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Polycomb-mediated repression of paternal chromosomes maintains haploid dosage in diploid embryos of Marchantia [RNA-seq]

ABSTRACT: Complex mechanisms regulate gene dosage throughout eukaryotic life cycles. Mechanisms controlling gene dosage have been extensively studied in animals, however it is unknown how generalizable these mechanisms are to diverse eukaryotes. Here, we use the haploid plant Marchantia polymorpha to assess gene dosage control in its short-lived diploid embryo. We show that throughout embryogenesis, paternal chromosomes are repressed resulting in functional haploidy. The paternal genome is targeted for genomic imprinting by the Polycomb mark H3K27me3 starting at fertilization, rendering the maternal genome in control of embryogenesis. Maintaining haploid gene dosage by this new form of imprinting is essential for embryonic development. Our findings illustrate how haploid-dominant species can regulate gene dosage through paternal chromosome inactivation and initiates the exploration of the link between life cycle history and gene dosage in a broader range of organisms.

ORGANISM(S): Marchantia polymorpha

PROVIDER: GSE193306 | GEO | 2022/08/23

REPOSITORIES: GEO

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Polycomb-mediated repression of paternal chromosomes maintains haploid dosage in diploid embryos of Marchantia [CUT&RUN]

Project description:Complex mechanisms regulate gene dosage throughout eukaryotic life cycles. Mechanisms controlling gene dosage have been extensively studied in animals, however it is unknown how generalizable these mechanisms are to diverse eukaryotes. Here, we use the haploid plant Marchantia polymorpha to assess gene dosage control in its short-lived diploid embryo. We show that throughout embryogenesis, paternal chromosomes are repressed resulting in functional haploidy. The paternal genome is targeted for genomic imprinting by the Polycomb mark H3K27me3 starting at fertilization, rendering the maternal genome in control of embryogenesis. Maintaining haploid gene dosage by this new form of imprinting is essential for embryonic development. Our findings illustrate how haploid-dominant species can regulate gene dosage through paternal chromosome inactivation and initiates the exploration of the link between life cycle history and gene dosage in a broader range of organisms.

2022-08-23 | GSE193305 | GEO

High-frequency generation of fertile transgenic mice from H19-Igf2 engineered androgenetic haploid embryonic stem cells

Project description:Recent success in the derivation of mouse haploid embryonic stem cells from androgenetic blastocysts (ahESCs) has provided new avenues for the generation of genetically modified animals. However, the efficiency to produce viable transgenic mice via intracytoplasmic ahESCs injection (ICAI) was very low, which may correlate with the aberrant regulation of imprinted genes. Here we designed to delete the paternal imprinted gene H19 by CRSPR-Cas9 system combined with homologous recombination. The H19 deleted (H19Î) ahESCs maintained haploidy and genome integrity, expressed pluripotency markers, differentiated into embryoid bodies (EBs), and contributed to chimeras after blastocyst injection. These cells exhibited similar imprinting features with sperm cells, and can produce fertile progenies after ICAI at a high efficiency. More importantly, it is feasible to perform genetic manipulations in H19Î ahESCs, and the genomic modifications can be properly transmitted to offspring. Our study will benefit the reproductive medicine in curing the hereditary genetic diseases and infertility in the future. The copy number variations of the two H19Î ahESC lines were analyzed by the SurePrint G3 Mouse CGH 4Ã180 K microarrays (Agilent). Wild-type OG-3 ahESCs were used as reference.

2015-11-05 | E-GEOD-67563 | biostudies-arrayexpress

Inhibition of Apoptosis Reduces Diploidization of Haploid Mouse Embryonic Stem Cells during the Differentiation

Project description:Phenotypes of haploid embryonic stem cells (haESCs) are dominant for recessive traits in mice. However, one major obstacle to their use is self-diploidization in daily culture. Although haESCs maintain haploidy well by deleting p53, whether they can sustain haploidy in differentiated status and the mechanism behind remain unknown. To address that, we induced p53-deficient haESCs into multiple differentiated lineages keeping a haploid status in vitro. Besides, haploid cells also remained in chimeric embryos and teratomas arising from p53-null haESCs. Transcriptome analysis revealed that apoptosis genes were down-regulated in p53-null haESCs, comparing to that in wild-type haESCs. Finally, we knocked-out p73, another apoptosis gene, and observed stabilization of haploidy in haESCs, either. These results indicated that the main mechanism of diploidization was apoptosis-related genes triggered cell death in haploid cell cultures. Thus, we can derive haploid somatic cells by manipulating apoptosis gene, facilitating genetic screens of lineage-specific development.

2020-04-07 | GSE148118 | GEO

High-frequency generation of fertile transgenic mice from H19-Igf2 engineered androgenetic haploid embryonic stem cells

Project description:Recent success in the derivation of mouse haploid embryonic stem cells from androgenetic blastocysts (ahESCs) has provided new avenues for the generation of genetically modified animals. However, the efficiency to produce viable transgenic mice via intracytoplasmic ahESCs injection (ICAI) was very low, which may correlate with the aberrant regulation of imprinted genes. Here we designed to delete the paternal imprinted gene H19 by CRSPR-Cas9 system combined with homologous recombination. The H19 deleted (H19Δ) ahESCs maintained haploidy and genome integrity, expressed pluripotency markers, differentiated into embryoid bodies (EBs), and contributed to chimeras after blastocyst injection. These cells exhibited similar imprinting features with sperm cells, and can produce fertile progenies after ICAI at a high efficiency. More importantly, it is feasible to perform genetic manipulations in H19Δ ahESCs, and the genomic modifications can be properly transmitted to offspring. Our study will benefit the reproductive medicine in curing the hereditary genetic diseases and infertility in the future.

2015-11-05 | GSE67563 | GEO

Genetic screening and multipotency in rhesus monkey haploid neural progenitor cells

Project description:Haploid embryonic stem cells (haESCs) have been extensively applied in forward and reverse genetic screening. However, a mammalian haploid somatic cell line is difficult to achieve because of spontaneous diploidization in differentiation. As a non-human primate species, monkeys are widely used in basic and pre-clinical research in which haploid cells are restricted to ESCs. Here, we report that rhesus monkey haESCs in an optimized culture medium show naïve-state pluripotency and stable haploidy. This model facilitated the derivation of haploid neural progenitor cells (haNPCs), which maintained haploidy and differentiation potential into neurons and glia for a long period in vitro. High-throughput trapping mutations can be efficiently introduced into haNPCs via piggyBac transposons. This system proves useful when identifying gene targets of neural toxicants via a proof-of-concept experiment. Using CRISPR/Cas9 editing, we confirmed that B4GALT6, from the candidate gene list, is a resistance gene of A803467 (a tetrodotoxin-like toxicant). This model is the first non-human primate haploid somatic cell line with proliferative ability, multipotency and an intact genome, thus providing a cellular resource for recessive genetic and potential drug screening.

2020-11-21 | GSE161862 | GEO

Zea mays Transcriptome or Gene expression

Project description:In many eukaryotes, reproduction involves contributions of genetic material from two parents. At some genes there are parent-of-origin differences in the expression of the maternal and paternal alleles of a gene and this is referred to as imprinting. The analysis of allele-specific expression in several maize hybrids allowed the comprehensive detection of imprinted genes. By comparing allelic expression patterns in multiple crosses, it was possible to observe allelic variation for imprinting in maize. The comparison of genes subject to imprinting in multiple plant species reveals limited conservation for imprinting. The subset of genes that exhibit conserved imprinting in maize and rice may play important, dosage-dependent roles in regulation of seed development. In this study, deep sequencing of RNA isolated from 14 days-after-pollination (DAP) endosperm tissue of five reciprocal hybrid pairs was performed to identify imprinted genes.

2013-11-14 | E-MTAB-4319 | biostudies-arrayexpress

Fundulus heteroclitus

Project description:Gene expression throughout vertebrate embryogenesis

| PRJNA126081 | ENA

Transcriptome profiling of an autopolyploidy series of Arabidopsis thaliana

Project description:Heterosis occurs where F1 offspring display superior characteristics to the parents. Heterosis is usually considered to result from crosses of genetically distinct (e.g. homozygous inbred) parents producing heterozygous F1 offspring. Most mechanistic models for heterosis require genetically heterozygous F1 hybrid offspring harbouring allelic diversity. Epigenetic or dosage models for heterosis could allow for heterosis effects in F1 offspring that display no allelic diversity with their parents. Reciprocal inter-ploidy crosses between diploid (2x) and tetraploid (4x) lines in the same genetic background generates genetically identical F1 triploids (3x). Such reciprocal F1 triploids differ according to whether the additional chromosome set is either maternally (maternal excess) or paternally inherited (paternal excess). Biomass accumulation and abiotic stress tolerance between the parental (2x and 4x) and reciprocal F1 triploid (3x) offspring of Arabidopsis thaliana accession C24 reveals a strong parental genome-dosage induced heterosis in the paternal-excess triploid F1 plants. In these F1 triploids, the circadian clock related genes CCA1 and TOC1, and the growth factors PIF4 and PIF5, display different expression levels compared to the non-heterotic maternal excess F1 triploid siblings. Whole transcriptome profiling reveals a paternal genome dosage effect on gene expression levels with strong enrichment for dysregulated abiotic stress-related genes in the paternal excess F1 triploids. This study demonstrates that heterosis can be triggered without allelic diversity in F1 triploid plants. Heterosis without heterozygosity in plants can be induced via an epigenetic “chromosome imprinting” like parental genome dosage effect requiring paternal transmission of an additional chromosome set 4 or 5 biological replicates per ploidy level, each replicate being a single two weeks old seedling

2014-08-01 | E-GEOD-52885 | biostudies-arrayexpress

Expression data from haploid and diploid epiblast stem cells

Project description:Haploid pluripotent stem cells, such as haploid embryonic stem cells (haESCs), facilitate the genetic study of recessive traits. In vitro, fish haESCs maintain haploidy in both undifferentiated and differentiated states, but whether mammalian haESCs can preserve pluripotency in the haploid state has not been tested. Here, we report that mouse haESCs can differentiate in vitro into haploid epiblast stem cells (haEpiSCs), which maintain an intact haploid genome, unlimited self-renewal potential, and durable pluripotency to differentiate into various tissues in vitro and in vivo. Mechanistically, the maintenance of self-renewal potential depends on the Activin/bFGF pathway. We further show that haEpiSCs can differentiate in vitro into haploid progenitor-like cells.

2015-07-15 | GSE62887 | GEO

A genetic screen identifies Etl4-deficiency capable of stabilizing the haploidy in embryonic stem cells

Project description:We performed a genome-wild loss-of-function screening and revealed several gene mutations could significantly reduce the rate of self-diploidization in haESCs. We further demonstrated that CRISPR/Cas9 mediated Etl4 knockout stabilizes the haploid state in different haploid cell lines. More interestingly, Etl4 deficiency could increase the mitochondrial oxidative phosphorylation (OXPHOS) capacity and decrease glycolysis in haESCs. Collectively, our study identifies Etl4 as a novel haploidy-related factor and suggests that the changes of energy metabolism is associated with self-diploidization.

2021-01-11 | GSE150215 | GEO

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