Tissue-specific developmental expression of OAX, a Xenopus repetitive element

Whitford, Kristin L.; Oakes, Jennifer A.; Scholnick, Joshua; Saha, Margaret S.

doi:10.1016/s0925-4773(00)00307-5

Cited by 6 publications

(8 citation statements)

References 25 publications

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“…Clones containing repetitive element sequences were also found at highest levels in the blastema and pseudoblastema libraries. Although the exact function of expressed genes containing repetitive elements remains unclear, studies have shown that genes of the OAX family of small RNAs exhibit distinct patterns of expression both spatially and temporally during early embryonic development (Whitford et al,2000). We found two independent cDNAs from the regeneration‐competent blastema library that share homology to the OAX element.…”

Section: Resultsmentioning

confidence: 99%

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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Section: Resultsmentioning

confidence: 99%

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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“…25 In the X. laevis embryo, tissue-, spatial-and stage-specific pattern was demonstrated for satellite 1 transcription, 75,76 also known as the X1-741 satellite DNA [25], or OAX (Oocyte Activation in Xenopus) region. 77,78 To summarize, transcripts of both strands of the X1-741 satellite DNA sequences were identified by ISH on X. laevis lampbrush chromosomes. 25 OAX / satellite 1 transcripts are absent until tailbud stage and cannot be revealed in adult liver or oocytes as demonstrated by RNase protection assay, dot blot hybridization and ISH in cryosections of whole-mount samples.…”

Section: Transcription Of Highly Repetitive Tandem Dna Sequences In Smentioning

confidence: 99%

“…25 OAX / satellite 1 transcripts are absent until tailbud stage and cannot be revealed in adult liver or oocytes as demonstrated by RNase protection assay, dot blot hybridization and ISH in cryosections of whole-mount samples. 75,76,78 The later stages of development are characterized by tissue-specific OAX / satellite 1 transcription. The non-coding RNA from both strands of the OAX transcripts was detected in the cement gland and somites.…”

Section: Transcription Of Highly Repetitive Tandem Dna Sequences In Smentioning

confidence: 99%

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Transcription of highly repetitive tandemly organized DNA in amphibians and birds: A historical overview and modern concepts

Trofimova

Krasikova

2016

RNA Biology

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Tandemly organized highly repetitive DNA sequences are crucial structural and functional elements of eukaryotic genomes. Despite extensive evidence, satellite DNA remains an enigmatic part of the eukaryotic genome, with biological role and significance of tandem repeat transcripts remaining rather obscure. Data on tandem repeats transcription in amphibian and avian model organisms is fragmentary despite their genomes being thoroughly characterized. Review systematically covers historical and modern data on transcription of amphibian and avian satellite DNA in somatic cells and during meiosis when chromosomes acquire special lampbrush form. We highlight how transcription of tandemly repetitive DNA sequences is organized in interphase nucleus and on lampbrush chromosomes. We offer LTR-activation hypotheses of widespread satellite DNA transcription initiation during oogenesis. Recent explanations are provided for the significance of high-yield production of non-coding RNA derived from tandemly organized highly repetitive DNA. In many cases the data on the transcription of satellite DNA can be extrapolated from lampbrush chromosomes to interphase chromosomes. Lampbrush chromosomes with applied novel technical approaches such as superresolution imaging, chromosome microdissection followed by high-throughput sequencing, dynamic observation in life-like conditions provide amazing opportunities for investigation mechanisms of the satellite DNA transcription.

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“…(e) Upregulated transposon-derived genes in the lungfish tail blastema Transposable elements and genes derived from retrotransposon have been previously implicated in regeneration in species as distantly related as sea cucumbers [40] and axolotls [41]. Two genes derived from transposons were found enriched in the tail blastema of Xenopus tadpoles [14]: oax, which is a Xenopus-specific repetitive element [42], and l1td1-like, which is similar to l1td1, a mammal-specific L1 transposon-derived gene previously identified as a marker of human embryonic stem cells [43]. We searched our lungfish dataset for transposon-derived genes and found 16 genes, including an ortholog of l1td1-like, the harbinger transposon-derived gene Harbi1, and the piggyBac transposon-derived gene Pgbd4 (figure 4e).…”

Section: (D) Genes Enriched In Lungfish Tail Blastema Versus Pectoralmentioning

confidence: 99%

Salamander-like tail regeneration in the West African lungfish

Verissimo

Perez

Dragalzew

et al. 2020

Preprint

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Salamanders, frog tadpoles, and lizards possess the remarkable ability to regenerate tails. The fossil record suggests that this capacity is an ancestral tetrapod trait, yet its evolutionary history remains unclear. Here we examine tail regeneration in a living representative of the sister group of tetrapods, the West African lungfish Protopterus annectens. We show that, as seen in salamanders, lungfish tail regeneration occurs via formation of a proliferative blastema and restores original structures including muscle, skeleton and spinal cord. Contrary to lizards and similar to salamanders, lungfish regenerate spinal cord neurons and reconstitute dorsoventral patterning of the tail.Similar to salamander and frog tadpoles, we show that Shh is required for lungfish tail regeneration. Through RNA-seq analysis of uninjured and regenerating tail blastema we show that lungfish deploy a genetic program comparable to that of tetrapods, showing upregulation of genes and signaling pathways previously implicated in amphibian and lizard tail regeneration. Furthermore, the tail blastema showed marked upregulation of genes encoding post-transcriptional RNA processing components and transposon-derived genes. Collectively, our study establishes the lungfish as a valuable research system for regenerative biology and provides insights into the evolution of cellular and molecular processes underlying vertebrate tail regeneration.

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Tissue-specific developmental expression of OAX, a Xenopus repetitive element

Cited by 6 publications

References 25 publications

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

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

Transcription of highly repetitive tandemly organized DNA in amphibians and birds: A historical overview and modern concepts

Salamander-like tail regeneration in the West African lungfish

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