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High throughput CRISPR perturbation screens identify epigenetic regulators impacting primordial germ cell development [CRISPRi]

ABSTRACT: High throughput CRISPR perturbation screens identify epigenetic regulators impacting primordial germ cell development [CRISPRi]

PROVIDER: PRJNA1080593 | ENA |

REPOSITORIES: ENA

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High throughput CRISPR perturbation screens identify epigenetic regulators impacting primordial germ cell development [CRISPRi]

Project description:There is concern that environmental factors underlie reported declines in fertility and reproductive parameters such as the number and quality of sperm and eggs. One possible mechanism is the perturbation of epigenetic landscapes in the germline. To explore this possibility, we utilized a highly scalable in vitro platform for the differentiation of embryonic stem cells (ESCs) into primordial germ cell-like cells (PGCLCs) to conduct a CRISPRi screen of epigenetic-related genes to identify those that specifically perturb the efficiency of PGCLC formation. This platform leveraged an ESC line containing 4 inducible transcription factors (Prdm1, Prdm14, Tfap2c, and Nanog) and a PGC reporter (Stella-eGFP) that enabled highly efficient, cytokine-free differentiation and quantification en masse. A total of 701 genes with distinct sgRNAs were screened, and 53 genes were identified that decreased the efficiency of PGCLC formation. NCOR2, a transcriptional repressor that acts via recruitment of Class I and Class IIa histone deacetylases (HDACs) to gene targets, was particularly potent in suppressing PGCLC differentiation. Consistent with evidence that histone deacetylation is crucial for germline differentiation, we found that HDAC inhibitors (HDACi), including the anti-convulsive drug valproic acid (VPA) and widely-available dietary supplement sodium butyrate (SB), also suppressed ESC>PGCLC differentiation. Transcriptome analyses of HDACi-treated, differentiating ESC>PGCLC cultures revealed suppression of germline-associated pathways and enhancement of somatic pathways. Additionally, exposure of developing mouse embryos to SB or VPA caused hypospermatogenesis. This work demonstrates the feasibility of conducting large scale functional screens of genes, chemical agents and possibly genetic variants that impact germline development and epigenome.

2025-09-04 | GSE259289 | GEO

High throughput CRISPR perturbation screens identify epigenetic regulators impacting primordial germ cell development [RNA-seq]

Project description:High throughput CRISPR perturbation screens identify epigenetic regulators impacting primordial germ cell development [RNA-seq]

| PRJNA1080592 | ENA

High throughput CRISPR perturbation screens identify epigenetic regulators impacting primordial germ cell development [RNA-seq]

2025-09-04 | GSE259290 | GEO

dHyperCas12a enables multiplexed CRISPRi screens

Project description:dHyperCas12a enables multiplexed CRISPRi screens

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Single-cell CRISPRi screens of breast cancer associated enhancers

Project description:This series contains the single-cell CRISPRi screens of MDA-MB-361 cells and MDA-MB-231 cells targeting 3512 enhancers associated breast cancer GWAS variants and somatic mutations.

2024-11-13 | GSE224986 | GEO

Single-cell CRISPRi screens of breast cancer associated enhancers

Project description:Single-cell CRISPRi screens of breast cancer associated enhancers

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CRISPR-based epigenome editing screens identify transcriptional and epigenetic regulators of human CD8 T cell function [Sorting-based CRISPR screens]

Project description:All bulk CRISPR based screens CD2 and B2M CRISPRi tiling screens (primary human CD8 T cells), IL2RA CRISPRa tiling screens (Jurkats), CRISPRi/a TF screens (primary human CD8 T cells), and CRISPR TFome KO (primary human T cells)

2023-08-31 | GSE241933 | GEO

CRISPRi-based screens in iAssembloids to elucidate neuron-glia interactions

Project description:The sheer complexity of the brain has complicated our ability to understand its cellular mechanisms in health and disease. Genome-wide association studies have uncovered genetic variants associated with specific neurological phenotypes and diseases. In addition, single-cell transcriptomics have provided molecular descriptions of specific brain cell types and the changes they undergo during disease. Although these approaches provide a giant leap forward towards understanding how genetic variation can lead to functional changes in the brain, they do not establish molecular mechanisms. To address this need, we developed a 3D co-culture system termed iAssembloids (induced multi-lineage assembloids) that enables the rapid generation of homogenous neuron-glia spheroids. We characterize these iAssembloids with immunohistochemistry and single-cell transcriptomics and combine them with large-scale CRISPRi-based screens. In our first application, we ask how glial and neuronal cells interact to control neuronal death and survival. Our CRISPRi-based screens identified that GSK3β inhibits the protective NRF2-mediated oxidative stress response in the presence of reactive oxygen species elicited by high neuronal activity, which was not previously found in 2D monoculture neuron screens. We also apply the platform to investigate the role of APOE- 4, a risk variant for Alzheimer’s Disease, in its effect on neuronal survival. We find that APOE- 4 expressing astrocytes may promote more neuronal activity as compared to APOE- 3 expressing astrocytes. This platform expands the toolbox for the unbiased identification of mechanisms of cell-cell interactions in brain health and disease.

2024-07-12 | GSE272093 | GEO

Dissecting the yeast heat shock response by CRISPRi/a

Project description:CRISPRi screens on the repression of 129 protein kinases and 161 transcription factors in S. cerevisiae. We quantify perturbation effects on cellular fitness at 23, 30 and 38°C, expression of the SSA1 Hsp70 chaperone (as proxy for heat shock response activity) and thermotolerance. The integration of these phenotypes allowed us to identify core signaling pathways of the HSR and their contributions to temperature-associated growth and heat resistance.

2021-07-01 | GSE155455 | GEO

Precise measurement of molecular phenotypes with barcode-based CRISPRi screens

Project description:Precise measurement of molecular phenotypes with barcode-based CRISPRi screens

| PRJNA1118732 | ENA