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RNA-seq following enhancer repression

ABSTRACT: Using RNA-seq to identify genes regulated by dCas9-KRAB mediated enhancer repression in NCI-H2009 lung adenocarcinoma cells

ORGANISM(S): Homo sapiens

PROVIDER: GSE72001 | GEO | 2015/10/26

SECONDARY ACCESSION(S): PRJNA292701

REPOSITORIES: GEO

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RNA-seq following enhancer repression

Project description:Using RNA-seq to identify genes regulated by dCas9-KRAB mediated enhancer repression in NCI-H2009 lung adenocarcinoma cells NCI-H2009 cells were first transfected with dCas9-KRAB fusion and subsequently transfected with no guide RNA (Empty), a guide RNA that has no target in the human genome (Dummy), and two separate guide RNAs (e3 #1 and e3 #2) recognizing the enhancer region of our study.

2015-10-26 | E-GEOD-72001 | biostudies-arrayexpress

Identifying functional enhancers regulating Cebpa expression and adipocyte differentiation (mRNA-Seq)

Project description:To explore the effect of enhancer repression on adipocyte differentiation in a transcriptome-wide manner, we infected cells with 1 mL lentiviruses medium containing dCas9-KRAB-En2-sgRNAs (Experimental group) or dCas9-KRAB (Control group) at the multiplicity of infection (MOI) of 100 for 12 h. We performed transcriptional profiling by RNA sequencing (RNA-seq) for dCas9-KRAB-En2 and dCas9-KRAB cells at day 7 of differentiation.

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RNA-seq of CSMD1 enhancer CRISPRi in LUHMES cells and differentiated neurons

Project description:we performed lentiviral CRISPR interference (CRISPRi) by recruiting dCas9 fused with the KRAB domain to the CSMD1 enhancer (fam3) in the neuronal precursor cell line – Lund human mesencephalic (LUHMES). Given that the expression of CSMD1 was not detectable in LUHMES cells we differentiated these cells into neurons. Differentiated neurons with CRISPRi of CSMD1 enhancer showed significantly higher expression of CSMD1 than control.

2022-06-30 | E-MTAB-8027 | biostudies-arrayexpress

Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements

Project description:Epigenome editing with the CRISPR/Cas9 platform is a promising technology to modulate gene expression to direct cell phenotype and to dissect the causal epigenetic mechanisms that direct gene regulation. Fusions of the nuclease-inactive dCas9 to the KRAB repressor domain (dCas9-KRAB) can effectively silence target gene expression. We targeted dCas9-KRAB to the HS2 enhancer, a distal regulatory element that orchestrates the expression of multiple globin genes. Genome-wide analyses demonstrated that localization of dCas9-KRAB to HS2 specifically induced H3K9 tri-methylation (H3K9me3) at that enhancer and reduced the chromatin accessibility of both the enhancer and its promoter targets. Targeted epigenetic modification of HS2 silenced the expression of multiple globin genes, with minimal off-target changes in gene expression. These results demonstrate that repression mediated by dCas9-KRAB is sufficiently specific to disrupt the activity of individual enhancers via local modification of the epigenome. This approach enables precise modulation of epigenetic function without modifying the underlying genome sequence.

2015-07-16 | GSE70973 | GEO

Epigenome Editing by CRISPR/Cas9 Repressors for Silencing of Distal Regulatory Elements

2015-10-19 | GSE71557 | GEO

Epigenome Editing by CRISPR/Cas9 Repressors for Silencing of Distal Regulatory Elements

2015-10-19 | GSE70671 | GEO

Identification of a novel enhancer of CEBPE essential for granulocytic differentiation

Project description:RNA-Seq of Control, dCas9-KRAB-EV, dCas9-KRAB-sg2 and dCas9-KRAB-sg5

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CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions [ChIP-seq]

Project description:ChIP-seq was performed to identify dCas9-KRAB binding sites in the presence of sgRNA (sgTGFB1_B9D2) targeting a region with rs1800469 between TGFB1 and B9D2 in H441 lung papillary adenocarcinoma cells.

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CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions [RNA-seq]

Project description:RNA-seq was performed to identify genes affected by CRISPRi (dCas9-KRAB) with sgRNA (sgTGFB1_B9D2) targeting a region that contains rs1800469 in an unbiased genome-wide fashion using H441 lung papillary adenocarcinoma cells.

2020-05-05 | GSE145529 | GEO

Super Enhancer Regulation of Cytokine-Induced Chemokine Production in Alcoholic Hepatitis [ChIP-Seq]

Project description:We performed histone modification ChIP-Seq in human liver explants and showed upregulation of multiple CXCL chemokines in AH. ChIP-Seq, chromosome conformation capture assays, and in silico analysis of published data identified a super enhancer for multiple CXCL genes. Targeting this super enhancer by dCas9-KRAB-mediated epigenome editing and Bromodomain and Extraterminal (BET) inhibitors decreased the expression of multiple CXCL genes.

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