Sauria SINEs: Novel Short Interspersed Retroposable Elements That Are Widespread in Reptile Genomes

Piskurek, Oliver; Austin, Christopher C.; Okada, Norihiro

doi:10.1007/s00239-005-0201-5

Cited by 57 publications

(60 citation statements)

References 80 publications

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“…PLEs are a widespread, yet poorly studied, class of transposable elements characterized by an endonuclease domain as well as an unusual but active reverse transcriptase domain with similarity to telomerases (Evgen'ev and Arkhipova 2005). Sauria SINEs are nonviral tRNA-derived repetitive sequences that are widespread in lizards and snakes (Piskurek et al 2006). These elements contain RNA polymerase III-specific internal promoter sequences whose activity can be enhanced by upstream genomic sequences.…”

Section: Discussion Accumulation Of Retrotransposons In Lizard Hox Gementioning

confidence: 99%

Atypical relaxation of structural constraints in Hox gene clusters of the green anole lizard

Di‐Poï¹,

Montoya‐Burgos²,

Duboule³

2009

Genome Res.

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Hox genes control many aspects of embryonic development in metazoans. Previous analyses of this gene family revealed a surprising diversity in terms of gene number and organization between various animal species. In vertebrates, Hox genes are grouped into tightly organized clusters, claimed to be devoid of repetitive sequences. Here, we report the genomic organization of the four Hox loci present in the green anole lizard and show that they have massively accumulated retrotransposons, leading to gene clusters larger in size when compared to other vertebrates. In addition, similar repeats are present in many other development-related gene-containing regions, also thought to be refractory to such repetitive elements. Transposable elements are major sources of genetic variations, including alterations of gene expression, and hence this situation, so far unique among vertebrates, may have been associated with the evolution of the spectacular realm of morphological variations in the body plans of Squamata. Finally, sequence alignments highlight some divergent evolution in highly conserved DNA regions between vertebrate Hox clusters, which may coincide with the emergence of mammalian-specific features.

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Section: Discussion Accumulation Of Retrotransposons In Lizard Hox Gementioning

confidence: 99%

Atypical relaxation of structural constraints in Hox gene clusters of the green anole lizard

Di‐Poï¹,

Montoya‐Burgos²,

Duboule³

2009

Genome Res.

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“…Our initial sequence analyses revealed that sequences of Sauria SINE subfamilies described for varanid lizards [Varanus indicus (mangrove monitor)] and snakes [Azemiops feae (Fea's viper)] are closely related to the TATV-SINE (12). These squamates belong to a clade recently defined as Toxicofera, referring to the presence of venom in this phylogenetic lineage (32,33).…”

Section: Resultsmentioning

confidence: 99%

“…Sauria SINEs are Ϸ350 nucleotides long and are widely distributed among lizards and snakes, the most diverse group of living reptiles (Squamata). They comprise a typical 5Ј tRNA-related region, a tRNA-unrelated region, and a 3Ј tail region (containing short tandem repeats) which is derived from ubiquitous squamate Bov-B LINEs (12). Using the complete TATV genome sequence (accession no.…”

Section: Resultsmentioning

confidence: 99%

Poxviruses as possible vectors for horizontal transfer of retroposons from reptiles to mammals

Piskurek

Okada²

2007

Proc. Natl. Acad. Sci. U.S.A.

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126

113

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Poxviruses (Poxviridae) are a family of double-stranded DNA viruses with no RNA stage. Members of the genus Orthopoxvirus (OPV) are highly invasive and virulent. It was recently shown that the taterapox virus (TATV) from a West African rodent is the sister of camelpox virus and therefore belongs to the clade closest to the variola virus (VARV), the etiological agent of smallpox. Although these OPVs are among the most dreaded pathogens on Earth, our current knowledge of their genomes, their origins, and their possible hosts is still very limited. Here, we report the horizontal transfer of a retroposon (known only from reptilian genomes) to the TATV genome. After isolating and analyzing different subfamilies of short interspersed elements (SINEs) from lizards and snakes, we identified a highly poisonous snake (Echis ocellatus) from West Africa as the closest species from which the SINE sequence discovered in the TATV genome (TATV-SINE) was transferred to the virus. We discovered direct repeats derived from the virus flanking the TATV-SINE, and the absence of any snake-derived DNA flanking the SINE. These data provide strong evidence that the TATV-SINE was actually transferred within the snake to the viral genome by retrotransposition and not by any horizontal transfer at the DNA level. We propose that the snake is another host for TATV, suggesting that VARV-related epidemiologically relevant viruses may have derived from our cold-blooded ancestors and that poxviruses are possible vectors for horizontal transfer of retroposons from reptiles to mammals.Bov-B long interspersed element ͉ lateral transfer ͉ Orthopoxvirus ͉ retrotransposition ͉ Sauria short interspersed element S hort interspersed elements (SINEs) are a type of retroposon (70-500 bp) that invade new genomic sites by a copy-andpaste mechanism through integration of a reverse-transcribed copy of RNA (1, 2). The retrotransposition of nonautonomous SINEs depends on the enzymatic retrotranspositional machinery of their autonomous partner long interspersed elements (LINEs), which encode a reverse transcriptase (RT) and endonuclease (EN). The mechanism of LINE retrotransposition (3) is termed ''target-primed reverse transcription'' (TPRT) and was adopted for partner SINE retrotransposition because the corresponding identical 3Ј tail sequence of a SINE is recognized by the RT of its partner LINE (4-6). In TPRT, the EN initiates a nick on one strand of the targeted DNA. Subsequently, the 3Ј OH introduced by this nick is used to prime cDNA synthesis, using an RNA transcript of a SINE or LINE as a template. TPRT usually results in a pair of direct repeats flanking the inserted retroposon, a hallmark of retrotransposition. SINE families and subfamilies, which are defined by the presence of diagnostic nucleotides, namely a set of specific nucleotides that differ from those of a consensus sequence, can be found specifically within members of a particular phylogenetic lineage. Their role as effective markers for elucidating evolutionary history has been demonstrated i...

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“…In sauropsids, the most intensively investigated TEs have been non-LTR retrotransposons (LINEs or retroposons), such as RTE clade (including Bov-B LINEs) [Zupunski et al, 2001;Gogolevsky et al, 2008;Novick et al, 2009;Piskurek et al, 2009], L2 clade [Lovsin et al, 2001;Novick et al, 2009;Piskurek et al, 2009], L1 clade [Kordis et al, 2006;Novick et al, 2009;Piskurek et al, 2009], R4 clade [Volff et al, 2001a;Novick et al, 2009;Piskurek et al, 2009], CR1 clade [Fantaccione et al, 2004;International Chicken Genome Sequencing Consortium, 2004;Wicker et al, 2005;Shedlock, 2006;Kaiser et al, 2007;Kriegs et al, 2007;Shedlock et al, 2007;Abrusan et al, 2008;Chapus and Edwards, 2009;Liu et al, 2009;Novick et al, 2009;Piskurek et al, 2009;Shan et al, 2009] and R2 clade [Kojima and Fujiwara, 2005]. Much research in sauropsids has been focused on SINEs, such as on the CR1 LINE/SINE pair in a lizard [Fantaccione et al, 2004], LF SINEs [Bejerano et al, 2006], AmnSINE1s [Nishihara et al, 2006;Hirakawa et al, 2009], Sauria SINEs [Piskurek et al, 2006[Piskurek et al, , 2009Piskurek and Okada, 2007;Gogolevsky et al, 2008;Kosushkin et al, 2008], polIII/SINE in turtles …”

Section: Investigations In the Genomics Era (From The Year 2000 To Thmentioning

confidence: 99%

Transposable Elements in Reptilian and Avian (Sauropsida) Genomes

Kordiš¹

2009

Cytogenet Genome Res

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Transposable elements (TEs) have profound effects on the structure, function and evolution of their host genomes. Our knowledge about these agents of genomic change in sauropsids, a sister group of mammals that includes all extant reptiles and birds, is still very limited. Invaluable information concerning the diversity, activity and repetitive landscapes in sauropsids has recently emerged from analyses of the draft genomes of chicken and Anolis and other preliminary reptilian genome sequencing projects. Avian and reptilian genomes differ significantly in the classes of TEs present, their fractional representation in the genome and by the level of TE activity. While lepidosaurian genomes contain many young, active TE families, the extant avian genomes have very few active TE lineages. Most reptilian genomes possess quite rich TE repertoires that differ considerably from those of birds and mammals, being more similar in diversity to that of lower vertebrates. The large amount of recently accumulated genome-wide data on TEs in diverse lineages of sauropsids has provided a remarkable opportunity to review current knowledge about TEs of sauropsids in their genomic context.

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Sauria SINEs: Novel Short Interspersed Retroposable Elements That Are Widespread in Reptile Genomes

Cited by 57 publications

References 80 publications

Atypical relaxation of structural constraints in Hox gene clusters of the green anole lizard

Atypical relaxation of structural constraints in Hox gene clusters of the green anole lizard

Poxviruses as possible vectors for horizontal transfer of retroposons from reptiles to mammals

Transposable Elements in Reptilian and Avian (Sauropsida) Genomes

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