ArticleNucleic acids research2023
BESST: a novel LncRNA knockout strategy with less genome perturbance.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Towards efficient perturbation for the noncoding genome.Nature communications · 2026Article
- Exploring the Clinical Landscape of Long Non-coding RNAs in Cancer Diagnosis and Therapy.Biochemical genetics · 2026Review
- Non-coding RNAs in lipid metabolism and their roles in atherosclerosis.Nature reviews. Cardiology · 2026Review
- Nuclear and cytoplasmic USP30-AS1 coordinately regulate breast cancer progression through HnRNPF/p21 and EZH2/c-Myc/p21 axes.Genes & diseases · 2026Article
- The long non-coding RNAFrontiers in nutrition · 2026Article
- Functional Genomic Screening Identifies lncRNA CNPY2-AS1 as a Regulator of Redox Metabolism and Antiviral Immunity.International journal of biological sciences · 2026Article
- Noncanonical target-strand cytosine base editing via engineered Un1Cas12f1 platform.Nature communications · 2025Article
- Long non-coding RNAs in cattle: implications for key meat and dairy production traits.Functional & integrative genomics · 2025Review
- Whole-transcriptome analysis reveals the profiles and roles of coding and non-coding RNAs during hair follicle cycling in Rex rabbits.BMC genomics · 2025Article
- Article
- LncRNAway: a web-based sgRNA design tool for precise and effective suppression of long noncoding RNAs.Nucleic acids research · 2024Article
- TheNon-coding RNA · 2023Article
- Functional knockout of long non-coding RNAs with genome editing.Frontiers in genetics · 2023Review
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Authors and funding
12 authors.
Funding
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Abstract
Long noncoding RNAs (lncRNAs) are >200 nt RNA transcripts without protein-coding potential. LncRNAs can be categorized into intergenic, intronic, bidirectional, sense, and antisense lncRNAs based on the genomic localization to nearby protein-coding genes. The current CRISPR-based lncRNA knockout strategy works efficiently for lncRNAs distant from the protein-coding gene, whereas it causes genomic perturbance inevitably due to technical limitations. In this study, we introduce a novel lncRNA knockout strategy, BESST, by deleting the genomic DNA fragment from the branch point to the 3' splicing site in the last intron of the target lncRNA. The BESST knockout exhibited comparable or superior repressive efficiency to RNA silencing or conventional promoter-exon1 deletion. Significantly, the BESST knockout strategy minimized the intervention of adjacent/overlap protein-coding genes by removing an average of ∼130 bp from genomic DNA. Our data also found that the BESST knockout strategy causes lncRNA nuclear retention, resulting in decapping and deadenylation of the lncRNA poly(A) tail. Further study revealed that PABPN1 is essential for the BESST-mediated decay and subsequent poly(A) deadenylation and decapping. Together, the BESST knockout strategy provides a versatile tool for investigating gene function by generating knockout cells or animals with high specificity and efficiency.
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