siRNAs with decreased off-target effect facilitate the identification of essential genes in cancer cells

Chunyan Li; Zhenzhen Liu; Fang Yang; Wensheng Liu; Di Wang; Encheng Dong; Yu Wang; Chung-I Wu; Xuemei Lu

doi:10.18632/oncotarget.4269

Oncotarget

Oncotarget (a primarily oncology-focused, peer-reviewed, open access journal) aims to maximize research impact through insightful peer-review; eliminate borders between specialties by linking different fields of oncology, cancer research and biomedical sciences; and foster application of basic and clinical science.

Its scope is unique. The term "oncotarget" encompasses all molecules, pathways, cellular functions, cell types, and even tissues that can be viewed as targets relevant to cancer as well as other diseases. The term was introduced in the inaugural Editorial, Introducing Oncotarget.

As of January 1, 2022, Oncotarget has shifted to a continuous publishing model. Papers will now be published continuously within yearly volumes in their final and complete form and then quickly released to Pubmed.

Subscribe to receive alerts once a paper has been published by Oncotarget.

Learn about our FREE

Post-Publication Promotion Services

50% on all publication fees until the end of 2024.

Impact Journals, LLC is the publisher of Oncotarget: www.impactjournals.com.

Impact Journals is a member of the Wellcome Trust List of Compliant Publishers.

Impact Journals is a member of the Society for Scholarly Publishing.

On December 23, 2022, Oncotarget server experienced a DDoS attack. As a result, Oncotarget site was inaccessible for a few hours. Oncotarget team swiftly dealt with the situation and took it under control. This malicious action will be reported to the FBI.

Research Papers:

siRNAs with decreased off-target effect facilitate the identification of essential genes in cancer cells

Chunyan Li, Zhenzhen Liu, Fang Yang, Wensheng Liu, Di Wang, Encheng Dong, Yu Wang, Chung-I Wu and Xuemei Lu _

PDF | HTML | Supplementary Files | How to cite

Oncotarget. 2015; 6:21603-21613. https://doi.org/10.18632/oncotarget.4269

Metrics: PDF 1643 views | HTML 2409 views | ?

Abstract

Chunyan Li1,*, Zhenzhen Liu1,2,*, Fang Yang1,*, Wensheng Liu1, Di Wang1, Encheng Dong1, Yu Wang1, Chung-I Wu1 and Xuemei Lu1

1 CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Chaoyang District, Beijing, P. R. China

2 University of Chinese Academy of Sciences, Shijingshan District, Beijing, P. R. China

* These authors have contributed equally to this work

Correspondence to:

Xuemei Lu, email:

Keywords: essential gene, siRNA, off-target, cell viability, transcriptome

Received: February 12, 2015 Accepted: May 13, 2015 Published: May 25, 2015

Abstract

Since the essential genes are crucial to the proliferation and survival of cancer cells, the interference of these genes is promising to be an option for cancer therapy to overcome heterogeneity. However, the essential genes are highly overestimated by RNA interference (RNAi) screenings, which is mainly caused by the pervasive off-target effect of small interference RNA (siRNA) and short hairpin RNA (shRNA). In the present study, we designed Match-Mismatch paired siRNAs to discriminate the on-target effect from off-target effect of siRNAs on cell viability. Only one of the 7 potential essential genes was validated as essential to cell viability, which demonstrates the high false positive rate in RNAi screenings. We modified the siRNA by introducing random nucleotides (N) into the guide strand to mitigate the off-target effect, without significantly compromising the on-target effect. The whole transcriptome profile analysis of cells transfected with siRNAs with or without Nindicates that siRNA-dN (with Ns on both the 2nd and the 18th bases of the guide strand) weakens the off-target effect by decreasing the unintended targets. The optimized siRNAs can be applied in the characterization of essential genes in cancer cells.

All site content, except where otherwise noted, is licensed under a Creative Commons Attribution 4.0 License.
PII: 4269

Publication Alerts

Post-Publication Promotion

Publication Discount

Research Papers:

siRNAs with decreased off-target effect facilitate the identification of essential genes in cancer cells

Abstract