Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA335860 | ENA |
REPOSITORIES: ENA
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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
Project description:MYC controls the transcription of large numbers of long non-coding RNAs. Since MYC is a ubiquitous oncoprotein, some of these long non-coding RNAs (lncRNAs) probably play a significant role in cancer. We applied CRISPRi to the identification of MYC-regulated lncRNAs that are required for MYC-driven cell proliferation in the P493-6 and RAMOS human lymphoid cell lines. We identified 320 non-coding loci that play a positive role in cell growth. Transcriptional repression of any one of these lncRNAs reduces the proliferative capacity of the cells. Selected hits were validated by RTqPCR and in CRISPRi-competition assays with individual GFP-expressing sgRNA-constructs. We also showed binding of MYC to the promoter of two candidate genes by chromatin immunoprecipitation. In the course of our studies, we discovered that the repressor domain SID derived from the MXD1 protein is highly effective in P493-6 and RAMOS cells in terms of the number of guides depleted in library screening and the extent of the induced transcriptional repression. In the cell lines used, it is superior to the KRAB repressor domain which serves routinely as transcriptional repressor domain in CRISPRi. The SID transcriptional repressor domain is effective as a fusion to the MS2 aptamer binding protein MCP allowing the construction of a doxycycline regulatable CRISPRi-system that allows controlled repression of targeted genes and will facilitate the functional analysis of growth-promoting lncRNAs.
2020-04-06 | GSE141482 | GEO
Project description:MYC controls the transcription of large numbers of long non-coding RNAs. Since MYC is a ubiquitous oncoprotein, some of these long non-coding RNAs (lncRNAs) probably play a significant role in cancer. We applied CRISPRi to the identification of MYC-regulated lncRNAs that are required for MYC-driven cell proliferation in the P493-6 and RAMOS human lymphoid cell lines. We identified 320 non-coding loci that play a positive role in cell growth. Transcriptional repression of any one of these lncRNAs reduces the proliferative capacity of the cells. Selected hits were validated by RTqPCR and in CRISPRi-competition assays with individual GFP-expressing sgRNA-constructs. We also showed binding of MYC to the promoter of two candidate genes by chromatin immunoprecipitation. In the course of our studies, we discovered that the repressor domain SID derived from the MXD1 protein is highly effective in P493-6 and RAMOS cells in terms of the number of guides depleted in library screening and the extent of the induced transcriptional repression. In the cell lines used, it is superior to the KRAB repressor domain which serves routinely as transcriptional repressor domain in CRISPRi. The SID transcriptional repressor domain is effective as a fusion to the MS2 aptamer binding protein MCP allowing the construction of a doxycycline regulatable CRISPRi-system that allows controlled repression of targeted genes and will facilitate the functional analysis of growth-promoting lncRNAs.
2020-04-06 | GSE141491 | GEO
Project description:There are over 15,000 long (>200 nucleotides) noncoding RNA (lncRNAs) genes in the human genome, but only few of them has been functionally characterized. Emerging evidence has shown that long non-coding RNAs (lncRNAs) modulate diverse biological processes and mediate tumor-promoting/suppressing effects and serve as independent diagnostic/prognostic biomarkers in cancer. However, the role and function mechanism of the lncRNA/RBP-mediated regulatory circuits in determining the functional characteristics of GSCs underlying GBM pathogenesis remains poorly understood. To fill this gap, we combined CRISPR (clustered regularly interspaced short palindromic repeat) interference (CRISPRi), with large-scale computational analysis of The Cancer Genome Atlas (TCGA) to systematically identify the functional lncRNAs with clinically relevant expression in GBM.
2023-08-09 | GSE213046 | GEO
Project description:Long non-coding RNAs (lncRNAs) are defined as non-protein-coding transcripts that are at least 200 nucleotides long. They are known to play pivotal roles in regulating gene expression, especially during stress responses in plants. We used a large collection of in-house transcriptome data from various soybean (Glycine max and Glycine soja) tissues treated under different conditions to perform a comprehensive identification of soybean lncRNAs. We also retrieved publicly available soybean transcriptome data that were of sufficient quality and sequencing depth to enrich our analysis. In total, RNA-seq data of 332 samples were used for this analysis. An integrated reference-based, de novo transcript assembly was developed that identified ~69,000 lncRNA gene loci. We showed that lncRNAs are distinct from both protein-coding transcripts and genomic background noise in terms of length, number of exons, transposable element composition, and sequence conservation level across legume species. The tissue-specific and time-specific transcriptional responses of the lncRNA genes under some stress conditions may suggest their biological relevance. The transcription start sites of lncRNA gene loci tend to be close to their nearest protein-coding genes, and they may be transcriptionally related to the protein-coding genes, particularly for antisense and intronic lncRNAs. A previously unreported subset of small peptide-coding transcripts was identified from these lncRNA loci via tandem mass spectrometry, which paved the way for investigating their functional roles. Our results also highlight the current inadequacy of the bioinformatic definition of lncRNA, which excludes those lncRNA gene loci with small open reading frames (ORFs) from being regarded as protein-coding.
2020-01-09 | PXD014553 | Pride
Project description:CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions
| PRJNA607514 | ENA
Project description:Pooled CRISPR-Cas9 screens have recently emerged as a powerful method for functionally characterizing regulatory elements in the non-coding genome, but off-target effects in these experiments have not been systematically evaluated. Here, we conducted multiple genome-scale CRISPR screens for essential CTCF loop anchors in the human K562 erythroid cell line. Surprisingly, the primary drivers of apparent ``hits'' in this screen were single guide RNAs (sgRNAs) with low sequence specificity. After removing these confounders, we found that no CTCF loop anchors among the ones we screened are essential for cell growth in culture. We also observed analogous effects in independent non-coding screens densely tiling regulatory elements and genomic neighborhoods near previously known essential genes. Strikingly, we found that low-specificity guides also result in strong confounding growth effects in screens employing epigenetic perturbations that do not cause DNA damage, such as CRISPRi and CRISPRa. Remarkably, the set of confounded guides is distinct for each perturbation mode. Promisingly, strict filtering of CRISPRi libraries using GuideScan-aggregate specificity scores removed these confounded sgRNAs and allowed for the identification of essential enhancers, which we validated extensively. Our stduy presents the first genome-scale functional characterization of CTCF binding sites in the human genome, while also identifying the limitations on and outlining the future prospects for the detailed functional dissection of regulatory elements in the genome using Cas9.
2019-07-01 | GSE131349 | GEO
Project description:Identification and Initial Functional Characterization of SENCR, a Long Non-Coding RNA Enriched in Human Vascular Cells
2019-05-14 | E-GEOD-51878 | ExpressionAtlas
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
Project description:A core task to understand the consequences of non-coding single nucleotide polymorphisms (SNP) is to identify their genotype specific binding of transcription factor (TF). Here, we generate a large-scale TF-SNP interaction map for a selection of 116 colorectal cancer (CRC) risk loci and validated TF binding to 10 putatively functional SNPs. Our data further revealed TF binding complexity adjacent to the 116 risk loci, adding an additional layer of understanding to regulatory networks associated with CRC relevant loci.
2017-03-30 | MSV000080810 | MassIVE