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RNA-seq on MCF7 cells induced with sgRNA vectors targeting CTCF binding elements

ABSTRACT: We performed a CRISPR-based functional genetic screen targeting CTCF binding elements (CBEs) located in the vicinity of ERα-bound enhancers. The screen identified four functional CBEs whose targeting resulted in a marked negative effect on the proliferation of MCF-7 cells (ERα-positive cells) but no significant effect on MDA-MB-231 (ERα-negative cells) cells. We then carried out RNA-seq analysis on MCF-7 cells induced with sgRNA vectors targeting these four CBEs: sgRNA_1118, sgRNA_1659, sgRNA_680 and sgRNA_810, as well as non-targeting sgRNA as control.

ORGANISM(S): Homo sapiens

PROVIDER: GSE124573 | GEO | 2019/11/01

REPOSITORIES: GEO

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GRO-seq on MCF7 cells induced with sgRNA vectors targeting CTCF binding elements

Project description:We performed a CRISPR-based functional genetic screen targeting CTCF binding elements (CBEs) located in the vicinity of ERα-bound enhancers. The screen identified four functional CBEs whose targeting resulted in a marked negative effect on the proliferation of MCF-7 cells (ERα-positive cells) but no significant effect on MDA-MB-231 (ERα-negative cells) cells. Here, we carried out GRO-seq analysis on MCF-7 cells induced with an sgRNA vector targeting one of the hits detected by the screen: sgRNA_1118, as well as non-targeting sgRNA and sg1830 as control.

2019-11-01 | GSE124572 | GEO

Genomic binding profiles of ERa in MCF-7 and T47D control or enhancer588-targeted cells

Project description:Estrogen Receptor a (ERa) bindning to DNA was profiled by ChIP-seq in MCF-7 and T47D cells transduced with either control sgRNA, or sgRNA targeting a specific enhancer region (enhancer588). ERa in MCF-7 and T47D control or enhancer588-targeted cells

2015-12-14 | E-GEOD-75779 | biostudies-arrayexpress

RNA-seq on MCF10A-YAP5SA cells (overexpressed constrictively activated YAP in MCF10A cells) transduced with sgRNAs vectors targeting the TEAD4 binding motif within the identified enhancers

Project description:We performed a CRISPR-based functional genetic screen targeting TEAD4 binding motif located within the YAP-bound enhancers. The screen identified seven functional enhancers whose targeting resulted in a marked negative effect on the proliferation of MCF10A-YAP-5SA cells (overexpressed constrictively activated YAP) but no significant effect on MCF10A (parental control) cells. We then carried out RNA-seq analysis on MCF10A-YAP-5SA cells transduced with sgRNA vectors targeting these seven enhancers (enhancers A, B, C, D, E, F, G) as well as the non-targeting sgRNA as control (NT).

2021-01-01 | GSE137981 | GEO

A CRISPR-Cas9 screen identifies essential CTCF anchor sites for Estrogen Receptor-driven breast cancer cell proliferation

Project description:Estrogen receptor α (ERα) is an enhancer activating transcription factor, a key driver of breast cancer, and a main target for cancer therapy. ER-mediated gene regulation requires proper chromatin-conformation to facilitate interactions between ER-bound enhancers and their target promoters. A major determinant of chromatin structure is the CCCTC-binding factor (CTCF), that dimerizes and together with cohesin stabilizes chromatin loops and forms the boundaries of topologically associated domains. However, whether CTCF-binding elements (CBEs) are essential for ER-driven cell proliferation is unknown. To address this question in a global manner, we implemented a CRISPR-based functional genetic screening approach targeting CBEs located in the vicinity of ERα-bound enhancers. We identified four functional CBEs and demonstrated the role of one in inducing chromatin conformation changes in favor of activation of PREX1, a key ERα target gene in breast cancer. Indeed, high PREX1 expression is a bona-fide marker of ER-dependency in cell lines, and associated with good outcome after anti-hormonal treatment. Altogether, our data show that distinct CTCF-mediated chromatin structures are required for ER- driven breast cancer cell proliferation.

2020-01-04 | GSE124667 | GEO

Genomic binding profiles of ERa in MCF-7 and T47D control or enhancer588-targeted cells

2015-12-14 | GSE75779 | GEO

Transcriptome analysis of TWIST1 sgRNA-treated human tumor endothelial cells

Project description:The global RNA expression was assayed on human glioblastoma-derived tumor endothelial cells (ECs) treated with CRISPR/sgRNA targeting Twist1 or control sequence.

2023-02-15 | GSE221950 | GEO

The effect of miRNA overexpression on gene expression profile of MCF-7 cells

Project description:To identify microRNAs impacting estrogen receptor ERα expression in breast cancer, we have screened ER-positive breast cancer cells with a library of pre-miRs, and systematically monitored the ERα expression by protein lysate microarrays. There was a significant enrichment of the in silico predicted ERα targeting microRNAs among the hits. The most potent pre-miRs miR-18a/b, miR-193b, miR-206, and miR-302c, were confirmed to directly target ERα and to repress estrogen-responsive genes. The effect of miRNA overexpression on gene expression profile of MCF-7 cells was studied. Furthermore, miR-18a and miR-18b showed increased expression in ERα-negative as compared to ERα-positive clinical tumors. In summary, we present systematic and direct functional and correlative clinical evidence on microRNAs inhibiting ERα signaling in breast cancer.

2009-08-18 | GSE14847 | GEO

Functional CRISPR Screen Identifies AP1-associated Enhancer regulating FOXF1 to modulate Oncogene-Induced Senescence

Project description:We carried out CRISPR-Cas9 functional screen focused on AP-1 bound enhancers that are activated upon oncogenic stress. The screen discovered Enh.AP1.OIS1 - an enhancer bound by AP1 that is required for activation of oncogene-induced senescence (OIS) response. We applied RNA-seq analysis to RASG12V-activated BJ cells transduced with either sgRNAs targeting AP-1 bound enhancer (sgRNA-69 or sgRNA71), or sgRNA targeting the target gene FOXF1 or non-targeting control sgRNA (sgNT)

2018-07-15 | GSE112458 | GEO

Screening of a heptamer-type sgRNA library for therapeutic agents against hematological malignancies.

Project description:tRNase ZL-utilizing efficacious gene silencing (TRUE gene silencing) is an RNA-mediated gene expression control technology that has therapeutic potential. This technology is based on the properties of tRNase ZL that it can cleave any target RNA at any desired site under the direction of an appropriate artificial small guide RNA (sgRNA) and that cytosolic tRNase ZL can modulate gene expression by cleaving mRNA under the direction of cellular 5M-bM-^@M-2-half-tRNA or microRNA as sgRNA. In order to estimate a number of potential therapeutic heptamer-type sgRNAs for hematological malignancies, we constructed an sgRNA library composed of 156 heptamer-type sgRNAs, and examined how the sgRNAs affect viability of leukemia and myeloma cells. And we found that 20 of the 156 sgRNAs can efficiently induce apoptosis in at least one of the cancer cell lines. Furthermore, we demonstrated that 4 of the 20 effective sgRNAs can reduce growth rates of HL60 cells in mouse xenograft models. DNA microarray analysis for changes in an mRNA profile by these four heptamer-type sgRNAs suggested at least one candidate target mRNA that contains a potential tRNase ZL target site for each sgRNA. Changes in gene expression in HL60 cells were measured after 18-hour incubation in the absence or presence of one of five different heptamer-type sgRNAs. *Heptamer sequences requested but not provided by submitter

2014-06-30 | E-GEOD-49578 | biostudies-arrayexpress

A screen for cis-regulatory elements for murine miR-142 using an sgRNA library prepared by Molecular Chipper technology

Project description:CRISPR-based loss-of-function screens have been proven powerful to identify genetic regulators in mammalian cells, but current approaches for single guide RNA (sgRNA) library construction are expensive and difficult to be adapted in most laboratories. Here, we present a Molecular Chipper technology for inexpensive and easily customizable sgRNA library generation, and a proof-of-principle screen that identifies novel cis-regulatory regions for miR-142 biogenesis. This method will be useful for functional interrogation of non-coding elements in mammalian genomes

2016-03-17 | GSE70011 | GEO

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