Computational detection and suppression of sequence-specific off-target phenotypes from whole genome RNAi screens

Nucleic Acids Research

Volumn 42, Issue 13, 2014, Pages 8214-8222

  Zhong, Rui ^a,b   Kim, Jimi ^b   Kim, Hyun Seok ^b,c   Kim, Minsoo ^a,b,d   Lum, Lawrence ^b   Levine, Beth ^e,f   Xiao, Guanghua ^a,b   White, Michael A ^b   Xie, Yang ^a,b  

^a Quantitative Biomedical Research Center   (United States)

^b Department of Clinical Sciences ^*  (United States)

^c Yonsei University College of Medicine   (South Korea)

^d UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^e Center for Autophagy Research   (United States)

^f HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC RNA; SMALL INTERFERING RNA;

3' UNTRANSLATED REGION; ALGORITHM; ARTICLE; CELL VIABILITY; COMPUTER INTERFACE; CONTROLLED STUDY; DATA ANALYSIS; DENATURATION; FUNCTIONAL GENOMICS; GENE TARGETING; HIGH THROUGHPUT SEQUENCING; MOLECULAR LIBRARY; PHENOTYPE; PRIORITY JOURNAL; RNA ANALYSIS; RNA INTERFERENCE; RNA SEQUENCE;

ALGORITHMS; BASE SEQUENCE; CELL LINE; GENOMICS; HUMANS; MICRORNAS; RNA INTERFERENCE; RNA, SMALL INTERFERING;

EID: 84905588593     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku306     Document Type: Article

References (13)

1. Whitehurst, A.W., Bodemann, B.O., Cardenas, J., Ferguson, D., Girard, L., Peyton, M., Minna, J.D., Michnoff, C., Hao, W., Roth, M.G. et al. (2007) Synthetic lethal screen identification of chemosensitizer loci in cancer cells. Nature, 446, 815-819.
2. Orvedahl, A., Sumpter, R. Jr, Xiao, G., Ng, A., Zou, Z., Tang, Y., Narimatsu, M., Gilpin, C., Sun, Q., Roth, M. et al. (2011) Image-based genome-wide siRNA screen identifies selective autophagy factors. Nature, 480, 113-117.
3. Ward, S.E., Kim, H.S., Komurov, K., Mendiratta, S., Tsai, P.L., Schmolke, M., Satterly, N., Manicassamy, B., Forst, C.V., Roth, M.G. et al. (2012) Host modulators of H1N1 cytopathogenicity. PLoS One, 7, e39284.
4. Tang, W., Dodge, M., Gundapaneni, D., Michnoff, C., Roth, M. and Lum, L. (2008) A genome-wide RNAi screen for Wnt/beta-catenin pathway components identifies unexpected roles for TCF transcription factors in cancer. Proc. Natl. Acad. Sci. U.S.A., 105, 9697-9702.
5. Kim, H.S., Mendiratta, S., Kim, J., Pecot, C.V., Larsen, J.E., Zubovych, I., Seo, B.Y., Kim, J., Eskiocak, B., Chung, H. et al. (2013) Systematic identification of molecular subtype-selective vulnerabilities in non-small cell lung cancer. Cell., 155, 552-566.
6. Birmingham, A., Anderson, E.M., Reynolds, A., Ilsley-Tyree, D., Leake, D., Fedorov, Y., Baskerville, S., Maksimova, E., Robinson, K., Karpilow, J. et al. (2006) 3' UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat. Methods, 3, 199-204.
7. Jackson, A.L., Burchard, J., Schelter, J., Chau, B.N., Cleary, M., Lim, L. and Linsley, P.S. (2006) Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity. RNA, 12, 1179-1187.
8. Sigoillot, F.D., Lyman, S., Huckins, J.F., Adamson, B., Chung, E., Quattrochi, B. and King, R.W. (2012) A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens. Nat. Methods, 9, 363-366.
9. Buehler, E., Khan, A.A., Marine, S., Rajaram, M., Bahl, A., Burchard, J. and Ferrer, M. (2012) siRNA off-target effects in genome-wide screens identify signaling pathway members. Sci. Rep., 2, 428.
10. Bartel, D.P. (2009) MicroRNAs: target recognition and regulatory functions. Cell, 136, 215-233.
11. Singh, N.K., Seo, B.Y., Vidyasagar, M., White, M.A. and Kim, H.S. (2013) siMacro: A fast and easy data processing tool for cell-based genomewide siRNA screens. Genomics Inform., 11, 55-57.
12. Shao, D.D., Tsherniak, A., Gopal, S., Weir, B.A., Tamayo, P., Stransky, N., Schumacher, S.E., Zack, T.I., Beroukhim, R., Garraway, L.A. et al. (2013) ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens. Genome Res., 23, 665-678.
13. Marine, S., Bahl, A., Ferrer, M. and Buehler, E. (2012) Common seed analysis to identify off-target effects in siRNA screens. J. Biomol. Screen., 17, 370-378.