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General Information
Symbol
copia
Species
D. melanogaster
Feature type
natural_transposable_element
FlyBase ID
FBte0000023
Sequences and Components
Complete element (bp)

5146

Terminal repeat (bp)

276

Component genes
Sequence Accessions
Sequence Ontology (SO)
Insertions and Copy Number
Copy number and comments

60 (Finnegan et al., 1978; Potter et al., 1979)

5143 in euchromatin of Release 3 genome annotation, of which 30 are full length.

Target Site Duplication
Size (bp)

5

Orthologs
Comments

Dwil\copia is virtually identical in sequence to copia despite melanogaster and willistoni being separated from a common ancestor by approximately 50 million years. Although copia is abundant in all melanogaster group species it displays a patchy distribution in willistoni. A recent horizontal transfer of copia from melanogaster to willistoni is indicated.

Age dependence of the copia transposition rate in males is positively associated with copia transcript abundance in testes. This type of age dependence indicates that copia transpositions do not occur in stem cells. Clusters of transpositions have been detected indicating pre-meiotic transposition. The physiological state of the host may affect expression and transposition of copia.

Transposable elements can be used to reveal cross-over events.

No transposition was detected in progeny after heat shock of parents.

Ufo has an effect on copia mRNA levels.

A lower proportion of copia, mdg1 and 412 element insertion sites on the X chromosome, from various populations of D.melanogaster and D.simulans, in comparison with autosomes suggests that selection against the detrimental effects of TE insertions in the major force containing TE copies in populations.

Dhyd\lola-like encodes a transcription factor that binds and interacts with an 18bp target DNA sequence within the copia enhancer sequences to activate transcription in Schneider cells.

Using copia LTR as a model, it is demonstrated that a regulatory region contained within the elements untranslated leader region (ULR) consists of multiple copies of an 8bp motif (TTGTGAAA) with similarity to the core sequence of the SV40 enhancer. Naturally occurring variation number of these motifs correlates with the enhancer strength of the ULR. Results indicate that inter-element selection may favour the evolution of more active enhancers within permissive genetic backgrounds.

Correlations between the rate of transposition and TE copy number are determined for copia and are found to be either zero or positive.

High rates of germ line copia transposition occur only in males by tissue-specific control of RNA levels (copia is transcribed at much higher levels in male germinal tissues that in the equivalent female tissue). Data suggests that transposition of copia is regulated at the RNA level and only occurs in tissues containing more than a relatively high threshold level of copia RNA.

Used in an investigation to address the relationship between retrotransposons and retroviruses and the coadaptation of these retroelements to their host genomes. Results indicate retrotransposons are heterogeneous in contrast to retroviruses, suggesting different modes of evolution by slippage-like mechanisms.

One of a class of genes with TATA-less promoters that have the conserved DPE sequence.

The behaviour of the retrotransposons copia, Dsim\copia and mdg1 has been analysed in hybrids between D.melanogaster and D.simulans. No somatic transposition events were detected in hybrid larvae.

Study of TE distribution (P-element, hobo, I-element, copia, mdg1, mdg3, 412, 297 and roo) along chromosome arms shows no global tendency for the TE site occupancy frequency to negatively follow the recombination rate, except for the 3L arm. The tendency for TE insertion number to increase from base to tip of some chromosome arms is simply explicable by a positive relationship with DNA content along the chromosomes. So for all TEs, except hobo, there is no relationship between distribution of TE insertion numbers weighted by DNA content and recombination rate. hobo insertion site number is positively correlated with recombination rate.

Endogenous transposable elements show more instability in sublines injected with exogenous viral particles than in transgenic sublines containing a foreign viral insert, all transposable elements are not equally sensitive to such genomic stress.

Larval copia RNA levels are variable among Drosophila species, transcripts are detected in D.melanogaster, but not in D.simulans, D.mauritiana, D.sechellia, D.yakuba, D.erecta or D.willistoni. Size variation mapping to the LTR and ULR in naturally occurring copia elements is likely generated by duplication and is of functional significance. Ecol\CAT reporter gene constructs indicate that regulatory sequences that influence copia expression are located within the elements 5' LTR and adjacent ULR.

copia transposition rate is positively and nonlinearly associated with copia copy number. Results postulate that the number of copia virus-like particles, necessary for copia transposition, could depend nonlinearly on copia copy number.

Excision of the copia retrotransposon can be influenced by heat shock.

The distribution of copia elements in heterochromatin has been studied by in situ hybridisation to mitotic chromosomes.

Phylogenetic analysis indicates that although D.melanogaster copia elements are distinct from those of D.simulans and D.mauritiana, the copia elements of these latter two species are not distinguishable from one another.

Experiments designed to compare the insertion patterns of copia and mdg1 revealed that crossing to marker strains led to heterogeneity in insertion patterns of the copia elements, with no significant polymorphism of the mdg1 insertions.

Spontaneous insertions and excisions of mdg1, copia, 412 and roo (excisions are outnumbered by insertions) occur during 65 generations of mass mating under laboratory conditions. Their contribution into variation for transposable element location does not seem great.

The distribution of a number of transposable elements has been studied in 10 Harwich mutation accumulation lines.

copia activity appears to be restricted to males. The X chromosome is the preferential target for copia insertions.

The distribution of transposable elements within heterochromatin indicates that they are major structural components of the heterochromatin.

The chromosomal distribution of a number of retrotransposons in an isolated population of D.melanogaster (from Ishigaki Island, Okinawa, Japan) has been determined.

The distribution of copia elements across the chromosomes has been analysed in individuals from a natural population of D.melanogaster.

copia enancer sequences are responsible for high level expression of copia in transient transfection assays using D.hydei- and D.melanogaster-derived cells. A 50kD factor that binds the enhancer sequences is identified by mobility shift assays and UV crosslinking experiments.

Estimating the genomic numbers of transposable elements demonstrates many families of element are over-represented in heterochromatin.

The spatial and temporal expression patterns of fifteen families of retrotransposons are analysed during embryogenesis and are found to be conserved. Results suggest that all families carry cis-acting elements that control their spatial and temporal expression patterns.

The copia and 412 transposable elements increase in copy number in aged adult tissue due to the activation of reverse transcriptase.

The insertion patterns of mdg1 and copia are sufficiently modified to allow the unambiguous detection of an alien genome income.

Rates of transposition and excision of the copia element have been determined.

Element copy numbers on inversion and standard chromosomes has been determined. The copy number is significantly higher within low frequency inversions than within the corresponding standard chromosome regions.

The copia 5' untranslated region contains binding sites for transcriptional regulation by homeoproteins.

The copia retrotransposon has been found unstable in the 2b3 stock.

All sequences necessary for developmentally regulated copia transcription are contained within the 3' LTR. Doa mutations increase accumulation of this transcript, therefore the site responsible for Doa interaction with copia also lies within the 3' LTR.

Polymorphism of transposable elements in inbred lines has been examined: P-element, gypsy, jockey, I-element, mdg1, 412, mdg3 and 297 sites are largely stable, whereas roo and copia sites are polymorphic.

Reduction of fitness, as implied from increase in sterility, accompanies high mobility of roo and copia in a semi-sterile inbred stock.

In a study of the distribution in the genome of 9 families of transposable element among chromosomes 2 and 3 of a natural population, it was found that the elements were distributed randomly in the distal section of chromosome arms, whereas some linkage disequilibrium was detected in proximal regions. Different elements tend to occupy different sites. The more proximal the site, the more likely the element was to show a non-random distribution.

Distribution of 9 families of transposable elements in a natural population was studied and the hypothesis that transposable element abundance is regulated primarily by deleterious fitness consequences of ectopic meiotic exchange was supported. Proximal euchromatin may only infrequently undergo exchange, and elements detected in population surveys of this kind tend to be inserted into sites where there is negligible effect on fitness.

copia is able to dosage compensate and the response shows developmental and position dependence. copia-initiated transcript within wa is dosage compensated in adults, but not in larvae.

Numbers of mdg1, mdg3, gypsy and copia have been studied in several strains of D.melanogaster and D.simulans. Mean number of mdg1 and copia sites are drastically reduced in D.simulans. Majority of mdg1 and copia sites, and one third of mdg3 sites, are in hot spots for insertion, particularly in D.simulans. Southern blot analysis indicates that the majority of mdg1 and copia are in the euchromatin of D.melanogaster but the heterochromatin of D.simulans.

One substock of inbred lines shows considerable heterogeneity of insertion sites of copia (frequency of insertions is 12% per haploid genome per generation) whereas mdg1, 412, mdg3, gypsy, 297 and HMS-Beagle were stable in all stocks examined.

Stability of 11 transposable element families compared by Southern blotting among individuals of lines that had been subjected to 30 generations of sister sib matings. 412, roo, blood, 297, 1731 and G-element all appear stable, whereas copia, hobo, I-element, gypsy and jockey elements show instability.

copia is capable of negatively regulating expression from its own promoter and is also able to positively regulate expression from Lsp1α in transient DNA co-transfection assays.

copia promoter elements show no enhancement of transcription by heat shock in cultured Drosophila cell lines.

Expression and processing of the copia\GIP gag precursor in E.coli cells generates a unique laminate structure in E.coli. copia protease in involved in cleaving the gag precursor, a mutation in the active site of the protease results in accumulation of the gag precursor and the laminate structure is not generated.

Reverse transcription of copia RNA is likely to occur in copia virus-like particles.

The gag gene products of copia are produced in far greater amounts than the pol and int gene products. Gene fusion constructs with Ecol\lacZ demonstrate that gag encoding RNA is expressed as protein in cultured cells at least ten fold more efficiently than the RNA containing pol and int reading frames.

copia elements are found in D.simulans, D.mauritiana and D.melanogaster but copia-encoded transcripts are only found in D.melanogaster. copia transcript level variation is found among natural populations of D.melanogaster : this is not due to variable copia copy number but may be due to the action of trans-acting controls.

The distribution of a number of transposable elements, including copia elements, in a D.melanogaster laboratory strain with a high frequency of spontaneous mutations and its derivatives, has been studied.

The 2kb copia RNA is generated through splicing and encodes sufficient information to make copia virus-like particles, VLPs, in Drosophila cultured cells. copia VLPs are produced through autocatalytic processing of the polyprotein precursor encoded by spliced 2kb RNA.

One end of tRNA:M-iΨ (a tRNA pseudogene homologous to the 5' half of an initiator tRNA) is joined directly to the 3' terminal sequence of copia. tRNA:M-iΨ may be a derivative of a reverse transcript of copia primer RNA.

Sequences located 5' to Sgs7, Sgs8, Sgs3, the Hsp70 genes at 87A and 87C and the copia coding region are similar to the sequence at -405 from Sgs4.

First described by Finnegan et al. (1978) as a sequence complementary to abundant polyA+ RNA in tissue culture cells. The map in Lindsley, Zimm, 1992: 1099 is taken from the sequence of Mount and Rubin (1985), and the sequence of the LTR is from Levis et al. (1980). The sequences of complete copia elements have been published by Mount and Rubin (1985) and by Emori et al. (1985). Virus-like particles containing full length copia RNAs have been found in tissue culture cells by Shiba and Saigo (1983). The major protein in these particles is translated from a 2 kb spliced mRNA (Yoshioka et al.). The sequence of this mRNA has been determined by Miller et al. (1989). This protein is released from the primary translation product by autocatalytic cleavage (Yoshioka et al.). Kikuchi et al. (1986) have shown that a fragment of the initiator methionine tRNA acts as a primer for reverse transcription of copia RNA in these particles. Sequences essential for copia expression are located on either side of the major transcriptional start sites (Sneddon and Flavell, 1989).

Other Information
Etymology
External Crossreferences and Linkouts ( 42 )
Synonyms and Secondary IDs (14)
Reported As
Symbol Synonym
BcDNA:RH07382
BcDNA:RH25742
BcDNA:SD10530
copia
(Kordyukova et al., 2020, Palazzo et al., 2019, Barckmann et al., 2018, Raje et al., 2018, Solares et al., 2018, Sun et al., 2018, Karam et al., 2017, Nefedova and Kim, 2017, Guida et al., 2016, Xu et al., 2016, Kofler et al., 2015, Molla-Herman et al., 2015, Rahman et al., 2015, Senti et al., 2015, Wang et al., 2015, Basquin et al., 2014, Kirsanov et al., 2014, Mirkovic-Hösle and Förstemann, 2014, Sytnikova et al., 2014, Cridland et al., 2013, Czech et al., 2013, Dönertas et al., 2013, Fedoseeva and Tchurikov, 2013, Muerdter et al., 2013, Fedoseeva et al., 2012, Kofler et al., 2012, Sienski et al., 2012, Tan et al., 2012, de Setta et al., 2011, Handler et al., 2011, Klenov et al., 2011, Nefedova et al., 2011, Pane et al., 2011, Petrov et al., 2011, Shpiz et al., 2011, Vu and Nuzhdin, 2011, Zhang et al., 2011, Díaz-González et al., 2010, Fedoseeva et al., 2010, Kotova et al., 2010, Lu and Clark, 2010, Deloger et al., 2009, Henikoff et al., 2009, Lau et al., 2009, Li et al., 2009, Malone et al., 2009, Steinbiss et al., 2009, Tchurikov et al., 2009, Brennecke et al., 2008, Chung et al., 2008, Czech et al., 2008, Iklé et al., 2008, Kawamura et al., 2008, Matyunina et al., 2008, Mugnier et al., 2008, Bergman and Bensasson, 2007, Brennecke et al., 2007, Fablet et al., 2007, Klenov et al., 2007, Lecuyer et al., 2007, Minervini et al., 2007, Nefedova and Kim, 2007, Alonso-Gonzalez et al., 2006, Athauda et al., 2006, Bergman et al., 2006, Ganko et al., 2006, Haynes et al., 2006, Saito et al., 2006, Kalmykova et al., 2005, Lipatov et al., 2005, Mito et al., 2005, Houle and Nuzhdin, 2004, Vagin et al., 2004, Alonso-Gonzalez et al., 2003, Dimitri et al., 2003, Fanti et al., 2003, Abe et al., 2001, Levinger and Varshavsky, 1982)
copia element
Secondary FlyBase IDs
  • FBgn0063664
  • FBgn0063660
  • FBgn0061364
  • FBgn0000349
  • FBtp0011420
References (346)