Name: analysis of translation in the developing mouse brain using polysome profiling
Uploaded: 2021-05-22T14:00:00
Description: Watch this Scientific Journal Video about Analysis of Translation in the Developing Mouse Brain using Polysome Profiling at JoVE.com

This work was funded by a NSERC Discovery Grant (RGPIN/04246-2018 to G.Y.). G.Y. is a Canada Research Chair. S.K. was funded by Mitacs Globalink Graduate Fellowship and ACHRI Graduate Student Scholarship.

All animal use was supervised by the Animal Care Committee at the University of Calgary. CD1 mice used for the experiment were purchased from commercial vendor.
1. Preparation of solutions
NOTE To prevent RNA degradation, spray workbench and all equipment with RNase decontamination solution. RNase-free tips are used for the experiment. All solutions are prepared in RNase-free water.
<ol>
	<li>Prepare cycloheximide stock solution (100 mg/mL) in DMSO and store at -2...

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Polysome profiling is a commonly used and powerful technique to assess the translational status at both single gene and genome-wide levels14 . In this report, we present a protocol of polysome profiling using a home-assembled platform and its application to analyze the developing mouse cortex. This cost-effective platform is easy to assemble and generate robust, reproducible sucrose gradients and polysome profiling with high sensitivity.
It is worthy to note that the pr...

During the development of the mammalian brain, neural stem cells proliferate and differentiate to generate neurons and glia1,2 . The perturbation of this process can lead to alterations in brain structure and function, as seen in many neurodevelopmental disorders3,4. The proper behavior of neural stem cells requires the orchestrated expression of specific genes5. While the epigenetic and transcriptional control of these genes has been intensively studied, recent findings suggest that gene regulation at other levels also contributes to the coordination of neural stem cell proliferation and differentiation6,7,8,9,10. Thus, addressing the translational control programs will greatly advance our understanding of the mechanisms underlying neural stem cell fate decision and brain development.
Three main techniques with different strengths have been widely applied to assess the translational status of mRNA, including ribosome profiling, translating ribosome affinity purification (TRAP) and polysome profiling. Ribosome profiling uses RNA sequencing to determine ribosome-protected mRNA fragments, allowing the global analysis of the number and location of translating ribosomes on each transcript to indirectly infer the translation rate by comparing it to transcript abundance11. TRAP takes advantage of epitope-tagged ribosomal proteins to capture ribosome-bound mRNAs12. Given that the tagged ribosomal proteins can be expressed in specific cell types using genetic approaches, TRAP allows the analysis of translation in a cell type-specific manner. In comparison, polysome profiling, which uses sucrose density gradient fractionation to separate free and poorly-translated portion (lighter monosomes) from those being actively translated by ribosomes (heavier polysomes), provides a direct measurement of ribosome density on mRNA13. One advantage this technique offers is its versatility to study the translation of specific mRNA of interest as well as genome-wide translatome analysis14.
In this paper, we describe a detailed protocol of polysome profiling to analyze the developing mouse cerebral cortex. We use a home-assembled system to prepare sucrose density gradients and collect fractions for downstream applications. The protocol presented here can be adapted easily to analyze other types of tissues and organisms.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1.5 mL RNA free microtubes</td>
			<td>Axygen</td>
			<td>MCT-150-C</td>
			<td></td>
		</tr>
		<tr>
			<td>10 cm dish</td>
			<td>Greiner-Bio</td>
			<td>664160</td>
			<td></td>
		</tr>
		<tr>
			<td>1M MgCl2</td>
			<td>Invitrogen</td>
			<td>AM9530G</td>
			<td></td>
		</tr>
		<tr>
			<td>21-23G needle</td>
			<td>BD</td>
			<td>305193</td>
			<td></td>
		</tr>
		<tr>
			<td>2M KCl</td>
			<td>Invitrogen</td>
			<td>AM8640G</td>
			<td></td>
		</tr>
		<tr>
			<td>30 mL syringe</td>
			<td>BD</td>
			<td>302832</td>
			<td></td>
		</tr>
		<tr>
			<td>Blunt end needle</td>
			<td>VWR</td>
			<td>20068-781</td>
			<td></td>
		</tr>
		<tr>
			<td>Breadboard</td>
			<td>Thorlabs</td>
			<td>MB2530/M</td>
			<td></td>
		</tr>
		<tr>
			<td>Bromophenol blue</td>
			<td>Sigma</td>
			<td>115-39-9</td>
			<td></td>
		</tr>
		<tr>
			<td>CD1 mouse</td>
			<td></td>
			<td>Charles River Laboratory</td>
			<td></td>
		</tr>
		<tr>
			<td>Curved tip forceps</td>
			<td>Sigma</td>
			<td>#Z168785</td>
			<td></td>
		</tr>
		<tr>
			<td>Cycloheximide</td>
			<td></td>
			<td>Sigma</td>
			<td>66-81-9</td>
		</tr>
		<tr>
			<td>Data acquisition software TracerDAQ</td>
			<td>Measurement Computing</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Digital converter</td>
			<td></td>
			<td>Measurement Computing</td>
			<td>USB-1208LS</td>
		</tr>
		<tr>
			<td>Direct-zol RNA miniprep kit</td>
			<td>Zymo</td>
			<td>R2070</td>
			<td></td>
		</tr>
		<tr>
			<td>Dithiothreitol (DTT)</td>
			<td>Bio-basic</td>
			<td>12-03-3483</td>
			<td></td>
		</tr>
		<tr>
			<td>DMSO</td>
			<td>Bioshop</td>
			<td>67-68-5</td>
			<td></td>
		</tr>
		<tr>
			<td>Dumont No.5 forceps</td>
			<td>Sigma</td>
			<td>#F6521</td>
			<td></td>
		</tr>
		<tr>
			<td>Fraction collector</td>
			<td>Bio-Rad</td>
			<td>Model 2110</td>
			<td></td>
		</tr>
		<tr>
			<td>HBSS</td>
			<td>Wisent</td>
			<td>311-513-CL</td>
			<td></td>
		</tr>
		<tr>
			<td>Linear stage actuator</td>
			<td>Rattmmotor</td>
			<td>CBX1605-100A</td>
			<td></td>
		</tr>
		<tr>
			<td>Luciferase control RNA</td>
			<td>Promega</td>
			<td>L4561</td>
			<td></td>
		</tr>
		<tr>
			<td>Maxima first strand cDNA synthesis kit</td>
			<td>Themo Fisher</td>
			<td>M1681</td>
			<td></td>
		</tr>
		<tr>
			<td>Miniature V-clamp</td>
			<td>Thorlabs</td>
			<td>VH1/M</td>
			<td></td>
		</tr>
		<tr>
			<td>Mini-series breadboard</td>
			<td>Thorlabs</td>
			<td>MSB7515/M</td>
			<td></td>
		</tr>
		<tr>
			<td>Mini-series optical post</td>
			<td>Thorlabs</td>
			<td>MS2R/M</td>
			<td></td>
		</tr>
		<tr>
			<td>Mini-series pedestal post holder base</td>
			<td>Thorlabs</td>
			<td>MBA1</td>
			<td></td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Bio-basic</td>
			<td>7647-14-5</td>
			<td></td>
		</tr>
		<tr>
			<td>Neurobasal media</td>
			<td>Gibco</td>
			<td>21103-049</td>
			<td></td>
		</tr>
		<tr>
			<td>&#216;12.7 mm aluminum post</td>
			<td>Thorlabs</td>
			<td>TRA150/M</td>
			<td></td>
		</tr>
		<tr>
			<td>Parafilm</td>
			<td>Bemis</td>
			<td>PM992</td>
			<td></td>
		</tr>
		<tr>
			<td>PerfeCTa SYBR green fastmix</td>
			<td>Quanta Bio</td>
			<td>CA101414-274</td>
			<td></td>
		</tr>
		<tr>
			<td>Phosphate buffered saline (PBS)</td>
			<td>Wisent</td>
			<td>311-010-CL</td>
			<td></td>
		</tr>
		<tr>
			<td>Puromycin</td>
			<td>Bioshop</td>
			<td>58-58-2</td>
			<td></td>
		</tr>
		<tr>
			<td>Right-angle clamp</td>
			<td>Thorlabs</td>
			<td>RA90/M</td>
			<td></td>
		</tr>
		<tr>
			<td>Right-angle &#216;1/2&#34; to &#216;6 mm post clamp</td>
			<td>Thorlabs</td>
			<td>RA90TR/M</td>
			<td></td>
		</tr>
		<tr>
			<td>Rnase AWAY</td>
			<td>Molecular BioProducts</td>
			<td>7002</td>
			<td></td>
		</tr>
		<tr>
			<td>RNase free tips</td>
			<td>Frogga Bio</td>
			<td>FT10, FT200, FT1000</td>
			<td></td>
		</tr>
		<tr>
			<td>RNase free water</td>
			<td>Wisent</td>
			<td>809-115-CL</td>
			<td></td>
		</tr>
		<tr>
			<td>RNasin</td>
			<td>Promega</td>
			<td>N2111</td>
			<td></td>
		</tr>
		<tr>
			<td>Slim right-angle bracket</td>
			<td>Thorlabs</td>
			<td>AB90B/M</td>
			<td></td>
		</tr>
		<tr>
			<td>Small V-clamp</td>
			<td>Thorlabs</td>
			<td>VC1/M</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium deoxycholate</td>
			<td>Sigma</td>
			<td>302-95-4</td>
			<td></td>
		</tr>
		<tr>
			<td>Stepper motor driver</td>
			<td>SongHe</td>
			<td>TB6600</td>
			<td></td>
		</tr>
		<tr>
			<td>Sucrose</td>
			<td>Bioshop</td>
			<td>57501</td>
			<td></td>
		</tr>
		<tr>
			<td>SW 41 Ti rotor</td>
			<td>Beckman Coulter</td>
			<td>331362</td>
			<td></td>
		</tr>
		<tr>
			<td>Syringe pump</td>
			<td>Harvard Apparatus</td>
			<td>70-4500</td>
			<td></td>
		</tr>
		<tr>
			<td>Syringe pump</td>
			<td>Harvard Apparatus</td>
			<td>70-4500</td>
			<td></td>
		</tr>
		<tr>
			<td>Triton-X-100</td>
			<td>Bio-basic</td>
			<td>9002-93-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Trizol</td>
			<td>Thermofisher Scientific</td>
			<td>15596018</td>
			<td></td>
		</tr>
		<tr>
			<td>Tube piercer</td>
			<td>Brandel</td>
			<td>BR-184</td>
			<td></td>
		</tr>
		<tr>
			<td>Ultracentrifuge</td>
			<td></td>
			<td>Beckman Coulter</td>
			<td>L8-70M</td>
		</tr>
		<tr>
			<td>Ultracentrifuge tubes</td>
			<td>Beckman Coulter</td>
			<td>331372</td>
			<td></td>
		</tr>
		<tr>
			<td>UltraPure 1M Tris-HCl pH 7.5</td>
			<td>Invitrogen</td>
			<td>15567-027</td>
			<td></td>
		</tr>
		<tr>
			<td>UNO project super starter kit</td>
			<td>Elegoo</td>
			<td>EL-KIT-003</td>
			<td></td>
		</tr>
		<tr>
			<td>UV monitor</td>
			<td>Bio-Rad</td>
			<td>EM-1 Econo</td>
			<td></td>
		</tr>
		<tr>
			<td>Vertical bracket</td>
			<td>Thorlabs</td>
			<td>VB01A/M</td>
			<td></td>
		</tr>
	</tbody>
</table>

analysis of translation in the developing mouse brain using polysome profiling

The proper development of the mammalian brain relies on a fine balance of neural stem cell proliferation and differentiation into different neural cell types. This balance is tightly controlled by gene expression that is fine-tuned at multiple levels, including transcription, post-transcription and translation. In this regard, a growing body of evidence highlights a critical role of translational regulation in coordinating neural stem cell fate decisions. Polysome fractionation is a powerful tool for the assessment of mRNA translational status at both global and individual gene levels. Here, we present an in-house polysome profiling pipeline to assess translational efficiency in cells from the developing mouse cerebral cortex. We describe the protocols for sucrose gradient preparation, tissue lysis, ultracentrifugation and fractionation-based analysis of mRNA translational status.

As a demonstration, the cortical lysate containing 75 &#181;g RNA (pooled from 8 embryos) was separated by the sucrose gradient into 12 fractions. Peaks of UV absorbance at 254 nm identified fractions containing the 40S subunit, 60S subunit, 80S monosome and polysomes (Figure 4A). Analysis of fractions by western blot for the large ribosomal subunit, Rpl10 showed its presence in the 60S subunit (fraction 3), monosome (fraction 4) and polysomes (fractions 5-12) (Figure 4B...

Watch this Scientific Journal Video about Analysis of Translation in the Developing Mouse Brain using Polysome Profiling at JoVE.com

Analysis of Translation in the Developing Mouse Brain using Polysome Profiling

The development of the mammalian brain requires proper control of gene expression at the level of translation. Here, we describe a polysome profiling system with an easy-to-assemble sucrose gradient-making and fractionation platform to assess the translational status of mRNAs in the developing brain.

The proper development of the mammalian brain relies on a fine balance of neural stem cell proliferation and differentiation into different neural cell ...

Translational regulation plays an important role in brain development. Polysome profiling provides a useful and powerful tool to assess the translational status of mRNA, making it possible to examine translational control functions during brain development. This method is an easy and low-cost approach to make sucrose gradients and assess polysome fractionation.In this protocol, it is used to analyze the developing mouse cortex. However, it can be easily adapted to study other systems. Begin by diluting 2.2 molar sucrose to prepare six 10 to 50%sucrose gradients.Fill a 30 milliliter syringe with approximately 16 milliliters of 10%sucrose, place it on the syringe pump and connect it to the needle. Make sure that there are no air bubbles in the syringe, tubing or needle, and wipe the tip of the needle to remove any residual solution. Move the motorized stage up such that the tip of the needle touches the center of the tube at the bottom.Set the syringe pump to a flow rate of two milliliters per minute for a volume of 2.3 milliliters. After dispensing 2.3 milliliters of 10%sucrose solution, move down the motorized stage and repeat the process for all six gradients. Then add 20%sucrose solution to the bottom of the tubes followed by 30, 40 and 50%Collect CD1 mouse embryos at embryonic day 12 and place them in a 10 centimeter plate containing ice cold HBSS on ice.Under the dissection scope, transfer one embryo to a six centimeter plate containing ice cold HBSS. Use 21 to 23 gauge needles to fix the position of the head by penetrating through the eyes at a 45 degree angle and apply a force to make sure the needles are fixed on the plate. Use number five forceps to remove the skin and skull working from the middle to the sides, then cut the olfactory bulbs and remove the meninges to expose the cortical tissues.Use curved forceps to cut the cortical tissues into two to three milliliters of neurobasal medium on ice. Pull the tissues from different embryos as needed. Tissues from eight to 10 embryos usually give approximately 200 micrograms of total RNA.Add cycloheximide to the neurobasal medium with the dissected tissues to a final concentration of 100 micrograms per milliliter and incubate at 37 degrees Celsius for 10 minutes. Centrifuge the tissue at 500 x g for five minutes at four degrees Celsius and discard the supernatant. Wash the tissues twice with ice cold PBS supplemented with 100 micrograms per milliliter cycloheximide.Add 500 microliters of cell lysis buffer supplemented with four microliters of RNase inhibitor and pipette up and down to resuspend the tissue. Use an insulin needle to gently lyse the tissue. Then incubate on ice for 10 minutes with brief vortexing every two to three minutes.After the incubation, centrifuge the lysate at 2000 x g for five minutes at four degrees Celsius and transfer the supernatant to a new centrifuge tube on ice. Repeat this process once more centrifuging at 13, 000 x g. After transferring the supernatant to a new centrifuge tube on ice, measure the RNA concentration in the tissue lysate using a UV-Vis spectrophotometer.Load the samples on top of the sucrose gradients by slowly dispensing the lysate to the walls of the ultracentrifuge tubes. Gently place the sucrose gradients in the buckets and ultracentrifuge the samples at 190, 000 x g and four degrees Celsius for 90 minutes. Place an empty ultracentrifuge tube on the tube piercer and gently penetrate the tube with the needle from the bottom.Fill a 30 milliliter syringe with 25 milliliters of 60%sucrose chase solution. Then gently press the syringe such that the chase solution fills the empty tube and goes through the 254 nanometer UV monitor to set the baseline for detection. Press auto zero on the UV monitor to register a baseline for detection, then press Play on the software to begin recording.Once the system establishes a baseline, pause recording on the software and retract the chase solution, making sure that no residual chase solution remains in the system. Load one sample tube on the tube piercer and gently penetrate the tube with the needle from the bottom. Begin recording on the software, make sure that there are no air bubbles in the line.Then start the syringe pump and the fraction collector to collect polysome fractions, setting the fractionator to 30 seconds. Collect the fractions into 1.5 milliliter tubes. The cortical lysate containing RNA pulled from eight embryos was separated by a sucrose gradient into 12 fractions.Peaks of UV absorbance at 254 nanometers identified fractions containing the 40S subunit 60S subunit and 80S monosome and polysomes. Analysis of the fractions by Western blot for the large ribosomal subunit Rpl10 showed its presence in the 60S subunit monosomes and polysomes. In contrast, cytoplasmic proteins, Gapdh and Csde1, were not associated with ribosomes, but were enriched in fractions containing free RNA.Consistent with the separation of proteins in different fractions, Gapdh and sox2 mRNAs were highly enriched in the fractions containing heavy polysomes, suggesting that these mRNAs are efficiently translated in the developing cortex. In contrast, rpl7 and rpl35 mRNAs were enriched in the fraction containing monosomes, suggesting repressed translation. To obtain reproducible results, it is important to maintain consistency in making sucrose gradients.The syringe pumps should be used to eject the sucrose. During fractionation and sample collection, it is important to wash the system with RNase-free water. This reduces any residual sucrose remaining from the previous sample.This method can be used to assess the translational status of mRNAs in various tissues. Using the platform, consistent gradients for polysome profiling can be obtained, which provides a low-cost solution for this classical and useful technique.

Research

JoVE Journal

Neuroscience

Mosaic Analysis of Gene Function in Postnatal Mouse Brain Development by Using Virus-based Cre Recombination

Normal brain function relies not only on embryonic development when major neuronal pathways are established, but also on postnatal 
development when ...

In vivo Electroporation of Developing Mouse Retina

In vivo Electroporation of Developing Mouse Retina

The functional characterization of genes expressed during mammalian retinal development remains a significant challenge.  Gene targeting to generate ...

Single-cell Profiling of Developing and Mature Retinal Neurons

Highly specialized, but exceedingly small populations of cells play important roles in many tissues. The identification of cell-type specific markers and ...

Visualization and Genetic Manipulation of Dendrites and Spines in the Mouse Cerebral Cortex and Hippocampus using In utero Electroporation

Visualization and Genetic Manipulation of Dendrites and Spines in the Mouse Cerebral Cortex and Hippocampus using In utero Electroporation

In utero electroporation (IUE) has become a powerful technique to study the development of different regions of the embryonic nervous system 1-5. To date ...

Assessing Cell Cycle Progression of Neural Stem and Progenitor Cells in the Mouse Developing Brain after Genotoxic Stress

Neurons of the cerebral cortex are generated during brain development from different types of neural stem and progenitor cells (NSPC), which form a ...

Live Imaging of Mitosis in the Developing Mouse Embryonic Cortex

Although of short duration, mitosis is a complex and dynamic multi-step process fundamental for development of organs including the brain. In the ...

Imaging Serotonergic Fibers in the Mouse Spinal Cord Using the CLARITY/CUBIC Technique

Long descending fibers to the spinal cord are essential for locomotion, pain perception, and other behaviors. The fiber termination pattern in the spinal ...

High Resolution Quantitative Synaptic Proteome Profiling of Mouse Brain Regions After Auditory Discrimination Learning

The molecular synaptic mechanisms underlying auditory learning and memory remain largely unknown. Here, the workflow of a proteomic study on auditory ...

Modelling Zika Virus Infection of the Developing Human Brain In Vitro Using Stem Cell Derived Cerebral Organoids

Modelling Zika Virus Infection of the Developing Human Brain In Vitro Using Stem Cell Derived Cerebral Organoids

The recent emergence of Zika virus (ZIKV) in susceptible populations has led to an abrupt increase in microcephaly and other neurodevelopmental conditions ...

Quantifying the Heterogeneous Distribution of a Synaptic Protein in the Mouse Brain Using Immunofluorescence

The presence, absence, or levels of specific synaptic proteins can severely influence synaptic transmission. In addition to elucidating the function of a ...