Expression profiling reveals off-target gene regulation by RNAi
Abstract
RNA interference is thought to require near-identity between the small interfering RNA (siRNA) and its cognate mRNA. Here, we used gene expression profiling to characterize the specificity of gene silencing by siRNAs in cultured human cells. Transcript profiles revealed siRNA-specific rather than target-specific signatures, including direct silencing of nontargeted genes containing as few as eleven contiguous nucleotides of identity to the siRNA. These results demonstrate that siRNAs may cross-react with targets of limited sequence similarity.
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The Argonaute-loaded miRNA programs the gene target specificity of miRISC, as nucleotides 2-7 (the seed sequence) are mainly responsible for determining target mRNA identity through base pairing.
“The Argonaute‐loaded miRNA programs the gene target specificity of the miRISC, as nucleotides 2‐7, referred to as the miRNA “seed” sequence, are mainly responsible for determining the target mRNA identity through base pairing (Grün, Wang, Langenberger, Gunsalus, & Rajewsky, 2005; Haley & Zamore, 2004; Jackson et al., 2003; Krek et al., 2005; Lewis, Burge, & Bartel, 2005; Lewis, Shih, Jones‐Rhoades”
From microRNA strand selection: Unwinding the rules (2021) · cites this paper as Jackson et al., 2003
CRISPRi avoids the widespread off-target effects that are intrinsic to RNAi-based screening.
“CRISPRi represents an important advance over RNAi, since it lacks the pervasive off-target effects (Gilbert et al., 2014) inherent to RNAi-based screening approaches (Adamson et al., 2012; Jackson et al., 2003; Kaelin, 2012).”
From CRISPR Interference-Based Platform for Multimodal Genetic Screens in Human iPSC-Derived Neurons (2019) · cites this paper as Jackson et al., 2003
RNAi is associated with off-target silencing of transcripts based on partial sequence complementarity.
“Another common issue associated with RNAi appears to be off-target silencing of transcripts based on partial sequence complementarity [8]”
From Advances in targeted degradation of endogenous proteins (2019) · cites this paper as [8]
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- Authors
- Jackson, A. L., Bartz, S. R., Schelter, J., Kobayashi, S. V., Burchard, J., Mao, M., Li, B., Cavet, G., & Linsley, P. S.
- Corresponding author
- Jackson, Aimee L
- Bartz, Steven R
- Venue
- Nature Biotechnology
- Published
- 2003-05-18
- Volume
- 21
- Issue
- 6
- Pages
- 635-637
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2017642141
- Cited by
- 2,370
- References
- 8
- Citations by year
- 2026: 37 · 2025: 59 · 2024: 60 · 2023: 49 · 2022: 77 · 2021: 63 · 2020: 77 · 2019: 63 · 2018: 67 · 2017: 77 · 2016: 59 · 2015: 95 · 2014: 95 · 2013: 96 · 2012: 121
- FWCI
- 65.28
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Interference and Gene Delivery
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- RNA interference, siRNA, gene expression profiling, siRNA specificity, sequence similarity, transcriptome, human cells
- MeSH terms
- Base Sequence, Gene Expression Regulation, HeLa Cells, Humans, Molecular Sequence Data, RNA, Messenger, Transformation, Genetic, Conserved Sequence, Gene Targeting, Gene Silencing, Gene Expression Profiling, RNA Interference, RNA, Small Interfering
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