A novel family of retrotransposons in Xenopus with a developmentally regulated expression

Shim, Sangwoo; Lee, Sung-Kuk; Han, Jin‐Kwan

doi:10.1002/(sici)1526-968x(200003)26:3<198::aid-gene5>3.3.co;2-s

Cited by 4 publications

(7 citation statements)

References 60 publications

(80 reference statements)

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“…Similarly, ABA and JA enhance the transcription of the barley element Bare1 and tobacco element Tto1 (Suoniemi et al 1996;Takeda et al 1998), while UV stress activates LTR retrotransposons in both Xenopus sp. (Shim et al 2000) and oat (Kimura et al 2001). During periods of high transpositional activity, some retrotransposon sequences are amplified to produce multi-copy, relatively homogeneous elements which then diverge, either by subsequent retrotransposition or by natural acquisition of mutations.…”

Section: Discussionmentioning

confidence: 99%

FaRE1: a transcriptionally active Ty1-copia retrotransposon in strawberry

Zhao

et al. 2009

J Plant Res

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Retrotransposons are ubiquitous in the plant kingdom and constitute a large fraction of many plant genomes. Although most retrotransposons from plants were thought to be transcriptionally silent in somatic tissues, evidence of activity under certain conditions is available in some cases. In this study, a complete LTR retrotransposon was isolated from the cultivated strawberry (Fragaria x ananassa) genome using genome walking. The element, named FaRE1, has all the features of a typical Ty1-copia retrotransposon. Its total length was 5,104 bp, comprising a single 3,891 bp open reading frame. It is represented by approximately 96 copies per genome, equivalent to approximately 0.33% of the genome. Transcription of FaRE1 was detected in leaf tissue treated with various phytohormones, such as naphthalene acetic acid, 2,4-dichlorophenoxyacetic acid or abscisic acid . To our knowledge, this is the first report of the isolation of a complete LTR retrotransposon with transcriptional activity in strawberry.

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Section: Discussionmentioning

confidence: 99%

FaRE1: a transcriptionally active Ty1-copia retrotransposon in strawberry

Zhao

et al. 2009

J Plant Res

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“…However, the expression profiles of TEs during development are different from each other. For example, Xretpos retrotransposon expression is zygotically activated, restricted to ventroposterior-specific regions, and induced by ventralizing manipulation, such as UV irradiation (53). Thus, the expression profile of XTERV1 differs from what has been reported to date concerning other TEs in Xenopus, and therefore, we can postulate that specific regulation cues might drive XTERV1 transcription during Xenopus development.…”

Section: Discussionmentioning

confidence: 87%

“…Several environmental clues (UV exposure, chemicals, drugs, and stress) or endogenous clues (such as hormonal balance) have been shown or suggested to influence the expression of endogenous retroviruses (51,53). Therefore, we quantified the expression levels of XTERV1 genes following various cellular stresses to characterize their regulation in comparison with the stress responses described for R. sylvatica FR47 (43).…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

Characterization of a Xenopus tropicalis Endogenous Retrovirus with Developmental and Stress-Dependent Expression

Sinzelle

Carradec

Paillard

et al. 2011

J Virol

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We report on the identification and characterization of XTERV1, a full-length endogenous retrovirus (ERV) within the genome of the western clawed frog (Xenopus tropicalis). XTERV1 contains all the basic genetic elements common to ERVs, including the classical 5-long terminal repeat (LTR)-gag-pol-env-3-LTR architecture, as well as conserved functional motifs inherent to each retroviral protein. Using phylogenetic analysis, we show that XTERV1 is related to the Epsilonretrovirus genus. The X. tropicalis genome harbors a single full-length copy with intact gag and pol open reading frames that localizes to the centromeric region of chromosome 5. About 10 full-length defective copies of XTERV1 are found interspersed in the genome, and 2 of them could be assigned to chromosomes 1 and 3. We find that XTERV1 genes are zygotically transcribed in a regulated spatiotemporal manner during frog development, including metamorphosis. Moreover, XTERV1 transcription is upregulated under certain cellular stress conditions, including cytotoxic and metabolic stresses. Interestingly, XTERV1 Env is found to be homologous to FR47, a protein upregulated following cold exposure in the freeze-tolerant wood frog (Rana sylvatica). In addition, we find that R. sylvatica FR47 mRNA originated from a retroviral element. We discuss the potential role(s) of ERVs in physiological processes in vertebrates.

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“…These include SINEs from mammals (Rudin and Thompson 2001), HIV-1 of humans (Valerie et al 1996) and some LTR retrotransposons from animals (Shim et al 2000), yeast (Boeke and Corces 1989;Bradshaw and McEntee 1989) and plants (Kimura et al 2001). The plant element OARE1 is a Copia retrotransposon from oat similar to BARE1 of barley.…”

Section: Reme1 Transcriptional Activationmentioning

confidence: 99%

“…Among the stress agents, UV light was reported to activate animal short interspersed nuclear elements (SINEs) (Rudin and Thompson 2001) and LTR retrotransposons in both Xenopus (Shim et al 2000) and plants (e.g., the Copia element OARE1 of oat; Kimura et al 2001). McClintock (1984) viewed the UV light -induced activation of maize transposons (Wessler 1996;Walbot 1999) as ''genomic stress.''…”

Section: Introductionmentioning

confidence: 99%

Reme1, a Copia retrotransposon in melon, is transcriptionally induced by UV light

et al. 2007

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For the first time, numerous sequences of Copia and Gypsy retrotransposons from the Cucumis melo genome have been obtained and analyzed. Phylogenetic analyses of sequences of both types of long terminal repeat (LTR) retrotransposons were carried out. The melon genome contains approximately 20,000 Gypsy and 6,800 Copia elements, comprising about 26% of its total size. Starting from a retrotransposon fragment, we have cloned and characterized an entire melon retrotransposon, named Reme1, which is 5,149 bp long. Reme1 belongs to the Superfamily Copia retrotransposons by its protein domain order and sequence similarity to other Copia elements of dicotyledons. The haploid genome of melon (var. "Piel de Sapo") contains about 120 copies of Reme1. Several copies of Reme1 are transcriptionally active, although at low levels, in melon leaves as analyzed by reverse-transcription PCR (RT-PCR) and sequencing. However, the transcript pool is considerably increased when melon leaves are treated with UV light, as has been seen for various retroelements in many organisms. The cDNAs of Reme1 transcripts showed less diversity than do Reme1 genomic sequences, suggesting that a subfamily of these elements is differentially responsive to UV.

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A novel family of retrotransposons in Xenopus with a developmentally regulated expression

Cited by 4 publications

References 60 publications

FaRE1: a transcriptionally active Ty1-copia retrotransposon in strawberry

FaRE1: a transcriptionally active Ty1-copia retrotransposon in strawberry

Characterization of a Xenopus tropicalis Endogenous Retrovirus with Developmental and Stress-Dependent Expression

Reme1, a Copia retrotransposon in melon, is transcriptionally induced by UV light

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