Abstract
Functional gene screening is a basic strategy for identifying candidate genes that are responsible for biological processes of interest to researchers. RNA-mediated interference (RNAi)-based screening is one such approach. Although the knockdown technique using siRNA is widely accepted, careful evaluation is required to avoid false positive candidates as much as possible, because various cellular responses can be caused by events other than the target gene disruption. In this chapter, we introduce a method for a relatively small-scale siRNA screening that is capable of finding RNA binding proteins that regulate a specific RNA that is a structural component of a nuclear compartment.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Justice MJ, Noveroske JK, Weber JS, Zheng B, Bradley A (1999) Mouse ENU mutagenesis. Hum Mol Genet 8(10):1955–1963
Thibault ST, Singer MA, Miyazaki WY, Milash B, Dompe NA, Singh CM, Buchholz R, Demsky M, Fawcett R, Francis-Lang HL, Ryner L, Cheung LM, Chong A, Erickson C, Fisher WW, Greer K, Hartouni SR, Howie E, Jakkula L, Joo D, Killpack K, Laufer A, Mazzotta J, Smith RD, Stevens LM, Stuber C, Tan LR, Ventura R, Woo A, Zakrajsek I, Zhao L, Chen F, Swimmer C, Kopczynski C, Duyk G, Winberg ML, Margolis J (2004) A complementary transposon tool kit for Drosophila melanogaster using P and piggyBac. Nat Genet 36(3):283–287
Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2(2006):0008
Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A, Entian KD, Flaherty P, Foury F, Garfinkel DJ, Gerstein M, Gotte D, Guldener U, Hegemann JH, Hempel S, Herman Z, Jaramillo DF, Kelly DE, Kelly SL, Kotter P, LaBonte D, Lamb DC, Lan N, Liang H, Liao H, Liu L, Luo C, Lussier M, Mao R, Menard P, Ooi SL, Revuelta JL, Roberts CJ, Rose M, Ross-Macdonald P, Scherens B, Schimmack G, Shafer B, Shoemaker DD, Sookhai-Mahadeo S, Storms RK, Strathern JN, Valle G, Voet M, Volckaert G, Wang CY, Ward TR, Wilhelmy J, Winzeler EA, Yang Y, Yen G, Youngman E, Yu K, Bussey H, Boeke JD, Snyder M, Philippsen P, Davis RW, Johnston M (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418(6896):387–391
Moffat J, Grueneberg DA, Yang X, Kim SY, Kloepfer AM, Hinkle G, Piqani B, Eisenhaure TM, Luo B, Grenier JK, Carpenter AE, Foo SY, Stewart SA, Stockwell BR, Hacohen N, Hahn WC, Lander ES, Sabatini DM, Root DE (2006) A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 124(6):1283–1298
Echeverri CJ, Perrimon N (2006) High-throughput RNAi screening in cultured cells: a user’s guide. Nat Rev Genet 7(5):373–384
Gaj T, Gersbach CA, Barbas CF 3rd (2013) ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 31(7):397–405
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Hasegawa, Y., Nakagawa, S. (2015). siRNA Screening of Nuclear Proteins. In: Nakagawa, S., Hirose, T. (eds) Nuclear Bodies and Noncoding RNAs. Methods in Molecular Biology, vol 1262. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2253-6_21
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2253-6_21
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2252-9
Online ISBN: 978-1-4939-2253-6
eBook Packages: Springer Protocols