This study was funded by the National Natural Science Foundation of China (31501898), the Science and Technology Program of Guangzhou (202102010465), the Guangzhou Higher Education Teaching Quality and Teaching Reform Project (2022JXGG057), and the Research project of the Open Online Course Steering Committee of Guangdong Provincial Universities (2022ZXKC381).

1. Silkworm species and rearing
<ol>
	<li>Rear at least 120 freshly hatched 1st instar silkworm larvae of B. mori P50 strain with fresh mulberry leaves at 25 &#177; 1 &#176;C, photoperiod 12 h Light:12 h Dark, and 75% &#177; 5% relative humidity.</li>
</ol>
2. Selection of silkworm larvae
<ol>
	<li>Pick day 1 of the 5th instar larvae for the RNAi experiment; the silkworm larvae grow fast after day 3 of the 5th instar, which is ideal for comparing the differences in the larval appearance. 
	NOTE: Alternatively, younger stages, such as the 3rd or 4th instar, could be used for the RNAi experiment. However, it requires constant dsRNA treatment until the 5th instar, which is relatively expensive and material costing.</li>
</ol>
3. Synthesis of dsRNA
<ol>
	<li>Identifying dsRNA target fragment: Select the coding sequence of a target gene and align it with other homologous genes to determine the conserved region. Design gene-specific primers in the non-conserved region for subsequent dsRNA target fragment amplification. For RNAi experiments in insects, the typical dsRNA target fragment is generally 400-600 bp. The minimum size could be 200 bp. 
	NOTE: To improve the efficiency and successful rate of RNAi experiments, some web-based tool can be used to design the dsRNA target, such as dsRNA Engineer (https://dsrna-engineer.cn/).</li>
	<li>Producing PCR product template: Add a T7 RNA polymerase promoter (5&#39;-TAATACGACTCACTATAGG-3&#39;) to the 5&#39;-end of either primer designed above. Perform standard PCR to amplify the dsRNA target fragment. Run a 1% agarose gel in 1x TAE to verify a single PCR product of the expected size. After that, purify the PCR product with a purification kit (Table of Materials) and use it for subsequent transcription. 
	NOTE: To store the target PCR product for long-term and obtain high yields, it is suggested to ligate the PCR product to a plasmid. The plasmid should be linearized before the PCR reaction.</li>
	<li>Generation of dsRNA: Use a T7 RNAi System (Table of Materials) to generate the dsRNA. Set up the reaction by adding the components at room temperature according to the manufacturer&#39;s instructions. Mix the reaction by pipetting gently and incubate at 37 &#176;C for 30 min. 
	NOTE: To maximize the yield, incubation at 37 &#176;C can be extended up to 2-6 h. For templates containing a secondary structure or GC-rich, incubation can be performed at 42 &#176;C instead to improve the yield of dsRNA.</li>
	<li>Annealing to form dsRNA: Incubate the reaction at 70 &#176;C for 10 min, then slowly cool to room temperature (~20 min). This will anneal the dsRNA.</li>
	<li>DNase and RNase treatment: Pipette 1 &#181;L of the supplied RNase solution to 199 &#181;L of nuclease-free water to make a freshly diluted RNase solution. Add 1 &#181;L of freshly diluted RNase solution and 1 &#181;L of the supplied RQ1 RNase-free DNase per 20 &#181;L reaction volume, mix gently, and incubate at 37 &#176;C for 30 min. The single-stranded RNA (ssRNA) and the template DNA in the reaction will be removed after this treatment.</li>
	<li>Alcohol precipitation: Add 1 volume of isopropanol or 2.5 volumes of 95% ethanol along with 0.1 volume of 3 M Sodium Acetate (pH 5.2) to the reaction. Mix the reaction by vortexing and incubate on ice for 5 min to form a cloudy mass. Spin at maximum speed in a centrifuge for 10 min to collect a white pellet at the bottom of the tube. Discard the supernatant and wash the pellet with 0.5 mL of cold 70% ethanol to remove the residual salt. Remove the ethanol after the wash. Allow the pellet to air dry at room temperature for 15 min. Resuspend the pellet with nuclease-free water in 2-5 times of the initial reaction volume. Store at -20 &#176;C or -70 &#176;C. 
	NOTE: The dsRNA pellet should not be overly dried, since this could make it difficult to fully resuspend. To ensure sufficient resuspension, a minimum of 2 volumes are needed.</li>
	<li>Quantity and quality check of dsRNA: Dilute the dsRNA in nuclease-free water at a ratio of 1:100 to 1:300. Determine the concentration of dsRNA using a microvolume spectrophotometer (Table of Materials) according to the manufacturer&#39;s instructions. To quantify dsRNA, multiply the concentration by the volume. To assess the quality of dsRNA, use agarose gel electrophoresis. Prepare a 1% agarose gel in 1x TAE and dilute the dsRNA at 1:50 with nuclease-free water. Use 5 &#181;L of diluted dsRNA per lane and stain the gel in 0.5 mg/mL ethidium bromide for at least 15 min for visualization. 
	NOTE: dsRNA migrates more slowly than dsDNA.</li>
</ol>
4. Preparation of the chitosan/dsRNA nanoparticles
<ol>
	<li>Make 100 mM sodium acetate (0.1 M NaC2H3O2 and 0.1 M acetic acid, pH 4.5 in deionized water) and 100 mM sodium sulfate (100 mM Na2SO4 in deionized water) buffer at room temperature.</li>
	<li>Dissolve commercialized chitosan (from shrimp shells, &#8805;75% deacetylated; Table of Materials) in 100 mM sodium acetate buffer to make a 0.02% (w/v) chitosan solution.</li>
	<li>Dissolve 20 &#181;g of dsRNA in 50 &#181;L of nuclease-free water and add it to 50 &#181;L of 100 mM sodium sulfate buffer to make a 100 &#181;L dsRNA solution.</li>
	<li>Add 100 &#181;L of chitosan solution to 100 &#181;L of dsRNA solution. Simultaneously, prepare a control by adding 100 &#181;L of chitosan solution to 100 &#181;L of 50 mM sodium sulfate. Mix and heat the mixtures at 55 &#176;C for 1 min.</li>
	<li>Vortex the mixture immediately with a high-speed vortex for 30 s to allow the formation of the nanoparticles.</li>
	<li>Centrifuge the mixture at 13,000 x g at room temperature for 10 min to obtain a white pellet. Transfer the supernatant to a fresh 1.5 mL tube. Let the pellet air-dry at room temperature for 10 min.</li>
	<li>Determine the concentration of dsRNA in the supernatant by using a microvolume spectrophotometer (Table of Materials). Use the supernatant from the control as a blank. Multiply the concentration by volume to calculate the total amount of dsRNA remaining in the supernatant. Calculate the percentage of dsRNA encapsulated in the nanoparticles by the amount remaining in the supernatant divided by the starting amount of dsRNA. 
	NOTE: Even though the nanoparticles could be kept for 4-37 &#176;C for at least 15 days before use14, it is suggested to use the nanoparticles as soon as possible.</li>
</ol>
5. Feeding the silkworm larvae with chitosan/dsRNA nanoparticles
<ol>
	<li>Pick freshly molted 5th instar silkworm larvae (i.e., Day 1 of the 5th instar) of the same size for the feeding experiment. Place the larvae individually into each well of a 6-well plate before closing the cover and starve for 24 h.</li>
	<li>Rinse fresh mulberry leaves with deionized water and dry them with clean kitchen paper. The mulberry leaves should be dry without water drops. Cut into 1 cm x 1 cm mulberry leaf discs.</li>
	<li>Dissolve chitosan/dsRNA nanoparticles into nuclease-free water at 500 ng/&#181;L prior to use. Dilute the control chitosan nanoparticles (prepared in 4.4) with same volume of nuclease-free water. Prepare naked dsRNA to 500 ng/&#181;L in nuclease-free water.</li>
	<li>Use the chitosan/dsRNA nanoparticles for RNAi knockdown experiment, the control chitosan nanoparticles as a blank/negative control. Use the naked dsRNA to compare the differences with chitosan/dsRNA nanoparticles.</li>
	<li>Coat 10 &#181;L of chitosan/dsRNA nanoparticles, chitosan, and naked dsRNA on the surface of each leaf disc, respectively. Air-dry the nanoparticle solution and dsRNA solution on the leaf discs at room temperature for 5 min.</li>
	<li>Feed each larva with one nanoparticle-coated or dsRNA-coated leaf disc per day. Provide nanoparticle-coated or dsRNA-coated leaf discs to the larvae continuously for 5 days. Fresh mulberry leaves can be provided after the coated leaf disc is fully eaten by the larvae each day.</li>
	<li>On day 6, anesthetize the larvae on ice until they do not move and dissect the larvae for sampling. Cut off the thorax with scissors on a clean Petri dish. Pull out the midgut with a tweezer. Remove the content in the midgut and wash the midgut in another Petri dish filled with nuclease-free water. Store the midgut in a 1.5 mL tube and keep at -70 &#176;C.</li>
</ol>
6. Confirmation of gene silencing
<ol>
	<li>Perform quantitative Real-time PCR (qRT-PCR) to calculate the relative transcript quantification. At least three biological replicates and three technical replicates for each biological replicate are required. At least two reference genes are recommended to normalize the relative transcript. A Bombyx Toll9-2 (BmToll9-2) gene is tested. Evaluate the gene silencing efficiency by comparing the mean value of the relative transcript to the control group and convert it to percentage. 
	NOTE: The qRT-PCR amplification condition, primer information, and relative transcript calculation can be found in our recent publication20.</li>
	<li>Analyze the RNAi phenotype to evaluate the gene silencing effect. Observe the size of the larvae and cocoons. Take photos daily to record appearances. 
	NOTE: RNAi can affect morphology, metamorphosis, physiology, and behavior. The observation of RNAi-related phenotypes depends on the genes targeted.</li>
</ol>

Nanoparticle-Mediated dsRNA Feeding for Gene Silencing in Silkworm Larvae

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The authors have nothing to disclose.

A proper stage is important for RNAi phenotype observation, depending on the genes targeted. Our preliminary results showed that Toll9-2 is involved in the growth of the silkworm. The size and weight of the silkworm larvae increase rapidly at the 5th instar21. Therefore, the 5th instar larvae are selected as the stage for the chitosan/dsRNA nanoparticles feeding experiment. It is also possible to select the 3rd or 4th instar larvae for feeding e...

The silkworm, Bombyx mori, is an insect domesticated more than 5000 years ago in China. Due to its ability to produce silk, the silkworm is an important economic insect in Chinese agriculture and sericulture. The silkworm is second only to the fruit fly as the model insect. As a model insect in Lepidoptera, the silkworm is easy to rear, with a large body size and plenty of mutants. Meanwhile, the silkworm is the first Lepidopteran insect with its complete genome sequenced1. A lot of databases providing information for genome2, transcriptome3, expressed sequence tag (EST)4, non-coding RNA5, and microsatellite6 are also available to the public. The above facts make the silkworm a perfect model for genetic research.
RNA interference (RNAi) is a cellular process in which double-stranded RNA (dsRNA) molecules bind and slice the complementary messenger RNA (mRNA), thereby achieving the silencing effect of the target gene. This mechanism is naturally present in bacteria to defend against the invasion of viruses7. Later, it was found that RNAi is conserved in animals, plants, and microbes. Due to its powerful sequence-specific silencing effect, RNAi is used in fundamental research to manipulate gene expression and study gene function. RNAi is achieved through the delivery of dsRNA into cells.
In insects, there are three common ways to deliver dsRNA, which are microinjection, feeding, and soaking8. At the moment, successful RNAi reports in the silkworms through naked dsRNA delivery are conducted by dsRNA injection9. The advantages of microinjection are the immediate delivery of dsRNA into the hemolymph and precise dsRNA amount control. However, certain disadvantages of microinjection also exist. For example, it is time-consuming, and it requires delicate devices. It is also important to optimize the injection needles, injection volume, and dsRNA amount. Therefore, an alternative way to deliver dsRNA to silkworms becomes necessary. Because an insect&#39;s exoskeleton is a water-tight barrier that is made of chitin, soaking insect larvae to achieve RNAi is rarely reported, which is not a good option for RNAi in insects. Feeding of dsRNA is labor-saving, cost-effective, and easy to perform10. This method is also applicable for high-throughput gene screening11. However, it is found that a DNA/RNA non-specific nuclease, namely BmdsRNase, is present in the midgut and midgut juice of the silkworm larvae12. This nuclease is shown to digest dsRNA, preferably13. Therefore, feeding naked dsRNA to the silkworm to silence the gene expression seems to be difficult.
Recently, nanoparticle-shielded dsRNA is proved to be a good alternative to increase the RNAi efficiency by feeding14. Chitosan is an inexpensive, nontoxic, and biodegradable polymer, which can be prepared by deacetylation of chitin, a naturally occurring and the second most abundant biopolymer after cellulose15. Because the amino group in the chitosan is positively charged and the phosphate group on the backbone of the dsRNA is negatively charged, the chitosan/dsRNA nanoparticles could be formed by self-assembly of polycations16. Chitosan/dsRNA nanoparticles are effective in achieving RNAi through larval feeding in mosquitos Aedes aegypti and Anopheles gambiae17, cotton spotted bollworm Earias vittella18 and carmine spider mite Tetranychus cinnabarinus19.
In order to develop a methodology for dsRNA delivery by feeding in silkworms to gain successful RNAi efficiency, this report focuses on describing step-by-step procedures on how to prepare the chitosan/dsRNA nanoparticles and feed the nanoparticles to the silkworm larvae. This methodology is relatively inexpensive, labor-saving and easy to follow, which can be adapted for gene silencing studies in other insects. We aim to provide an easier protocol for the Lepidopteran dsRNA delivery method with higher RNAi efficiency.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1.5 mL centrifuge tube</td>
			<td>Sangon</td>
			<td>F601620</td>
			<td>for dsRNA or nanoparticles reaction</td>
		</tr>
		<tr>
			<td>10 &#956;l pipette</td>
			<td>Eppendorf</td>
			<td>P13473G</td>
			<td>to aspirate or resuspend liquid</td>
		</tr>
		<tr>
			<td>100 &#956;l pipette</td>
			<td>Eppendorf</td>
			<td>Q12115G</td>
			<td>to aspirate or resuspend liquid</td>
		</tr>
		<tr>
			<td>2.5 &#956;l pipette</td>
			<td>Eppendorf</td>
			<td>P20777G</td>
			<td>to aspirate or resuspend liquid</td>
		</tr>
		<tr>
			<td>20 &#956;l pipette</td>
			<td>Eppendorf</td>
			<td>H19229E</td>
			<td>to aspirate or resuspend liquid</td>
		</tr>
		<tr>
			<td>200 &#956;l pipette</td>
			<td>Eppendorf</td>
			<td>H20588E</td>
			<td>to aspirate or resuspend liquid</td>
		</tr>
		<tr>
			<td>6-well Clear TC-treated Multiple Well Plates</td>
			<td>Costar</td>
			<td>3516</td>
			<td>for silkworm rearing individually</td>
		</tr>
		<tr>
			<td>Acetic acid</td>
			<td>Aladdin</td>
			<td>A116165</td>
			<td>to make TAE</td>
		</tr>
		<tr>
			<td>Agarose M</td>
			<td>BBI Life Sciences</td>
			<td>A610013</td>
			<td>for agarose gel electrophosis</td>
		</tr>
		<tr>
			<td>Analytical balance</td>
			<td>Sartorius</td>
			<td>BSA224S</td>
			<td>to weight ingredients</td>
		</tr>
		<tr>
			<td>Centrifuge&#160;</td>
			<td>Sartorius</td>
			<td>Centrisart A-14C</td>
			<td>to centrifuge to form dsRNA or nanoparticles</td>
		</tr>
		<tr>
			<td>Chitosan</td>
			<td>Sigma-Aldrich</td>
			<td>C3646</td>
			<td>to combine with dsRNA for preparation of nanoparticles</td>
		</tr>
		<tr>
			<td>EDTA</td>
			<td>Sangon</td>
			<td>A500895</td>
			<td>to make TAE</td>
		</tr>
		<tr>
			<td>Ethanol</td>
			<td>Aladdin</td>
			<td>E130059</td>
			<td>to make TAE, or for dsRNA precipitation</td>
		</tr>
		<tr>
			<td>Freezer</td>
			<td>Siemens</td>
			<td>iQ300</td>
			<td>to store dsRNA or nanoparticles</td>
		</tr>
		<tr>
			<td>GoTaq Green Master Mix</td>
			<td>Promega</td>
			<td>M712</td>
			<td>for PCR reaction</td>
		</tr>
		<tr>
			<td>GoTaq qPCR Master Mix</td>
			<td>Promega</td>
			<td>A6002</td>
			<td>for qRT-PCR reaction</td>
		</tr>
		<tr>
			<td>Isopropanol&#160;</td>
			<td>Aladdin</td>
			<td>I112011</td>
			<td>for dsRNA precipitation</td>
		</tr>
		<tr>
			<td>NanoDrop Microvolume UV-Vis Spectrophotometer</td>
			<td>ThermoFisher</td>
			<td>One</td>
			<td>to determine the concentration of dsRNA</td>
		</tr>
		<tr>
			<td>ph meter</td>
			<td>Sartorius</td>
			<td>&#160;PB-10</td>
			<td>to prepare buffers</td>
		</tr>
		<tr>
			<td>SanPrep Column PCR Product Purification Kit</td>
			<td>Sangon</td>
			<td>B518141</td>
			<td>for PCR product purification</td>
		</tr>
		<tr>
			<td>Sodium acetate</td>
			<td>Sigma-Aldrich</td>
			<td>S2889</td>
			<td>to make 100 mM sodium acetate buffer</td>
		</tr>
		<tr>
			<td>Sodium sulfate&#160;</td>
			<td>Sigma-Aldrich</td>
			<td>239313</td>
			<td>to make 100 mM sodium sulfate buffer</td>
		</tr>
		<tr>
			<td>T7 RiboMAX Express RNAi System</td>
			<td>Promega</td>
			<td>P1700</td>
			<td>for dsRNA synthesis</td>
		</tr>
		<tr>
			<td>ThermoMixer</td>
			<td>Eppendorf</td>
			<td>C</td>
			<td>for dsRNA generation or nanoparticles heating</td>
		</tr>
		<tr>
			<td>Tris</td>
			<td>Sangon</td>
			<td>A501492</td>
			<td>to make TAE</td>
		</tr>
		<tr>
			<td>Vortex&#160;</td>
			<td>IKA</td>
			<td>Vortex 3</td>
			<td>to prepare chitosan/dsRNA nanoparticles</td>
		</tr>
	</tbody>
</table>

larval rna interference in silkworm bombyx mori through chitosan/dsrna nanoparticle delivery

The silkworm, Bombyx mori, is an important economic insect with thousands of years of history in China. Meanwhile, the silkworm is the model insect of Lepidoptera with a good accumulation of basic research. It is also the first insect in Lepidoptera with its complete genome sequenced and assembled, which provides a solid foundation for gene functional study. Although RNA interference (RNAi) is widely used in reverse gene functional study, it is refractory in silkworms and other Lepidopteran species. Previous successful RNAi-related research to deliver double-stranded RNA (dsRNA) was performed through injection only. Delivery of dsRNA through feeding is never reported. In this article, we describe step-by-step procedures to prepare the chitosan/dsRNA nanoparticles, which are fed to the silkworm larvae by ingestion. The protocol includes (i) selection of the proper stage of silkworm larvae, (ii) synthesis of dsRNA, (iii) preparation of the chitosan/dsRNA nanoparticles, and (iv) feeding the silkworm larvae with chitosan/dsRNA nanoparticles. Representative results, including gene transcript confirmation and phenotype observation, are presented. dsRNA feeding is a simple technique for RNAi in silkworm larvae. Since silkworm larvae are easy to rear and large enough to operate, it provides a good model to demonstrate larval RNAi in insects. In addition, the simplicity of this technique stimulates more student involvement in research, making silkworm larvae an ideal genetic system for use in a classroom setting.

To evaluate the RNAi efficiency, an immune gene targeting BmToll9-2 was chosen for analysis. BmToll9-2 gene is well characterized in the lab, and gene silencing by dsRNA injection results in lighter and smaller larvae in our recent publication20. To confirm the RNAi efficacy by ingestion through chitosan/dsRNA nanoparticles, chitosan nanoparticles were used as a control, and naked dsRNA was compared at the same time.
Compared with the control, chitosan...

Author Spotlight: Advancing Gene Silencing Research in Silkworms with dsRNA Delivery Through Feeding Chitosan Nanoparticles

Presented here is a protocol for chitosan/dsRNA nanoparticle delivery in silkworm Bombyx mori larvae to induce gene silencing through ingestion.

Larval RNA Interference in Silkworm Bombyx mori through Chitosan/dsRNA Nanoparticle Delivery

The silkworm, Bombyx mori, is an important economic insect with thousands of years of history in China. Meanwhile, the silkworm is the model insect of ...

larval-rna-interference-silkworm-bombyx-mori-through-chitosandsrna

Research

JoVE Journal

Biology

1.7K Views.  Guangzhou University. Presented here is a protocol for chitosan/dsRNA nanoparticle delivery in silkworm Bombyx mori larvae to induce gene silencing through ingestion.

Video: Author Spotlight: Advancing Gene Silencing Research in Silkworms with dsRNA Delivery Through Feeding Chitosan Nanoparticles

Dissection of Larval CNS in Drosophila Melanogaster

The central nervous system (CNS) of Drosophila larvae is complex and poorly understood.  One way to investigate the CNS is to use immunohistochemistry to examine the expression of various novel and marker proteins.  Staining of whole larvae is impractical because the tough cuticle prevents antibodies from penetrating inside the body cavity.  In order to stain these tissues it is necessary to dissect the animal prior to fixing and staining.  In this article we demonstrate how to dissect Drosophila larvae without damaging the CNS.  Begin by tearing the larva in half with a pair of fine forceps, and then turn the cuticle "inside-out" to expose the CNS.  If the dissection is performed carefully the CNS will remain attached to the cuticle.  We usually keep the CNS attached to the cuticle throughout the fixation and staining steps, and only completely remove the CNS from the cuticle just prior to mounting the samples on glass slides.  We also show some representative images of a larval CNS stained with Eve, a transcription factor expressed in a subset of neurons in the CNS.  The article concludes with a discussion of some of the practical uses of this technique and the potential difficulties that may arise.

In this article we demonstrate how to dissect the central nervous system from third instar Drosophila larvae.

The central nervous system (CNS) of Drosophila larvae is complex and poorly understood.  One way to investigate the CNS is to use immunohistochemistry 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 ...

Using RNA-mediated Interference Feeding Strategy to Screen for Genes Involved in Body Size Regulation in the Nematode C. elegans

Double-strand RNA-mediated interference (RNAi) is an effective strategy to knock down target gene expression1-3. It has been applied to many model systems including plants, invertebrates and vertebrates. There are various methods to achieve RNAi in vivo4,5. For example, the target gene may be transformed into an RNAi vector, and then either permanently or transiently transformed into cell lines or primary cells to achieve gene knockdown effects; alternatively synthesized double-strand oligonucleotides from specific target genes (RNAi oligos) may be transiently transformed into cell lines or primary cells to silence target genes; or synthesized double-strand RNA molecules may be microinjected into an organism. Since the nematode C. elegans uses bacteria as a food source, feeding the animals with bacteria expressing double-strand RNA against target genes provides a viable strategy6. Here we present an RNAi feeding method to score body size phenotype. Body size in C. elegans is regulated primarily by the TGF- &beta; - like ligand DBL-1, so this assay is appropriate for identification of TGF-&beta; signaling components7. We used different strains including two RNAi hypersensitive strains to repeat the RNAi feeding experiments. Our results showed that rrf-3 strain gave us the best expected RNAi phenotype. The method is easy to perform, reproducible, and easily quantified. Furthermore, our protocol minimizes the use of specialized equipment, so it is suitable for smaller laboratories or those at predominantly undergraduate institutions.

Using RNA-mediated Interference Feeding Strategy to Screen for Genes Involved in Body Size Regulation in the Nematode C. elegans

We demonstrate how to use the RNAi feeding technique to knock down target genes and score body size phenotype in C. elegans. This method could be used for a large scale screen to identify potential genetic components of interest, such as those involved in body size regulation by DBL-1/TGF-&beta; signaling.

Double-strand RNA-mediated interference (RNAi) is an effective strategy to knock down target gene expression1-3. It has been applied to many model systems ...

Larval RNA Interference in the Red Flour Beetle, Tribolium castaneum

The red flour beetle, Tribolium&#160;castaneum, offers a repertoire of experimental tools for genetic and developmental studies, including a fully annotated genome sequence, transposon-based transgenesis, and effective RNA interference (RNAi). Among these advantages, RNAi-based gene knockdown techniques are at the core of Tribolium research. T. castaneum show a robust systemic RNAi response, making it possible to perform RNAi at any life stage by simply injecting double-stranded RNA (dsRNA) into the beetle&#8217;s body cavity.
In this report, we provide an overview of our larval RNAi technique in T. castaneum. The protocol includes (i) isolation of the proper stage of T. castaneum larvae for injection, (ii) preparation for the injection setting, and (iii) dsRNA injection. Larval RNAi is a simple, but powerful technique that provides us with quick access to loss-of-function phenotypes, including multiple gene knockdown phenotypes as well as a series of hypomorphic phenotypes. Since virtually all T. castaneum tissues are susceptible to extracellular dsRNA, the larval RNAi technique allows researchers to study a wide variety of tissues in diverse contexts, including the genetic basis of organismal responses to the outside environment. In addition, the simplicity of this technique stimulates more student involvement in research, making T. castaneum an ideal genetic system for use in a classroom setting.

Larval RNA Interference in the Red Flour Beetle, Tribolium castaneum

RNA interference (RNAi)-based gene knockdown techniques are at the core of Tribolium research. Here, we provide an overview of our larval RNAi technique in Tribolium castaneum. Larval RNAi is a simple, but powerful technique that provides quick access to loss-of-function phenotypes, allowing researchers to study gene functions in diverse contexts.

The red flour beetle, Tribolium&#160;castaneum, offers a repertoire of experimental tools for genetic and developmental studies, including a fully ...

Chitosan/Interfering RNA Nanoparticle Mediated Gene Silencing in Disease Vector Mosquito Larvae

Vector mosquitoes inflict more human suffering than any other organism&#8212;and kill more than one million people each year. The mosquito genome projects facilitated research in new facets of mosquito biology, including functional genetic studies in the primary African malaria vector Anopheles gambiae and the dengue and yellow fever vector Aedes aegypti. RNA interference- (RNAi-) mediated gene silencing has been used to target genes of interest in both of these disease vector mosquito species. Here, we describe a procedure for preparation of chitosan/interfering RNA nanoparticles that are combined with food and ingested by larvae. This technically straightforward, high-throughput, and relatively inexpensive methodology, which is compatible with long double stranded RNA (dsRNA) or small interfering RNA (siRNA) molecules, has been used for the successful knockdown of a number of different genes in A. gambiae and A. aegypti larvae. Following larval feedings, knockdown, which is verified through qRT-PCR or in situ hybridization, can persist at least through the late pupal stage. This methodology may be applicable to a wide variety of mosquito and other insect species, including agricultural pests, as well as other non-model organisms. In addition to its utility in the research laboratory, in the future, chitosan, an inexpensive, non-toxic and biodegradable polymer, could potentially be utilized in the field.

Here we describe a procedure for inhibiting gene function in disease vector mosquitoes through the use of chitosan/interfering RNA nanoparticles that are ingested by larvae.

Vector mosquitoes inflict more human suffering than any other organism&#8212;and kill more than one million people each year. The mosquito genome projects ...

Absolute Quantification of Plasma MicroRNA Levels in Cynomolgus Monkeys, Using Quantitative Real-time Reverse Transcription PCR

RT-qPCR is one of the most common methods to assess individual target miRNAs. MiRNAs levels are generally measured relative to a reference sample. This approach is appropriate for examining physiological changes in target gene expression levels. However, absolute quantification using better statistical analysis is preferable for a comprehensive assessment of gene expression levels. Absolute quantification is still not in common use. This report describes a protocol for measuring the absolute levels of plasma miRNA, using RT-qPCR with or without pre-amplification.
A fixed volume (200 &#181;L) of EDTA-plasma was prepared from the blood collected from the femoral vein of conscious cynomolgus monkeys (n = 50). Total RNA was extracted using commercially available system. Plasma miRNAs were quantified by probe-based RT-qPCR assays which contains miRNA-specific forward/reverse PCR primer and probe. Standard curves for absolute quantification were generated using commercially available synthetic RNA oligonucleotides. A synthetic cel-miR-238 was used as an external control for normalization and quality assessment. The miRNAs that showed quantification cycle (Cq) values above 35 were pre-amplified prior to the qPCR step.
Among the 8 miRNAs examined, miR-122, miR-133a, and miR-192 were detectable without pre-amplification, whereas miR-1, miR-206, and miR-499a required pre-amplification because of their low expression levels. MiR-208a and miR-208b were not detectable even after pre-amplification. Sample processing efficiency was evaluated by the Cq values of the spiked cel-miR-238. In this assay method, technical variation was estimated to be less than 3-fold and the lower limit of quantification (LLOQ) was 102 copy/&#181;L, for most of the examined miRNAs.
This protocol provides a better estimate of the quantity of plasma miRNAs, and allows quality assessment of corresponding data from different studies. Considering the low number of miRNAs in body fluids, pre-amplification is useful to enhance detection of poorly expressed miRNAs.

This report describes a protocol for measuring the absolute levels of plasma miRNA, using quantitative real-time reverse transcription PCR with or without pre-amplification. This protocol affords better understanding of the quantity of plasma miRNAs and allows qualitative assessment of corresponding data from different studies or laboratories.

RT-qPCR is one of the most common methods to assess individual target miRNAs. MiRNAs levels are generally measured relative to a reference sample. This ...

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 ...

TChIP-Seq: Cell-Type-Specific Epigenome Profiling

Epigenetic regulation plays central roles in gene expression. Since histone modification was discovered in the 1960s, its physiological and pathological functions have been extensively studied. Indeed, the advent of next-generation deep sequencing and chromatin immunoprecipitation (ChIP) via specific histone modification antibodies has revolutionized our view of epigenetic regulation across the genome. Conversely, tissues typically consist of diverse cell types, and their complex mixture poses analytic challenges to investigating the epigenome in a particular cell type. To address the cell type-specific chromatin state in a genome-wide manner, we recently developed tandem chromatin immunoprecipitation sequencing (tChIP-Seq), which is based on the selective purification of chromatin by tagged core histone proteins from cell types of interest, followed by ChIP-Seq. The goal of this protocol is the introduction of best practices of tChIP-Seq. This technique provides a versatile tool for tissue-specific epigenome investigation in diverse histone modifications and model organisms.

We describe a step-by-step protocol for tandem chromatin immunoprecipitation sequencing (tChIP-Seq) that enables the analysis of cell-type-specific genome-wide histone modification.

Epigenetic regulation plays central roles in gene expression. Since histone modification was discovered in the 1960s, its physiological and pathological ...

Nuclei Isolation from Adult Mouse Kidney for Single-Nucleus RNA-Sequencing

The kidneys regulate diverse biological processes such as water, electrolyte, and acid-base homeostasis. Physiological functions of the kidney are executed by multiple cell types arranged in a complex architecture across the corticomedullary axis of the organ. Recent advances in single-cell transcriptomics have accelerated the understanding of cell type-specific gene expression in renal physiology and disease. However, enzyme-based tissue dissociation protocols, which are frequently utilized for single-cell RNA-sequencing (scRNA-seq), require mostly fresh (non-archived) tissue, introduce transcriptional stress responses, and favor the selection of abundant cell types of the kidney cortex resulting in an underrepresentation of cells of the medulla.
Here, we present a protocol that avoids these problems. The protocol is based on nuclei isolation at 4 &#176;C from frozen kidney tissue. Nuclei are isolated from a central piece of the mouse kidney comprised of the cortex, outer medulla, and inner medulla. This reduces the overrepresentation of cortical cells typical for whole-kidney samples for the benefit of medullary cells such that data will represent the entire corticomedullary axis at sufficient abundance. The protocol is simple, rapid, and adaptable and provides a step towards the standardization of single-nuclei transcriptomics in kidney research.

Here, we present a protocol to isolate high-quality nuclei from frozen mouse kidneys that improve the representation of medullary kidney cell types and avoids the gene expression artifacts from enzymatic tissue dissociation.