ArticleNucleic acids research2018
Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
73 citing papers in PubMed.
- To scramble or not: Steric blocking 2'-MOE/PS control antisense oligonucleotides across cellular models.Molecular therapy. Nucleic acids · 2026Article
- Direct roles of long non-coding RNAs in transcription activation.Nature structural & molecular biology · 2026Review
- LINC01116, a hypoxia-lncRNA marker of pathological lymphangiogenesis and poor prognosis in lung adenocarcinoma.Molecular oncology · 2026Article
- Leveraging human genetic variation to therapeutically target hundreds of genes with dominant & dispensable disease alleles.medRxiv : the preprint server for health sciences · 2026Article
- RSRC2 is a novel RNA-binding protein that safeguards mitotic fidelity by interacting with the lncRNA C1QTNF1-AS1.Nucleic acids research · 2026Article
- In Vivo CRISPR Interference Screen Reveals Long Noncoding RNA Portfolio Crucial for Cutaneous Squamous Cell Carcinoma Tumor Growth.The Journal of investigative dermatology · 2026Article
- Gene Editing of Pluripotent Stem Cell-Derived Hepatic Cells for Liver Disease Modeling and Therapeutic Development.Biomolecules & therapeutics · 2026Review
- Reshaping tumor immune microenvironment through ROS-responsive prodrug polyplexes via synergistic effect of CRISPRi system and epigenetic inhibitor for breast cancer therapy.Materials today. Bio · 2025Article
- CRISPR-based Transcriptional Regulation: Technologies, Applications, and Future Directions.DNA · 2025Article
- Review
- SUMO conjugation to promoter-proximal sequence elements-associated proteins impacts on snRNA transcription.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Unraveling the advances of non-coding RNAs on the tumor microenvironment: innovative strategies for cancer therapies.Journal of translational medicine · 2025Review
- Integrating datasets to dissectData in brief · 2025Article
- The Interface of Gene Editing with Regenerative Medicine.Engineering (Beijing, China) · 2025Article
- Arrayed CRISPRi library to suppress genes required for Schizosaccharomyces pombe viability.The Journal of cell biology · 2025Article
- Targeting and engineering long non-coding RNAs for cancer therapy.Nature reviews. Genetics · 2024Review
- LncRNA Functional Screening in Organismal Development.Non-coding RNA · 2023Review
- Review
- Long non-coding RNAs in retinal neovascularization: current research and future directions.Graefe's archive for clinical and experimental ophthalmology = Albrecht von Graefes Archiv fur klinische und experimentelle Ophthalmologie · 2023Review
- Functional knockout of long non-coding RNAs with genome editing.Frontiers in genetics · 2023Review
13 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Loss-of-function (LOF) methods such as RNA interference (RNAi), antisense oligonucleotides or CRISPR-based genome editing provide unparalleled power for studying the biological function of genes of interest. However, a major concern is non-specific targeting, which involves depletion of transcripts other than those intended. Little work has been performed to characterize the off-target effects of these common LOF methods at the whole-transcriptome level. Here, we experimentally compared the non-specific activity of RNAi, antisense oligonucleotides and CRISPR interference (CRISPRi). All three methods yielded non-negligible off-target effects in gene expression, with CRISPRi also exhibiting strong clonal effects. As an illustrative example, we evaluated the performance of each method for determining the role of an uncharacterized long noncoding RNA (lncRNA). Several LOF methods successfully depleted the candidate lncRNA but yielded different sets of differentially expressed genes as well as a different cellular phenotype upon depletion. Similar discrepancies between methods were observed with a protein-coding gene (Ch-TOG/CKAP5) and another lncRNA (MALAT1). We suggest that the differences between methods arise due to method-specific off-target effects and provide guidelines for mitigating such effects in functional studies. Our recommendations provide a framework with which off-target effects can be managed to improve functional characterization of genes of interest.
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Registered trials
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