ArticleProceedings of the National Academy of Sciences of the United States of America2015
Next-generation libraries for robust RNA interference-based genome-wide screens.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
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- Integrative multiomic approaches reveal ZMAT3 and p21 as conserved hubs in the p53 tumor suppression network.Cell death and differentiation · 2025Article
- BBANsh: a deep learning architecture based on BERT and bilinear attention networks to identify potent shRNA.Briefings in bioinformatics · 2025Article
- Analysis of Processing, Post-Maturation, and By-Products of shRNA in Gene and Cell Therapy Applications.Methods and protocols · 2025Article
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- A Novel CRISPR Interference Effector Enabling Functional Gene Characterization with Synthetic Guide RNAs.The CRISPR journal · 2022Article
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- ZetaSuite: computational analysis of two-dimensional high-throughput data from multi-target screens and single-cell transcriptomics.Genome biology · 2022Article
- Selective vulnerabilities in the proteostasis network of castration-resistant prostate cancer.Cell chemical biology · 2022Article
- Degradome-focused RNA interference screens to identify proteases important for breast cancer cell growth.Frontiers in oncology · 2022Article
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- Functional genomics screen identifies proteostasis targets that modulate prion protein (PrP) stability.Cell stress & chaperones · 2021Article
- Identification of a long non-coding RNA regulator of liver carcinoma cell survival.Cell death & disease · 2021Article
- Targeting alternative splicing by RNAi: from the differential impact on splice variants to triggering artificial pre-mRNA splicing.Nucleic acids research · 2021Article
- In Vivo Genome-Wide Pooled RNAi Screens in Cancer Cells to Identify Determinants of Chemotherapy/Drug Response.Methods in molecular biology (Clifton, N.J.) · 2021Article
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Authors and funding
11 authors.
Funding
Abstract
Genetic screening based on loss-of-function phenotypes is a powerful discovery tool in biology. Although the recent development of clustered regularly interspaced short palindromic repeats (CRISPR)-based screening approaches in mammalian cell culture has enormous potential, RNA interference (RNAi)-based screening remains the method of choice in several biological contexts. We previously demonstrated that ultracomplex pooled short-hairpin RNA (shRNA) libraries can largely overcome the problem of RNAi off-target effects in genome-wide screens. Here, we systematically optimize several aspects of our shRNA library, including the promoter and microRNA context for shRNA expression, selection of guide strands, and features relevant for postscreen sample preparation for deep sequencing. We present next-generation high-complexity libraries targeting human and mouse protein-coding genes, which we grouped into 12 sublibraries based on biological function. A pilot screen suggests that our next-generation RNAi library performs comparably to current CRISPR interference (CRISPRi)-based approaches and can yield complementary results with high sensitivity and high specificity.
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