A Database of Drosophila Genes & Genomes

FB2013_03, released May 7th, 2013
 

Dmel\hobo

General Information
Symbol Dmel\hobo Species D.melanogaster
Name hobo element FlyBase ID FBte0000154
Feature type natural transposable element
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Description
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FB2013_03
FB2013_02
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hide Sequences & Components
Complete element (bp)
2959
(Kaminker et al., 2002)
3016
 
Terminal repeat (bp)
12
 
Reference sequence transposon_sequence_set.embl.txt.gz
Component genes
hobo\T
 
hide Sequence Accessions
DDBJ/EMBL/GenBank
 
hide Sequence Ontology (SO)
Transposon type
terminal_inverted_repeat_element
(Kaminker et al., 2002, Souames et al., 2003)
transposable_element
(Kaminker et al., 2002, )
hide Insertions & Copy Number
Copy number
and comments
0-50 (McGinnis and Beckendorf, 1983; Streck et al., 1986).
 
24 in euchromatin of Release 3 genome annotation, of which 1 is full length.
(Kaminker et al., 2002)
Search for
Target Site Duplication
Size (bp)
8
(Linheiro and Bergman, 2012, )
hide Orthologs
Curated drosophilid orthologs
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
(Arca and Savakis, 2000)
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999, Loreto et al., 1997)
(Biemont and Cizeron, 1999)
(Simmons, 1992, Daniels et al., 1990, Arca and Savakis, 2000, Biemont and Cizeron, 1999)
 
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
(Daniels et al., 1990, Arca and Savakis, 2000, Periquet, 1994.2.7, Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
(Simmons, 1992, Daniels et al., 1990)
(Arca and Savakis, 2000, Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
(Biemont and Cizeron, 1999)
(Loreto et al., 1997)
(Arca and Savakis, 2000, Biemont and Cizeron, 1999)
hide Comments
Euchromatic hobo-related sequences have been found to be in fixed positions in six E strains analysed, at 38C, 42B, 55A, 79E, 80B, 82C, 84C and 84D. The hobo related sequences from Oregon-R and iso-1 are substantially diverged and rearranged and cannot code for a functional hobo\T.
(Galindo et al., 2001)
Sequences flanking a donor hobo do not influence subsequent integration site preference, whereas sequences contained within 31bp flanking an integration hot spot have a significant effect on the frequency of integration into that site. The lack of a common sequence motif in the DNA flanking several hot spots suggests that higher order DNA structural characteristics of the DNA and/or chromatin may influence integration site selection by the hobo.
(Saville et al., 1999)
GD sterility, hobo mobilisation and male recombination have been investigated for 13 strains of D.melanogaster.
(Bonnivard et al., 1997)
The hobo transposable element is capable of mediating germline transformation in D.virilis.
(Gomez and Handler, 1997)
Molecular and GD sterility tests are not sufficient to classify strains in the hobo system. All the components of the dysgenic syndrome must be taken into account.
(Bazin and Higuet, 1996)
hobo mediated inversions result from homologous pairing and recombination between a pair of hobos in reverse orientation.
(Eggleston et al., 1996)
Several Drosophilid and tephritid species are permissive for hobo motility, tephritid species harbour hobo-related elements. hobo excision occurred in the absence, as well as the presence, of hobo\T in both insect families. This suggests that cross-mobilisation systems exist in a broad range of insects.
(Handler and Gomez, 1996)
The function of hobo transposon in tephritid species is tested in transient embryonic excision assays. Wild-type and mutant strains of A.suspensa, B.dorsalis, B.cucurbitae, C.capitata and T.curvicauda all support hobo excision or deletion both in the presence and absence of co-injected hobo transposase source. This indicates a permissive state for hobo motility and the existance of endogenous systems capable of mobilising hobo.
(Handler and Gomez, 1996)
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.
(Hoogland and Biemont, 1996)
D.virilis can be genetically transformed with vectors based on the hobo.
(Lozovskaya et al., 1996)
The distribution of hobos in heterochromatin has been studied by in situ hybridisation to mitotic chromosomes.
(Carmena and Gonzalez, 1995)
Inversion present in the Uc-1 X chromosome are produced by ectopic recombination between a pair of hobos in opposite orientation.
(Eggleston et al., 1995)
Mobility of the hobo transposon has been assayed using an in vivo transient assay in several Drosophila species. In D.melanogaster devoid of hobos, excision occurs only after co-injection of a helper plasmid. In species confirmed not to contain hobo, excision occurred at significant rates both in the presence and absence of co-injected helper plasmid. hobo is capable of functioning in the soma during embryogenesis, and its mobility is unrestricted in drosophilids. Drosophilids not containing hobo are able to mobilize hobo, presumably by a hobo-related cross-mobilizing system. The cross-mobilizing system in D.virilis is not functionally identical to hobo with respect to excision sequence specificity.
(Handler and Gomez, 1995)
The distribution of a number of transposable elements has been studied in 10 Harwich mutation accumulation lines.
(Nuzhdin and Mackay, 1995)
The spread of hobos is temperature-dependent, being more efficient at 25oC than 21oC. hobos introduced into the genome by transformation have the ability to confer the features of bona fide hobo wild strains and reinforce the hypothesis of genome invasion.
(Periquet et al., 1995)
The distribution of transposable elements within heterochromatin indicates that they are major structural components of the heterochromatin.
(Pimpinelli et al., 1995)
Invasion kinetics of hobos are studied, most integration sites are already described for several transposons but some are hotspots for hobos.
(Ladeveze et al., 1994)
A modified hobo introduced into embryos of the housefly, M.domestica, and the Queensland fruitfly, B.tryoni, is capable of transposition and transposition products have all the landmarks of hobo transposition products recovered from D.melanogaster.
(O'Brochta et al., 1994)
The transposition behaviour of hobos has been analysed in two laboratory strains.
(Yannopoulos et al., 1994)
The distribution and copy number of P-elements and hobos has been studied in long-term D.melanogaster cage populations kept under different culture conditions.
(Yannopoulos et al., 1994)
hobo excision is similar to Ac and Tam3 element excision in plants, the empty donor sites are very similar. hobos can be mobilised in M.domestica in the absence of hobo-encoded transposase as M.domestica has hobo-transposase-like factors.
(Atkinson et al., 1993)
In a cross screen that was well defined with respect to its P-element components and specifically designed to mobilise and recover P-element insertion mutations the study instead mobilised hobos and hobo insertion mutations are isolated instead.
(Locke et al., 1993)
Interactions between hobos are responsible for the instability of the Uc unstable X chromosome. Interactions between widely separated elements produce gross rearrangements and interactions between nearby elements cause regional instabilities, which may arise when a copy of hobo transposes a short distance, creating a pair of hobos that can interact to produce small rearrangements.
(Sheen et al., 1993)
P-element and hobo enhancer trap constructs insert into the genome with different patterns of insertions. hobos may be used effectively for enhancer trap mutagenesis into genes that are resistant to P-element inserts.
(Smith et al., 1993)
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.
(di Franco et al., 1992)
hobos occupy both cytological breakpoints of 3 out of 4 endemic inversions sampled from natural populations of D.melanogaster in the Hawaiian islands. The fourth has a hobo at one breakpoint. This is direct evidence that transposable elements are responsible for causing specific rearrangements found in nature, and that chromosome rearrangements can arise in nature in a manner predicted by the results of hybrid dysgenic crosses in the laboratory.
(Lyttle and Haymer, 1992)
The pattern of occurrence of hobos in D.melanogaster and D.simulans is polymorphic. Most tested strains in both species have both complete (3.0kb) and smaller hobos, although in both species some strains completely lack such canonical hobos.
(Boussy and Daniels, 1991)
46 strains derived from American and French natural populations have been tested for the presence of hobos by Southern blotting and a gonadal dysgenesis assay. The oldest available strains show weak hybridisation to the hobo probe and have neither hobo-activity potential or hobo-repression potential. In contrast all recently collected strains have hobo sequences and have a strong hobo-repression potential but no strong hobo-activity potential.
(Pascual and Periquet, 1991)
Southern blot analysis of 134 species of the genus Drosophila shows that hobo sequences are limited to the melanogaster and montium subgroups of the melanogaster-species group. Of the hobo-bearing species, only D.melanogaster, D.simulans and D.mauritiana contain potentially complete hobos, while D.sechellia contains sequences that probably represent internally deleted hobos.
(Daniels et al., 1990)
Transposition rates of mobile elements in lines AW and JH, in which spontaneous mutations have accumulated for about 400 generations, are studied. 412 and 17.6 elements rate of transposition is very low, I-element and hobo insertions occur much more frequently.
(Harada et al., 1990)
Deleted versions of the hobo found in natural populations fall into three classes by restriction mapping: Oh (1,870bp), Th1 (1,510bp) and Th2 (1,490bp).
(Periquet et al., 1990)
"pHFL1" is able to mediate germ-line transformation of a marked hobo element (H{har1}) and therefore is an autonomous fully functional hobo.
(Blackman et al., 1989)
The hobo family of transposable elements can promote high rates of chromosomal instability.
(Blackman et al., 1987)
First described by McGinnis and Beckendorf (1983) as being associated with the Sgs4 allele in the strain Stromsvreten 8. The sequence and map in Lindsley, Zimm, 1992: 1102 are of hobo100 (Streck et al., 1986). This element contains a single long open reading frame that reads from left to right. Blackman et al. (1989) have identified a fully functional hobo element and have used it to introduce a marked element into the genome. Some strains appear to lack hobo elements, whereas others have 10-50 copies. These are called 'E' and 'H' strains, respectively (Streck et al., 1986). The frequency of hobo activity is elevated in some strains and in some cases is increased in the progeny of crosses between E and H strains (Yannopoulos et al., 1987; Blackman et al.). Lim (1988) has evidence that recurring chromosome aberrations that he has found on an unstable X chromosome are due to recombination between hobo elements that lie at the breakpoints. The majority of strains derived from natural populations before the mid-1950's harbor few hobo homologous sequences. In contrast almost all present-day populations carry numerous hobo elements and two specific deletion-derivative elements called Th1 and Th2 (Periquet, Hamelin, Bigot and Lepissier, 1989).
 
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hide External Crossreferences
Sequence Crossreferences
DDBJ/EMBL/GenBank
 
Other Crossreferences
hide Synonyms & Secondary IDs ( 9 )
Reported As
Symbol Synonym
38C.13
(McGill Drosophila Genome Project, 2001.9.25)
HDC12224
 
H-element
(Greil et al., 2003, FlyBase, 1996-)
HFL1
(Aravind, 2000, Calvi, 1994.10.30)
Hobo
(Yan et al., 2002, Rizzon et al., 2002, Haoudi and Mason, 2000, Ronsseray et al., 2000, Golubovsky and Kaidanov, 1995, Twombly et al., 2009)
hobo
(Kovalenko et al., 2006, Zakharenko et al., 2006, Linheiro and Bergman, 2012, Souames et al., 2003, Aulard et al., 2004, Pane et al., 2011, Petrov et al., 2011, Boussy and Itoh, 2004, Brennecke et al., 2007, Kim et al., 2011, Brennecke et al., 2008, Kawamura et al., 2008, Malone et al., 2009, Alonso-Gonzalez et al., 2006, Torres et al., 2006, de Freitas Ortiz and Loreto, 2009, Kikuno et al., 2006, Zakharenko et al., 2007, Li et al., 2009, Bazin et al., 2004, Ortiz and Silva Loreto, 2008, O'Brochta et al., 2009, Zakharenko and Perepelkina, 2009, Ruiz and Carareto, 2003, Tan et al., 2012, Sienski et al., 2012)
HOBO
(Gunawardane et al., 2007)
Hobo transposon
(Parkhurst and Delidakis, 2003)
Name Synonym
hobo element
(Aulard et al., 2004, Bazin et al., 2004)
Secondary FlyBase IDs
  • FBgn0001210
  • FBtp0011431
hide References ( 212 )
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hide Recent research papers ( 6 )
Linheiro and Bergman, 2012, PLoS ONE 7(2): e30008
Whole Genome Resequencing Reveals Natural Target Site Preferences of Transposable Elements in Drosophila melanogaster. [FBrf0217478]
Sienski et al., 2012, Cell 151(5): 964--980
Transcriptional silencing of transposons by piwi and maelstrom and its impact on chromatin state and gene expression. [FBrf0220033]
Tan et al., 2012, Hum. Mol. Genet. 21(1): 57--65
Retrotransposon activation contributes to fragile X premutation rCGG-mediated neurodegeneration. [FBrf0216915]
Kim et al., 2011, Genetica 139(8): 985--997
DNA sequence requirements for hobo transposable element transposition in Drosophila melanogaster. [FBrf0216280]
Pane et al., 2011, EMBO J. 30(22): 4601--4615
The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline. [FBrf0217070]
Petrov et al., 2011, Mol. Biol. Evol. 28(5): 1633--1644
Population genomics of transposable elements in Drosophila melanogaster. [FBrf0214125]
Show all research papers ...
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