Najmeh Nikpour and Fiona Alum provided suggestions and edited this manuscript. Department of Biochemistry at McGill University supported HM and VM with the CIHR Training Initiative in Chemical Biology. This work was supported by Canadian Institute of Health Research (CIHR) grant 119464 (to R. S.).

The protocol below describes the procedure for performing the fluorescence-based RNA editing assay. The assay can be performed in a single PCR tube, 96-well, or 384-well plates depending on the scope of the experiment. Subsequently the fluorescence signal can be read on a suitable real time PCR detection system. The assay here is described in the context of 384-well plates.
1. Culturing T. brucei Cells
<ol>
	<li>Prepare a growth medium for T. brucei procyclic form cells. For 1 L of medium:
	<ol>
		<li>Dissolve 25.4 g SDM-79 powder in 800 ml miliQ water.</li>
		<li>Add 2 g of NaHCO3 and pH to 7.3 with 10 M NaOH.</li>
		<li>Add nanopure water to a final volume of 900 ml, filter sterilize.</li>
		<li>Add Fetal Bovine Serum (FBS), penicillin-streptomycin solution and hemin (2.5 mg/ml) to final concentrations of 10% (v/v), 100 U/ml and 7.5 mg/L respectively.</li>
	</ol>
	</li>
	<li>Grow 300 ml of T. brucei 1.7A wild type (procyclic form) cells at 28 &#176;C, shaking at 70 rpm to a density of 1.5 x 107 cells/ml. NOTE: This should produce 3 ml of active editosome with ~0.5 mg of total protein, sufficient for 600 editing reactions.</li>
	<li>Harvest the cells by centrifugation at 6,000 x g for 10 min at 4 &#176;C.</li>
	<li>Wash the pellet with 50 ml of chilled PBSG buffer (10 mM Na2HPO4, 10 mM NaH2PO4, 145 mM NaCl, and 6 mM glucose), and spin down the cells again by centrifugation at 10,000 x g for 10 min at 4 &#176;C.</li>
</ol>
2. Isolation of Crude Mitochondria
NOTE: All the steps should be performed on ice or at 4 &#176;C to preserve editosome activity.
<ol>
	<li>Resuspend the harvested cells in 30 ml of DTE buffer (1 mM Tris-HCl pH 8.0 and 1 mM EDTA). Use a 40 ml sterile Dounce homogenizer (pre-chilled) to disrupt the cell membrane by stroking up and down at least 10 times on ice.</li>
	<li>Immediately add 4.3 ml of 60% sucrose (w/v; i.e. 1.75 M) to the homogenate to a final concentration of 0.25 M. Centrifuge at 15,800 x g for 10 min at 4 &#176;C, to preferentially bring down mitochondria.</li>
	<li>Resuspend the mitochondrial pellet in 4.6 ml of STM buffer (20 mM Tris-HCl pH 8.0, 250 mM sucrose and 2 mM MgCl2). Add 13.8 &#956;l of 0.1 M CaCl2 and 4 &#956;l of RNase-free DNase I to final concentrations of 0.3 mM and 9 U/ml, respectively. Incubate the mixture for 1 hr on ice.</li>
	<li>Add 4.6 ml of STE buffer (20 mM Tris-HCl pH 8.0, 250 mM sucrose and 2 mM EDTA) to inactivate the DNase I. Centrifuge at 15,800 x g for 10 min at 4 &#176;C.</li>
	<li>Resuspend the pellet in 400 &#956;l of lysis buffer (10 mM Tris-HCl pH 7.2, 10 mM MgCl2, 100 mM KCl, 1 &#181;g/ml pepstatin, 1 mM DTT, and 1x complete EDTA-free protease inhibitor) and transfer to a microfuge tube.</li>
	<li>Add 10% Triton X-100 to a final concentration of 1% and incubate the lysate for 15 min at 4 &#176;C on a tube rotator.</li>
	<li>Clear the mitochondrial lysate by centrifuging twice at 17,000 x g for 15 min at 4&#160;&#176;C; retaining the cleared supernatant each time.</li>
</ol>
3. Editosome Purification
<ol>
	<li>Pour a 10 ml 10%-30% (v/v) linear glycerol gradient (Table 1) in an ultracentrifuge tube using 2x HHE gradient buffer (40 mM HEPES pH 7.9, 20 mM Mg(OAc)2, 100 mM KCl, and 2 mM EDTA) and a gradient maker by following the instruction manual.</li>
	<li>Carefully remove 500 &#956;l of solution from the top of the glycerol gradient and gently load 500 &#956;l of the cleared mitochondrial lysate. Spin at 178,000 x g for 6 hr at 4 &#176;C using an ultracentrifuge.</li>
	<li>Collect 500 &#181;l fractions sequentially from the top to the bottom of the gradient at 4 &#176;C. Then snap freeze the fractions using liquid nitrogen and store at -80 &#176;C until usage.</li>
</ol>
4. RNA Preparation
<ol>
	<li>Anneal the respective DNA template containing sequence complementary to T7 promoter sequence (Table 2) with a T7 promoter oligonucleotide (5&#8217;-TAATACGACTCACTATAGGG-3&#8217;) in a 1:1 molar ratio by heating at 90 &#176;C for 3 min and cooling at RT for at least 10 min.</li>
	<li>Transcribe RNA using an in vitro transcription kit by following the instruction manual.</li>
	<li>Stop the transcription reaction by adding equal volume of 7 M urea dye (7 M urea, 0.05% Xylene Cynol, and 0.05% Bromophenol blue). Run on a filter sterilized 9% denaturing polyacrylamide gel (9% acrylamide, 7 M urea, 1x TBE) .</li>
	<li>Use the ultraviolet (UV) shadowing with a shortwave UV lamp to locate and excise respective RNA. Place the excised gel piece in a microfuge tube and add 400 &#181;l of gel elution buffer (20 mM Tris-HCl pH 7.5, 250 mM NaOAc, 1 mM EDTA and 0.25% SDS). Elute overnight at RT on a tube rotator.</li>
	<li>Precipitate the eluted RNA by adding 1 ml of cold 100% ethanol and incubating either at -80 &#176;C for 30 min or -20 &#176;C overnight.</li>
	<li>Centrifuge at 16,000 x g for 30 min at 4 &#176;C, to pellet down the RNA.</li>
	<li>Wash the pellet with 1 ml of 75% ethanol. Centrifuge at 16,000 x g for 20 min at 4 &#176;C.</li>
	<li>Resuspend the RNA pellet appropriately in RNase free water to achieve the desired concentrations, as shown in Table 2.</li>
</ol>
5. Fluorescence-based RNA Editing Assay
<ol>
	<li>For a single reaction, combine 1 pmol (1 &#181;l) of preA6Rbz and 2.5 pmol (1 &#181;l) of gA6Rbz (1:2.5 molar ratio) in a microfuge tube, incubate at 70 &#186;C for 3 min and let it sit at RT for at least 10 min.</li>
	<li>Meanwhile prepare a master mix using Table 3, without the preA6Rbz and gA6Rbz, for the editing reaction containing 1x HHE buffer (25 mM HEPES pH 7.9, 10 mM Mg(OAc)2, 50 mM KCl and 10 mM EDTA), 1 mM ATP, 5 mM CaCl2, 16 ng/&#181;l of Torula yeast RNA, 0.1% Triton X-100, and the purified editosome.</li>
	<li>Add annealed preA6Rbz and gA6Rbz to complete the master mix.</li>
	<li>Dispense 18 &#181;l of the master mix (Table 3) into wells containing either 2 &#181;l of RNase-free water (wells with no compounds) or 2 &#181;l of 200 &#181;M chemical compounds and include control samples in the plate according to Figure 5.</li>
	<li>Seal the plate with a plate sealer and spin the plate down, to remove any air bubbles. Incubate at 28 &#176;C for 4 hr.</li>
	<li>Add 25 pmol (2 &#181;l) of gA6Rbz competitor to each well. Place a fresh sealer, spin the plate down and place it on a real-time PCR machine. Program the following experiment: 
	Step 1: 85 &#176;C for 5 min; Step 2: 24 &#176;C for 10 min; Step 3: Stop.</li>
	<li>Add 15 pmol (1 &#181;l) of FRET substrate to each well to a final volume of 23 &#181;l. Seal the plate with a fresh sealer. Quickly spin the plate and place it back on the real-time PCR machine.</li>
	<li>Program a new experiment with the following steps: 
	Step 1: 37 &#176;C for 1 min; Step 2: Read; Step 3: Go to Step 1, 40 times; Step 4: Stop.</li>
	<li>Setup the plate by selecting all the wells that require reading and choose the FAM filter. Input volume as 23 &#956;l and start the run.</li>
	<li>Calculate the slope of the values obtained from each well/sample to obtain a kinetic measurement by plotting the slopes on a bar graph for analysis. NOTE: A kinetic read improves the signal-to-noise ratio between the sample and the background; as the background sample would have a slope close to zero. An end point reading has higher background noise.</li>
</ol>

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D., Stuart, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA+editing:+transfer+of+genetic+information+from+gRNA+to+precursor+mRNA+in+vitro.">RNA editing: transfer of genetic information from gRNA to precursor mRNA in vitro.</a> Science. 266, 114-117 (1994).</li><li>Weng, J., 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=Guide+RNA-binding+complex+from+mitochondria+of+trypanosomatids.">Guide RNA-binding complex from mitochondria of trypanosomatids.</a> Molecular. 32, 198-209 (2008).</li><li>Hashimi, H., Zikova, A., Panigrahi, A. K., Stuart, K. 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The authors have nothing to disclose.

A novel high-throughput screening method to identify inhibitors against the RNA editing complex of Trypanosomes was presented, providing a new tool for drug discovery to counter diseases caused by trypanosomatids. FRET-based ribozyme assay has been extensively used for different purposes20-22; however, we have utilized the capacity of FRET-based ribozyme assay for in vitro monitoring of RNA editing activity19. This assay could potentially be adapted to other types of RNA editing in eukaryot...

The process of RNA editing, a post-transcriptional mRNA modification, was first discovered in trypanosomatids1. Since then, substantial work has been conducted in studying the mechanism behind RNA editing in Trypanosoma brucei2,3. In a series of enzymatic reactions, the editosome, a core complex of about 20 proteins, creates mature mitochondrial mRNAs for multiple components of the energy generating oxidative phosphorylation system. The order of catalytic events is endonucleolytic cleavage, uridylate (U) addition or deletion, and ligation, as dictated by guide RNAs (gRNAs)4.
In addition to the core editosome complex proteins, a number of accessory factors have also been identified5-7. These proteins are mostly seen grouped in independent complexes. However, the order of protein assembly in the core editosome complex and the interaction patterns of the core complex with the accessory complexes are yet to be determined. Targeting the RNA editing process in trypanosomatids may provide chemical dissectors that aid in studying the assembly and function of the editosome complex. Furthermore, functional studies on several editosome proteins have shown essentiality across different life stages, indicating their potential as drug targets8-12. Therefore, the found inhibitors of the editosome may also act as lead compounds against trypanosomatids. This is timely, as drugs currently available against diseases caused by trypanosomatid are toxic, inefficient and expensive13,14.
An efficient and convenient in vitro assay is necessary to explore the chemical universe for specific inhibitors that block RNA editing. Three assays have been developed and used to monitor editosome activities: (a) full round in vitro RNA editing assay15, (b) pre-cleaved in vitro RNA editing assay16,17, and (c) hammerhead ribozyme (HHR)-based assay18. The first two assays rely on direct visualization of the edited product (ATPase 6 mRNA) with the help of radioactivity. The HHR-based assay uses a modified version of the ATPase 6 mRNA that is modeled to behave as a ribozyme upon editing. The functional ribozyme then specifically cleaves a radiolabeled RNA substrate, serving as a reporter. Recently, Moshiri et al. developed a &#8216;mix and measure&#8217; HHR-based in vitro reporter assay to monitor RNA editing where the radiolabeled RNA substrate is replaced with a fluorescence resonance energy transfer (FRET) substrate19. The principle advantages of this assay are: (a) it is a rapid and convenient mix and measure type of assay, as the production of active ribozyme and substrate cleavage occur simultaneously in the same tube in low volume (i.e. 20 &#956;l), (b) it avoids the use of radioactively labeled materials, (c) sensitivity that is afforded by fluorescence instrumentation in a micro-titer plate format, and (d) a high signal to noise ratio. Using this assay, the effect of known RNA editing ligase inhibitors against purified editosome was confirmed19. This experiment validated the assay for rapid identification of RNA editing inhibitors, primarily against whole editosomes from T. brucei.
Figure 1 is a detailed step-by-step schematic of the fluorescence-based in vitro RNA editing assay. This protocol can either be used for monitoring RNA editing in vitro or easily be adapted for screening compound libraries of various scales.

<table border="0" cellpadding="0" cellspacing="0" width="979">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:391px;">Name of Material/ Equipment</td>
			<td style="width:203px;">Company</td>
			<td style="width:139px;">Catalog Number</td>
			<td style="width:248px;">Comments/Description</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">SDM-79 Medium</td>
			<td>Gibco by life technologies</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="23">
			<td height="23" style="height:23px;">Fetal Bovine Serum</td>
			<td>life technologies</td>
			<td style="width:139px;">12483-020</td>
			<td>heat inactivation at 550C for 1 h</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:391px;">Hemin, minimum 80%</td>
			<td style="width:203px;">Sigma</td>
			<td style="width:139px;">H5533-10G</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:391px;">Penicillin-Streptomycin Sollution</td>
			<td style="width:203px;">Fisher Scientific</td>
			<td style="width:139px;">MT-30-002-CI</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:391px;">Dnase 1 recombinant, Rnase Free&#160;</td>
			<td style="width:203px;">Roche</td>
			<td style="width:139px;">4716728001</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:391px;">T7 RiboMax Express Large&#160; scale RNA&#160; production system</td>
			<td style="width:203px;">Promega</td>
			<td style="width:139px;">P1320</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:391px;">Kimble Kontes Dounce Tissue Grinders&#160;&#160;</td>
			<td style="width:203px;">Fisher Scientific</td>
			<td style="width:139px;">K885300-0040&#160;&#160;</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:391px;">Gradient Master, ver 5.25&#160;</td>
			<td style="width:203px;">Biocomp</td>
			<td style="width:139px;">107-201M</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:391px;">Ultra Clear Tube, 13.2ML</td>
			<td style="width:203px;">Beckman Coulter</td>
			<td style="width:139px;">344059</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:391px;">Optima L-100XP&#160; Ultracentrifuge&#160;</td>
			<td style="width:203px;">Beckman Coulter</td>
			<td style="width:139px;">392052</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:391px;">SW 41 Ti ROTOR</td>
			<td style="width:203px;">Beckman Coulter</td>
			<td style="width:139px;">331336</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:391px;">MicroSeal &#39;B&#39; Seal, Seals</td>
			<td style="width:203px;">Biorad</td>
			<td style="width:139px;">MSB1001</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:391px;">CFX 384 Touch Real-Time PCR Detection System</td>
			<td style="width:203px;">Biorad</td>
			<td style="width:139px;">185-5484</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:391px;">Acryl/Bis solution (19: 1), 40% (w/v)</td>
			<td style="width:203px;">Bio Basic</td>
			<td style="width:139px;">A0006-500ML</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:391px;">Urea, Molecular biology grade, 1Kg</td>
			<td style="width:203px;">life technologies</td>
			<td style="width:139px;">AM9902</td>
			<td style="width:248px;"></td>
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rna catalyst as a reporter for screening drugs against rna editing in trypanosomes

Substantial progress has been made in determining the mechanism of mitochondrial RNA editing in trypanosomes. Similarly, considerable progress has been made in identifying the components of the editosome complex that catalyze RNA editing. However, it is still not clear how those proteins work together. Chemical compounds obtained from a high-throughput screen against the editosome may block or affect one or more steps in the editing cycle. Therefore, the identification of new chemical compounds will generate valuable molecular probes for dissecting the editosome function and assembly. In previous studies, in vitro editing assays were carried out using radio-labeled RNA. These assays are time consuming, inefficient and unsuitable for high-throughput purposes. Here, a homogenous fluorescence-based &#8220;mix and measure&#8221; hammerhead ribozyme in vitro reporter assay to monitor RNA editing, is presented. Only as a consequence of RNA editing of the hammerhead ribozyme a fluorescence resonance energy transfer (FRET) oligoribonucleotide substrate undergoes cleavage. This in turn results in separation of the fluorophore from the quencher thereby producing a signal. In contrast, when the editosome function is inhibited, the fluorescence signal will be quenched. This is a highly sensitive and simple assay that should be generally applicable to monitor in vitro RNA editing or high throughput screening of chemicals that can inhibit the editosome function.

To demonstrate the necessary steps required for setting up a large-scale screen, Figures 2-5 are representative control experiments related to the quality of the assay. These are essential control experiments for a consistent assay over several days of screening or for comparison of different screens.
Assessing the Fluorescence Signal-to-noise Ratio
To ensure the stability and quality of the &#64258;uorescein-labeled oligoribonucleo...

Watch this Scientific Journal Video about RNA Catalyst as a Reporter for Screening Drugs against RNA Editing in Trypanosomes at JoVE.com

RNA Catalyst as a Reporter for Screening Drugs against RNA Editing in Trypanosomes

A highly sensitive ribozyme-based assay, applicable to high-throughput screening of chemicals targeting the unique process of RNA editing in trypanosomatid pathogens, is described in this paper. Inhibitors can be used as tools for hypothesis-driven analysis of the RNA editing process and ultimately as therapeutics.

Substantial progress has been made in determining the mechanism of mitochondrial RNA editing in trypanosomes. Similarly, considerable progress has been ...

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JoVE Journal

Biology

8.4K vues.  McGill University. A highly sensitive ribozyme-based assay, applicable to high-throughput screening of chemicals targeting the unique process of RNA editing in trypanosomatid pathogens, is described in this paper. Inhibitors can be used as tools for hypothesis-driven analysis of the RNA editing process and ultimately as therapeutics.

Vidéo: RNA Catalyst as a Reporter for Screening Drugs against RNA Editing in Trypanosomes

Visualizing RNA Localization in Xenopus Oocytes

RNA localization is a conserved mechanism of establishing cell polarity. Vg1 mRNA localizes to the vegetal pole of Xenopus laevis oocytes and acts to spatially restrict gene expression of Vg1 protein. Tight control of Vg1 distribution in this manner is required for proper germ layer specification in the developing embryo. RNA sequence elements in the 3' UTR of the mRNA, the Vg1 localization element (VLE) are required and sufficient to direct transport. To study the recognition and transport of Vg1 mRNA in vivo, we have developed an imaging technique that allows extensive analysis of trans-factor directed transport mechanisms via a simple visual readout. 
To visualize RNA localization, we synthesize fluorescently labeled VLE RNA and microinject this transcript into individual oocytes. After oocyte culture to allow transport of the injected RNA, oocytes are fixed and dehydrated prior to imaging by confocal microscopy. Visualization of mRNA localization patterns provides a readout for monitoring the complete pathway of RNA transport and for identifying roles in directing RNA transport for cis-acting elements within the transcript and trans-acting factors that bind to the VLE (Lewis et al., 2008, Messitt et al., 2008). We have extended this technique through co-localization with additional RNAs and proteins (Gagnon and Mowry, 2009, Messitt et al., 2008), and in combination with disruption of motor proteins and the cytoskeleton (Messitt et al., 2008) to probe mechanisms underlying mRNA localization.

Visualizing RNA Localization in Xenopus Oocytes

Visualization of in vivo RNA transport is accomplished by microinjection of fluorescently labeled RNA transcripts into Xenopus oocytes, followed by confocal microscopy.

RNA localization is a conserved mechanism of establishing cell polarity.  Vg1 mRNA localizes to the vegetal pole of Xenopus laevis oocytes and acts to ...

In vitro Transcription and Capping of Gaussia Luciferase mRNA Followed by HeLa Cell Transfection

In vitro transcription is the synthesis of RNA transcripts by RNA polymerase from a linear DNA template containing the corresponding promoter sequence (T7, T3, SP6) and the gene to be transcribed (Figure 1A). A typical transcription reaction consists of the template DNA, RNA polymerase, ribonucleotide triphosphates, RNase inhibitor and buffer containing Mg2+ ions.
Large amounts of high quality RNA are often required for a variety of applications. Use of in vitro transcription has been reported for RNA structure and function studies such as splicing1, RNAi experiments in mammalian cells2, antisense RNA amplification by the "Eberwine method"3, microarray analysis4 and for RNA vaccine studies5. The technique can also be used for producing radiolabeled and dye labeled probes6. Warren, et al. recently reported reprogramming of human cells by transfection with in vitro transcribed capped RNA7. The T7 High Yield RNA Synthesis Kit from New England Biolabs has been designed to synthesize up to 180 &mu;g RNA per 20 &mu;l reaction. RNA of length up to 10kb has been successfully transcribed using this kit. Linearized plasmid DNA, PCR products and synthetic DNA oligonucleotides can be used as templates for transcription as long as they have the T7 promoter sequence upstream of the gene to be transcribed.
Addition of a 5' end cap structure to the RNA is an important process in eukaryotes. It is essential for RNA stability8, efficient translation9, nuclear transport10 and splicing11. The process involves addition of a 7-methylguanosine cap at the 5' triphosphate end of the RNA. RNA capping can be carried out post-transcriptionally using capping enzymes or co-transcriptionally using cap analogs. In the enzymatic method, the mRNA is capped using the Vaccinia virus capping enzyme12,13. The enzyme adds on a 7-methylguanosine cap at the 5' end of the RNA using GTP and S-adenosyl methionine as donors (cap 0 structure). Both methods yield functionally active capped RNA suitable for transfection or other applications14 such as generating viral genomic RNA for reverse-genetic systems15 and crystallographic studies of cap binding proteins such as eIF4E16.
In the method described below, the T7 High Yield RNA Synthesis Kit from NEB is used to synthesize capped and uncapped RNA transcripts of Gaussia luciferase (GLuc) and Cypridina luciferase (CLuc). A portion of the uncapped GLuc RNA is capped using the Vaccinia Capping System (NEB). A linearized plasmid containing the GLuc or CLuc gene and T7 promoter is used as the template DNA. The transcribed RNA is transfected into HeLa cells and cell culture supernatants are assayed for luciferase activity. Capped CLuc RNA is used as the internal control to normalize GLuc expression.

In vitro Transcription and Capping of Gaussia Luciferase mRNA Followed by HeLa Cell Transfection

This method describes high yield in vitro synthesis of both capped and uncapped mRNA from a linearized plasmid containing the Gaussia luciferase (GLuc) gene. The RNA is purified and a fraction of the uncapped RNA is enzymatically capped using the Vaccinia virus capping enzyme. In the final step, the mRNA is transfected into HeLa cells and cell culture supernatants are assayed for luciferase activity.

In vitro transcription is the synthesis of RNA transcripts by RNA polymerase from a linear DNA template containing the corresponding promoter sequence ...

Chromatin Isolation by RNA Purification (ChIRP)

Long noncoding RNAs are key regulators of chromatin states for important biological processes such as dosage compensation, imprinting, and developmental gene expression 1,2,3,4,5,6,7. The recent discovery of thousands of lncRNAs in association with specific chromatin modification complexes, such as Polycomb Repressive Complex 2 (PRC2) that mediates histone H3 lysine 27 trimethylation (H3K27me3), suggests broad roles for numerous lncRNAs in managing chromatin states in a gene-specific fashion 8,9. While some lncRNAs are thought to work in cis on neighboring genes, other lncRNAs work in trans to regulate distantly located genes. For instance, Drosophila lncRNAs roX1 and roX2 bind numerous regions on the X chromosome of male cells, and are critical for dosage compensation 10,11. However, the exact locations of their binding sites are not known at high resolution. Similarly, human lncRNA HOTAIR can affect PRC2 occupancy on hundreds of genes genome-wide 3,12,13, but how specificity is achieved is unclear. LncRNAs can also serve as modular scaffolds to recruit the assembly of multiple protein complexes. The classic trans-acting RNA scaffold is the TERC RNA that serves as the template and scaffold for the telomerase complex 14; HOTAIR can also serve as a scaffold for PRC2 and a H3K4 demethylase complex 13.
Prior studies mapping RNA occupancy at chromatin have revealed substantial insights 15,16, but only at a single gene locus at a time. The occupancy sites of most lncRNAs are not known, and the roles of lncRNAs in chromatin regulation have been mostly inferred from the indirect effects of lncRNA perturbation. Just as chromatin immunoprecipitation followed by microarray or deep sequencing (ChIP-chip or ChIP-seq, respectively) has greatly improved our understanding of protein-DNA interactions on a genomic scale, here we illustrate a recently published strategy to map long RNA occupancy genome-wide at high resolution 17. This method, Chromatin Isolation by RNA Purification (ChIRP) (Figure 1), is based on affinity capture of target lncRNA:chromatin complex by tiling antisense-oligos, which then generates a map of genomic binding sites at a resolution of several hundred bases with high sensitivity and low background. ChIRP is applicable to many lncRNAs because the design of affinity-probes is straightforward given the RNA sequence and requires no knowledge of the RNA's structure or functional domains.

Chromatin Isolation by RNA Purification ChIRP

ChIRP is a novel and rapid technique to map genomic binding sites of long noncoding RNAs (lncRNAs). The method takes advantage of the specificity of anti-sense tiling oligonucleotides to allow the enumeration of lncRNA-bound genomic sites.

Long noncoding RNAs are key regulators of chromatin states for important biological processes such as dosage compensation, imprinting, and developmental ...

Substrate Generation for Endonucleases of CRISPR/Cas Systems

The interaction of viruses and their prokaryotic hosts shaped the evolution of bacterial and archaeal life. Prokaryotes developed several strategies to evade viral attacks that include restriction modification, abortive infection and CRISPR/Cas systems. These adaptive immune systems found in many Bacteria and most Archaea consist of clustered regularly interspaced short palindromic repeat (CRISPR) sequences and a number of CRISPR associated (Cas) genes (Fig. 1) 1-3. Different sets of Cas proteins and repeats define at least three major divergent types of CRISPR/Cas systems 4. The universal proteins Cas1 and Cas2 are proposed to be involved in the uptake of viral DNA that will generate a new spacer element between two repeats at the 5' terminus of an extending CRISPR cluster 5. The entire cluster is transcribed into a precursor-crRNA containing all spacer and repeat sequences and is subsequently processed by an enzyme of the diverse Cas6 family into smaller crRNAs 6-8. These crRNAs consist of the spacer sequence flanked by a 5' terminal (8 nucleotides) and a 3' terminal tag derived from the repeat sequence 9. A repeated infection of the virus can now be blocked as the new crRNA will be directed by a Cas protein complex (Cascade) to the viral DNA and identify it as such via base complementarity10. Finally, for CRISPR/Cas type 1 systems, the nuclease Cas3 will destroy the detected invader DNA 11,12 .
These processes define CRISPR/Cas as an adaptive immune system of prokaryotes and opened a fascinating research field for the study of the involved Cas proteins. The function of many Cas proteins is still elusive and the causes for the apparent diversity of the CRISPR/Cas systems remain to be illuminated. Potential activities of most Cas proteins were predicted via detailed computational analyses. A major fraction of Cas proteins are either shown or proposed to function as endonucleases 4.
Here, we present methods to generate crRNAs and precursor-cRNAs for the study of Cas endoribonucleases. Different endonuclease assays require either short repeat sequences that can directly be synthesized as RNA oligonucleotides or longer crRNA and pre-crRNA sequences that are generated via in vitro T7 RNA polymerase run-off transcription. This methodology allows the incorporation of radioactive nucleotides for the generation of internally labeled endonuclease substrates and the creation of synthetic or mutant crRNAs. Cas6 endonuclease activity is utilized to mature pre-crRNAs into crRNAs with 5'-hydroxyl and a 2',3'-cyclic phosphate termini.

CRISPR/Cas systems mediate adaptive immunity in Bacteria and Archaea. Many Cas proteins are proposed to act as endoribonucleases acting on crRNA precursors of varying length. Here we illustrate three different approaches to generate pre-crRNA substrates for the biochemical analysis of Cas endonuclease activity.

The  interaction of viruses and their prokaryotic hosts shaped the evolution of  bacterial and archaeal life. Prokaryotes developed several strategies to ...

Depletion of Ribosomal RNA for Mosquito Gut Metagenomic RNA-seq

The mosquito gut accommodates dynamic microbial communities across different stages of the insect's life cycle. Characterization of the genetic capacity and functionality of the gut community will provide insight into the effects of gut microbiota on mosquito life traits. Metagenomic RNA-Seq has become an important tool to analyze transcriptomes from various microbes present in a microbial community. Messenger RNA usually comprises only 1-3% of total RNA, while rRNA constitutes approximately 90%. It is challenging to enrich messenger RNA from a metagenomic microbial RNA sample because most prokaryotic mRNA species lack stable poly(A) tails. This prevents oligo d(T) mediated mRNA isolation. Here, we describe a protocol that employs sample derived rRNA capture probes to remove rRNA from a metagenomic total RNA sample. To begin, both mosquito and microbial small and large subunit rRNA fragments are amplified from a metagenomic community DNA sample. Then, the community specific biotinylated antisense ribosomal RNA probes are synthesized in vitro using T7 RNA polymerase. The biotinylated rRNA probes are hybridized to the total RNA. The hybrids are captured by streptavidin-coated beads and removed from the total RNA. This subtraction-based protocol efficiently removes both mosquito and microbial rRNA from the total RNA sample. The mRNA enriched sample is further processed for RNA amplification and RNA-Seq.

A ribosomal RNA (rRNA) depletion protocol was developed to enrich messenger RNA (mRNA) for RNA-seq of the mosquito gut metatranscriptome. Sample specific rRNA probes, which were used to remove rRNA via subtraction, were created from the mosquito and its gut microbes. Performance of the protocol can result in the removal of approximately 90-99% of rRNA.

The mosquito gut accommodates dynamic microbial communities across different stages of the insect's life cycle. Characterization of the genetic capacity ...

RNA In situ Hybridization in Whole Mount Embryos and Cell Histology Adapted for Marine Elasmobranchs

Marine elasmobranchs are valued animal models for biomedical and genomic studies as they are the most primitive vertebrates to have adaptive immunity and have unique mechanisms for osmoregulation 1-3. As the most primitive living jawed-vertebrates with paired appendages, elasmobranchs are an evolutionarily important model, especially for studies in evolution and development. Marine elasmobranchs have also been used to study aquatic toxicology and stress physiology in relationship to climate change 4. Thus, development and adaptation of methodologies is needed to facilitate and expand the use of these primitive vertebrates to multiple biological disciplines. Here I present the successful adaptation of RNA whole mount in situ hybridization and histological techniques to study gene expression and cell histology in elasmobranchs.
Monitoring gene expression is a hallmark tool of developmental biologists, and is widely used to investigate developmental processes 5. RNA whole mount in situ hybridization allows for the visualization and localization of specific gene transcripts in tissues of the developing embryo. The expression pattern of a gene's message can provide insight into what developmental processes and cell fate decisions a gene may control. By comparing the expression pattern of a gene at different developmental stages, insight can be gained into how the role of a gene changes during development.
While whole mount in situ's provides a means to localize gene expression to tissue, histological techniques allow for the identification of differentiated cell types and tissues. Histological stains have varied functions. General stains are used to highlight cell morphology, for example hematoxylin and eosin for general staining of nuclei and cytoplasm, respectively. Other stains can highlight specific cell types. For example, the alcian blue stain reported in this paper is a widely used cationic stain to identify mucosaccharides. Staining of the digestive tract with alcian blue can identify the distribution of goblet cells that produce mucosaccharides. Variations in mucosaccharide constituents on short peptides distinguish goblet cells by function within the digestive tract 6. By using RNA whole mount in situ's and histochemical methods concurrently, cell fate decisions can be linked to gene-specific expression.
Although RNA in situ's and histochemistry are widely used by researchers, their adaptation and use in marine elasmobranchs have met limited and varied success. Here I present protocols developed for elasmobranchs and used on a regular basis in my laboratory. Although further modification of the RNA in situ's hybridization method may be needed to adapt to different species, the protocols described here provide a strong starting point for researchers wanting to adapt the use of marine elasmobranchs to their scientific inquiries.

RNA In situ Hybridization in Whole Mount Embryos and Cell Histology Adapted for Marine Elasmobranchs

By combining methods for RNA whole mount in situ hybridization and histology, gene expression can be linked with cell fate decisions in the developing embryo. These methods have been adapted to marine elasmobranchs and facilitate the use of these animals as model organisms for biomedical, toxicology and comparative studies.

Marine  elasmobranchs are valued animal models for biomedical and genomic studies as  they are the most primitive vertebrates to have adaptive immunity ...

A Chemical Screening Procedure for Glucocorticoid Signaling with a Zebrafish Larva Luciferase Reporter System

Glucocorticoid stress hormones and their artificial derivatives are widely used drugs to treat inflammation, but long-term treatment with glucocorticoids can lead to severe side effects. Test systems are needed to search for novel compounds influencing glucocorticoid signaling in vivo or to determine unwanted effects of compounds on the glucocorticoid signaling pathway. We have established a transgenic zebrafish assay which allows the measurement of glucocorticoid signaling activity in vivo and in real-time, the GRIZLY assay (Glucocorticoid Responsive In vivo Zebrafish Luciferase activitY). The luciferase-based assay detects effects on glucocorticoid signaling with high sensitivity and specificity, including effects by compounds that require metabolization or affect endogenous glucocorticoid production. We present here a detailed protocol for conducting chemical screens with this assay. We describe data acquisition, normalization, and analysis, placing a focus on quality control and data visualization. The assay provides a simple, time-resolved, and quantitative readout. It can be operated as a stand-alone platform, but is also easily integrated into high-throughput screening workflows. It furthermore allows for many applications beyond chemical screening, such as environmental monitoring of endocrine disruptors or stress research.

We describe the procedure and data analysis of a chemical screening system for glucocorticoid stress hormone signaling using zebrafish larvae: the Glucocorticoid Responsive In vivo Zebrafish Luciferase activitY (GRIZLY) assay. The assay sensitively and specifically detects effects on glucocorticoid signaling by compounds that require metabolization or affect endogenous glucocorticoid production.

Glucocorticoid stress hormones and their artificial derivatives are widely used drugs to treat inflammation, but long-term treatment with glucocorticoids ...

Detection of RNA-binding Proteins by In Vitro RNA Pull-down in Adipocyte Culture

RNA-binding proteins (RBPs) are emerging as a regulatory layer in the development and function of adipose. RBPs play a key role in the gene expression regulation at posttranscriptional levels by affecting the stability and translational efficiency of target mRNAs. RNA pull-down technique has been widely used to study RNA-protein interaction, which is necessary to elucidate the mechanism underlying RBPs&#39; as well as long non-coding RNAs&#39; (lncRNAs) function. However, the high lipid abundance in adipocytes poses a technical challenge in conducting this experiment. Here a detailed RNA pull-down protocol is optimized for primary adipocyte culture. An RNA fragment from androgen receptor&#39;s (AR) 3&#39; untranslated region (3&#39;UTR) containing an adenylate-uridylate-rich elementwas used as an example to demonstrate how to retrieve its RBP partner, HuR protein, from adipocyte lystate. The method described here can be applied to detect the interactions between RBPs and noncoding RNAs, as well as between RBPs and coding RNAs.

Detection of RNA-binding Proteins by In Vitro RNA Pull-down in Adipocyte Culture

An RNA pull-down protocol is optimized here for detection of interactions between RNA-binding proteins (RBPs) and noncoding as well as coding RNAs. An RNA fragment from androgen receptor (AR) was used as an example to demonstrate how to retrieve its RBP from lystate of primary brown adipocytes.

RNA-binding proteins (RBPs) are emerging as a regulatory layer in the development and function of adipose. RBPs play a key role in the gene expression ...

Practical Use of RNA Interference: Oral Delivery of Double-stranded RNA in Liposome Carriers for Cockroaches

RNA interference (RNAi) has been widely applied for uncovering the biological functions of numerous genes, and has been envisaged as a pest control tool operating by disruption of essential gene expression. Although different methods, such as injection, feeding, and soaking, have been reported for successful delivery of double-stranded RNA (dsRNA), the efficiency of RNAi through oral delivery of dsRNA is highly variable among different insect groups. The German cockroach, Blattella germanica, is highly sensitive to the injection of dsRNA, as shown by many studies published previously. The present study describes a method to demonstrate that the dsRNA encapsulated with liposome carriers is sufficient to retard the degradation of dsRNA by midgut juice. Notably, the continuous feeding of dsRNA encapsulated by liposomes significantly reduces the tubulin expression in the midgut, and led to the death of cockroaches. In conclusion, the formulation and utilization of dsRNA lipoplexes, which protect dsRNA against nucleases, could be a practical use of RNAi for insect pest control in the future.

This manuscript demonstrates the depletion of gene expression in the midgut of the German cockroach through oral ingestion of double-stranded RNA encapsulated in liposomes.

RNA interference (RNAi) has been widely applied for uncovering the biological functions of numerous genes, and has been envisaged as a pest control tool ...

Imaging FITC-dextran as a Reporter for Regulated Exocytosis

Regulated exocytosis is a process by which cargo, which is stored in secretory granules (SGs), is released in response to a secretory trigger. Regulated exocytosis is fundamental for intercellular communication and is a key mechanism for the secretion of neurotransmitters, hormones, inflammatory mediators, and other compounds, by a variety of cells. At least three distinct mechanisms are known for regulated exocytosis: full exocytosis, where a single SG fully fuses with the plasma membrane, kiss-and-run exocytosis, where a single SG transiently fuses with the plasma membrane, and compound exocytosis, where several SGs fuse with each other, prior to or after SG fusion with the plasma membrane. The type of regulated exocytosis undertaken by a cell is often dictated by the type of secretory trigger. However, in many cells, a single secretory trigger can activate multiple modes of regulated exocytosis simultaneously. Despite their abundance and importance across cell types and species, the mechanisms that determine the different modes of secretion are largely unresolved. One of the main challenges in investigating the different modes of regulated exocytosis, is the difficulty in distinguishing between them as well as exploring them separately. Here we describe the use of fluorescein isothiocyanate (FITC)-dextran as an exocytosis reporter, and live cell imaging, to differentiate between the different pathways of regulated exocytosis, focusing on compound exocytosis, based on the robustness and duration of the exocytic events.

Here we detail a method for live cell imaging of regulated exocytosis. This method utilizes FITC-dextran, which accumulates in lysosome-related organelles, as a reporter. This simple method also allows distinguishing between different modes of regulated exocytosis in cells that are difficult to manipulate genetically.

Regulated exocytosis is a process by which cargo, which is stored in secretory granules (SGs), is released in response to a secretory trigger. Regulated ...