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Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE140621 | GEO | 2020/03/22

REPOSITORIES: GEO

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Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage.

Project description:Zinc finger protein Zscan4 is selectively expressed in mouse two-cell (2C) embryos undergoing zygotic genome activation (ZGA) and in a rare subpopulation of embryonic stem cells with 2C-like features. Here, we show that Zscan4 specifically recognizes a subset of (CA)n microsatellites, repeat sequences prone to genomic instability. Zscan4-associated microsatellite regions are characterized by low nuclease sensitivity and high histone occupancy. In vitro, Zscan4 binds nucleosomes and protects them from disassembly upon torsional strain. Furthermore, Zscan4 depletion leads to elevated DNA damage in 2C mouse embryos in a transcription-dependent manner. Together, our results identify Zscan4 as a DNA sequence-dependent microsatellite binding factor and suggest a developmentally regulated mechanism, which protects fragile genomic regions from DNA damage at a time of embryogenesis associated with high transcriptional burden and genomic stress.

| S-EPMC7083622 | biostudies-literature

Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage [ATAC-seq]

Project description:ATAC-seq from mouse ESC with stably integrated Zscan4c-GFP reporter.

2020-03-22 | GSE140620 | GEO

Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage [ChIP-seq]

Project description:Genome-wide binding analysis of Zscan4 showed sequence-specific occupancy at (CA)n microsatellite repeats in 2C-like cells. Genome-wide occupancy profiling of FACT subunit SSRP1 in curaxin-treated mouse ESC demonstrated re-localization from transcription start sites to Zscan4 binding sites.

2020-03-22 | GSE140619 | GEO

Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage [RNA-seq]

Project description:2C-like cells or pluripotent cells were isolated from Zprom::GFP and Zprom::GFP-Zscan4 mouse ESC reporter lines to measure changes in gene expression.

2020-03-22 | GSE140615 | GEO

Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage

Project description:Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage

| PRJNA590251 | ENA

Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage [RNA-seq]

Project description:Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage [RNA-seq]

| PRJNA590258 | ENA

Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage [ATAC-seq]

Project description:Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage [ATAC-seq]

| PRJNA590256 | ENA

Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage [ChIP-seq]

Project description:Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage [ChIP-seq]

| PRJNA590257 | ENA

Dnmt1 binds and represses genomic retroelements via DNA methylation in mouse early embryos.

Project description:Genome-wide passive DNA demethylation in cleavage-stage mouse embryos is related to the cytoplasmic localization of the maintenance methyltransferase DNMT1. However, recent studies provided evidences of the nuclear localization of DNMT1 and its contribution to the maintenance of methylation levels of imprinted regions and other genomic loci in early embryos. Using the DNA adenine methylase identification method, we identified Dnmt1-binding regions in four- and eight-cell embryos. The unbiased distribution of Dnmt1 peaks in the genic regions (promoters and CpG islands) as well as the absence of a correlation between the Dnmt1 peaks and the expression levels of the peak-associated genes refutes the active participation of Dnmt1 in the transcriptional regulation of genes in the early developmental period. Instead, Dnmt1 was found to associate with genomic retroelements in a greatly biased fashion, particularly with the LINE1 (long interspersed nuclear elements) and ERVK (endogenous retrovirus type K) sequences. Transcriptomic analysis revealed that the transcripts of the Dnmt1-enriched retroelements were overrepresented in Dnmt1 knockdown embryos. Finally, methyl-CpG-binding domain sequencing proved that the Dnmt1-enriched retroelements, which were densely methylated in wild-type embryos, became demethylated in the Dnmt1-depleted embryos. Our results indicate that Dnmt1 is involved in the repression of retroelements through DNA methylation in early mouse development.

| S-EPMC7470951 | biostudies-literature

The tardigrade damage suppressor protein binds to nucleosomes and protects DNA from hydroxyl radicals.

Project description:Tardigrades, also known as water bears, are animals that can survive extreme conditions. The tardigrade Ramazzottius varieornatus contains a unique nuclear protein termed Dsup, for damage suppressor, which can increase the resistance of human cells to DNA damage under conditions, such as ionizing radiation or hydrogen peroxide treatment, that generate hydroxyl radicals. Here we find that R. varieornatus Dsup is a nucleosome-binding protein that protects chromatin from hydroxyl radicals. Moreover, a Dsup ortholog from the tardigrade Hypsibius exemplaris similarly binds to nucleosomes and protects DNA from hydroxyl radicals. Strikingly, a conserved region in Dsup proteins exhibits sequence similarity to the nucleosome-binding domain of vertebrate HMGN proteins and is functionally important for nucleosome binding and hydroxyl radical protection. These findings suggest that Dsup promotes the survival of tardigrades under diverse conditions by a direct mechanism that involves binding to nucleosomes and protecting chromosomal DNA from hydroxyl radicals.

| S-EPMC6773438 | biostudies-literature

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