Name: electrophoretic mobility shift assay (emsa) for the study of rna-protein interactions: the ire/irp example
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Description: Watch this Scientific Journal Video about Electrophoretic Mobility Shift Assay EMSA for the Study of RNA-Protein Interactions: The IRE/IRP Example at JoVE.com

This work was supported by a grant from the Canadian Institutes for Health Research (MOP-86514).

Experimental procedures with mice were approved by the Animal Care Committee of McGill University (protocol 4966).
1. Preparation of Protein Extracts from Cultured Cells
<ol>
	<li>Wash cultured cells twice with 10&#160;ml of ice-cold phosphate buffered saline (PBS).</li>
	<li>Scrape adherent cells with either a rubber policeman or a plastic cell scraper in 1&#160;ml of ice-cold PBS, transfer suspension into a 1.5&#160;ml microcentrifuge tube.</li>
	<li>Spin in a microcentrifuge for 5&#160;mi...

<ol>
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L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Iron-responsive+elements:+regulatory+RNA+sequences+that+control+mRNA+levels+and+translation.">Iron-responsive elements: regulatory RNA sequences that control mRNA levels and translation.</a> Science. 240, 924-928 (1988).</li><li>Dandekar, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+a+novel+iron-responsive+element+in+murine+and+human+erythroid+d-aminolevulinic+acid+synthase+mRNA.">Identification of a novel iron-responsive element in murine and human erythroid d-aminolevulinic acid synthase mRNA.</a> EMBO J. 10, 1903-1909 (1991).</li><li>Gray, N. K., Pantopoulos, K., Dandekar, T., Ackrell, B. A. C., Hentze, M. 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Biol. 14, 420-426 (2007).</li><li>Sanchez, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Iron+regulation+and+the+cell+cycle:+Identification+of+an+iron-responsive+element+in+the+3'-untranslated+region+of+human+cell+division+cycle+14A+mRNA+by+a+refined+microarray-based+screening+strategy.">Iron regulation and the cell cycle: Identification of an iron-responsive element in the 3'-untranslated region of human cell division cycle 14A mRNA by a refined microarray-based screening strategy.</a> J. Biol. Chem. 281, 22865-22874 (2006).</li><li>Santos, C. O., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+iron+responsive+element-like+stem-loop+regulates+alpha-hemoglobin-stabilizing+protein+mRNA.">An iron responsive element-like stem-loop regulates alpha-hemoglobin-stabilizing protein mRNA.</a> J Biol Chem. 283, 26956-26964 (2008).</li><li>Liu, Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Siderophore-mediated+iron+trafficking+in+humans+is+regulated+by+iron.">Siderophore-mediated iron trafficking in humans is regulated by iron.</a> J Mol Med (Berl. 90, 1209-1221 (2012).</li><li>Gray, N. K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recombinant+iron+regulatory+factor+functions+as+an+iron-responsive+element-binding+protein,+a+translational+repressor+and+an+aconitase.+A+functional+assay+for+translational+repression+and+direct+demonstration+of+the+iron+switch.">Recombinant iron regulatory factor functions as an iron-responsive element-binding protein, a translational repressor and an aconitase. A functional assay for translational repression and direct demonstration of the iron switch.</a> Eur. J. Biochem. 218, 657-667 (1993).</li><li>Bradford, M. 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B., Klausner, R. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Oxidation-reduction+and+the+molecular+mechanism+of+a+regulated+RNA-protein+interaction.">Oxidation-reduction and the molecular mechanism of a regulated RNA-protein interaction.</a> Science. 244, 357-359 (1989).</li><li>Meyron-Holtz, E. G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genetic+ablations+of+iron+regulatory+proteins+1+and+2+reveal+why+iron+regulatory+protein+2+dominates+iron+homeostasis.">Genetic ablations of iron regulatory proteins 1 and 2 reveal why iron regulatory protein 2 dominates iron homeostasis.</a> EMBO J. 23, 386-395 (2004).</li><li>Huang, F. W., Pinkus, J. L., Pinkus, G. S., Fleming, M. D., Andrews, N. 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Herein, we describe a protocol that has been developed to study the IRE-binding activities of IRP1 and IRP2, and we show representative data. By using different probes, this protocol can also be adjusted for the study of other RNA-binding proteins. A critical step is the size of the probe. Usage of long probes, which is common when the exact binding site is unknown, can result in RNA/protein complexes that do not migrate differently than the free RNA. In this case, it is advisable to remove unbound RNA by treatment with ...

The EMSA was originally developed to study the association of DNA-binding proteins with target DNA sequences1,2. The principle is similar for RNA/protein interactions3, which is the focus of this article. Briefly, RNA is negatively charged and will migrate towards the anode during non-denaturing electrophoresis in polyacrylamide (or agarose) gels. Migration within the gel depends on the size of the RNA, which is proportional to its charge. Specific binding of a protein to RNA alters its mobility, and the complex migrates slower compared to the free RNA. This is mainly due to an increase in the molecular mass, but also to alterations in the charge and possibly conformation. Utilizing a labeled RNA as probe allows easy monitoring of the &#8220;gel retardation&#8221; or &#8220;bandshift&#8221;. Usage of 32P-labeled RNA probes is very common and offers high sensitivity. The migration of RNA/protein complexes and free RNA are detected by autoradiography. Drawbacks are the short half-life of 32P (14.29 days), the gradual deterioration of the quality of the probe due to radiolysis, the requirement of a radioactivity license and infrastructure for radioactivity work, and potential biosafety concerns. Therefore, alternative non-isotopic methods for labeling the RNA probe have been developed, for instance with fluorophores or biotin, which enable detection by fluorescent or chemiluminescent imaging4,5. Limitations of these methods are the higher cost and often reduced sensitivity compared to isotopic labeling, and the potential of non-isotopic labels to interfere with the RNA/protein interaction. Non-denaturing polyacrylamide gels are suitable for most EMSA applications and are commonly used. On occasion, agarose gels may pose an alternative for the analysis of large complexes.
The major advantage of EMSA is that it combines simplicity, sensitivity, and robustness4. The assay can be completed within a few hours and does not require sophisticated instrumentation. RNA/protein interactions can be detected by EMSA at concentrations as low as 0.1 nM or less, and within a broad range of binding conditions (pH&#160;4.0 - 9.5, monovalent salt concentration 1 - 300&#160;mM, and temperature 0 - 60&#160;&#176;C).
RNA/protein complex formation can also be studied by the filter-binding assay. This is a simple, fast, and inexpensive procedure based on the retention of RNA/protein complexes in a nitrocellulose filter, while a free RNA probe passes through6. Compared to EMSA, it is limited in cases where the RNA probe contains multiple binding sites, or the crude extract contains more than one RNA-binding proteins that bind to the probe at the same site. While multiple RNA/protein interactions will escape detection by the filter-binding assay, they can be readily visualized by EMSA. In some cases, visualization is even possible when two RNA/protein complexes co-migrate (for instance, human IRP1/IRE and IRP2/IRE complexes), by adding an antibody against one of the RNA-binding proteins to the EMSA reaction, yielding further retardation on the gel (&#8220;supershift&#8221;)7.
The EMSA has been widely used to study IRP1 and IRP2, which are post-transcriptional regulators of iron metabolism8-10. They operate by binding to IREs, phylogenetically conserved hairpin structures within the UTRs of several mRNAs11. IREs were first discovered in the mRNAs encoding ferritin12 and transferrin receptor 1 (TfR1)13, proteins of iron storage and uptake, respectively. Later on, IREs were found in erythroid-specific aminolevulinate synthase (ALAS2)14, mitochondrial aconitase15, ferroportin16, divalent metal transporter 1 (DMT1)17, hypoxia inducible factor 2&#945; (HIF2&#945;)18, and other mRNAs19-21. The prototype H- and L-ferritin mRNAs contain one IRE in their 5&#8217; UTR, while TfR1 mRNA contains multiple IREs in its 3&#8217; UTR. IRE/IRP interactions specifically inhibit ferritin mRNA translation by sterically blocking its association of the 43S ribosomal subunit; moreover, they stabilize TfR1 mRNA against endonucleolytic cleavage. IRP1 and IRP2 share extensive sequence similarity and exhibit high IRE-binding activity in iron-starved cells. In iron-replete cells, IRP1 assembles a cubane Fe-S cluster that converts it to cytosolic aconitase at the expense of its IRE-binding activity, while IRP2 undergoes proteasomal degradation. Thus, the IRE/IRP interactions depend upon the cellular iron status, but are also regulated by other signals, such as H2O2, nitric oxide (NO) or hypoxia. Here, we describe the protocol for assessing IRE-binding activity from crude cell and tissue extracts by EMSA. We used a 32P-labeled H-ferritin IRE probe that was generated by in vitro transcription from a plasmid DNA template (I-12.CAT), where the IRE sequence was originally introduced in sense orientation downstream of the T7 RNA polymerase site by cloning of annealed synthetic oligonucleotides 22.

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			<td height="17" style="height:17px;width:195px;">Name of the Materials&#160;</td>
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			<td height="17" style="height:17px;">BioRad Protein Assay</td>
			<td>BIORAD</td>
			<td>500-0006</td>
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			<td height="17" style="height:17px;">T7 RNA polymerase</td>
			<td>Thermoscientific</td>
			<td>EPO111</td>
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			<td height="17" style="height:17px;">Rnase Inhibitor</td>
			<td>Invitrogen</td>
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			<td>Perkin-Elmer</td>
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			<td height="17" style="height:17px;">Scintillation liquid</td>
			<td>Beckman Coulter</td>
			<td align="right">141349</td>
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			<td height="17" style="height:17px;">heparin</td>
			<td>SIGMA</td>
			<td>H0777</td>
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			<td height="17" style="height:17px;">Rnase T1</td>
			<td>Thermoscientific</td>
			<td>EN0541</td>
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		<tr height="17">
			<td height="17" style="height:17px;"></td>
			<td></td>
			<td></td>
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			<td height="17" style="height:17px;">Name of the Equipments&#160;</td>
			<td>Company</td>
			<td>Catalog Number&#160;</td>
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			<td height="17" style="height:17px;">Tissue Ruptor</td>
			<td>Qiagen</td>
			<td align="right">9001271</td>
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			<td height="17" style="height:17px;">Scintillation counter</td>
			<td>Beckman Coulter</td>
			<td>LS6500</td>
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			<td height="17" style="height:17px;">Protean II xi Cell&#160;&#160;</td>
			<td>BIORAD</td>
			<td>165-1834</td>
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			<td height="17" style="height:17px;">20 wells combs 1.5mm thick</td>
			<td>BIORAD</td>
			<td>165-1868</td>
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			<td height="17" style="height:17px;">1.5 mm spacers</td>
			<td>BIORAD</td>
			<td>165-1849</td>
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		<tr height="17">
			<td height="17" style="height:17px;">PowerPac</td>
			<td>BIORAD</td>
			<td>164-5070</td>
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electrophoretic mobility shift assay (emsa) for the study of rna-protein interactions: the ire/irp example

RNA/protein interactions are critical for post-transcriptional regulatory pathways. Among the best-characterized cytosolic RNA-binding proteins are iron regulatory proteins, IRP1 and IRP2. They bind to iron responsive elements (IREs) within the untranslated regions (UTRs) of several target mRNAs, thereby controlling the mRNAs translation or stability. IRE/IRP interactions have been widely studied by EMSA. Here, we describe the EMSA protocol for analyzing the IRE-binding activity of IRP1 and IRP2, which can be generalized to assess the activity of other RNA-binding proteins as well. A crude protein lysate containing an RNA-binding protein, or a purified preparation of this protein, is incubated with an excess of32 P-labeled RNA probe, allowing for complex formation. Heparin is added to preclude non-specific protein to probe binding. Subsequently, the mixture is analyzed by non-denaturing electrophoresis on a polyacrylamide gel. The free probe migrates fast, while the RNA/protein complex exhibits retarded mobility; hence, the procedure is also called &#8220;gel retardation&#8221; or &#8220;bandshift&#8221; assay. After completion of the electrophoresis, the gel is dried and RNA/protein complexes, as well as free probe, are detected by autoradiography. The overall goal of the protocol is to detect and quantify IRE/IRP and other RNA/protein interactions. Moreover, EMSA can also be used to determine specificity, binding affinity, and stoichiometry of the RNA/protein interaction under investigation.

A radiolabeled IRE probe was prepared, as described in sections 3 and 4 of the protocol. The sequence of the probe was 5&#39;-GGGCGAAUUC GAGCUCGGUA CCCGGGGAUC CUGCUUCAAC AGUGCUUGGA CGGAUCCU-3&#39;; the bolded nucleotides represent an unpaired C residue and the loop, which are critical IRE features. The specific radioactivity of the probe was 4.5 x 109 cpm/&#956;g of RNA.
To assess the effects of iron perturbations on IRE-binding activity, murine RAW...

Watch this Scientific Journal Video about Electrophoretic Mobility Shift Assay EMSA for the Study of RNA-Protein Interactions: The IRE/IRP Example at JoVE.com

Electrophoretic Mobility Shift Assay EMSA for the Study of RNA-Protein Interactions: The IRE/IRP Example

Here we present a protocol to analyze RNA/protein interactions. The electrophoretic mobility shift assay (EMSA) is based on the differential migration of RNA/protein complexes and free RNA during native gel electrophoresis. By using a radiolabeled RNA probe, RNA/protein complexes can be visualized by autoradiography.

Electrophoretic Mobility Shift Assay (EMSA) for the Study of RNA-Protein Interactions: The IRE/IRP Example

RNA/protein interactions are critical for post-transcriptional regulatory pathways. Among the best-characterized cytosolic RNA-binding proteins are iron ...

Research

JoVE Journal

Biology

Testing Visual Sensitivity to the Speed and Direction of Motion in Lizards

Testing visual sensitivity in any species provides basic information regarding behaviour, evolution, and ecology. However, testing specific features of ...

Optimized Fibrin Gel Bead Assay for the Study of Angiogenesis

Angiogenesis is a complex multi-step process, where, in response to angiogenic stimuli, new vessels are created from the existing vasculature.  These ...

Computer-Generated Animal Model Stimuli

Communication between animals is diverse and complex. Animals may communicate using auditory, seismic, chemosensory, electrical, or visual signals. In ...

Do-It-Yourself Device for Recovery of Cryopreserved Samples Accidentally Dropped into Cryogenic Storage Tanks

Liquid nitrogen is colorless, odorless, extremely cold (-196 &deg;C) liquid kept under pressure. It is commonly used as a cryogenic fluid for long term ...

A Liquid Phase Affinity Capture Assay Using Magnetic Beads to Study Protein-Protein Interaction: The Poliovirus-Nanobody Example

In this article, a simple, quantitative, liquid phase affinity capture assay is presented. Provided that one protein can be tagged and another protein ...

The MultiBac Protein Complex Production Platform at the EMBL

Proteomics  research revealed the impressive complexity of eukaryotic proteomes in  unprecedented detail. It is now a commonly accepted notion that ...

Budding Yeast Protein Extraction and Purification for the Study of Function, Interactions, and Post-translational Modifications

Homogenization by bead beating is a fast and efficient way to release DNA, RNA, proteins, and metabolites from budding yeast cells, which are notoriously ...

Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions

The paper describes the combination of optical tweezers and single molecule fluorescence detection for the study of protein-DNA interaction. The method ...

Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo

Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo

Intricate gene regulatory networks orchestrate biological processes and developmental transitions in plants. Selective transcriptional activation and ...

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Population and family-based genetic studies typically result in the identification of genetic variants that are statistically associated with a clinical ...