Name: mission esirna for rnai screening in mammalian cells
Uploaded: 2010-05-12T17:45:00
Duration: 15 min 31 s
Description: Watch this Scientific Journal Video about MISSION esiRNA for RNAi Screening in Mammalian Cells at JoVE.com

We would like to acknowledge members of the Buchholz laboratory and the Sigma-Aldrich RNAi-team for discussion. We would like to thank the Max Planck Society and the Bundesministerium f&uuml;r Bildung und Forschung grands Go-Bio [0315105] for support.
MISSION &reg; is a registered trademark of Sigma-Aldrich Biotechnology L.P.

1. High-quality MISSION esiRNA libraries
<ol>
	<li>For every gene of interest the most susceptible and specific target region for RNAi is chosen utilizing the DEQOR algorithm (http://cluster-1.mpi-cbg.de/Deqor/deqor.html).4 DEQOR scores the silencing potential of all possible 21 nucleotides long siRNAs in a target-mRNA based on state-of-the art design-constraints4. In addition, each potential siRNA is analyzed for possible cross-reactivity with other genes by performing a BLAST search against the transcriptome of the organism studied. The program thereby provides an analysis of the overall quality and cross-silencing capacities of the potential esiRNA (300-600 bp length).</li>
	<li>The chosen region of the target-gene cDNA is amplified by PCR using gene-specific primers flanked by bacteriophage RNA-polymerase-promoter sequences.</li>
	<li>Every PCR product used for MISSION esiRNA production is verified for identity by sequencing and for purity by Caliper Labchip analysis.</li>
	<li>Long double-stranded RNA is transcribed from the PCR-product by RNA polymerase, followed by an annealing of the transcribed strands.</li>
	<li>esiRNAs are prepared by limited enzymatic digestion of the long double-stranded RNA using RNaseIII followed by purification via anion-exchange chromatography utilizing Q-sepharose spin columns.</li>
	<li>esiRNAs are precipitated and resuspended in TE buffer. The yield is measured by UV-absorption measurements and the concentration is adjusted by dissolving in an appropriate volume of TE buffer. The overall quality of the final product is checked by Caliper Labchip analysis.</li>
</ol>
2. Choosing a cell line and optimizing transfection for screening
<ol>
	<li>Titrate amounts of esiRNA (use Eg5 as positive and renilla-luciferase as negative control) and increasing amounts of transfection reagent in a 384-well plate, add cells and incubate for 48 hours. Eg5 is a kinesin motor protein required for bipolar spindle assembly and depletion leads to a mitotic arrest. Repeat this procedure for different transfection reagents and cell lines. Here, we use HeLa cells cultured following standard procedures and oligofectamine (Invitrogen) as transfection reagent.</li>
	<li>For choosing the optimal transfection conditions count the cells transfected with Eg5 esiRNAs that show a mitotic arrest (round shape) and the total number of cells transfected with renilla-luciferase (RLUC) esiRNA by light microscopy. Choose the condition with the least toxicity for RLUC and the most pronounced phenotype for Eg5. An alternative method for optimizing transfection conditions involves a stable cell line expressing EGFP (or another suitable reporter gene) under the control of a constitutive active promoter. After transfection of an esiRNA against EGFP (or another reporter gene) and RLUC (or another suitable negative control esiRNA) measure knock-down efficacy and toxicity by e.g. fluorescence assisted cell sorting (FACS). Make sure that the used esiRNA for EGFP is fully complementary to the target-mRNA.</li>
</ol>
3. Setting Up the Primary screen5,6
<ol>
	<li>Optimize the pipetting accuracy for all used components on an automated pipetting station (e.g. Aquarius, Tecan and WellMate, Matrix). Because pipetting parameters change depending on the type of solution, volume and plate type this optimization has to be repeated for every step separately. If possible, the pipetting station should be placed under a laminar flow hood to avoid contaminations. All used components should be sanitized before use either by autoclaving if applicable or by spraying with 75% ethanol. Optimize wash-protocols so that cross-contamination from well to well is excluded. Details for the optimization of automated pipetting cannot be give for space-constraints and depend largely on the utilized pipetting station. For further information refer to the manufactures protocol.</li>
	<li>Transfect cells in 384-well format using the optimized conditions from above with esiRNAs for Eg5 and RLUC. Use an alternating pattern for Eg5 and RLUC esiRNA covering the whole plate.</li>
	<li>After incubation for 48 hours fix the cells with cold 100% ethanol, rehydrate in PBS for 15 minutes, stain for 25 minutes in PBS containing 1 &mu;g/ml DAPI and 100 &mu;g/ml RNase A (Qiagen). Finally wash with PBS and store at 4&deg;C.</li>
	<li>Measure intensity of DAPI-fluorescence by microscopy e.g. on an Olympus ScanR system. Generate a histogram by plotting DAPI intensity against cell number and evaluate the cell cycle distribution by calculating the percentage of cells with the DNA-content 2N for G1-phase; &lt; 2N &gt; 4N for S-phase; 4N for G2/M-phase and &gt; 4N for aneuploidy/polyploidy.</li>
	<li>Evaluate the homogeneity of the results over the plate. Further optimization is needed if results differ significantly to exclude position effects. A common problem when using multi-well plates is enhanced evaporation at the edge wells during incubation time. This leads to different experimental conditions in different wells, which often translates to plate-position specific effects. For this reason, we recommend to leave all edge wells empty for a screen. To further minimize evaporation make sure that the incubators are kept at high humidity. We also routinely employ evaporation barriers such as Corning Breathable Sealing Tape which block evaporation. Also other resources for position effects have to be taken into consideration, e.g. technical variation of the readout system (microscope, plate reader, etc) or variations in liquid handling (gradients, inhomogeneity of solutions, etc).</li>
	<li>The statistical differences between positive and negative controls provide a measure for the significance of the assay employed. A large difference between negative control (or background noise; mock-control) and sample has to be established before starting the actual screening. A good measure for the statistical significance is the Z-factor. The Z-factor is calculated following the equation: 
 Z = 1- (3 SD[sample] + 3 SD[mock]) * (|Av[sample] - Av[mock]|)-1; with SD: standard deviation; Av: average. A Z-factor of 1 &gt; Z &gt; 0.5 indicates a statistically significant separation of negative controls (and noise) from the positive controls7.</li>
</ol>
4. Primary screen
<ol>
	<li>Prepare 384-well tissue culture plates for transfection of esiRNAs utilizing the optimized conditions from above. Here, we use 15ng esiRNA per well dissolved in 5&mu;l TE buffer. At least eight control positions per plate should be loaded with suitable positive and negative controls for the biological process studied (here: Eg5 and RLUC). To avoid position effects the edge wells are loaded with 5&mu;l TE buffer only.</li>
	<li>Add 5&mu;l OptiMEM (Invitrogen) containing 0.2&mu;l Oligofectamine per well, mix and incubate for 20 minutes at room temperature.</li>
	<li>Add cell suspension onto the transfection mixture (here: 40&mu;l of a HeLa cell suspension at 25 cells/&mu;l concentration; equivalent to 1000 cells per well) and incubate for 72 hours.</li>
	<li>Measure DNA-content on an automated microscope (Olympus ScanR, see above). Evaluate using Z-score statistics for hit selection: Z-scores are calculated for all sample esiRNAs using the signal for the negative control as reference. Note, the Z-score is not the same as the Z-factor. Z-scores provide a statistical measure for significance of sample values in comparison to a (mock-) control. It is calculated following the equation: 
 Z = (value[Sample] - average[mock]) * standard-deviation[mock]-1. 
 For hit selection a threshold has to be applied. Typically, a significance criteria like: 2 &lt; Z &lt; -2 is used, but depending on the quality of the dataset, the studied biological process or simply the scope of the screen, different thresholds may be applicable. Beside the fairly easy Z-score statistics also more elaborate mathematical evaluation methods can be used (a first inside into the wide field of statistical evaluation of screening data can be found in Malo et al.8).</li>
</ol>
5. Secondary screen and hit validation
<ol>
	<li>A secondary screen follows the primary screen to eliminate false positives due to experimental errors or off-target effects. For the selected hits the same procedure as used in the primary screen should be repeated for a bigger number of replicates (3-5) to allow a better statistical evaluation.</li>
	<li>For verified hits a secondary non-overlapping esiRNA (or another non-overlapping silencing trigger) against the targets identified in the initial screens should be used. The same assay and read-out should be applied as for the primary screen.</li>
	<li>Ultimately the selected genes can be validated by cross-species RNAi rescue9. Thereby a bacterial artificial chromosome (BAC) encoding e.g. the mouse ortholog of the gene is stably transfected into cells. BAC-constructs preserve a gene in its genomic context and allow for a nearly-physiological expression. RNAi against the endogenous human gene will leave the mouse transgene expression unaltered which rescues the RNAi-phenotype. RNAi-rescue provides the gold-standard for the verification of RNAi phenotypes available to date.</li>
	<li>Finally, the validated candidates are studied in more detail to eventually derive mechanistic understanding. In many cases RNAi can be used in these experiments, e.g. in secondary, more elaborate assays.</li>
</ol>

<ol>
	<li>Ghildiyal, M., Zamore, P. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Small+silencing+RNAs:+an+expanding+universe.">Small silencing RNAs: an expanding universe.</a> Nat Rev Genet. 10, 94-108 (2009).</li><li>Jackson, A. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Expression+profiling+reveals+off-target+gene+regulation+by+RNAi.">Expression profiling reveals off-target gene regulation by RNAi.</a> Nat Biotechnol. 21, 635-637 (2003).</li><li>Echeverri, C. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Minimizing+the+risk+of+reporting+false+positives+in+large-scale+RNAi+screens.">Minimizing the risk of reporting false positives in large-scale RNAi screens.</a> Nat Methods. 3, 777-779 (2006).</li><li>Henschel, A., Buchholz, F., Habermann, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DEQOR:+a+web-based+tool+for+the+design+and+quality+control+of+siRNAs.">DEQOR: a web-based tool for the design and quality control of siRNAs.</a> Nucleic Acids Res. 32, W113-W120 (2004).</li><li>Kittler, R., Pelletier, L., Buchholz, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Systems+biology+of+mammalian+cell+division.">Systems biology of mammalian cell division.</a> Cell Cycle. 7, 2123-2128 (2008).</li><li>Kittler, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genome-scale+RNAi+profiling+of+cell+division+in+human+tissue+culture+cells.">Genome-scale RNAi profiling of cell division in human tissue culture cells.</a> Nat Cell Biol. 9, 1401-1412 (2007).</li><li>Zhang, J. H., Chung, T. D., Oldenburg, K. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Simple+Statistical+Parameter+for+Use+in+Evaluation+and+Validation+of+High+Throughput+Screening+Assays.">A Simple Statistical Parameter for Use in Evaluation and Validation of High Throughput Screening Assays.</a> J Biomol Screen. 4, 67-73 (1999).</li><li>Malo, N., Hanley, J. A., Cerquozzi, S., Pelletier, J., Nadon, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Statistical+practice+in+high-throughput+screening+data+analysis.">Statistical practice in high-throughput screening data analysis.</a> Nat Biotechnol. 24, 167-175 (2006).</li><li>Kittler, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA+interference+rescue+by+bacterial+artificial+chromosome+transgenesis+in+mammalian+tissue+culture+cells.">RNA interference rescue by bacterial artificial chromosome transgenesis in mammalian tissue culture cells.</a> Proc Natl Acad Sci U S A. 102, 2396-2401 (2005).</li><li>Kittler, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genome-wide+resources+for+endoribonuclease-prepared+short+interfering+RNAs+for+specific+loss-of-function+studies.">Genome-wide resources for endoribonuclease-prepared short interfering RNAs for specific loss-of-function studies.</a> Nat Methods. 4, 337-344 (2007).</li></ol>

Authors declare financial relationships with commercial entities that might have an interest in the submitted work.

RNA interference has become a standard technique to study loss-of-function phenotypes. Large-scale collections of RNAi-mediators are available from different suppliers and provide an easy, cost-effective and rapid method for gene-silencing. This opened the gate for systematic screening for key-players in many biological processes allowing a genome-scale perspective on a wide range of different species and cell types.
High false positive and false negative rates are a common challenge in RNAi screens. To address this problem, considerable efforts have been invested to improve the efficacy and in particular the specificity of the silencing triggers. An important discovery was that a pool of different siRNAs targeting the same transcript greatly enhances target specificity. Because a very complex pool of different siRNAs is produced by the endoribonuclease, esiRNAs are high target specificity triggers, reducing the false positive rate in RNAi screens. esiRNAs have also demonstrated to achieve efficient knockdowns, reducing also the false negative rate.
Because RNAi screens are technically demanding, they will likely remain challenging to perform on a routine basis for some time. However, as reagents and instruments get better and more laboratories share their expertise, the use of RNAi screens in modern biology are deemed to increase in the future.

<table border="1">
<tr>
<td>Material Name</td>
<td>Type</td>
<td>Company</td>
<td>Catalogue Number</td>
<td>Comments</td>
</tr>	
<tr>
<td>MISSION esiRNA</td>
<td>&nbsp;</td>
<td>Sigma-Aldrich</td>
<td>&nbsp;</td>
<td>For additional information contact: rnai@sial.com</td>
</tr>
<tr>
<td>Wellmate</td>
<td>&nbsp;</td>
<td>ThermoScientific</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>Breathable sealing tape</td>
<td>&nbsp;</td>
<td>Corning</td>
<td>Breathable Sealing Tape, Sterile (Product #3345)</td>
<td>&nbsp;</td>
<tr>
<td>OptiMEM</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td><a href="http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&N4=E7023|SIAL&N5=SEARCH_CONCAT_PNO|BRAND_KEY&F=SPEC&cm_sp=affiliate-_-Jove-_-12346">Ethanol</a></td>
<td>&nbsp;</td>
<td>Sigma-Aldrich</td>
<td>E7023</td>
<td>200 proof (absolute), for molecular biology</td>
</tr>
<tr>
<td><a href="http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&N4=P5493|SIGMA&N5=SEARCH_CONCAT_PNO|BRAND_KEY&F=SPEC&cm_sp=affiliate-_-Jove-_-12347">Phosphate buffered saline</a></td>
<td>&nbsp;</td>
<td>Sigma-Aldrich</td>
<td>P5493</td>
<td>BioReagent, 10x concentrate, suitable for cell culture, for molecular biology</td>
</tr>
<tr>
<td><a href="http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&N4=D8417|SIGMA&N5=SEARCH_CONCAT_PNO|BRAND_KEY&F=SPEC&cm_sp=affiliate-_-Jove-_-12348">4&#x2032;,6-Diamidino-2-phenylindole dihydrochloride</a></td>
<td>&nbsp;</td>
<td>Sigma-Aldrich</td>
<td>D8417</td>
<td>Poweder, BioReagent, suitable for cell culture, >98% (HPLC and TLC)</td>
</tr>
<tr>
<td><a href="http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&N4=R6513|SIGMA&N5=SEARCH_CONCAT_PNO|BRAND_KEY&F=SPEC&cm_sp=affiliate-_-Jove-_-12349">Ribonuclease A from bovine pancreas</a></td>
<td>&nbsp;</td>
<td>Sigma-Aldrich</td>
<td>R6513</td>
<td>For molecular biology, &ge;70 Kunitz units/mg protein, lyophilized powder</td>
</tr>
<tr>
<td><a href="http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&N4=T9285|SIGMA&N5=SEARCH_CONCAT_PNO|BRAND_KEY&F=SPEC&cm_sp=affiliate-_-Jove-_-12350">Tris-EDTA buffer solution</a></td>
<td>&nbsp;</td>
<td>Sigma-Aldrich</td>
<td>T9285
</td>
<td>100 x, for molecular biology</td>
</tr>
</table>

mission esirna for rnai screening in mammalian cells

RNA interference (RNAi) is a basic cellular mechanism for the control of gene expression. RNAi is induced by short double-stranded RNAs also known as small interfering RNAs (siRNAs). The short double-stranded RNAs originate from longer double stranded precursors by the activity of Dicer, a protein of the RNase III family of endonucleases. The resulting fragments are components of the RNA-induced silencing complex (RISC), directing it to the cognate target mRNA. RISC cleaves the target mRNA thereby reducing the expression of the encoded protein1,2,3. RNAi has become a powerful and widely used experimental method for loss of gene function studies in mammalian cells utilizing small interfering RNAs.
Currently two main methods are available for the production of small interfering RNAs. One method involves chemical synthesis, whereas an alternative method employs endonucleolytic cleavage of target specific long double-stranded RNAs by RNase III in vitro. Thereby, a diverse pool of siRNA-like oligonucleotides is produced which is also known as endoribonuclease-prepared siRNA or esiRNA. A comparison of efficacy of chemically derived siRNAs and esiRNAs shows that both triggers are potent in target-gene silencing. Differences can, however, be seen when comparing specificity. Many single chemically synthesized siRNAs produce prominent off-target effects, whereas the complex mixture inherent in esiRNAs leads to a more specific knockdown10.
In this study, we present the design of genome-scale MISSION esiRNA libraries and its utilization for RNAi screening exemplified by a DNA-content screen for the identification of genes involved in cell cycle progression. We show how to optimize the transfection protocol and the assay for screening in high throughput. We also demonstrate how large data-sets can be evaluated statistically and present methods to validate primary hits. Finally, we give potential starting points for further functional characterizations of validated hits.

Watch this Scientific Journal Video about MISSION esiRNA for RNAi Screening in Mammalian Cells at JoVE.com

MISSION esiRNA for RNAi Screening in Mammalian Cells

Here we use a human esiRNA library in a high-throughput screen for genes involved in cell division. We demonstrate how to set up and conduct an esiRNA screens, as well as how to analyze and validate the results.

RNA interference (RNAi) is a basic cellular mechanism for the control of gene expression. RNAi is induced by short double-stranded RNAs also known as ...

mission-esirna-for-rnai-screening-in-mammalian-cells

Research

JoVE Journal

Biology

Protocol for RNAi Assays in Adult Mosquitoes (A. gambiae)

Reverse genetic approaches have proven extremely useful for determining  which genes underly resistance to vector pathogens in mosquitoes.  This video protocol illustrates a method used by the Dimopoulos lab to inject dsRNA into Anopheles gambiae mosquitoes, which harbor the malaria parasite.  The technique manipulating the injection setup and injecting dsRNA into the thorax is illustrated.

Protocol for RNAi Assays in Adult Mosquitoes A. gambiae

Reverse genetic approaches have proven extremely useful for determining which genes underly resistance to vector pathogens in mosquitoes. This video protocol illustrates a method used by the Dimopoulos lab to inject dsRNA into Anopheles gambiae mosquitoes, which harbor the malaria parasite. The technique manipulating the injection setup and injecting dsRNA into the thorax is illustrated.

Reverse genetic approaches have proven extremely useful for determining  which genes underly resistance to vector pathogens in mosquitoes.  This video ...

Bacterial Delivery of RNAi Effectors: Transkingdom RNAi

RNA interference (RNAi) represents a high effective mechanism for specific inhibition of mRNA expression. Besides its potential as a powerful laboratory tool, the RNAi pathway appears to be promising for therapeutic utilization. For development of RNA interference (RNAi)-based therapies, delivery of RNAi-mediating agents to target cells is one of the major obstacles. A novel strategy to overcome this hurdle is transkingdom RNAi (tkRNAi). This technology uses non-pathogenic bacteria, e.g. Escherichia coli, to produce and deliver therapeutic short hairpin RNA (shRNA) into target cells to induce RNAi. A first-generation tkRNAi-mediating vector, TRIP, contains the bacteriophage T7 promoter for expression regulation of a therapeutic shRNA of interest. Furthermore, TRIP has the Inv locus from Yersinia pseudotuberculosis that encodes invasin, which permits natural noninvasive bacteria to enter &beta;1-integrin-positive mammalian cells and the HlyA gene from Listeria monocytogenes, which produces listeriolysin O. This enzyme allows the therapeutic shRNA to escape from entry vesicles within the cytoplasm of the target cell. TRIP constructs are introduced into a competent non-pathogenic Escherichia coli strain, which encodes T7 RNA polymerase necessary for the T7 promoter-driven synthesis of shRNAs. A well-characterized cancer-associated target molecule for different RNAi strategies is ABCB1 (MDR1/P-glycoprotein, MDR1/P-gp). This ABC-transporter acts as a drug extrusion pump and mediates the "classical" ABCB1-mediated multidrug resistance (MDR) phenotype of human cancer cells which is characterized by a specific cross resistance pattern. Different ABCB1-expressing MDR cancer cells were treated with anti-ABCB1 shRNA expression vector bearing E. coli. This procedure resulted in activation of the RNAi pathways within the cancer cells and a considerable down regulation of the ABCB1 encoding mRNA as well as the corresponding drug extrusion pump. Accordingly, drug accumulation was enhanced in the pristine drug-resistant cancer cells and the MDR phenotype was reversed. By means of this model the data provide the proof-of-concept that tkRNAi is suitable for modulation of cancer-associated factors, e.g. ABCB1, in human cancer cells.

For development of RNA interference (RNAi)-based therapies, a novel strategy was developed, transkingdom RNAi (tkRNAi). This technology uses non-pathogenic bacteria to produce and deliver therapeutic short hairpin RNA (shRNA) into target cells. Here, tkRNAi was successfully applied for reversal of classical ABCB1-mediated multidrug resistance (MDR) of cancer cells.

RNA interference (RNAi) represents a high effective mechanism for specific inhibition of mRNA expression. Besides its potential as a powerful laboratory ...

Mutagenesis and Functional Analysis of Ion Channels Heterologously Expressed in Mammalian Cells

We will demonstrate how to study the functional effects of introducing a point mutation in an ion channel. We study G protein-gated inwardly rectifying potassium (referred to as GIRK) channels, which are important for regulating the excitability of neurons. There are four different mammalian GIRK channel subunits (GIRK1-GIRK4) - we focus on GIRK2 because it forms a homotetramer. Stimulation of different types of G protein-coupled receptors (GPCRs), such as the muscarinic receptor (M2R), leads to activation of GIRK channels. Alcohol also directly activates GIRK channels. We will show how to mutate one amino acid by specifically changing one or more nucleotides in the cDNA for the GIRK channel. This mutated cDNA sequence will be amplified in bacteria, purified, and the presence of the point mutation will be confirmed by DNA sequencing. The cDNAs for the mutated and wild-type GIRK channels will be transfected into human embryonic kidney HEK293T cells cultured in vitro. Lastly, whole-cell patch-clamp electrophysiology will be used to study the macroscopic potassium currents through the ectopically expressed wild-type or mutated GIRK channels. In this experiment, we will examine the effect of a L257W mutation in GIRK2 channels on M2R-dependent and alcohol-dependent activation.

We will demonstrate how to study the effect of a single point mutation on the function of an ion channel.

We will demonstrate how to study the functional effects of introducing a point mutation in an ion channel. We study G protein-gated inwardly rectifying ...

MISSION LentiPlex Pooled shRNA Library Screening in Mammalian Cells

RNA interference (RNAi) is an intrinsic cellular mechanism for the regulation of gene expression. Harnessing the innate power of this system enables us to knockdown gene expression levels in loss of gene function studies.
There are two main methods for performing RNAi. The first is the use of small interfering RNAs (siRNAs) that are chemically synthesized, and the second utilizes short-hairpin RNAs (shRNAs) encoded within plasmids 1. The latter can be transfected into cells directly or packaged into replication incompetent lentiviral particles. The main advantages of using lentiviral shRNAs is the ease of introduction into a wide variety of cell types, their ability to stably integrate into the genome for long term gene knockdown and selection, and their efficacy in conducting high-throughput loss of function screens. To facilitate this we have created the LentiPlex pooled shRNA library.
The MISSION LentiPlex Human shRNA Pooled Library is a genome-wide lentiviral pool produced using a proprietary process. The library consists of over 75,000 shRNA constructs from the TRC collection targeting 15,000+ human genes 2. Each library is tested for shRNA representation before product release to ensure robust library coverage. The library is provided in a ready-to-use lentiviral format at titers of at least 5 x 108 TU/ml via p24 assay and is pre-divided into ten subpools of approximately 8,000 shRNA constructs each. Amplification and sequencing primers are also provided for downstream target identification.
Previous studies established a synergistic antitumor activity of TRAIL when combined with Paclitaxel in A549 cells, a human lung carcinoma cell line 3, 4. In this study we demonstrate the application of a pooled LentiPlex shRNA library to rapidly conduct a positive selection screen for genes involved in the cytotoxicity of A549 cells when exposed to TRAIL and Paclitaxel. One barrier often encountered with high-throughput screens is the cost and difficulty in deconvolution; we also detail a cost-effective polyclonal approach utilizing traditional sequencing.

Here we use a human LentiPlex pooled library and traditional sequencing methods to identify gene targets promoting cell survival. We demonstrate how to set up and deconvolute a LentiPlex screen and validate the results.

RNA interference (RNAi) is an intrinsic cellular mechanism for the regulation of gene expression. Harnessing the innate power of this system enables us to ...

RNAi Screening to Identify Postembryonic Phenotypes in C. elegans

C. elegans has proven to be a valuable model system for the discovery and functional characterization of many genes and gene pathways1. More sophisticated tools and resources for studies in this system are facilitating continued discovery of genes with more subtle phenotypes or roles. 
Here we present a generalized protocol we adapted for identifying C. elegans genes with postembryonic phenotypes of interest using RNAi2. This procedure is easily modified to assay the phenotype of choice, whether by light or fluorescence optics on a dissecting or compound microscope. This screening protocol capitalizes on the physical assets of the organism and molecular tools the C. elegans research community has produced. As an example, we demonstrate the use of an integrated transgene that expresses a fluorescent product in an RNAi screen to identify genes required for the normal localization of this product in late stage larvae and adults. First, we used a commercially available genomic RNAi library with full-length cDNA inserts. This library facilitates the rapid identification of multiple candidates by RNAi reduction of the candidate gene product. Second, we generated an integrated transgene that expresses our fluorecently tagged protein of interest in an RNAi-sensitive background. Third, by exposing hatched animals to RNAi, this screen permits identification of gene products that have a vital embryonic role that would otherwise mask a post-embryonic role in regulating the protein of interest. Lastly, this screen uses a compound microscope equipped for single cell resolution.

RNAi Screening to Identify Postembryonic Phenotypes in C. elegans

We describe a sensitized method to identify postembryonic regulators of protein expression and localization in C. elegans using an RNAi-based genomic screen and an integrated transgene that expresses a functional, fluorescently tagged protein.

C. elegans has proven to be a valuable model system for the discovery and functional characterization of many genes and gene pathways1. More sophisticated ...

Analysis of Cell Cycle Position in Mammalian Cells

The regulation of cell proliferation is central to tissue morphogenesis during the development of multicellular organisms. Furthermore, loss of control of cell proliferation underlies the pathology of diseases like cancer. As such there is great need to be able to investigate cell proliferation and quantitate the proportion of cells in each phase of the cell cycle. It is also of vital importance to indistinguishably identify cells that are replicating their DNA within a larger population. Since a cell&prime;s decision to proliferate is made in the G1 phase immediately before initiating DNA synthesis and progressing through the rest of the cell cycle, detection of DNA synthesis at this stage allows for an unambiguous determination of the status of growth regulation in cell culture experiments.
DNA content in cells can be readily quantitated by flow cytometry of cells stained with propidium iodide, a fluorescent DNA intercalating dye. Similarly, active DNA synthesis can be quantitated by culturing cells in the presence of radioactive thymidine, harvesting the cells, and measuring the incorporation of radioactivity into an acid insoluble fraction. We have considerable expertise with cell cycle analysis and recommend a different approach. We Investigate cell proliferation using bromodeoxyuridine/fluorodeoxyuridine (abbreviated simply as BrdU) staining that detects the incorporation of these thymine analogs into recently synthesized DNA. Labeling and staining cells with BrdU, combined with total DNA staining by propidium iodide and analysis by flow cytometry1 offers the most accurate measure of cells in the various stages of the cell cycle. It is our preferred method because it combines the detection of active DNA synthesis, through antibody based staining of BrdU, with total DNA content from propidium iodide. This allows for the clear separation of cells in G1 from early S phase, or late S phase from G2/M. Furthermore, this approach can be utilized to investigate the effects of many different cell stimuli and pharmacologic agents on the regulation of progression through these different cell cycle phases.
In this report we describe methods for labeling and staining cultured cells, as well as their analysis by flow cytometry. We also include experimental examples of how this method can be used to measure the effects of growth inhibiting signals from cytokines such as TGF-&beta;1, and proliferative inhibitors such as the cyclin dependent kinase inhibitor, p27KIP1. We also include an alternate protocol that allows for the analysis of cell cycle position in a sub-population of cells within a larger culture5. In this case, we demonstrate how to detect a cell cycle arrest in cells transfected with the retinoblastoma gene even when greatly outnumbered by untransfected cells in the same culture. These examples illustrate the many ways that DNA staining and flow cytometry can be utilized and adapted to investigate fundamental questions of mammalian cell cycle control.

Determining the cell cycle position of a population of cells, or understanding how signals affect proliferation, can be readily measured by flow cytometry using this protocol. We report a simple experimental approach to staining cells and quantifying their position in the cell cycle.

The regulation of cell proliferation is central to tissue morphogenesis during the development of multicellular organisms. Furthermore, loss of control of ...

Visualization of Endoplasmic Reticulum Localized mRNAs in Mammalian Cells

In eukaryotes, most of the messenger RNAs (mRNAs) that encode secreted and membrane proteins are localized to the surface of the endoplasmic reticulum (ER). However, the visualization of these mRNAs can be challenging. This is especially true when only a fraction of the mRNA is ER-associated and their distribution to this organelle is obstructed by non-targeted (i.e. "free") transcripts. In order to monitor ER-associated mRNAs, we have developed a method in which cells are treated with a short exposure to a digitonin extraction solution that selectively permeabilizes the plasma membrane, and thus removes the cytoplasmic contents, while simultaneously maintaining the integrity of the ER. When this method is coupled with fluorescent in situ hybridization (FISH), one can clearly visualize ER-bound mRNAs by fluorescent microscopy. Using this protocol the degree of ER-association for either bulk poly(A) transcripts or specific mRNAs can be assessed and even quantified. In the process, one can use this assay to investigate the nature of mRNA-ER interactions.

Here we describe a method to visualize endoplasmic reticulum-associated mRNAs in mammalian tissue culture cells. This technique involves the selective permeabilization of the plasma membrane with digitonin to remove cytoplasmic contents followed by fluorescent in situ hybridization to detect either bulk poly(A) mRNA or specific transcripts.

In eukaryotes, most of the messenger RNAs (mRNAs) that encode secreted and membrane proteins are localized to the surface of the endoplasmic reticulum ...

siRNA Screening to Identify Ubiquitin and Ubiquitin-like System Regulators of Biological Pathways in Cultured Mammalian Cells

Post-translational modification of proteins with ubiquitin and ubiquitin-like molecules (UBLs) is emerging as a dynamic cellular signaling network that regulates diverse biological pathways including the hypoxia response, proteostasis, the DNA damage response and transcription.&#160; To better understand how UBLs regulate pathways relevant to human disease, we have compiled a human siRNA &#8220;ubiquitome&#8221; library consisting of 1,186 siRNA duplex pools targeting all known and predicted components of UBL system pathways. This library can be screened against a range of cell lines expressing reporters of diverse biological pathways to determine which UBL components act as positive or negative regulators of the pathway in question.&#160; Here, we describe a protocol utilizing this library to identify ubiquitome-regulators of the HIF1A-mediated cellular response to hypoxia using a transcription-based luciferase reporter.&#160; An initial assay development stage is performed to establish suitable screening parameters of the cell line before performing the screen in three stages: primary, secondary and tertiary/deconvolution screening. &#160;The use of targeted over whole genome siRNA libraries is becoming increasingly popular as it offers the advantage of reporting only on members of the pathway with which the investigators are most interested.&#160; Despite inherent limitations of siRNA screening, in particular false-positives caused by siRNA off-target effects, the identification of genuine novel regulators of the pathways in question outweigh these shortcomings, which can be overcome by performing a series of carefully undertaken control experiments.

Here, we describe a methodology to perform a targeted siRNA &#8220;ubiquitome&#8221; screen to identify novel ubiquitin and ubiquitin-like regulators of the HIF1A-mediated cellular response to hypoxia.&#160; This can be adapted to any biological pathway where a robust read out of reporter activity is available.

Post-translational modification of proteins with ubiquitin and ubiquitin-like molecules (UBLs) is emerging as a dynamic cellular signaling network that ...

Measurement of Heme Synthesis Levels in Mammalian Cells

Heme serves as the prosthetic group for a wide variety of proteins known as hemoproteins, such as hemoglobin, myoglobin and cytochromes. It is involved in various molecular and cellular processes such as gene transcription, translation, cell differentiation and cell proliferation. The biosynthesis levels of heme vary across different tissues and cell types and is altered in diseased conditions such as anemia, neuropathy and cancer. This technique uses [4-14C] 5-aminolevulinic acid ([14C] 5-ALA), one of the early precursors in the heme biosynthesis pathway to measure the levels of heme synthesis in mammalian cells. This assay involves incubation of cells with [14C] 5-ALA followed by extraction of heme and measurement of the radioactivity incorporated into heme. This procedure is accurate and quick. This method measures the relative levels of heme biosynthesis rather than the total heme content. To demonstrate the use of this technique the levels of heme biosynthesis were measured in several mammalian cell lines.

Altered intracellular heme levels are associated with common diseases such as cancer. Thus, there is a need to measure heme biosynthesis levels in diverse cells. The goal of this protocol is to provide a fast and sensitive method to measure and compare the levels of heme synthesis in different cells.

Heme serves as the prosthetic group for a wide variety of proteins known as hemoproteins, such as hemoglobin, myoglobin and cytochromes. It is involved in ...

Massively Parallel Reporter Assays in Cultured Mammalian Cells

The genetic reporter assay is a well-established and powerful tool for dissecting the relationship between DNA sequences and their gene regulatory activities. The potential throughput of this assay has, however, been limited by the need to individually clone and assay the activity of each sequence on interest using protein fluorescence or enzymatic activity as a proxy for regulatory activity. Advances in high-throughput DNA synthesis and sequencing technologies have recently made it possible to overcome these limitations by multiplexing the construction and interrogation of large libraries of reporter constructs. This protocol describes implementation of a Massively Parallel Reporter Assay (MPRA) that allows direct comparison of hundreds of thousands of putative regulatory sequences in a single cell culture dish.

The genetic reporter assay is a well-established and powerful tool for dissecting the relationship between DNA sequences and their gene regulatory activities. Coupling candidate regulatory elements to reporter genes that carry identifying sequence tags enables massive parallelization of these assays.