A novel family of retrotransposons inXenopus 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>3.0.co;2-0

Cited by 9 publications

(5 citation statements)

References 72 publications

(59 reference statements)

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“…These three retrotransposons are 1a11 13 (GenBank accession number: L11263.1), λ-olt 2-1 14 (GenBank accession number: AF145965.1) and xretpos(L) 14 (GenBank accession number: AF057166.1). λ-olt 2-1 and xretpos(L) show 95% nucleotide sequence identity in 1595 nucleotides 14 . These retrotransposons start to be activated soon after the midblastula transition.…”

Section: Resultsmentioning

confidence: 99%

“…All three retrotransposons, 1a11, λ-olt 2-1 and xretpos(L) , have been found as LTR retrotransposons in Xenopus laevis 13 14 . 1a11 encodes a 71 kDa protein, which shows similarity to the viral structure protein Gag.…”

Section: Discussionmentioning

confidence: 98%

“…The Xenopus genome seems to contain approximately 200 copies of xretpos(L) LTR, 15 copies of the xretpos(L) open reading frame, and 50 copies of the complete xretpos(L) 14 . Again, the published expression analysis data of xretpos(L) support our qPCR data 14 ( Fig. 1b ).…”

Section: Discussionmentioning

confidence: 99%

“…All three retrotransposons have in common that they show no amino acid homology to the conserved pol gene. Since the pol gene encodes proteins needed for transposition (protease, reverse transcriptase, and integrase), it is likely that 1a11 , λ-olt 2-1 and xretpos(L) have lost their ability to transpose 14 .…”

Section: Discussionmentioning

confidence: 99%

“…In gene expression database several retrotransposon transcripts of Xenopus laevis could be identified. In addition, the expression of a few retrotransposons was reported to be developmentally regulated 13 14 . Based on this knowledge, we further investigated the expression of retrotransposons in Xenopus laevis and found retrotransposons whose expression is upregulated in early embryos.…”

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confidence: 99%

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Histone H3 lysine 9 trimethylation is required for suppressing the expression of an embryonically activated retrotransposon in Xenopus laevis

Herberg

Simeone

Oikawa

et al. 2015

Sci Rep

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Transposable elements in the genome are generally silenced in differentiated somatic cells. However, increasing evidence indicates that some of them are actively transcribed in early embryos and the proper regulation of retrotransposon expression is essential for normal development. Although their developmentally regulated expression has been shown, the mechanisms controlling retrotransposon expression in early embryos are still not well understood. Here, we observe a dynamic expression pattern of retrotransposons with three out of ten examined retrotransposons (1a11, λ-olt 2-1 and xretpos(L)) being transcribed solely during early embryonic development. We also identified a transcript that contains the long terminal repeat (LTR) of λ-olt 2-1 and shows a similar expression pattern to λ-olt 2-1 in early Xenopus embryos. All three retrotransposons are transcribed by RNA polymerase II. Although their expression levels decline during development, the LTRs are marked by histone H3 lysine 4 trimethylation. Furthermore, retrotransposons, especially λ-olt 2-1, are enriched with histone H3 lysine 9 trimethylation (H3K9me3) when their expression is repressed. Overexpression of lysine-specific demethylase 4d removes H3K9me3 marks from Xenopus embryos and inhibits the repression of λ-olt 2-1 after gastrulation. Thus, our study shows that H3K9me3 is important for silencing the developmentally regulated retrotransposon in Xenopus laevis.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 98%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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Histone H3 lysine 9 trimethylation is required for suppressing the expression of an embryonically activated retrotransposon in Xenopus laevis

Herberg

Simeone

Oikawa

et al. 2015

Sci Rep

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Identification of genes expressed during Xenopus laevis limb regeneration by using subtractive hybridization

King

Nguyen

Calley

et al. 2003

Developmental Dynamics

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Suppression polymerase chain reaction-based subtractive hybridization was used to identify genes that are expressed during Xenopus laevis hindlimb regeneration. Subtractions were done by using RNAs extracted from the regeneration-competent stage (stage 53) and regeneration-incompetent stage (stage 59) of limb development. Forward and reverse subtractions were done between stage 53 7-day blastema and stage 53 contralateral limb (competent stage), stage 59 7-day pseudoblastema and stage 59 contralateral limb (incompetent stage), and stage 53 7-day blastema and stage 59 7-day pseudoblastema. Several thousand clones were analyzed from the various subtracted libraries, either by random selection and sequencing (1,920) or by screening subtracted cDNA clones (6,150), arrayed on nylon membranes, with tissue-specific probes. Several hundred clones were identified from the array screens whose expression levels were at least twofold higher in experimental tissue vs. control tissue (e.g., blastema vs. limb) and selected for sequencing. In addition, primers were designed to assay several of the randomly selected clones and used to assess the level of expression of these genes during regeneration and normal limb development. Approximately half of the selected clones were differentially expressed, as expected, including several that demonstrate blastema-specific enhancement of expression. Three distinct categories of expression were identified in our screens: (1) clones that are expressed in both regeneration-competent blastemas and -incompetent pseudoblastemas, (2) clones that are expressed at highest levels in regeneration-competent blastemas, and (3) clones that are expressed at highest levels in regeneration-incompetent pseudoblastemas. Characterizing the role of each of these three categories of genes will be important in furthering our understanding of the process of tissue regeneration. Developmental Dynamics 226:398 -409, 2003.

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Polymorphism of a new Ty1-copia retrotransposon in durum wheat under salt and light stresses

et al. 2010

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Long terminal repeat retrotransposons are the most abundant mobile elements in the plant genome and play an important role in the genome reorganization induced by environmental challenges. Their success depends on the ability of their promoters to respond to different signaling pathways that regulate plant adaptation to biotic and abiotic stresses. We have isolated a new Ty1-copia-like retrotransposon, named Ttd1a from the Triticum durum L. genome. To get insight into stress activation pathways in Ttd1a, we investigated the effect of salt and light stresses by RT-PCR and S-SAP profiling. We screened for Ttd1a insertion polymorphisms in plants grown to stress and showed that one new insertion was located near the resistance gene. Our analysis showed that the activation and mobilization of Ttd1a was controlled by salt and light stresses, which strengthened the hypothesis that stress mobilization of this element might play a role in the defense response to environmental stresses.

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A novel family of retrotransposons inXenopus with a developmentally regulated expression

Cited by 9 publications

References 72 publications

Histone H3 lysine 9 trimethylation is required for suppressing the expression of an embryonically activated retrotransposon in Xenopus laevis

Histone H3 lysine 9 trimethylation is required for suppressing the expression of an embryonically activated retrotransposon in Xenopus laevis

Identification of genes expressed during Xenopus laevis limb regeneration by using subtractive hybridization

Polymorphism of a new Ty1-copia retrotransposon in durum wheat under salt and light stresses

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