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

Herberg, Sarah; Simeone, Angela; Oikawa, Mami; Jullien, Jérôme; Bradshaw, Charles R.; Teperek, Marta; Gurdon, J. B.; Miyamoto, Kazuaki

doi:10.1038/srep14236

Cited by 9 publications

(7 citation statements)

References 41 publications

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“…In order to judge off target effects, we chose a non-coding sequence that has high homology to a protein coding gene. During bioinformatic searches for transcripts upregulated after the midblastula transition, we found a transcript that carries 87% sequence similarity with an exon of mars2 (NCBI: NM_001086369.1), but does not seem to encode any proteins ( Fig 4A ) [ 28 ]. Hereafter this transcript is referred to as mars2 -like ( mars2-l , see Materials and Methods ).…”

Section: Resultsmentioning

confidence: 99%

The Expression of TALEN before Fertilization Provides a Rapid Knock-Out Phenotype in Xenopus laevis Founder Embryos

Miyamoto

Suzuki

et al. 2015

PLoS ONE

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Recent advances in genome editing using programmable nucleases have revolutionized gene targeting in various organisms. Successful gene knock-out has been shown in Xenopus, a widely used model organism, although a system enabling less mosaic knock-out in founder embryos (F0) needs to be explored in order to judge phenotypes in the F0 generation. Here, we injected modified highly active transcription activator-like effector nuclease (TALEN) mRNA to oocytes at the germinal vesicle (GV) stage, followed by in vitro maturation and intracytoplasmic sperm injection, to achieve a full knock-out in F0 embryos. Unlike conventional injection methods to fertilized embryos, the injection of TALEN mRNA into GV oocytes allows expression of nucleases before fertilization, enabling them to work from an earlier stage. Using this procedure, most of developed embryos showed full knock-out phenotypes of the pigmentation gene tyrosinase and/or embryonic lethal gene pax6 in the founder generation. In addition, our method permitted a large 1 kb deletion. Thus, we describe nearly complete gene knock-out phenotypes in Xenopus laevis F0 embryos. The presented method will help to accelerate the production of knock-out frogs since we can bypass an extra generation of about 1 year in Xenopus laevis. Meantime, our method provides a unique opportunity to rapidly test the developmental effects of disrupting those genes that do not permit growth to an adult able to reproduce. In addition, the protocol shown here is considerably less invasive than the previously used host transfer since our protocol does not require surgery. The experimental scheme presented is potentially applicable to other organisms such as mammals and fish to resolve common issues of mosaicism in founders.

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Section: Resultsmentioning

confidence: 99%

The Expression of TALEN before Fertilization Provides a Rapid Knock-Out Phenotype in Xenopus laevis Founder Embryos

Miyamoto

Suzuki

et al. 2015

PLoS ONE

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“…The appearance of H3K27me3 during the late gastrula, long after loss of competence, suggests H3K27me3 is not a feature of loss of competence to Wnt during dorsal induction. Furthermore, H3K9me3 at sia and Xnr3 was barely detectable above background in dorsal and ventral cells compared to control genes xretpos(L) and 1a11, retrotransposons that have acquired H3K9me3 by the gastrula stage (Herberg et al, 2015), and there was no detectable enrichment in ventral halves ( Figure 3C). These findings do not support a role for H3K9me3 or H3K27me3 in the loss of competence to respond to Wnt signaling at sia or Xnr3.…”

Section: Repressive Histone Modifications Are Not Associated With Losmentioning

confidence: 98%

“…; Xnr3 primers from (Blythe et al, 2010); ox gene primers from (Nakamura et al, 2016). For ChIP-qPCR: Sia, Xnr3, and Gsc primers are from (Blythe et al, 2010); 1a11, Xretropos, and olt2 primers are from (Herberg et al, 2015). Reagent or resource Source Identifier Antibodies IgG Abcam 171870 H3K9ac Cell Signaling 9671S H3K9me3…”

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confidence: 99%

Chromatin accessibility and histone acetylation in the regulation of competence in early development

Esmaeili

Blythe²,

Tobias

et al. 2019

Preprint

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As development proceeds, inductive cues are interpreted by competent tissues in a spatially and temporally restricted manner. While key inductive signaling pathways within competent cells are well-described at a molecular level, the mechanisms by which tissues lose responsiveness to inductive signals are not well understood. Localized activation of Wnt signaling before zygotic gene activation in Xenopus laevis leads to dorsal development, but competence to induce dorsal genes in response to Wnts is lost by the late blastula stage. We hypothesize that loss of competence is mediated by changes in histone modifications leading to a loss of chromatin accessibility at the promoters of Wnt target genes. We use ATAC-seq to evaluate genome-wide changes in chromatin accessibility across several developmental stages. Based on overlap with p300 binding, we identify thousands of putative cis-regulatory elements at the gastrula stage, including sites that lose accessibility by the end of gastrulation and are enriched for pluripotency factor binding motifs. Dorsal Wnt target gene promoters are not accessible after the loss of competence in the early gastrula while genes involved in mesoderm and neural crest development maintain accessibility at their promoters. Inhibition of histone deacetylases increases acetylation at the promoters of dorsal Wnt target genes and extends competence for dorsal gene induction by Wnt signaling. Histone deacetylase inhibition, however, is not sufficient to extend competence for mesoderm or neural crest induction. These data suggest that chromatin state regulates the loss of competence to inductive signals in a context-dependent manner.

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“…It has been shown that H3K9me3 is required for repression of retrotransposons in gastrulating Xenopus embryos (Herberg et al 2015). Furthermore, also in frogs small RNAs are involved in repression of TEs by mediating deposition of H3K9me3 and H4K20me3 (Faunes et al 2012; Harding et al 2014).…”

Section: Introductionmentioning

confidence: 99%

Heterochromatic histone modifications at transposons in Xenopus tropicalis embryos

Kruijsbergen

Hontelez

Elurbe

et al. 2017

Developmental Biology

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Summary Transposable elements are parasitic genomic elements that can be deleterious for host gene function and genome integrity. Heterochromatic histone modifications are involved in the repression of transposons. However, it remains unknown how these histone modifications mark different types of transposons during embryonic development. Here we document the variety of heterochromatic epigenetic signatures at parasitic elements during development in Xenopus tropicalis, using genome-wide ChIP-sequencing data and ChIP-qPCR analysis. We show that specific subsets of transposons in various families and subfamilies are marked by different combinations of the heterochromatic histone modifications H4K20me3, H3K9me2/3 and H3K27me3. Many DNA transposons are marked at the blastula stage already, whereas at retrotransposons the histone modifications generally accumulate at the gastrula stage or later. Furthermore, transposons marked by H3K9me3 and H4K20me3 are more prominent in gene deserts. Using intra-subfamily divergence as a proxy for age, we show that relatively young DNA transposons are preferentially marked by early embryonic H4K20me3 and H3K27me3. In contrast, relatively young retrotransposons are marked by increasing H3K9me3 and H4K20me3 during development, and are also linked to piRNA-sized small non-coding RNAs. Our results implicate distinct repression mechanisms that operate in a transposon-selective and developmental stage-specific fashion.

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

Cited by 9 publications

References 41 publications

The Expression of TALEN before Fertilization Provides a Rapid Knock-Out Phenotype in Xenopus laevis Founder Embryos

The Expression of TALEN before Fertilization Provides a Rapid Knock-Out Phenotype in Xenopus laevis Founder Embryos

Chromatin accessibility and histone acetylation in the regulation of competence in early development

Heterochromatic histone modifications at transposons in Xenopus tropicalis embryos

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