. MGLR-3 is ubiquitous regardless of the host of origin.

Amino Acid Sequence↗
PubMed1994

Similar origins of two mouse minisatellites within transposon-like LTRs.

Tandem arrays of simple sequence repeat units are among the most unstable regions of mammalian genomes. Mutational instability at such loci depends on both repeat unit sequence and DNA sequences external to the tandem array, which have been recently implicated in polarized variability at human minisatellites. The characteristics of DNA sequences flanking the mouse minisatellite Ms6-hm have been investigated. This locus has a high mutation rate both in the germline and during early somatic development and is composed of a hypervariable tandem array of 500-2000 pentanucleotide repeat units flanked by a transposon-like long terminal repeat sequence of the mouse transcript (MT) family. A subpopulation of MT elements in the mouse genome are shown to flank a 1.1-kb internal sequence, consistent with their classification within a newly defined mammalian retrotransposon-like superfamily (MaLR). A second mouse minisatellite, Hm-2, also originates from within a MaLR LTR. Hm-2 is related to Ms6-hm in repeat unit sequence and profiles of germline and somatic instability; at both loci the tandem array has amplified from precisely the same point within the LTR. The similar origins of Ms6-hm and Hm-2 suggest that flanking MaLR sequences may be involved in mutational processes at these loci.

Animals↗
PubMed1995

Complete sequence of the 43-kb human ribosomal DNA repeat: analysis of the intergenic spacer.

We have sequenced the remaining 12.4 kb of the 30-kb human ribosomal DNA intergenic spacer (IGS), which allows us to piece together both a complete IGS and a 43-kb rDNA unit. The sequence of the complete IGS reveals a collection of sequence motifs that can be correlated with functions known or expected to reside in the rDNA repeat: modulation of transcription, recombination, initiation of DNA replication, and chromosomal organization. Finally, we find that IGS accumulates variation at a much higher rate than the transcribed regions. This finding leads us to correlate sequence character with types of mutation and sequence context with rate of mutation.

Animals↗
PubMed1995

Mapping of retrotransposon sequences in the unstable region surrounding the spinal muscular atrophy locus in 5q13.

The mutation that underlies the autosomal recessive disorder spinal muscular atrophy (SMA) is located on chromosome 5q13. Recent studies show that SMA patients frequently have deletions and rearrangements in this region compared to normal controls. During the isolation of candidate cDNAs for the disease, we identified a sequence that shows high homology to the THE-1 retrotransposon gene family. Using YAC fragmentation techniques, we have refined the localization of this sequence to the domain known to show instability in SMA patients. The implication of these results for the mechanism of the mutation in SMA is discussed.

Base Sequence↗