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CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions

ABSTRACT: CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions

PROVIDER: PRJNA607514 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11112538_1.fastq.gz	Fastqsanger.gz
	SRR11112538_2.fastq.gz	Fastqsanger.gz
	SRR11112539_1.fastq.gz	Fastqsanger.gz
	SRR11112539_2.fastq.gz	Fastqsanger.gz
	SRR11112540_1.fastq.gz	Fastqsanger.gz

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

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

| PRJNA607516 | ENA

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

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

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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

CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions.

Project description:Genome-wide association studies have identified lung disease-associated loci; however, the functions of such loci are not well understood in part because the majority of such loci are located at non-coding regions. Hi-C, ChIP-seq and eQTL data predict potential roles (e.g. enhancer) of such loci; however, they do not elucidate the molecular function. To determine whether these loci function as gene-regulatory regions, CRISPR interference (CRISPRi; CRISPR/dCas9-KRAB) has been recently used. Here, we applied CRISPRi along with Hi-C, ChIP-seq and eQTL to determine the functional roles of loci established as highly associated with asthma, cystic fibrosis (CF), chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF). Notably, Hi-C, ChIP-seq and eQTL predicted that non-coding regions located at chromosome 19q13 or chromosome 17q21 harboring single-nucleotide polymorphisms (SNPs) linked to asthma/CF/COPD and chromosome 11p15 harboring an SNP linked to IPF interact with nearby genes and function as enhancers; however, CRISPRi indicated that the regions with rs1800469, rs2241712, rs12603332 and rs35705950, but not others, regulate the expression of nearby genes (single or multiple genes). These data indicate that CRISPRi is useful to precisely determine the roles of non-coding regions harboring lung disease-associated loci as to whether they function as gene-regulatory regions at a genomic level.

| S-EPMC7252574 | biostudies-literature

CRISPRi-based genome-scale identification of functional long non-coding RNA loci in human cells

Project description:The human genome produces thousands of long non-coding RNAs (lncRNAs) – transcripts >200 nucleotides long that do not encode proteins. While critical roles in normal biology and disease have been revealed for a subset of lncRNAs, the function of the vast majority remains untested. Here, we developed a CRISPR interference (CRISPRi) platform targeting 16,401 lncRNA loci in 7 diverse cell lines including 6 transformed cell lines and human induced pluripotent stem cells (iPSCs). Large-scale screening identified 499 lncRNA loci required for robust cellular growth, of which 89% showed growth modifying function exclusively in one cell type. We further found that lncRNA knockdown can perturb complex transcriptional networks in a cell type-specific manner. These data underscore the functional importance and cell type-specificity of many lncRNAs.

2016-12-01 | GSE85011 | GEO

Mapping the functional impact of non-coding regulatory elements in primary T cells through single-cell CRISPR screens

Project description:The vast majority of complex disease associations cannot be cleanly mapped to a gene, as they often lie within the non-cding fraction of the genome. Immune disease-associated variants are enriched within regulatory elements, such as distal enhancers, found in T cell-specific open chromatin regions. To identify the genes modulated by these regulatory elements, we developed a CRISPRi-based single-cell functional screening approach in primary human CD4+ T cells. We performed a proof-of-concept screen targeting 45 non-coding regulatory elements and 35 transcription start sites, each targeted by 4 different gRNAs. We profiled approximately 250,000 CD4+ T cell single-cell transcriptomes using 3' 10X Genomics.

2024-01-08 | E-MTAB-13324 | biostudies-arrayexpress

CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-05-05 | GSE145530 | GEO

CRISPRi Screen of Long Non-coding RNAs Identifies LINC03045 Regulating Glioblastoma Invasion

Project description:Introduction: Glioblastoma (GBM) invasion studies have focused on coding genes, while few studies evaluate long non-coding RNAs (lncRNAs), transcripts without protein-coding potential, for role in GBM invasion. We leveraged CRISPR-interference (CRISPRi) to evaluate invasive function of GBM-associated lncRNAs in an unbiased functional screen, characterizing and exploring the mechanism of identified candidates. Methods: We implemented a CRISPRi lncRNA loss-of-function screen evaluating association of lncRNA knockdown (KD) with invasion capacity in Matrigel. Top screen candidates were validated using CRISPRi and oligonucleotide(ASO)-mediated knockdown in three tumor lines. Clinical relevance of candidates was assessed via The Cancer Genome Atlas(TCGA) and Genotype-Tissue Expression(GTEx) survival analysis. Mediators of lncRNA effect were identified via differential expression analysis following lncRNA KD and assessed for tumor invasion using knockdown and rescue experiments. Results: Forty-eight lncRNAs were significantly associated with 33-83% decrease in invasion (p<0.01) upon knockdown. The top candidate, LINC03045, identified from effect size and p-value, demonstrated 82.7% decrease in tumor cell invasion upon knockdown, while LINC03045 expression was significantly associated with patient survival and tumor grade(p<0.0001). RNAseq analysis of LINC03045 knockdown revealed that WASF3, previously implicated in tumor invasion studies, was highly correlated with lncRNA expression, while WASF3 KD was associated with significant decrease in invasion. Finally, WASF3 overexpression demonstrated rescue of invasive function lost with LINC03045 KD. Conclusion: CRISPRi screening identified LINC03045, a previously unannotated lncRNA, as critical to GBM invasion. Gene expression is significantly associated with tumor grade and survival. RNA-seq and mechanistic studies suggest that this novel lncRNA may regulate invasion via WASF3.

2024-06-03 | GSE268342 | GEO

Gene expression profiling (RNA-seq) experiment where CRISPRi guides were designed to target the human rs2650492 variant, the promoter of GAPDH, and a non-coding region near TUFM in HEK293t cells

Project description:CRISPRi guides were designed to target genomic regions of interest in HEK293t cells. Four guides were designed per region (see processed file). These regions were an enhancer located in the 3’UTR of SBK1 which harbors the obesity GWAS variant rs2650492, the promoter of GAPDH as a positive control, and a non-coding region near TUFM as a negative control. We also provide transcriptomes for Cas9 transfected cells only. Genes proximal to rs2650492 were assessed for differential expression. This experiment was performed with technical replicates where each replicate is a unique transfection and library preparation.

2021-07-14 | E-MTAB-10460 | biostudies-arrayexpress

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.

2020-05-05 | GSE145528 | GEO

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