Abstract
The lack of specific pharmacological tools to interrogate the functional role of palmitoyl acyltransferases (zDHHCs) in mammalian cells has significantly hampered the understanding of this important gene family. Gene silencing by RNA interference (RNAi) is a process in eukaryotes that allows specific knockdown of the expression of proteins by targeting their coding mRNA. RNAi can thus be used as a proteomic tool to study the functional role of specific zDHHCs in cells by analyzing the effects of endogenous zDHHC knockdown on their protein targets or pathways. Here we describe the application of short interfering RNA (siRNA), a class of short (20–25 base pairs) double-stranded RNAs, to knockdown endogenous zDHHC enzymes expressed in human embryonic kidney (HEK293) cells and subsequent validation of knockdown efficiency using RT-qPCR to quantify zDHHC mRNA levels.
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References
Elbashir SM, Harborth J, Lendeckel W et al (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411(6836):494–498
Ipsaro JJ, Joshua-Tor L (2015) From guide to target: molecular insights into eukaryotic RNA-interference machinery. Nat Struct Mol Biol 22(1):20–28
Sioud M (2015) RNA interference: mechanisms, technical challenges, and therapeutic opportunities. Methods Mol Biol 1218:1–15
Carthew RW, Sontheimer EJ (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136(4):642–655
Licatalosi DD, Darnell RB (2010) RNA processing and its regulation: global insights into biological networks. Nat Rev Genet 11(1):75–87
Chamberlain LH, Shipston MJ (2015) The physiology of protein S-acylation. Physiol Rev 95(2):341–376
Greaves J, Chamberlain LH (2011) DHHC palmitoyl transferases: substrate interactions and (patho)physiology. Trends Biochem Sci 36(5):245–253
Fukata Y, Fukata M (2010) Protein palmitoylation in neuronal development and synaptic plasticity. Nat Rev Neurosci 11(3):161–175
Tafer H (2014) Bioinformatics of siRNA design. Methods Mol Biol 1097(Chapter 22):477–490
Naito Y, Ui-Tei K (2012) siRNA design software for a target gene-specific RNA interference. Front Genet 3:102
Tian L, McClafferty H, Knaus H-G, Ruth P, Shipston MJ (2012) Distinct acyl protein transferases and thioesterases control surface expression of calcium-activated potassium channels. J Biol Chem 287(18):14718–14725
Tian L, McClafferty H, Jeffries O, Shipston MJ (2010) Multiple palmitoyltransferases are required for palmitoylation-dependent regulation of large conductance calcium- and voltage-activated potassium channels. J Biol Chem 285(31):23954–23962
Tian L, Jeffries O, McClafferty H et al (2008) Palmitoylation gates phosphorylation-dependent regulation of BK potassium channels. Proc Natl Acad Sci U S A 105(52):21006–21011
Jeffries O, Geiger N, Rowe IC et al (2010) Palmitoylation of the S0-S1 linker regulates cell surface expression of voltage- and calcium-activated potassium (BK) channels. J Biol Chem 285(43):33307–33314
Shipston MJ, Tian L (2016) Posttranscriptional and posttranslational regulation of BK channels. Int Rev Neurobiol 128:91–126
Bustin SA, Benes V, Garson JA et al (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55(4):611–622
Thornton B, Basu C (2011) Real-time PCR (qPCR) primer design using free online software. Biochem Mol Biol Educ 39(2):145–154
Acknowledgments
This work is dedicated to the memory of our colleague Lijun Tian, who developed and optimized the siRNA approach in the laboratory, and died in service before the writing of this chapter. The work was supported by the Wellcome Trust, British Heart Foundation, and Diabetes UK.
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McClafferty, H., Shipston, M.J. (2019). siRNA Knockdown of Mammalian zDHHCs and Validation of mRNA Expression by RT-qPCR. In: Linder, M. (eds) Protein Lipidation. Methods in Molecular Biology, vol 2009. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9532-5_12
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DOI: https://doi.org/10.1007/978-1-4939-9532-5_12
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