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Identifying regulators of parental imprinting by CRISPR/Cas9 screening in haploid human embryonic stem cells

ABSTRACT: Identifying regulators of parental imprinting by CRISPR/Cas9 screening in haploid human embryonic stem cells

PROVIDER: PRJEB48075 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR7017660.fastq.gz	Fastqsanger.gz
	ERR7017651.fastq.gz	Fastqsanger.gz
	ERR7017661.fastq.gz	Fastqsanger.gz
	ERR7017652.fastq.gz	Fastqsanger.gz
	ERR7017662.fastq.gz	Fastqsanger.gz

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Similar Datasets

Identifying regulators of parental imprinting by CRISPR/Cas9 screening in haploid human embryonic stem cells

Project description:To search for factors regulating paternally imprinted genes (PEGs), we performed a genome-wide loss-of-function CRISPR/Cas9 screen in haploid parthenogenetic ESCs. This by staining a pooled CRISPR library with a PEG10 antibody and next FACS-sorted for cells that presented de-novo PEG10 expression.

2021-10-21 | E-MTAB-11014 | biostudies-arrayexpress

Identifying regulators of parental imprinting by CRISPR/Cas9 screening in haploid human embryonic stem cells

Project description:In mammals, imprinted genes are regulated by differentially methylated regions (DMRs) that are inherited from germ cells, leading to monoallelic expression in accordance with parent-of-origin. Yet, it is largely unknown how imprinted DMRs are maintained in human embryos despite global DNA demethylation following fertilization. Here, we explored the mechanisms involved in imprinting regulation by employing human parthenogenetic embryonic stem cells (hpESCs), which lack paternal alleles. We show that although global loss of DNA methylation in hpESCs affects most imprinted DMRs, many paternally-expressed genes (PEGs) remain repressed. To search for factors regulating PEGs, we performed a genome-wide CRISPR/Cas9 screen in haploid hpESCs. This revealed ATF7IP as an essential repressor of a set of PEGs, which we further show is also required for silencing sperm-specific genes. Our study reinforces an important role for histone modifications in regulating imprinted genes and suggests a link between parental imprinting and germ cell identity. Genetic imprinting ensures monoallelic gene expression critical for normal embryonic development. Here the authors take advantage of human haploid parthenogenic embryonic stem cells lacking paternal alleles to identify, by genome-wide screening, factors involved in the regulation of imprinted genes.

| S-EPMC8602306 | biostudies-literature

BALANCED GENE DOSAGE CONTROL RATHER THAN PARENTAL ORIGIN UNDERPINS GENOMIC IMPRINTING

Project description:Mammalian parental imprinting represents an exquisite form of epigenetic control regulating the parent-specific monoallelic expression of genes in clusters. While imprinting perturbations are widely associated with developmental abnormalities, the intricate regional interplay between imprinted genes makes interpreting the contribution of gene dosage effects to phenotypes a challenging task. Using mouse models with distinct deletions in an intergenic region controlling imprinting across the Dlk1-Dio3 domain, we link changes in genetic and epigenetic states to allelic-expression and phenotypic outcome in vivo. This determined how hierarchical interactions between regulatory elements orchestrate robust parent-specific expression, with implications for non-imprinted gene regulation. Strikingly, flipping imprinting on the parental chromosomes by crossing genotypes of complete and partial intergenic element deletions, rescues the lethality of each deletion on its own. Our work indicates that parental origin of an epigenetic state is irrelevant as long as appropriate balanced gene expression is established and maintained at imprinted loci.

2022-07-09 | GSE207600 | GEO

Establishment of monkey imprinted differentially methylated regions map by comparative analysis of parthenogenetic haploid embryonic stem cells and sperms

Project description:Genomic imprinting is a important biological process, which leads to parental specific gene expressions. Improper gene imprinting results in several developmental abnormalities, cancer and other diseases. Studies in mice indicated genomic imprinting establishment relied on parental allele-specific DNA methylation during gametogenesis. Despite the fact that genomic imprinting is highly conserved in mammalian, the species specific pattern exists. Until now, except that of in mouse, informations about imprinting patterns is little, especially in primates. Through generation genome-wide 5mC and 5hmC profiles for two types of haploid genomes from rhesus monkeys, including parthenogenetic haploid ESCs ( PG ha ESCs) (derived from rhesus monkey parthenogenetic embryos) and sperms. We clearly characterized and distinguished methylome (5mC) from hydroxymethylome (5hmC)(which can not discriminate from methylome in traditional bisulfite (BS) sequencing) in haploid genomes. Based on these information, we determined distribution patterns of 5mC and 5hmC in ha ESCs and sperms. Interestingly, both 5hmC levels and distribution patterns were similar in ha ESCs and sperms, and 5hmC which is enriched in the regions with low 5mC frequency. Meanwhile through comparing DNA methylation and hydroxymethylation status between sperms and ha ESCs, we first provided a fundamental information of monkey imprinted differentially methylated regions (DMRs) distribution in monkey chromosomes. Second, we observed that DMRs did not overlap with hydroxymethylated regions (DMR or DhMR), suggesting that establishment of imprinted regions was not interfered by 5hmC. Our results demonstrate DNA methylation profiling of PG ha ESCs and sperms can be uesed as a powerful and effective method to map and characterize imprinted regions in non-human primates genome.

2016-12-08 | GSE75817 | GEO

Dynamics of parental genomic imprinting during human male germ cell development

Project description:It is generally assumed that parental DNA imprinting is complete before the onset of meiosis in human spermatogenesis. Conversely, we here demonstrate dynamic DNA methylation in multiple imprinted regions during meiosis and subsequent maturation of spermatids. This suggests a role for these genes in spermatogenesis and has implications for the effectiveness and safety of assisted conception using testicular sperm.

2021-06-26 | GSE175576 | GEO

BALANCED GENE DOSAGE CONTROL RATHER THAN PARENTAL ORIGIN UNDERPINS GENOMIC IMPRINTING

Project description:BALANCED GENE DOSAGE CONTROL RATHER THAN PARENTAL ORIGIN UNDERPINS GENOMIC IMPRINTING

| PRJNA856294 | ENA

Dynamics of parental genomic imprinting during human male germ cell development

Project description:Dynamics of parental genomic imprinting during human male germ cell development

| PRJNA732925 | ENA

Identifying the differentially expressed genes between ADI-PEG20 resistant and parental Ju77 cell line

Project description:Identifying the differentially expressed genes between ADI-PEG20 resistant and parental Ju77 cell line

2016-07-12 | GSE73970 | GEO

Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta (RNA-seq)

Project description:Given the possible critical importance of placental gene imprinting and random monoallelic expression on fetal and infant health, most of those genes must be identified, in order to understand the risks that the baby might meet during pregnancy and after birth. Therefore, the aim of the current study was to introduce a workflow and tools for analyzing imprinted and random monoallelic gene expression in human placenta, by applying whole-transcriptome (WT) RNA sequencing of placental tissue and genotyping of coding DNA variants in family trios. Ten family trios, each with a healthy spontaneous single-term pregnancy, were recruited. Total RNA was extracted for WT analysis, providing the full sequence information for the placental transcriptome. Parental and child blood DNA genotypes were analyzed by exome SNP genotyping microarrays, mapping the inheritance and estimating the abundance of parental expressed alleles. Imprinted genes showed consistent expression from either parental allele, as demonstrated by the SNP content of sequenced transcripts, while monoallelically expressed genes had random activity of parental alleles. We revealed 4 novel possible imprinted genes (LGALS8, LGALS14, PAPPA2 and SPTLC3) and confirmed the imprinting of 4 genes (AIM1, PEG10, RHOBTB3 and ZFAT-AS1) in human placenta. The major finding was the identification of 4 genes (ABP1, BCLAF1, IFI30 and ZFAT) with random allelic bias, expressing one of the parental alleles preferentially. The main functions of the imprinted and monoallelically expressed genes included: i) mediating cellular apoptosis and tissue development; ii) regulating inflammation and immune system; iii) facilitating metabolic processes; and iv) regulating cell cycle. Placentas from ten family trios were analysed using RNA-Seq.

2014-09-01 | E-GEOD-56524 | biostudies-arrayexpress

Transcription profiling of barley seedling leaves from Steptoe x Morex doubled-haploid lines and from the parental cultivars

Project description:We measured mRNA abundance in the seedling leaves of 35 recombinant Steptoe x Morex doubled-haploid lines (no replicates) and in parental genotypes, Steptoe and Morex, 3 replicates each, total 41 chip.

2007-04-11 | E-TABM-111 | biostudies-arrayexpress

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