Abstract
RNAi screening has gained popularity in recent years, due to its usefulness in systematic investigations of biological pathways. Combined with high-content screening and advances in imaging and analysis methods, it can enable detailed genetic characterization of cellular processes such as protein glycosylation, a major function of the Golgi apparatus. Glycosylation concerns about one third of all human proteins and regulates various cellular behaviors. Yet the methods available to study it are limited and not easily accessible. In this chapter, we detail a step-by-step method to systematically and quantitatively investigate glycosylation using fluorescent lectin staining, following high-throughput RNAi-based downregulation of gene activities. We also provide a workflow for downstream analysis of the data generated.
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References
Moffat J, Sabatini DM (2006) Building mammalian signalling pathways with RNAi screens. Nat Rev Mol Cell Biol 7(3):177–187, Nature Publishing Group
Falschlehner C, Steinbrink S, Erdmann G, Boutros M (2010) High-throughput RNAi screening to dissect cellular pathways: a how-to guide. Biotechnol J 5(4):368–376
Mohr SE, Perrimon N (2012) RNAi screening: new approaches, understandings, and organisms. Wiley Interdiscip Rev RNA 3(2):145–158
Taylor DL (2010) A personal perspective on high-content screening (HCS): from the beginning. J Biomol Screen 15(7):720–725
Fuchs F, Pau G, Kranz D, Sklyar O, Budjan C, Steinbrink S et al (2010) Clustering phenotype populations by genome-wide RNAi and multiparametric imaging. Mol Syst Biol 6:1–13
Ohtsubo K, Marth JD (2006) Glycosylation in cellular mechanisms of health and disease. Cell 126(5):855–867
Varki A, Cummings RD, Esko JD, Freeze HH, Stanley P, Bertozzi CR et al (2009) Structural analysis of glycans, 2nd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
Sharon N (2004) History of lectins: from hemagglutinins to biological recognition molecules. Glycobiology 14(11):53R–62R
Varki A, Cummings RD, Esko JD, Freeze HH, Stanley P, Bertozzi CR et al (2009) Antibodies and lectins in glycan analysis, 2nd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
Torres BV, McCrumb DK, Smith DF (1988) Glycolipid-lectin interactions: reactivity of lectins from Helix pomatia, Wisteria floribunda, and Dolichos biflorus with glycolipids containing N-acetylgalactosamine. Arch Biochem Biophys 262(1):1–11
Piller V, Piller F, Cartron JP (1990) Comparison of the carbohydrate-binding specificities of seven N-acetyl-D-galactosamine-recognizing lectins. Eur J Biochem 191(2):461–466
Swamy MJ, Gupta D, Mahanta SK, Surolia A (1991) Further characterization of the saccharide specificity of peanut (Arachis hypogaea) agglutinin. Carbohydr Res 213:59–67
Brockhausen I (2006) Mucin-type O-glycans in human colon and breast cancer: glycodynamics and functions. EMBO Rep 7(6):599–604
Bennett EP, Mandel U, Clausen H, Gerken TA, Fritz TA, Tabak LA (2012) Control of mucin-type O-glycosylation: a classification of the polypeptide GalNAc-transferase gene family. Glycobiology 22(6):736–756
Debray H, Decout D, Strecker G, Spik G, Montreuil J (1981) Specificity of twelve lectins towards oligosaccharides and glycopeptides related to N-glycosylproteins. Eur J Biochem 117(1):41–55
Miyoshi E, Moriwaki K, Nakagawa T (2007) Biological function of fucosylation in cancer biology. J Biochem 143(6):725–729
Kaladas PM, Kabat EA, Iglesias JL, Lis H, Sharon N (1982) Immunochemical studies on the combining site of the D-galactose/N-acetyl-D-galactosamine specific lectin from Erythrina cristagalli seeds. Arch Biochem Biophys 217(2):624–637
Cummings RD, Kornfeld S (1982) Characterization of the structural determinants required for the high affinity interaction of asparagine-linked oligosaccharides with immobilized Phaseolus vulgaris leukoagglutinating and erythroagglutinating lectins. J Biol Chem 257(19):11230–11234
Schwarz RE, Wojciechowicz DC, Park PY, Paty PB (1996) Phytohemagglutinin-L (PHA-L) lectin surface binding of N-linked beta 1–6 carbohydrate and its relationship to activated mutant ras in human pancreatic cancer cell lines. Cancer Lett 107(2):285–291
Crowley JF, Goldstein IJ, Arnarp J, Lönngren J (1984) Carbohydrate binding studies on the lectin from Datura stramonium seeds. Arch Biochem Biophys 231(2):524–533
Cummings RD, Kornfeld S (1984) The distribution of repeating [Gal beta 1,4GlcNAc beta 1,3] sequences in asparagine-linked oligosaccharides of the mouse lymphoma cell lines BW5147 and PHAR 2.1. J Biol Chem 259(10):6253–6260
Sun Q, Kang X, Zhang Y, Zhou H, Dai Z, Lu W et al (2009) DSA affinity glycoproteome of human liver tissue. Arch Biochem Biophys 484(1):24–29
Geisler C, Jarvis DL (2011) Effective glycoanalysis with Maackia amurensis lectins requires a clear understanding of their binding specificities. Glycobiology 21(8):988–993
Chia J, Goh G, Racine V, Ng S, Kumar P, Bard F (2012) RNAi screening reveals a large signaling network controlling the Golgi apparatus in human cells. Mol Syst Biol 8:629
Rinderle SJ, Goldstein IJ, Matta KL, Ratcliffe RM (1989) Isolation and characterization of amaranthin, a lectin present in the seeds of Amaranthus caudatus, that recognizes the T- (or cryptic T)-antigen. J Biol Chem 264(27):16123–16131
Gill DJ, Chia J, Senewiratne J, Bard F (2010) Regulation of O-glycosylation through Golgi-to-ER relocation of initiation enzymes. J Cell Biol 189(5):843–858
Chia J, Tham KM, Gill DJ, Bard-Chapeau EA, Bard FA (2014) ERK8 is a negative regulator of O-GalNAc glycosylation and cell migration. Elife 3:e01828
Gill DJ, Tham KM, Chia J, Wang SC, Steentoft C, Clausen H et al (2013) Initiation of GalNAc-type O-glycosylation in the endoplasmic reticulum promotes cancer cell invasiveness. Proc Natl Acad Sci 110(34):E3152–E3161
Cullen BR (2006) Enhancing and confirming the specificity of RNAi experiments. Nat Cell Biol 3(9):677–681
Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O et al (2006) Cell Profiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol 7(10):R100
Kumar P, Goh G, Wongphayak S, Moreau D, Bard F (2013) ScreenSifter: analysis and visualization of RNAi screening data. BMC Bioinformatics 14:290
Boutros M, Brás LP, Huber W (2006) Analysis of cell-based RNAi screens. Genome Biol 7(7):R66
Birmingham A, Selfors LM, Forster T, Wrobel D, Kennedy CJ, Shanks E et al (2009) Statistical methods for analysis of high-throughput RNA interference screens. Nat Methods 6(8):569–575
Chung N, Zhang XD, Kreamer A, Locco L, Kuan P-F, Bartz S et al (2008) Median absolute deviation to improve hit selection for genome-scale RNAi screens. J Biomol Screen 13(2):149–158
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Goh, G.Y., Bard, F.A. (2015). RNAi Screens for Genes Involved in Golgi Glycosylation. In: Tang, B. (eds) Membrane Trafficking. Methods in Molecular Biology, vol 1270. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2309-0_28
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DOI: https://doi.org/10.1007/978-1-4939-2309-0_28
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